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.t5 isoform g11823.t5 18589994 18591160
chr_1 g11823 g11823.t5 exon g11823.t5.exon1 18589994 18590878
chr_1 g11823 g11823.t5 cds g11823.t5.CDS1 18589994 18590878
chr_1 g11823 g11823.t5 exon g11823.t5.exon2 18591089 18591160
chr_1 g11823 g11823.t5 cds g11823.t5.CDS2 18591089 18591160
chr_1 g11823 g11823.t5 TSS g11823.t5 18591259 18591259
chr_1 g11823 g11823.t5 TTS g11823.t5 NA NA

Sequences

>g11823.t5 Gene=g11823 Length=957
ATGAGTGAAAATGTTGATAGTGATCTTCTGTATGAAGATTTTCAAAATGAAGACCAAAAG
GAATTTAATAATGAAAGTTATGGGCATGTACAAGAAGATGATTTATATGATGACGTTCTT
ACATCGGGATCAAACAATATAAACAGTGAGAATAATGCGTCCTCAGAACATAATGCAGAA
ACAGAAACTAATGGAAATTATCAAGGAAACATGCATAATATTGCAAAAAGATTTCAACTT
TACGTTGGAAATCTAACTTGGTGGACAACTGATTCTGATATTACTGATGCAGTTATCGCT
ACAGGTGTCAATGACTTTCAAGAAGTAAAATTTTTTGAAAATCGTGCCAATGGTCAATCC
AAAGGCTTCTGTGTAATCTCGCTTGGATCTGAAGCTAGCATGCGAATTGTTTTAGAGAAC
TTGCCGAAAAAAGAACTAAACGGACAAACTCCAATTGTCACATTACCTACAAAACAAGCA
TTGAATCAGTTTGAAAGTCAGCAAAAAACAAGACCTACTCCTCCTGTTCCAAATCCAAAT
CAGCAGAAAACGAGTGGAATAGCTAATAGCGGTCCAAATAACTTGATGAACCCAAATATG
CCGCTTCAAATGCATCCACGAATGATGAATCCACCTATGCGAGGAAACATGCAAAATCCT
CCGATGATGAATCCAAATATGCAACAAAGGATGCCCTTATCGCCGCAAATGAATCATGCT
CCGCAAATGAACAATATGCGATTTCAAAATAATTGGAATAATGGTCCTATTCGTCCACCG
ATTCACCCAAATGGCATGCAAAATAATAATCGACCGCCACCTCCAATGAATATGCCACCA
CAAGGTCATCCCATGCCAAATAATATGATGAATAGGCCAATGAATATGCCACCATCTGGA
AGACCACCTTTTGGTCCTAATCCTAATCGACCAATGCATCCAAATTTCAATCAACAT

>g11823.t5 Gene=g11823 Length=319
MSENVDSDLLYEDFQNEDQKEFNNESYGHVQEDDLYDDVLTSGSNNINSENNASSEHNAE
TETNGNYQGNMHNIAKRFQLYVGNLTWWTTDSDITDAVIATGVNDFQEVKFFENRANGQS
KGFCVISLGSEASMRIVLENLPKKELNGQTPIVTLPTKQALNQFESQQKTRPTPPVPNPN
QQKTSGIANSGPNNLMNPNMPLQMHPRMMNPPMRGNMQNPPMMNPNMQQRMPLSPQMNHA
PQMNNMRFQNNWNNGPIRPPIHPNGMQNNNRPPPPMNMPPQGHPMPNNMMNRPMNMPPSG
RPPFGPNPNRPMHPNFNQH

Protein features from InterProScan

Transcript Database ID Name Start End E.value
6 g11823.t5 CDD cd12643 RRM_CFIm68 79 154 6.72839E-48
5 g11823.t5 Gene3D G3DSA:3.30.70.330 - 79 169 1.1E-17
8 g11823.t5 MobiDBLite mobidb-lite consensus disorder prediction 165 193 -
9 g11823.t5 MobiDBLite mobidb-lite consensus disorder prediction 294 319 -
10 g11823.t5 MobiDBLite mobidb-lite consensus disorder prediction 296 310 -
2 g11823.t5 PANTHER PTHR23204 CLEAVAGE AND POLYADENYLATION SPECIFIC FACTOR 17 316 9.6E-59
3 g11823.t5 PANTHER PTHR23204:SF7 CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR SUBUNIT 6 17 316 9.6E-59
1 g11823.t5 Pfam PF00076 RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) 80 150 5.5E-7
11 g11823.t5 ProSiteProfiles PS50102 Eukaryotic RNA Recognition Motif (RRM) profile. 78 158 9.763
7 g11823.t5 SMART SM00360 rrm1_1 79 154 1.2E-9
4 g11823.t5 SUPERFAMILY SSF54928 RNA-binding domain, RBD 77 172 6.52E-14

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:0003676 nucleic acid 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