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.t9 TSS g11153.t9 14352304 14352304
chr_1 g11153 g11153.t9 isoform g11153.t9 14352379 14354570
chr_1 g11153 g11153.t9 exon g11153.t9.exon1 14352379 14352740
chr_1 g11153 g11153.t9 cds g11153.t9.CDS1 14352612 14352740
chr_1 g11153 g11153.t9 exon g11153.t9.exon2 14352797 14353387
chr_1 g11153 g11153.t9 cds g11153.t9.CDS2 14352797 14353387
chr_1 g11153 g11153.t9 exon g11153.t9.exon3 14354172 14354570
chr_1 g11153 g11153.t9 cds g11153.t9.CDS3 14354172 14354570
chr_1 g11153 g11153.t9 TTS g11153.t9 14354634 14354634

Sequences

>g11153.t9 Gene=g11153 Length=1352
ATGAAAGACATTGAAATATTAGATCCAACAAACACAACGAAAAACCGAGAATTATTGCAT
AGACTTATTATAAGGTAAGAAAAAGAATAAATTTACGTTTATGAAATTACCGGCAGAAAA
AAATTATTTTCAGCCAACTTTTCTATGATGGTTATGCTGCGGTTGCTGCAGAATTAGCAA
ATAGTATTAGAACAGAACCACCTTGTCCTCCAAGTAACCGTTTATATCAAATTATGCTGA
ATGGTTTACAAAATGAAGGAAAGAAAGAAACTATTATTGAATCTGATGATATGGATTTAC
CCGGAATTGATCTTGAATTTCAAGCTGACGCAACTTGTGTTGCTCCCGAACCTGCGACTT
ATGAAACTGCTTATGTGACTAGTCACAAGCATGCATGTCGTTCAGGATCATTTAGTTTTG
ATGGACAATTAGTCGCTACAGGATCGGTAGATGCTTCAATTAAAATACTTGATGTGGAAA
GAATGTTAGCAAAGTCAGCTCCGGAAGAAACTGACACACGTGAGCAGCAACAAGGACATC
CTGTTATTCGTACACTCTATGACCATACAGATGAAGTAGCTTTTCTCGAATTTCATCCAA
GTTCTCAAATTCTTGCTAGTGGTTCACGCGATATGACGGTGAAATTATTTGATATCAGTA
AAGCAAGTGTAAAGAAAGCACATAAAACATTCACTGATTGTGAGCCTGTGCGAAGTTTAT
CTTTTCATCCTACGGGCGATTATTTGGCAGTAGCTACAGATCATCATTTACTTAGAGTTT
ATGATATCAACACTGGTCAATGCTTTGTTAGTGCAATACCAATGCAACATCATAAAGGAG
CTATCAATTGTGTTAAATATGCCATAAATGGAAAACTGTATGCTACAGGTTCAATTGATG
GTTCGATTAAGATTTGGGATGGTGTTAGTGGAAGATGCATTAATACATTTATTGATGCTC
ATAGTGGTTCTGAAATTTATTCTGTATCATTTTCAAAGAATGGTAAATATTTGCTGAGTT
CAGGAAAAGATTCTTTAGTAAAGCTTTGGGAATTAAGTACAAGTAGAGCATTGATTGCAT
ATACGGGTGCAGGCACAACAGGCAAACAAGAGCATAGCACACAAGCAGTTTTCAATCACA
CAGAAGATTTTGTTCTGTTTCCTGATGAAGCAACAACCTCATTGTGTGCATGGAATTCAC
GTAATGCCAGTCGTTGTCATCTCATGAGTTTGGGGCATAATGGTCCAGTTCGATTTCTTA
TTCATTCTCCTGTTTCTCCTGCATTTCTCACATGCTCTGATGATTTTCGTGCTCGCTTTT
GGGTTAGACGAACAGCAGTTAATCAATATTAA

>g11153.t9 Gene=g11153 Length=372
MLNGLQNEGKKETIIESDDMDLPGIDLEFQADATCVAPEPATYETAYVTSHKHACRSGSF
SFDGQLVATGSVDASIKILDVERMLAKSAPEETDTREQQQGHPVIRTLYDHTDEVAFLEF
HPSSQILASGSRDMTVKLFDISKASVKKAHKTFTDCEPVRSLSFHPTGDYLAVATDHHLL
RVYDINTGQCFVSAIPMQHHKGAINCVKYAINGKLYATGSIDGSIKIWDGVSGRCINTFI
DAHSGSEIYSVSFSKNGKYLLSSGKDSLVKLWELSTSRALIAYTGAGTTGKQEHSTQAVF
NHTEDFVLFPDEATTSLCAWNSRNASRCHLMSLGHNGPVRFLIHSPVSPAFLTCSDDFRA
RFWVRRTAVNQY

Protein features from InterProScan

Transcript Database ID Name Start End E.value
11 g11153.t9 CDD cd00200 WD40 44 363 9.05841E-53
9 g11153.t9 Gene3D G3DSA:2.130.10.10 - 45 197 4.0E-29
10 g11153.t9 Gene3D G3DSA:2.130.10.10 - 198 363 3.6E-28
4 g11153.t9 PANTHER PTHR44133 CLEAVAGE STIMULATION FACTOR SUBUNIT 1 23 367 1.6E-149
6 g11153.t9 PRINTS PR00320 G protein beta WD-40 repeat signature 127 141 6.3E-6
5 g11153.t9 PRINTS PR00320 G protein beta WD-40 repeat signature 216 230 6.3E-6
7 g11153.t9 PRINTS PR00320 G protein beta WD-40 repeat signature 260 274 6.3E-6
2 g11153.t9 Pfam PF00400 WD domain, G-beta repeat 50 78 0.1
3 g11153.t9 Pfam PF12894 Anaphase-promoting complex subunit 4 WD40 domain 119 208 9.2E-7
1 g11153.t9 Pfam PF00400 WD domain, G-beta repeat 233 272 2.0E-6
12 g11153.t9 ProSitePatterns PS00678 Trp-Asp (WD) repeats signature. 260 274 -
19 g11153.t9 ProSiteProfiles PS50294 Trp-Asp (WD) repeats circular profile. 48 372 37.044
23 g11153.t9 ProSiteProfiles PS50082 Trp-Asp (WD) repeats profile. 48 82 8.737
22 g11153.t9 ProSiteProfiles PS50082 Trp-Asp (WD) repeats profile. 108 149 12.814
20 g11153.t9 ProSiteProfiles PS50082 Trp-Asp (WD) repeats profile. 197 238 14.519
21 g11153.t9 ProSiteProfiles PS50082 Trp-Asp (WD) repeats profile. 248 282 12.614
15 g11153.t9 SMART SM00320 WD40_4 42 80 0.027
17 g11153.t9 SMART SM00320 WD40_4 101 140 4.8E-7
13 g11153.t9 SMART SM00320 WD40_4 146 184 0.011
18 g11153.t9 SMART SM00320 WD40_4 187 229 9.5E-6
14 g11153.t9 SMART SM00320 WD40_4 232 273 8.2E-8
16 g11153.t9 SMART SM00320 WD40_4 326 364 2.0
8 g11153.t9 SUPERFAMILY SSF50978 WD40 repeat-like 44 363 2.29E-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