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Encyclopedia of C. elegans 3'UTRs and their regulatory elements

experiment: Encyclopedia of C. elegans 3'UTRs and their regulatory elements project: The 3' UTRome PI: Fabio Piano Labs: Fabio Piano, John Kim
The 3' untranslated region (3'UTR) constitutes a major site of post-transcriptional regulation of gene expression. Sequence elements in the 3'UTR interact with trans-acting regulators such as microRNAs that affect translation and stability. The overall aim is to use a 3'RACE cloning-sequencing stragety to identify the 3'UTRs of C. elegans transcripts and explore their heterogeneity in different developmental stages and tissues.

All features generated by this experiment:
Feature Export
Exon ? 21355
This represents 21353 unique Exons
TAB CSV GFF3 (for UCSC) SEQ
Gene ? 20220
This represents 19958 unique Genes
TAB CSV GFF3 (for UCSC) SEQ
MRNA ? 3720 TAB CSV GFF3 SEQ
PolyASignalSequence ? 27135
This represents 21718 unique PolyASignalSequences
TAB CSV GFF3 (for UCSC) SEQ
Transcript ? 27417 TAB CSV GFF3 SEQ
ThreePrimeRACEClone ? 2700 TAB CSV GFF3 SEQ
PolyASite ? 35382
This represents 27773 unique PolyASites
TAB CSV GFF3 (for UCSC) SEQ
EST ? 2694 TAB CSV GFF3 SEQ
ThreePrimeRST ? 2700 TAB CSV GFF3 SEQ
ThreePrimeUST ? 2700 TAB CSV GFF3 SEQ
ThreePrimeUTR ? 24055
This represents 22993 unique ThreePrimeUTRs
TAB CSV GFF3 (for UCSC) SEQ
All GBrowse tracks generated for this experiment:
GBrowse tracks: by chromosome
All 60 tracks I II III IV V X
GFF3 for the experiment (with Genes, UTRs, Transcripts, mRNA) (for UCSC) All entries in public repositories generated by this experiment
There are 41 Sample creation, RNA-seq and RACE submissions for this experiment:
DCC id Name developmental stage strain temperature tissue Embargoed until Features, GBrowse and Data Files
modENCODE_2332


Related to: modENCODE_2460

3' UTR Staged 454 Sequencing - hermaphrodite adult - alignments Adult 20dC 70hr post-L1 stage larvae [ALL]
N2 [ALL]
20 degree celsius [ALL]
embargo expired
GBrowse tracks: YA_herm.ws220.sam_sorted


1 files Download data files
modENCODE_2465


Related to: modENCODE_2331

3' UTR Staged 454 Sequencing - embryo - sequences Mixed Embryos 20dC [ALL]
N2 [ALL]
20 degree celsius [ALL]
embargo expired GEO: GSM446651
Download data files
modENCODE_2333


Related to: modENCODE_2459

3' UTR Staged 454 Sequencing - male adult - alignments Adult male 20dC 70hr post-L1 stage larvae [ALL]
CB1489 [ALL]
20 degree celsius [ALL]
embargo expired
GBrowse tracks: YM_male.ws220.sam_sorted


1 files Download data files
modENCODE_2460


Related to: modENCODE_2332

3' UTR Staged 454 Sequencing - hermaphrodite adult - sequences Adult 20dC 70hr post-L1 stage larvae [ALL]
N2 [ALL]
20 degree celsius [ALL]
embargo expired GEO: GSM446656
Download data files
modENCODE_2330


Related to: modENCODE_2458

3' UTR Staged 454 Sequencing - L4 - alignments L4 20dC 45hr post-L1 stage larvae [ALL]
N2 [ALL]
20 degree celsius [ALL]
embargo expired
GBrowse tracks: L4.ws220.sam_sorted


1 files Download data files
modENCODE_2457


Related to: modENCODE_2329

3' UTR Staged 454 Sequencing - L3 - sequences L3 20dC 30hr post-L1 stage larvae [ALL]
N2 [ALL]
20 degree celsius [ALL]
embargo expired GEO: GSM446654
Download data files
modENCODE_2331


Related to: modENCODE_2465

3' UTR Staged 454 Sequencing - embryo - alignments Mixed Embryos 20dC [ALL]
N2 [ALL]
20 degree celsius [ALL]
embargo expired
GBrowse tracks: E.ws220.sam_sorted


1 files Download data files
modENCODE_2458


Related to: modENCODE_2330

3' UTR Staged 454 Sequencing - L4 - sequences L4 20dC 45hr post-L1 stage larvae [ALL]
N2 [ALL]
20 degree celsius [ALL]
embargo expired GEO: GSM446655
Download data files
modENCODE_2831

small RNA 454 sequencing of N2 young adults young Adult 25dC [ALL]
N2 [ALL]
25 degree celsius [ALL]
embargo expired
GBrowse tracks: miRNA_young_adult.ws220.sam.gz_sorted


3 files Download data files
modENCODE_2328


Related to: modENCODE_2456

3' UTR Staged 454 Sequencing - L2 - alignments L2 20dC 20hr post-L1 stage larvae [ALL]
N2 [ALL]
20 degree celsius [ALL]
embargo expired
GBrowse tracks: L2.ws220.sam_sorted


1 files Download data files
modENCODE_2832

small RNA 454 sequencing of fer-1 unfertilized oocytes Adult male 20dC 70hr post-L1 stage larvae [ALL]
BA1 [ALL]
25 degree celsius [ALL]
unfertilized oocytes [ALL]
embargo expired
GBrowse tracks: miRNA_oocytes.ws220.sam.gz_sorted


1 files Download data files
modENCODE_2484


Related to: modENCODE_2501

3' UTRome Solexa sequencing & alignment Mixed Worm Stages [ALL]
N2 [ALL]
25 degree celsius [ALL]
embargo expired
GBrowse tracks: F_bowtie.map.sam.gz_sorted
C_bowtie.map.sam.gz_sorted
A_bowtie.map.sam.gz_sorted
H_bowtie.map.sam.gz_sorted
G_bowtie.map.sam.gz_sorted
D_bowtie.map.sam.gz_sorted
GEO: GSM469439


6 files Download data files
modENCODE_2455


Related to: modENCODE_2327

3' UTR Staged 454 Sequencing - L1 - sequences L1 20dC 8hr post-L1 stage larvae [ALL]
N2 [ALL]
20 degree celsius [ALL]
embargo expired GEO: GSM446652
Download data files
modENCODE_2329


Related to: modENCODE_2457

3' UTR Staged 454 Sequencing - L3 - alignments L3 20dC 30hr post-L1 stage larvae [ALL]
N2 [ALL]
20 degree celsius [ALL]
embargo expired
GBrowse tracks: L3.ws220.sam_sorted


1 files Download data files
modENCODE_3404

utrome 454 minipools Mixed Worm Stages [ALL]
N2 [ALL]
25 degree celsius [ALL]
embargo expired
GBrowse tracks: minipool1.sam.bam.sorted
minipool2.sam.bam.sorted


2 files Download data files
modENCODE_2456


Related to: modENCODE_2328

3' UTR Staged 454 Sequencing - L2 - sequences L2 20dC 20hr post-L1 stage larvae [ALL]
N2 [ALL]
20 degree celsius [ALL]
embargo expired GEO: GSM446653
Download data files
modENCODE_2829

small RNA 454 sequencing of him-8 sperm Adult male 20dC 70hr post-L1 stage larvae [ALL]
CB1489 [ALL]
25 degree celsius [ALL]
spermatids [ALL]
embargo expired
GBrowse tracks: miRNA_spermatids.ws220.sam.gz_sorted


3 files Download data files
modENCODE_2828

small RNA 454 sequencing of glp-4(bn2) young Adult 25dC [ALL]
SS104 [ALL]
25 degree celsius [ALL]
embargo expired
GBrowse tracks: miRNA-glp-4.ws220.sam.gz_sorted


3 files Download data files
modENCODE_2327


Related to: modENCODE_2455

3' UTR Staged 454 Sequencing - L1 - alignments L1 20dC 8hr post-L1 stage larvae [ALL]
N2 [ALL]
20 degree celsius [ALL]
embargo expired
GBrowse tracks: L1.ws220.sam_sorted


1 files Download data files
modENCODE_2501


Related to: modENCODE_2482
modENCODE_2484

3' UTRome sample pools Mixed Worm Stages [ALL]
N2 [ALL]
25 degree celsius [ALL]
embargo expired

1 files Download data files
modENCODE_2830

small RNA Illumina sequencing of fer-1 unfertilized oocytes Adult male 20dC 70hr post-L1 stage larvae [ALL]
BA1 [ALL]
25 degree celsius [ALL]
unfertilized oocytes [ALL]
embargo expired
GBrowse tracks: miRNA_oocytes_solexa.ws220.sam.gz_sorted


2 files Download data files
modENCODE_2826

small RNA Illumina sequencing of N2 embryos Mixed Embryos 20dC [ALL]
N2 [ALL]
25 degree celsius [ALL]
embargo expired
GBrowse tracks: miRNA_embryos_solexa.ws220.sam.gz_sorted


4 files Download data files
modENCODE_2825

small RNA Illumina sequencing of N2 whole worms Mixed Worm Stages [ALL]
N2 [ALL]
25 degree celsius [ALL]
embargo expired
GBrowse tracks: miRNA_mixed_stage_solexa.ws220.sam.gz_sorted


2 files Download data files
modENCODE_2827

small RNA 454 sequencing of eri-1(mg366) young Adult 25dC [ALL]
GR1373 [ALL]
25 degree celsius [ALL]
embargo expired
GBrowse tracks: miRNA_eri-1.ws220.sam.gz_sorted
GEO: ???


1 files Download data files
modENCODE_2482


Related to: modENCODE_2501

3' UTRome 454 sequencing & alignment Mixed Worm Stages [ALL]
N2 [ALL]
25 degree celsius [ALL]
embargo expired
GBrowse tracks: marco2_A_sorted
marco1_V1_sorted
marco1_H_sorted
marco1_F_sorted
marco2_H_sorted
marco1_G_sorted
marco1_E_sorted
marco2_G_sorted
marco1_D_sorted
marco2_F_sorted
marco2_D_sorted
marco1_C_sorted
marco2_E_sorted
marco2_C_sorted
marco1_B_sorted
marco2_B_sorted
marco1_A_sorted
GEO: GSM469976


17 files Download data files
modENCODE_2337


Related to: modENCODE_2463

3' UTR Staged 454 Sequencing - daf-9 - alignments Dauer Larvae [ALL]
DR2281 [ALL]
20 degree celsius [ALL]
embargo expired
GBrowse tracks: L33daf09.ws220.sam_sorted


1 files Download data files
modENCODE_2822

small RNA Illumina sequencing of glp-4(bn2) young Adult 25dC [ALL]
SS104 [ALL]
25 degree celsius [ALL]
embargo expired
GBrowse tracks: miRNA-glp-4_solexa.ws220.sam.gz_sorted


2 files Download data files
modENCODE_2462


Related to: modENCODE_2336

3' UTR Staged 454 Sequencing - daf-7 - sequences Dauer Larvae [ALL]
CB1372 [ALL]
20 degree celsius [ALL]
embargo expired GEO: GSM446659
Download data files
modENCODE_2823

small RNA Illumina sequencing of him-8 sperm Adult male 20dC 70hr post-L1 stage larvae [ALL]
CB1489 [ALL]
25 degree celsius [ALL]
spermatids [ALL]
embargo expired
GBrowse tracks: miRNA_spermatids_solexa.ws220.sam.gz_sorted


2 files Download data files
modENCODE_2463


Related to: modENCODE_2337

3' UTR Staged 454 Sequencing - daf-9 - sequences Dauer Larvae [ALL]
DR2281 [ALL]
20 degree celsius [ALL]
embargo expired GEO: GSM446660
Download data files
modENCODE_515


Related to: modENCODE_2934

3'UTRome CEUP1 sequences, alignments, annotation Mixed Worm Stages [ALL]
N2 [ALL]
20 degree celsius [ALL]
embargo expired
? Gene: 2630   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
? MRNA: 3720   export: TAB   CSV GFF3 SEQ    create LIST
? ThreePrimeRACEClone: 2700   export: TAB   CSV GFF3 SEQ    create LIST
? PolyASite: 2700   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
? EST: 2694   export: TAB   CSV GFF3 SEQ    create LIST
? ThreePrimeRST: 2700   export: TAB   CSV GFF3 SEQ    create LIST
? ThreePrimeUST: 2700   export: TAB   CSV GFF3 SEQ    create LIST
? ThreePrimeUTR: 2700   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
[full gff3]   [find nearby features]
GBrowse tracks: CEUP1_three_prime_UTR_3373_515
CEUP1_polyA_site_3373_515
CEUP1_UST_match_3373_515
CEUP1_RST_match_3373_515
Trace Archive: 2216286010
Trace Archive: 2216286011
Trace Archive: 2216286013
Trace Archive: 2216286014
Trace Archive: 2216286015
...All entries in public repositories generated by this submission



1 files Download data files
modENCODE_2464


Related to: modENCODE_2334

3' UTR Staged 454 Sequencing - daf-11 - sequences Dauer Larvae [ALL]
DR47 [ALL]
20 degree celsius [ALL]
embargo expired GEO: GSM446661
Download data files
modENCODE_2335


Related to: modENCODE_2461

3' UTR Staged 454 Sequencing - daf-2 - alignments Dauer Larvae [ALL]
CB1370 [ALL]
20 degree celsius [ALL]
embargo expired
GBrowse tracks: L33daf02.ws220.sam_sorted


1 files Download data files
modENCODE_2461


Related to: modENCODE_2335

3' UTR Staged 454 Sequencing - daf-2 - sequences Dauer Larvae [ALL]
CB1370 [ALL]
20 degree celsius [ALL]
embargo expired GEO: GSM446658
Download data files
modENCODE_896


Related to: modENCODE_992

3'UTR 454 sequencing pilot - Level 1 L1 20dC 8hr post-L1 stage larvae [ALL]
L2 20dC 20hr post-L1 stage larvae [ALL]
L3 20dC 30hr post-L1 stage larvae [ALL]
L4 20dC 45hr post-L1 stage larvae [ALL]
Mixed Embryos 20dC [ALL]
...
all 6 developmental stages
N2 [ALL]
20 degree celsius [ALL]
embargo expired GEO: GSM443959
GEO: GSM443960
GEO: GSM443961
GEO: GSM443962
GEO: GSM443963
...All entries in public repositories generated by this submission

Download data files
modENCODE_2745

UTRome V2 3UTRs multiple evidences embargo expired
? Gene: 20214   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
? Exon: 21355   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
? PolyASignalSequence: 27135   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
? Transcript: 27417   export: TAB   CSV GFF3 SEQ    create LIST
? PolyASite: 32682   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
? ThreePrimeUTR: 21355   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
[full gff3]   [find nearby features]
GBrowse tracks: UTRome_V2_3_three_prime_UTR_6102_2745
UTRome_V2_3_polyA_signal_sequence_6102_2745
UTRome_V2_3_polyA_site_6102_2745


1 files Download data files
modENCODE_2336


Related to: modENCODE_2462

3' UTR Staged 454 Sequencing - daf-7 - alignments Dauer Larvae [ALL]
CB1372 [ALL]
20 degree celsius [ALL]
embargo expired
GBrowse tracks: L33daf07.ws220.sam_sorted


1 files Download data files
modENCODE_992


Related to: modENCODE_896

3' UTR 454 sequencing pilot - alignments L1 20dC 8hr post-L1 stage larvae [ALL]
L2 20dC 20hr post-L1 stage larvae [ALL]
L3 20dC 30hr post-L1 stage larvae [ALL]
L4 20dC 45hr post-L1 stage larvae [ALL]
Mixed Embryos 20dC [ALL]
...
all 6 developmental stages
N2 [ALL]
20 degree celsius [ALL]
embargo expired
GBrowse tracks: YA_herm_pilot.sam_sorted
emb_pilot.sam_sorted
L2_pilot.sam_sorted
L1_pilot.sam_sorted
L3_pilot.sam_sorted
L4_pilot.sam_sorted


6 files Download data files
modENCODE_2821

small RNA Illumina sequencing of eri-1(mg366) young Adult 25dC [ALL]
GR1373 [ALL]
25 degree celsius [ALL]
embargo expired
GBrowse tracks: miRNA_eri-1_solexa.ws220.sam.gz_sorted


2 files Download data files
modENCODE_2459


Related to: modENCODE_2333

3' UTR Staged 454 Sequencing - male adult - sequences Adult male 20dC 70hr post-L1 stage larvae [ALL]
CB1489 [ALL]
20 degree celsius [ALL]
embargo expired GEO: GSM446657
Download data files
modENCODE_2334


Related to: modENCODE_2464

3' UTR Staged 454 Sequencing - daf-11 - alignments Dauer Larvae [ALL]
DR47 [ALL]
20 degree celsius [ALL]
embargo expired
GBrowse tracks: L33daf11.ws220.sam_sorted


1 files Download data files