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.t7 TSS g11153.t7 14352304 14352304
chr_1 g11153 g11153.t7 isoform g11153.t7 14352379 14353391
chr_1 g11153 g11153.t7 exon g11153.t7.exon1 14352379 14352452
chr_1 g11153 g11153.t7 cds g11153.t7.CDS1 14352379 14352452
chr_1 g11153 g11153.t7 exon g11153.t7.exon2 14352512 14352740
chr_1 g11153 g11153.t7 cds g11153.t7.CDS2 14352512 14352740
chr_1 g11153 g11153.t7 exon g11153.t7.exon3 14352797 14353391
chr_1 g11153 g11153.t7 cds g11153.t7.CDS3 14352797 14353390
chr_1 g11153 g11153.t7 TTS g11153.t7 NA NA

Sequences

>g11153.t7 Gene=g11153 Length=898
ATGAAAGACATTGAAATATTAGATCCAACAAACACAACGAAAAACCGAGAATTATTGCAT
AGACTTATTATAAGCCAACTTTTCTATGATGGTTATGCTGCGGTTGCTGCAGAATTAGCA
AATAGTATTAGAACAGAACCACCTTGTCCTCCAAGTAACCGTTTATATCAAATTATGCTG
AATGGTTTACAAAATGAAGGAAAGAAAGAAACTATTATTGAATCTGATGATATGGATTTA
CCCGGAATTGATCTTGAATTTCAAGCTGACGCAACTTGTGTTGCTCCCGAACCTGCGACT
TATGAAACTGCTTATGTGACTAGTCACAAGCATGCATGTCGTTCAGGATCATTTAGTTTT
GATGGACAATTAGTCGCTACAGGATCGGTAGATGCTTCAATTAAAATACTTGATGTGGAA
AGAATGTTAGCAAAGTCAGCTCCGGAAGAAACTGACACACGTGAGCAGCAACAAGGACAT
CCTGTTATTCGTACACTCTATGACCATACAGATGAAGTAGCTTTTCTCGAATTTCATCCA
AGTTCTCAAATTCTTGCTAGTGGTTCACGCGATATGACGGTGAAATTATTTGATATCAGT
AAAGCAAGTGTAAAGAAAGCACATAAAACATTCACTGATTGTGAGCCTGTGCGAAGTTTA
TCTTTTCATCCTACGGGCGATTATTTGGCAGTAGCTACAGATCATCATTTACTTAGAGTT
TATGATATCAACACTGGTCAATGCTTTGTTAGTGCAATACCAATGCAACATCATAAAGGA
GCTATCAATTGTGTTAAATATGCCATAAATGGAAAACTGTATGCTACAGGTTCAATTGAT
GGTTCGATTAAGATTTGGGATGGTGTTAGTGGAAGATGCATTAATACATTTATTGTAA

>g11153.t7 Gene=g11153 Length=299
MKDIEILDPTNTTKNRELLHRLIISQLFYDGYAAVAAELANSIRTEPPCPPSNRLYQIML
NGLQNEGKKETIIESDDMDLPGIDLEFQADATCVAPEPATYETAYVTSHKHACRSGSFSF
DGQLVATGSVDASIKILDVERMLAKSAPEETDTREQQQGHPVIRTLYDHTDEVAFLEFHP
SSQILASGSRDMTVKLFDISKASVKKAHKTFTDCEPVRSLSFHPTGDYLAVATDHHLLRV
YDINTGQCFVSAIPMQHHKGAINCVKYAINGKLYATGSIDGSIKIWDGVSGRCINTFIV

Protein features from InterProScan

Transcript Database ID Name Start End E.value
16 g11153.t7 Gene3D G3DSA:1.20.960.50 - 1 66 0.0000000
15 g11153.t7 Gene3D G3DSA:2.130.10.10 - 87 299 0.0000000
6 g11153.t7 PANTHER PTHR44133 CLEAVAGE STIMULATION FACTOR SUBUNIT 1 10 297 0.0000000
9 g11153.t7 PRINTS PR00320 G protein beta WD-40 repeat signature 125 139 0.0000440
8 g11153.t7 PRINTS PR00320 G protein beta WD-40 repeat signature 185 199 0.0000440
7 g11153.t7 PRINTS PR00320 G protein beta WD-40 repeat signature 274 288 0.0000440
1 g11153.t7 Pfam PF16699 Cleavage stimulation factor subunit 1, dimerisation domain 12 66 0.0000000
4 g11153.t7 Pfam PF00400 WD domain, G-beta repeat 108 136 0.0750000
3 g11153.t7 Pfam PF00400 WD domain, G-beta repeat 163 198 0.0003400
2 g11153.t7 Pfam PF00400 WD domain, G-beta repeat 207 237 0.0210000
5 g11153.t7 Pfam PF00400 WD domain, G-beta repeat 257 287 0.0000810
17 g11153.t7 ProSiteProfiles PS50294 Trp-Asp (WD) repeats circular profile. 106 296 27.6850000
19 g11153.t7 ProSiteProfiles PS50082 Trp-Asp (WD) repeats profile. 106 140 8.7370000
18 g11153.t7 ProSiteProfiles PS50082 Trp-Asp (WD) repeats profile. 166 207 12.8140000
20 g11153.t7 ProSiteProfiles PS50082 Trp-Asp (WD) repeats profile. 255 296 14.5190000
13 g11153.t7 SMART SM00320 WD40_4 100 138 0.0270000
12 g11153.t7 SMART SM00320 WD40_4 159 198 0.0000005
14 g11153.t7 SMART SM00320 WD40_4 204 242 0.0110000
11 g11153.t7 SMART SM00320 WD40_4 245 287 0.0000095
10 g11153.t7 SUPERFAMILY SSF50978 WD40 repeat-like 104 297 0.0000000

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

This gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).

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