Gene loci information

Transcript annotation

  • This transcript has been annotated as Cleavage and polyadenylation specificity factor subunit 5.

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_2 g8566 g8566.t7 TSS g8566.t7 31362597 31362597
chr_2 g8566 g8566.t7 isoform g8566.t7 31362796 31365376
chr_2 g8566 g8566.t7 exon g8566.t7.exon1 31362796 31362964
chr_2 g8566 g8566.t7 cds g8566.t7.CDS1 31362912 31362964
chr_2 g8566 g8566.t7 exon g8566.t7.exon2 31363020 31363284
chr_2 g8566 g8566.t7 cds g8566.t7.CDS2 31363020 31363284
chr_2 g8566 g8566.t7 exon g8566.t7.exon3 31363907 31364084
chr_2 g8566 g8566.t7 cds g8566.t7.CDS3 31363907 31364084
chr_2 g8566 g8566.t7 exon g8566.t7.exon4 31364908 31365016
chr_2 g8566 g8566.t7 cds g8566.t7.CDS4 31364908 31365016
chr_2 g8566 g8566.t7 exon g8566.t7.exon5 31365078 31365376
chr_2 g8566 g8566.t7 cds g8566.t7.CDS5 31365078 31365099
chr_2 g8566 g8566.t7 TTS g8566.t7 NA NA

Sequences

>g8566.t7 Gene=g8566 Length=1020
ATGTCTGGTGAGTATGAGTGCAATCTTTTTCTCAAATAGTTTAATGGAAGAAATTTTCTT
TAGGAGCTGGTTGGCCAAAAAGAAGTACATCTTCTTCTAGTGATCAATCGCAAGCAATGA
CAAAAACACCTATAAGTCAGTCACTTACACTCAACAGAACAATAAATTTATATCCATTGA
CAAACTACACGTTTGGAACGAAAGAGCCATTATTTGAAAAAGATCCATCGGTTCCTGTAA
GATTCCAGAGAATGCGAGATGAGTTTGTCAAAATTGGGATGAGAAGATCAGTTGAAGGAT
GCTTGCTAGTTCATGAACATGGTTTACCTCATGTTTTATTGTTACAACTTGGAACAATGT
TCTTTAAACTTCCCGGTGGTGAATTGAATGCAGGCGAAGATGAAGTCGATGGACTGAAAA
GACTTTTGACAGAAACTTTAGGACAACCATCGGGATCTGCAGGAACATCATCATGCAATT
GGATTATTGAAGAATGTATTGGTAATTGGTATAGACCGAATTTTGAGCCGCCCGTTTATC
CGTATCTGGTTCCTCACATCACAAAGCCAAAGGAACATAAAAGATTATTTTTAGTTCAAC
TACAGGAAAAGGCACTCTTTGCTGTTCCAAAGAACTACAAGTTAGTAGCTGCACCTTTGT
TTGAGTTGTATGACAATTCGCAAGGCTATGGACCCATAATATCGTCACTTCCACAAGCGT
TATTTAACTTTATTTACATGTAAATGTAAATGTGAAATGATAAAGTCATGAAAACTTAAA
AGCTACGTTTTCTGTAACATTTAAGAAGTATCATTGTCATAAGGATATCATGAAATGTAA
ACGCTGAAAAAAGAAAACTAATATTGACAATTAGGCGTTAATTTTTAAGAATATAGTCTC
GATTCATCCACACATTGTATCTCCCTTTTGCATTATTTTTTTATGCTCTTTTTCTTTGAA
ATGTCATTATACCTTTAAAGTAATATAAAATAAAATTGTAATTGATAATTAAAATCAACA

>g8566.t7 Gene=g8566 Length=208
MTKTPISQSLTLNRTINLYPLTNYTFGTKEPLFEKDPSVPVRFQRMRDEFVKIGMRRSVE
GCLLVHEHGLPHVLLLQLGTMFFKLPGGELNAGEDEVDGLKRLLTETLGQPSGSAGTSSC
NWIIEECIGNWYRPNFEPPVYPYLVPHITKPKEHKRLFLVQLQEKALFAVPKNYKLVAAP
LFELYDNSQGYGPIISSLPQALFNFIYM

Protein features from InterProScan

Transcript Database ID Name Start End E.value
5 g8566.t7 Gene3D G3DSA:3.90.79.10 Nucleoside Triphosphate Pyrophosphohydrolase 14 208 0.0000000
2 g8566.t7 PANTHER PTHR13047:SF0 CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR SUBUNIT 5 10 203 0.0000000
3 g8566.t7 PANTHER PTHR13047 PRE-MRNA CLEAVAGE FACTOR IM, 25KD SUBUNIT 10 203 0.0000000
7 g8566.t7 PIRSF PIRSF017888 CPSF-25 1 208 0.0000000
1 g8566.t7 Pfam PF13869 Nucleotide hydrolase 15 204 0.0000000
6 g8566.t7 ProSiteProfiles PS51462 Nudix hydrolase domain profile. 55 184 9.8420000
4 g8566.t7 SUPERFAMILY SSF55811 Nudix 56 164 0.0000054

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:0003729 mRNA binding MF
GO:0016787 hydrolase activity MF
GO:0006378 mRNA polyadenylation BP
GO:0005849 mRNA cleavage factor complex CC

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