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.t6 TSS g8566.t6 31362597 31362597
chr_2 g8566 g8566.t6 isoform g8566.t6 31362796 31365099
chr_2 g8566 g8566.t6 exon g8566.t6.exon1 31362796 31362802
chr_2 g8566 g8566.t6 cds g8566.t6.CDS1 31362796 31362802
chr_2 g8566 g8566.t6 exon g8566.t6.exon2 31362859 31362964
chr_2 g8566 g8566.t6 cds g8566.t6.CDS2 31362859 31362964
chr_2 g8566 g8566.t6 exon g8566.t6.exon3 31363020 31363284
chr_2 g8566 g8566.t6 cds g8566.t6.CDS3 31363020 31363284
chr_2 g8566 g8566.t6 exon g8566.t6.exon4 31363907 31364084
chr_2 g8566 g8566.t6 cds g8566.t6.CDS4 31363907 31364084
chr_2 g8566 g8566.t6 exon g8566.t6.exon5 31364908 31365016
chr_2 g8566 g8566.t6 cds g8566.t6.CDS5 31364908 31365016
chr_2 g8566 g8566.t6 exon g8566.t6.exon6 31365078 31365099
chr_2 g8566 g8566.t6 cds g8566.t6.CDS6 31365078 31365099
chr_2 g8566 g8566.t6 TTS g8566.t6 31365371 31365371

Sequences

>g8566.t6 Gene=g8566 Length=687
ATGTCTGGAGCTGGTTGGCCAAAAAGAAGTACATCTTCTTCTAGTGATCAATCGCAAGCA
ATGACAAAAACACCTATAAGTCAGTCACTTACACTCAACAGAACAATAAATTTATATCCA
TTGACAAACTACACGTTTGGAACGAAAGAGCCATTATTTGAAAAAGATCCATCGGTTCCT
GTAAGATTCCAGAGAATGCGAGATGAGTTTGTCAAAATTGGGATGAGAAGATCAGTTGAA
GGATGCTTGCTAGTTCATGAACATGGTTTACCTCATGTTTTATTGTTACAACTTGGAACA
ATGTTCTTTAAACTTCCCGGTGGTGAATTGAATGCAGGCGAAGATGAAGTCGATGGACTG
AAAAGACTTTTGACAGAAACTTTAGGACAACCATCGGGATCTGCAGGAACATCATCATGC
AATTGGATTATTGAAGAATGTATTGGTAATTGGTATAGACCGAATTTTGAGCCGCCCGTT
TATCCGTATCTGGTTCCTCACATCACAAAGCCAAAGGAACATAAAAGATTATTTTTAGTT
CAACTACAGGAAAAGGCACTCTTTGCTGTTCCAAAGAACTACAAGTTAGTAGCTGCACCT
TTGTTTGAGTTGTATGACAATTCGCAAGGCTATGGACCCATAATATCGTCACTTCCACAA
GCGTTATTTAACTTTATTTACATGTAA

>g8566.t6 Gene=g8566 Length=228
MSGAGWPKRSTSSSSDQSQAMTKTPISQSLTLNRTINLYPLTNYTFGTKEPLFEKDPSVP
VRFQRMRDEFVKIGMRRSVEGCLLVHEHGLPHVLLLQLGTMFFKLPGGELNAGEDEVDGL
KRLLTETLGQPSGSAGTSSCNWIIEECIGNWYRPNFEPPVYPYLVPHITKPKEHKRLFLV
QLQEKALFAVPKNYKLVAAPLFELYDNSQGYGPIISSLPQALFNFIYM

Protein features from InterProScan

Transcript Database ID Name Start End E.value
6 g8566.t6 Gene3D G3DSA:3.90.79.10 Nucleoside Triphosphate Pyrophosphohydrolase 34 228 2.0E-81
5 g8566.t6 MobiDBLite mobidb-lite consensus disorder prediction 1 26 -
2 g8566.t6 PANTHER PTHR13047:SF0 CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR SUBUNIT 5 30 223 5.9E-87
3 g8566.t6 PANTHER PTHR13047 PRE-MRNA CLEAVAGE FACTOR IM, 25KD SUBUNIT 30 223 5.9E-87
8 g8566.t6 PIRSF PIRSF017888 CPSF-25 7 228 3.6E-85
1 g8566.t6 Pfam PF13869 Nucleotide hydrolase 35 224 5.2E-72
7 g8566.t6 ProSiteProfiles PS51462 Nudix hydrolase domain profile. 75 204 9.842
4 g8566.t6 SUPERFAMILY SSF55811 Nudix 76 184 6.96E-6

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. There were no conditions that were differentially expressed