General information for g1172.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Cleavage stimulation factor subunit 2.
Parent gene
- The parent gene g1172 is located on chr_3: 8485688..8487626 (+ 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_3 | g1172 | g1172.t1 | TSS | g1172.t1 | 8484402 | 8484402 |
| chr_3 | g1172 | g1172.t1 | isoform | g1172.t1 | 8484493 | 8485688 |
| chr_3 | g1172 | g1172.t1 | exon | g1172.t1.exon1 | 8484493 | 8484550 |
| chr_3 | g1172 | g1172.t1 | cds | g1172.t1.CDS1 | 8484493 | 8484550 |
| chr_3 | g1172 | g1172.t1 | exon | g1172.t1.exon2 | 8484616 | 8485688 |
| chr_3 | g1172 | g1172.t1 | cds | g1172.t1.CDS2 | 8484616 | 8485688 |
| chr_3 | g1172 | g1172.t1 | TTS | g1172.t1 | 8485773 | 8485773 |
Sequences
>g1172.t1 Gene=g1172 Length=1131
ATGGTTGACAAGAATAATGACCAATCTATTATGGATAAGTCTATGCGATCAGTCTTCGTT
GGTAATATACCTTACGAAGCGACAGAAGAGAAATTAAAGGATATATTTAGTGAAGTAGGG
CCAGTTATTTCTCTAAAACTTGTATTTGATCGTGAAAGCGGAAAGCCAAAAGGATATGGA
TTTTGTGAATATAAAGATCAAGAAACTGCATTGTCGGCAATGAGAAATTTAAACGGCTAT
GAAATTGGTGGACGAACATTACGTGTTGATAATGCTTGTACTGAAAAATCTCGAATGGAA
ATGGCAGCACTTTTGTCAGGTCCACAAGTTGAAAATCCTTATGGAGAGCATTGTTCACCT
GAAGAGGCTCCAGAAATTATAAGCAAGACGATAGCTTCTTTACCTCCCGAGCAAATGTAT
GAACTAATGAAACAAATGAAGCAATGCATTCAAAATAATCCTCATGAAGCACGACAGATG
CTTATTCAAAACCCTCAACTTTCATATGCACTGTTGCAAGCTCAAGTAGTTATGAGGATC
ATTGATTCATCAACAGCTGTCTCTTTTCTGTTCAAACCGAATGTTATGCCGCCAGTTTTA
ACAACTCAATCGACAACCCAAAGTGTTCAATCTATGATGAATACAACTTTGGCAAGTATG
GGACAAGCACCATTAAATCCTGCCGTCTCATTTCCACAAGATGTCGATTTACGTTCAGTT
GTTGATCCACGTTTAAGCAGACAGCAAGCTGCTCCGATGGATATGGATATGAGAATGATG
CAAATTCCTCCGGCATTTGATCAGAGAGCTGCTGCTACAACTGCTCAACCAACAGCACCA
CCTCAGAGAGCATTCCCGAGCGATCCTAGACAGAGAGGAAATGATTCAAGAGATCCGAGA
CAAAAAGCTCAACAACAGCAGCAGCAACAACAACAACAAGCTCAAAGTAATTCACTTGCT
GCACAATTACATAGAGGTATTCAAAATGATGCAAGTGACCAAGAGAAAGCTGCATTGATT
ATGCAAGTACTGAAATTGACAGATGAGCAAATTGCTATTTTACCGCCTGAACAGCGTGCA
AGCATTCTTGTATTAAAAGAACAAATTGCAAAAAGTGCAAGTTTGAAATAA
>g1172.t1 Gene=g1172 Length=376
MVDKNNDQSIMDKSMRSVFVGNIPYEATEEKLKDIFSEVGPVISLKLVFDRESGKPKGYG
FCEYKDQETALSAMRNLNGYEIGGRTLRVDNACTEKSRMEMAALLSGPQVENPYGEHCSP
EEAPEIISKTIASLPPEQMYELMKQMKQCIQNNPHEARQMLIQNPQLSYALLQAQVVMRI
IDSSTAVSFLFKPNVMPPVLTTQSTTQSVQSMMNTTLASMGQAPLNPAVSFPQDVDLRSV
VDPRLSRQQAAPMDMDMRMMQIPPAFDQRAAATTAQPTAPPQRAFPSDPRQRGNDSRDPR
QKAQQQQQQQQQQAQSNSLAAQLHRGIQNDASDQEKAALIMQVLKLTDEQIAILPPEQRA
SILVLKEQIAKSASLK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 11 | g1172.t1 | CDD | cd12671 | RRM_CSTF2_CSTF2T | 18 | 92 | 4.12202E-54 |
| 9 | g1172.t1 | Gene3D | G3DSA:3.30.70.330 | - | 2 | 103 | 1.2E-30 |
| 10 | g1172.t1 | Gene3D | G3DSA:1.10.20.70 | - | 330 | 374 | 3.7E-23 |
| 13 | g1172.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 268 | 321 | - |
| 14 | g1172.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 300 | 321 | - |
| 5 | g1172.t1 | PANTHER | PTHR45735:SF6 | CLEAVAGE STIMULATION FACTOR SUBUNIT 2 | 10 | 229 | 7.0E-105 |
| 7 | g1172.t1 | PANTHER | PTHR45735 | CLEAVAGE STIMULATION FACTOR SUBUNIT 2 | 10 | 229 | 7.0E-105 |
| 4 | g1172.t1 | PANTHER | PTHR45735:SF6 | CLEAVAGE STIMULATION FACTOR SUBUNIT 2 | 323 | 373 | 7.0E-105 |
| 6 | g1172.t1 | PANTHER | PTHR45735 | CLEAVAGE STIMULATION FACTOR SUBUNIT 2 | 323 | 373 | 7.0E-105 |
| 2 | g1172.t1 | Pfam | PF00076 | RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) | 18 | 88 | 1.7E-24 |
| 1 | g1172.t1 | Pfam | PF14327 | Hinge domain of cleavage stimulation factor subunit 2 | 112 | 188 | 1.9E-30 |
| 3 | g1172.t1 | Pfam | PF14304 | Transcription termination and cleavage factor C-terminal | 333 | 372 | 7.6E-19 |
| 15 | g1172.t1 | ProSiteProfiles | PS50102 | Eukaryotic RNA Recognition Motif (RRM) profile. | 16 | 94 | 20.952 |
| 12 | g1172.t1 | SMART | SM00360 | rrm1_1 | 17 | 90 | 2.1E-29 |
| 8 | g1172.t1 | SUPERFAMILY | SSF54928 | RNA-binding domain, RBD | 7 | 109 | 3.36E-32 |
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:0003723 | RNA binding | MF |
| GO:0005847 | mRNA cleavage and polyadenylation specificity factor complex | CC |
| GO:0031124 | mRNA 3’-end processing | BP |
| GO:0006378 | mRNA polyadenylation | BP |
| GO:0003676 | nucleic acid binding | MF |
KEGG
Orthology
- This transcript has been annotated with K14407 (cleavage stimulation factor subunit 2)
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.
