Gene loci information

Transcript annotation

  • This transcript has been annotated as Cleavage stimulation factor subunit 1.

Parent gene

Gene structure

  • The exon-intron structure of all isoforms are indicated below. CDS regions are colored in green. TSS and TTs that were predicted with CTR-Seq data are indicated in solid circle and squares, respectively. More specific data are shown in the table below.

Chromosome Gene Transcript Category ID Start End
chr_1 g11153 g11153.t1 TSS g11153.t1 14352304 14352304
chr_1 g11153 g11153.t1 isoform g11153.t1 14352379 14354570
chr_1 g11153 g11153.t1 exon g11153.t1.exon1 14352379 14352452
chr_1 g11153 g11153.t1 cds g11153.t1.CDS1 14352379 14352452
chr_1 g11153 g11153.t1 exon g11153.t1.exon2 14352512 14352740
chr_1 g11153 g11153.t1 cds g11153.t1.CDS2 14352512 14352740
chr_1 g11153 g11153.t1 exon g11153.t1.exon3 14352797 14353387
chr_1 g11153 g11153.t1 cds g11153.t1.CDS3 14352797 14353387
chr_1 g11153 g11153.t1 exon g11153.t1.exon4 14354172 14354570
chr_1 g11153 g11153.t1 cds g11153.t1.CDS4 14354172 14354570
chr_1 g11153 g11153.t1 TTS g11153.t1 14354634 14354634

Sequences

>g11153.t1 Gene=g11153 Length=1293
ATGAAAGACATTGAAATATTAGATCCAACAAACACAACGAAAAACCGAGAATTATTGCAT
AGACTTATTATAAGCCAACTTTTCTATGATGGTTATGCTGCGGTTGCTGCAGAATTAGCA
AATAGTATTAGAACAGAACCACCTTGTCCTCCAAGTAACCGTTTATATCAAATTATGCTG
AATGGTTTACAAAATGAAGGAAAGAAAGAAACTATTATTGAATCTGATGATATGGATTTA
CCCGGAATTGATCTTGAATTTCAAGCTGACGCAACTTGTGTTGCTCCCGAACCTGCGACT
TATGAAACTGCTTATGTGACTAGTCACAAGCATGCATGTCGTTCAGGATCATTTAGTTTT
GATGGACAATTAGTCGCTACAGGATCGGTAGATGCTTCAATTAAAATACTTGATGTGGAA
AGAATGTTAGCAAAGTCAGCTCCGGAAGAAACTGACACACGTGAGCAGCAACAAGGACAT
CCTGTTATTCGTACACTCTATGACCATACAGATGAAGTAGCTTTTCTCGAATTTCATCCA
AGTTCTCAAATTCTTGCTAGTGGTTCACGCGATATGACGGTGAAATTATTTGATATCAGT
AAAGCAAGTGTAAAGAAAGCACATAAAACATTCACTGATTGTGAGCCTGTGCGAAGTTTA
TCTTTTCATCCTACGGGCGATTATTTGGCAGTAGCTACAGATCATCATTTACTTAGAGTT
TATGATATCAACACTGGTCAATGCTTTGTTAGTGCAATACCAATGCAACATCATAAAGGA
GCTATCAATTGTGTTAAATATGCCATAAATGGAAAACTGTATGCTACAGGTTCAATTGAT
GGTTCGATTAAGATTTGGGATGGTGTTAGTGGAAGATGCATTAATACATTTATTGATGCT
CATAGTGGTTCTGAAATTTATTCTGTATCATTTTCAAAGAATGGTAAATATTTGCTGAGT
TCAGGAAAAGATTCTTTAGTAAAGCTTTGGGAATTAAGTACAAGTAGAGCATTGATTGCA
TATACGGGTGCAGGCACAACAGGCAAACAAGAGCATAGCACACAAGCAGTTTTCAATCAC
ACAGAAGATTTTGTTCTGTTTCCTGATGAAGCAACAACCTCATTGTGTGCATGGAATTCA
CGTAATGCCAGTCGTTGTCATCTCATGAGTTTGGGGCATAATGGTCCAGTTCGATTTCTT
ATTCATTCTCCTGTTTCTCCTGCATTTCTCACATGCTCTGATGATTTTCGTGCTCGCTTT
TGGGTTAGACGAACAGCAGTTAATCAATATTAA

>g11153.t1 Gene=g11153 Length=430
MKDIEILDPTNTTKNRELLHRLIISQLFYDGYAAVAAELANSIRTEPPCPPSNRLYQIML
NGLQNEGKKETIIESDDMDLPGIDLEFQADATCVAPEPATYETAYVTSHKHACRSGSFSF
DGQLVATGSVDASIKILDVERMLAKSAPEETDTREQQQGHPVIRTLYDHTDEVAFLEFHP
SSQILASGSRDMTVKLFDISKASVKKAHKTFTDCEPVRSLSFHPTGDYLAVATDHHLLRV
YDINTGQCFVSAIPMQHHKGAINCVKYAINGKLYATGSIDGSIKIWDGVSGRCINTFIDA
HSGSEIYSVSFSKNGKYLLSSGKDSLVKLWELSTSRALIAYTGAGTTGKQEHSTQAVFNH
TEDFVLFPDEATTSLCAWNSRNASRCHLMSLGHNGPVRFLIHSPVSPAFLTCSDDFRARF
WVRRTAVNQY

Protein features from InterProScan

Transcript Database ID Name Start End E.value
15 g11153.t1 CDD cd00200 WD40 102 421 5.84932E-54
14 g11153.t1 Gene3D G3DSA:1.20.960.50 - 1 66 6.6E-24
13 g11153.t1 Gene3D G3DSA:2.130.10.10 - 103 254 5.4E-29
12 g11153.t1 Gene3D G3DSA:2.130.10.10 - 255 421 5.0E-28
7 g11153.t1 PANTHER PTHR44133 CLEAVAGE STIMULATION FACTOR SUBUNIT 1 10 425 2.5E-162
9 g11153.t1 PRINTS PR00320 G protein beta WD-40 repeat signature 185 199 9.2E-6
8 g11153.t1 PRINTS PR00320 G protein beta WD-40 repeat signature 274 288 9.2E-6
10 g11153.t1 PRINTS PR00320 G protein beta WD-40 repeat signature 318 332 9.2E-6
1 g11153.t1 Pfam PF16699 Cleavage stimulation factor subunit 1, dimerisation domain 12 66 4.9E-23
4 g11153.t1 Pfam PF00400 WD domain, G-beta repeat 108 136 0.12
3 g11153.t1 Pfam PF00400 WD domain, G-beta repeat 163 198 5.7E-4
2 g11153.t1 Pfam PF00400 WD domain, G-beta repeat 207 237 0.035
5 g11153.t1 Pfam PF00400 WD domain, G-beta repeat 257 287 1.3E-4
6 g11153.t1 Pfam PF00400 WD domain, G-beta repeat 291 330 2.5E-6
16 g11153.t1 ProSitePatterns PS00678 Trp-Asp (WD) repeats signature. 318 332 -
23 g11153.t1 ProSiteProfiles PS50294 Trp-Asp (WD) repeats circular profile. 106 430 37.044
25 g11153.t1 ProSiteProfiles PS50082 Trp-Asp (WD) repeats profile. 106 140 8.737
24 g11153.t1 ProSiteProfiles PS50082 Trp-Asp (WD) repeats profile. 166 207 12.814
26 g11153.t1 ProSiteProfiles PS50082 Trp-Asp (WD) repeats profile. 255 296 14.519
27 g11153.t1 ProSiteProfiles PS50082 Trp-Asp (WD) repeats profile. 306 340 12.614
20 g11153.t1 SMART SM00320 WD40_4 100 138 0.027
18 g11153.t1 SMART SM00320 WD40_4 159 198 4.8E-7
21 g11153.t1 SMART SM00320 WD40_4 204 242 0.011
17 g11153.t1 SMART SM00320 WD40_4 245 287 9.5E-6
22 g11153.t1 SMART SM00320 WD40_4 290 331 8.2E-8
19 g11153.t1 SMART SM00320 WD40_4 384 422 2.0
11 g11153.t1 SUPERFAMILY SSF50978 WD40 repeat-like 102 421 2.6E-59

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

GO terms from InterProScan

GOID TERM ONTOLOGY
GO:0005515 protein binding MF

KEGG

Orthology

Pathway

  • This transcript belongs to the following pathways

Expression

Transcript expression in Pv11 cells

TPM values are indicated as average +/- STDEV.

Differential expression

Differentially expressed genes were identified with DESeq2 using the ‘run_DE_analysis.pl’ script from Trinity. Transcripts were determined as differentially expressed when (1) FDR < 0.05 (2) fold change > 2 (TPM calculated by RSEM). DE information and fold change between conditions are indicated in the plot below.

Raw TPM values