Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Cleavage and polyadenylation specificity factor subunit CG7185.

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 g11823 g11823.t2 isoform g11823.t2 18587917 18589591
chr_1 g11823 g11823.t2 exon g11823.t2.exon1 18587917 18588547
chr_1 g11823 g11823.t2 cds g11823.t2.CDS1 18588415 18588547
chr_1 g11823 g11823.t2 exon g11823.t2.exon2 18588999 18589591
chr_1 g11823 g11823.t2 cds g11823.t2.CDS2 18588999 18589585
chr_1 g11823 g11823.t2 TSS g11823.t2 NA NA
chr_1 g11823 g11823.t2 TTS g11823.t2 NA NA

Sequences

>g11823.t2 Gene=g11823 Length=1224
AATATTATGCCACCACGAGGACCTCCTATGCCACCAATGAATAATCAAGGTCCACCGGCA
CCACATGTGAATCCTGCTTTCTTCAATCAAGGACCTGTGCAAAATATCGTACCTCCTCCA
GGAAATCATTTTAATCAAGCACCGAGACCAATGTGGGGAGGCAATAAAATGCCAAATGTT
TTCGATCAAGCAACTGGCGGACCGCCTACAGGTGTTCCTAATCAACAACCAATTAGTGAA
ACTGAATTTGAAGAAATTATGAGTCGTAATAGAACTGTTAGTAGTTCTGCGATCGCACGT
GCTGTTTCTGATGCGGCTGCTGGAGAATATAGTAGTGCTATAGAAACTCTTGCTACAACA
ATTTCATTAATAAAGCAATCAAAAGTTGCTAATGATGAGCGTTGCAAAATTTTGATCAAT
TCATTGCAAGATACATTGCAAGGTATAGAAGCAAAAAGCTTTAATCGTCGAGATAGATCT
GAGAGATCTAGATCACGTGAAAGACGTCGAAGAAGAGAAAGATCAAACTCTCGCTCATAT
AGACGATCAAGGAGTCGTGAACATCGTGATCATCGTGATAGAGGAAGAGATGATAACAGC
AGAAGTCGTCCACGCAAATCAGCTGAACCATCAGGTGAAAATTCAGAGAACTTCAAACGT
TCTTATGATGACCGTAATCGCGATTCAGACAGATATCGTGATCGTGAAACCAGAAATCGT
CACTAGGCATTATTATTATTAATAATAAATAAAATCATTATACATCGCACCCAAATTTTT
ATTTACATAGGATTAATTTAATTATCTACATTTAAAGTCAAAAAATTAAAAAGAGATCAA
CAATAGAGTGACACAATCTGAAAATGAGACGAAAGGAAGAAGTTTTATAAACTTTGAATC
CATAACTTTTTTTAGAATATGTATGCATGACTATATGTGAAATAATTTTAATTATGTTAC
TTATCATAACATTAATGGCTAGATCATTTTTTTGATTGATTGAACGAATAAATTTAGCTG
AAAATGAAAAAAAAATGTGTTTAAGAAAATACAAAAATTAATGTTGAGACTGAAGAAAAT
AGAACTTTTACTAATTGTCTTTATTTAGATAGTTTAAAACCTTTCATGAATCAATAATAC
TCATTTACTCTGTAAAGAAAGAAAAATTCTTCAACAAAATTAACTTGTTTCACTTTAAGT
CTCATTCTTAAATTTTTTATTCTC

>g11823.t2 Gene=g11823 Length=239
MPPRGPPMPPMNNQGPPAPHVNPAFFNQGPVQNIVPPPGNHFNQAPRPMWGGNKMPNVFD
QATGGPPTGVPNQQPISETEFEEIMSRNRTVSSSAIARAVSDAAAGEYSSAIETLATTIS
LIKQSKVANDERCKILINSLQDTLQGIEAKSFNRRDRSERSRSRERRRRRERSNSRSYRR
SRSREHRDHRDRGRDDNSRSRPRKSAEPSGENSENFKRSYDDRNRDSDRYRDRETRNRH

Protein features from InterProScan

Transcript Database ID Name Start End E.value
6 g11823.t2 MobiDBLite mobidb-lite consensus disorder prediction 1 23 -
7 g11823.t2 MobiDBLite mobidb-lite consensus disorder prediction 1 17 -
5 g11823.t2 MobiDBLite mobidb-lite consensus disorder prediction 151 239 -
4 g11823.t2 MobiDBLite mobidb-lite consensus disorder prediction 161 187 -
3 g11823.t2 MobiDBLite mobidb-lite consensus disorder prediction 188 239 -
1 g11823.t2 PANTHER PTHR23204 CLEAVAGE AND POLYADENYLATION SPECIFIC FACTOR 2 203 2.6E-48
2 g11823.t2 PANTHER PTHR23204:SF3 CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR SUBUNIT 6 2 203 2.6E-48

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:0005849 mRNA cleavage factor complex CC

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