General information for g11823.t4
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Cleavage and polyadenylation specificity factor subunit CG7185.
Parent gene
- The parent gene g11823 is located on chr_1: 18589994..18591160 (- 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_1 | g11823 | g11823.t4 | isoform | g11823.t4 | 18589994 | 18590859 |
| chr_1 | g11823 | g11823.t4 | exon | g11823.t4.exon1 | 18589994 | 18590859 |
| chr_1 | g11823 | g11823.t4 | cds | g11823.t4.CDS1 | 18589994 | 18590740 |
| chr_1 | g11823 | g11823.t4 | TSS | g11823.t4 | 18591259 | 18591259 |
| chr_1 | g11823 | g11823.t4 | TTS | g11823.t4 | NA | NA |
Sequences
>g11823.t4 Gene=g11823 Length=866
AAGAAGATGATTTATATGATGACGTTCTTACATCGGGATCAAACAATATAAACAGTGAGA
ATAATGCGTCCTCAGAACATAATGCAGAAACAGAAACTAATGGAAATTATCAAGGAAACA
TGCATAATATTGCAAAAAGATTTCAACTTTACGTTGGAAATCTAACTTGGTGGACAACTG
ATTCTGATATTACTGATGCAGTTATCGCTACAGGTGTCAATGACTTTCAAGAAGTAAAAT
TTTTTGAAAATCGTGCCAATGGTCAATCCAAAGGCTTCTGTGTAATCTCGCTTGGATCTG
AAGCTAGCATGCGAATTGTTTTAGAGAACTTGCCGAAAAAAGAACTAAACGGACAAACTC
CAATTGTCACATTACCTACAAAACAAGCATTGAATCAGTTTGAAAGTCAGCAAAAAACAA
GACCTACTCCTCCTGTTCCAAATCCAAATCAGCAGAAAACGAGTGGAATAGCTAATAGCG
GTCCAAATAACTTGATGAACCCAAATATGCCGCTTCAAATGCATCCACGAATGATGAATC
CACCTATGCGAGGAAACATGCAAAATCCTCCGATGATGAATCCAAATATGCAACAAAGGA
TGCCCTTATCGCCGCAAATGAATCATGCTCCGCAAATGAACAATATGCGATTTCAAAATA
ATTGGAATAATGGTCCTATTCGTCCACCGATTCACCCAAATGGCATGCAAAATAATAATC
GACCGCCACCTCCAATGAATATGCCACCACAAGGTCATCCCATGCCAAATAATATGATGA
ATAGGCCAATGAATATGCCACCATCTGGAAGACCACCTTTTGGTCCTAATCCTAATCGAC
CAATGCATCCAAATTTCAATCAACAT
>g11823.t4 Gene=g11823 Length=249
MHNIAKRFQLYVGNLTWWTTDSDITDAVIATGVNDFQEVKFFENRANGQSKGFCVISLGS
EASMRIVLENLPKKELNGQTPIVTLPTKQALNQFESQQKTRPTPPVPNPNQQKTSGIANS
GPNNLMNPNMPLQMHPRMMNPPMRGNMQNPPMMNPNMQQRMPLSPQMNHAPQMNNMRFQN
NWNNGPIRPPIHPNGMQNNNRPPPPMNMPPQGHPMPNNMMNRPMNMPPSGRPPFGPNPNR
PMHPNFNQH
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g11823.t4 | CDD | cd12643 | RRM_CFIm68 | 9 | 84 | 2.70321E-49 |
| 5 | g11823.t4 | Gene3D | G3DSA:3.30.70.330 | - | 9 | 99 | 6.9E-18 |
| 8 | g11823.t4 | MobiDBLite | mobidb-lite | consensus disorder prediction | 95 | 123 | - |
| 10 | g11823.t4 | MobiDBLite | mobidb-lite | consensus disorder prediction | 224 | 249 | - |
| 9 | g11823.t4 | MobiDBLite | mobidb-lite | consensus disorder prediction | 226 | 240 | - |
| 2 | g11823.t4 | PANTHER | PTHR23204 | CLEAVAGE AND POLYADENYLATION SPECIFIC FACTOR | 5 | 246 | 7.6E-49 |
| 3 | g11823.t4 | PANTHER | PTHR23204:SF7 | CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR SUBUNIT 6 | 5 | 246 | 7.6E-49 |
| 1 | g11823.t4 | Pfam | PF00076 | RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) | 10 | 80 | 3.5E-7 |
| 11 | g11823.t4 | ProSiteProfiles | PS50102 | Eukaryotic RNA Recognition Motif (RRM) profile. | 8 | 88 | 9.763 |
| 7 | g11823.t4 | SMART | SM00360 | rrm1_1 | 9 | 84 | 1.2E-9 |
| 4 | g11823.t4 | SUPERFAMILY | SSF54928 | RNA-binding domain, RBD | 8 | 102 | 4.25E-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
This gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).
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.
