General information for g8566.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Cleavage and polyadenylation specificity factor subunit 5.
Parent gene
- The parent gene g8566 is located on chr_2: 31363989..31365376 (+ strand)
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.t1 | TSS | g8566.t1 | 31362597 | 31362597 |
| chr_2 | g8566 | g8566.t1 | isoform | g8566.t1 | 31362796 | 31365099 |
| chr_2 | g8566 | g8566.t1 | exon | g8566.t1.exon1 | 31362796 | 31362802 |
| chr_2 | g8566 | g8566.t1 | cds | g8566.t1.CDS1 | 31362796 | 31362802 |
| chr_2 | g8566 | g8566.t1 | exon | g8566.t1.exon2 | 31362859 | 31362964 |
| chr_2 | g8566 | g8566.t1 | cds | g8566.t1.CDS2 | 31362859 | 31362964 |
| chr_2 | g8566 | g8566.t1 | exon | g8566.t1.exon3 | 31363020 | 31363284 |
| chr_2 | g8566 | g8566.t1 | cds | g8566.t1.CDS3 | 31363020 | 31363284 |
| chr_2 | g8566 | g8566.t1 | exon | g8566.t1.exon4 | 31363907 | 31364084 |
| chr_2 | g8566 | g8566.t1 | cds | g8566.t1.CDS4 | 31363907 | 31364084 |
| chr_2 | g8566 | g8566.t1 | exon | g8566.t1.exon5 | 31364908 | 31365022 |
| chr_2 | g8566 | g8566.t1 | cds | g8566.t1.CDS5 | 31364908 | 31365022 |
| chr_2 | g8566 | g8566.t1 | exon | g8566.t1.exon6 | 31365078 | 31365099 |
| chr_2 | g8566 | g8566.t1 | cds | g8566.t1.CDS6 | 31365078 | 31365099 |
| chr_2 | g8566 | g8566.t1 | TTS | g8566.t1 | 31365371 | 31365371 |
Sequences
>g8566.t1 Gene=g8566 Length=693
ATGTCTGGAGCTGGTTGGCCAAAAAGAAGTACATCTTCTTCTAGTGATCAATCGCAAGCA
ATGACAAAAACACCTATAAGTCAGTCACTTACACTCAACAGAACAATAAATTTATATCCA
TTGACAAACTACACGTTTGGAACGAAAGAGCCATTATTTGAAAAAGATCCATCGGTTCCT
GTAAGATTCCAGAGAATGCGAGATGAGTTTGTCAAAATTGGGATGAGAAGATCAGTTGAA
GGATGCTTGCTAGTTCATGAACATGGTTTACCTCATGTTTTATTGTTACAACTTGGAACA
ATGTTCTTTAAACTTCCCGGTGGTGAATTGAATGCAGGCGAAGATGAAGTCGATGGACTG
AAAAGACTTTTGACAGAAACTTTAGGACAACCATCGGGATCTGCAGGAACATCATCATGC
AATTGGATTATTGAAGAATGTATTGGTAATTGGTATAGACCGAATTTTGAGCCGCCCGTT
TATCCGTATCTGGTTCCTCACATCACAAAGCCAAAGGAACATAAAAGATTATTTTTAGTT
CAACTACAGGAAAAGGCACTCTTTGCTGTTCCAAAGAACTACAAGTTAGTAGCTGCACCT
TTGTTTGAGTTGTATGACAATTCGCAAGGCTATGGACCCATAATATCGTCACTTCCACAA
GCGTTGTGTCGATTTAACTTTATTTACATGTAA
>g8566.t1 Gene=g8566 Length=230
MSGAGWPKRSTSSSSDQSQAMTKTPISQSLTLNRTINLYPLTNYTFGTKEPLFEKDPSVP
VRFQRMRDEFVKIGMRRSVEGCLLVHEHGLPHVLLLQLGTMFFKLPGGELNAGEDEVDGL
KRLLTETLGQPSGSAGTSSCNWIIEECIGNWYRPNFEPPVYPYLVPHITKPKEHKRLFLV
QLQEKALFAVPKNYKLVAAPLFELYDNSQGYGPIISSLPQALCRFNFIYM
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g8566.t1 | Gene3D | G3DSA:3.90.79.10 | Nucleoside Triphosphate Pyrophosphohydrolase | 34 | 230 | 5.5E-85 |
| 5 | g8566.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 26 | - |
| 2 | g8566.t1 | PANTHER | PTHR13047:SF0 | CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR SUBUNIT 5 | 30 | 230 | 8.4E-90 |
| 3 | g8566.t1 | PANTHER | PTHR13047 | PRE-MRNA CLEAVAGE FACTOR IM, 25KD SUBUNIT | 30 | 230 | 8.4E-90 |
| 8 | g8566.t1 | PIRSF | PIRSF017888 | CPSF-25 | 7 | 230 | 5.3E-88 |
| 1 | g8566.t1 | Pfam | PF13869 | Nucleotide hydrolase | 35 | 225 | 2.7E-73 |
| 7 | g8566.t1 | ProSiteProfiles | PS51462 | Nudix hydrolase domain profile. | 75 | 204 | 9.842 |
| 4 | g8566.t1 | SUPERFAMILY | SSF55811 | Nudix | 76 | 184 | 7.11E-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
- This transcript has been annotated with K14397 (cleavage and polyadenylation specificity factor subunit 5)
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.
