General information for g11823.t3
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.t3 | TTS | g11823.t3 | 18588115 | 18588115 |
| chr_1 | g11823 | g11823.t3 | isoform | g11823.t3 | 18588415 | 18591160 |
| chr_1 | g11823 | g11823.t3 | exon | g11823.t3.exon1 | 18588415 | 18588770 |
| chr_1 | g11823 | g11823.t3 | exon | g11823.t3.exon2 | 18588995 | 18589591 |
| chr_1 | g11823 | g11823.t3 | cds | g11823.t3.CDS1 | 18588995 | 18589591 |
| chr_1 | g11823 | g11823.t3 | exon | g11823.t3.exon3 | 18589994 | 18590878 |
| chr_1 | g11823 | g11823.t3 | cds | g11823.t3.CDS2 | 18589994 | 18590878 |
| chr_1 | g11823 | g11823.t3 | exon | g11823.t3.exon4 | 18591089 | 18591160 |
| chr_1 | g11823 | g11823.t3 | cds | g11823.t3.CDS3 | 18591089 | 18591160 |
| chr_1 | g11823 | g11823.t3 | TSS | g11823.t3 | 18591259 | 18591259 |
Sequences
>g11823.t3 Gene=g11823 Length=1910
ATGAGTGAAAATGTTGATAGTGATCTTCTGTATGAAGATTTTCAAAATGAAGACCAAAAG
GAATTTAATAATGAAAGTTATGGGCATGTACAAGAAGATGATTTATATGATGACGTTCTT
ACATCGGGATCAAACAATATAAACAGTGAGAATAATGCGTCCTCAGAACATAATGCAGAA
ACAGAAACTAATGGAAATTATCAAGGAAACATGCATAATATTGCAAAAAGATTTCAACTT
TACGTTGGAAATCTAACTTGGTGGACAACTGATTCTGATATTACTGATGCAGTTATCGCT
ACAGGTGTCAATGACTTTCAAGAAGTAAAATTTTTTGAAAATCGTGCCAATGGTCAATCC
AAAGGCTTCTGTGTAATCTCGCTTGGATCTGAAGCTAGCATGCGAATTGTTTTAGAGAAC
TTGCCGAAAAAAGAACTAAACGGACAAACTCCAATTGTCACATTACCTACAAAACAAGCA
TTGAATCAGTTTGAAAGTCAGCAAAAAACAAGACCTACTCCTCCTGTTCCAAATCCAAAT
CAGCAGAAAACGAGTGGAATAGCTAATAGCGGTCCAAATAACTTGATGAACCCAAATATG
CCGCTTCAAATGCATCCACGAATGATGAATCCACCTATGCGAGGAAACATGCAAAATCCT
CCGATGATGAATCCAAATATGCAACAAAGGATGCCCTTATCGCCGCAAATGAATCATGCT
CCGCAAATGAACAATATGCGATTTCAAAATAATTGGAATAATGGTCCTATTCGTCCACCG
ATTCACCCAAATGGCATGCAAAATAATAATCGACCGCCACCTCCAATGAATATGCCACCA
CAAGGTCATCCCATGCCAAATAATATGATGAATAGGCCAATGAATATGCCACCATCTGGA
AGACCACCTTTTGGTCCTAATCCTAATCGACCAATGCATCCAAATTTCAATCAACATAAT
ATTATGCCACCACGAGGACCTCCTATGCCACCAATGAATAATCAAGGTCCACCGGCACCA
CATGTGAATCCTGCTTTCTTCAATCAAGGACCTGTGCAAAATATCGTACCTCCTCCAGGA
AATCATTTTAATCAAGCACCGAGACCAATGTGGGGAGGCAATAAAATGCCAAATGTTTTC
GATCAAGCAACTGGCGGACCGCCTACAGGTGTTCCTAATCAACAACCAATTAGTGAAACT
GAATTTGAAGAAATTATGAGTCGTAATAGAACTGTTAGTAGTTCTGCGATCGCACGTGCT
GTTTCTGATGCGGCTGCTGGAGAATATAGTAGTGCTATAGAAACTCTTGCTACAACAATT
TCATTAATAAAGCAATCAAAAGTTGCTAATGATGAGCGTTGCAAAATTTTGATCAATTCA
TTGCAAGATACATTGCAAGGTATAGAAGCAAAAAGCTTTAATCGTCGAGATAGATCTGAG
AGATCTAGATCACGTGAAAGACGTCGAAGAAGAGAAAGATCAAACTCTCGCTCATATAGA
CGATCAAGGAGTCGTGAACATCGTGATCATCGTGATAGAGGAAGAGATGAGTAATCGTTA
TTATGGTGGTGAAAACTATCATCGTGATACACGTGAACGCTCAAGATCAAGAGATCGCGG
AAATGCAGAACATTATCGAGGAGGCGATGAAAGGTATTATCTGTCTTGTCCCCTCTACTT
ATTTTAAATACATTGGAAATGATTCATTGAAGAATAATTAATAGAAAGTTATTTATCTTA
CAAATTTAAAAAAAAATTAATTTCATTTTTTTTGCAGTAACAGCAGAAGTCGTCCACGCA
AATCAGCTGAACCATCAGGTGAAAATTCAGAGAACTTCAAACGTTCTTATGATGACCGTA
ATCGCGATTCAGACAGATATCGTGATCGTGAAACCAGAAATCGTCACTAG
>g11823.t3 Gene=g11823 Length=517
MSENVDSDLLYEDFQNEDQKEFNNESYGHVQEDDLYDDVLTSGSNNINSENNASSEHNAE
TETNGNYQGNMHNIAKRFQLYVGNLTWWTTDSDITDAVIATGVNDFQEVKFFENRANGQS
KGFCVISLGSEASMRIVLENLPKKELNGQTPIVTLPTKQALNQFESQQKTRPTPPVPNPN
QQKTSGIANSGPNNLMNPNMPLQMHPRMMNPPMRGNMQNPPMMNPNMQQRMPLSPQMNHA
PQMNNMRFQNNWNNGPIRPPIHPNGMQNNNRPPPPMNMPPQGHPMPNNMMNRPMNMPPSG
RPPFGPNPNRPMHPNFNQHNIMPPRGPPMPPMNNQGPPAPHVNPAFFNQGPVQNIVPPPG
NHFNQAPRPMWGGNKMPNVFDQATGGPPTGVPNQQPISETEFEEIMSRNRTVSSSAIARA
VSDAAAGEYSSAIETLATTISLIKQSKVANDERCKILINSLQDTLQGIEAKSFNRRDRSE
RSRSRERRRRRERSNSRSYRRSRSREHRDHRDRGRDE
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g11823.t3 | CDD | cd12643 | RRM_CFIm68 | 79 | 154 | 1.69513E-46 |
| 5 | g11823.t3 | Gene3D | G3DSA:3.30.70.330 | - | 79 | 169 | 2.6E-17 |
| 8 | g11823.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 165 | 193 | - |
| 9 | g11823.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 471 | 517 | - |
| 10 | g11823.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 482 | 508 | - |
| 2 | g11823.t3 | PANTHER | PTHR23204 | CLEAVAGE AND POLYADENYLATION SPECIFIC FACTOR | 17 | 516 | 2.9E-96 |
| 3 | g11823.t3 | PANTHER | PTHR23204:SF7 | CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR SUBUNIT 6 | 17 | 516 | 2.9E-96 |
| 1 | g11823.t3 | Pfam | PF00076 | RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) | 80 | 150 | 1.2E-6 |
| 11 | g11823.t3 | ProSiteProfiles | PS50102 | Eukaryotic RNA Recognition Motif (RRM) profile. | 78 | 158 | 9.763 |
| 7 | g11823.t3 | SMART | SM00360 | rrm1_1 | 79 | 154 | 1.2E-9 |
| 4 | g11823.t3 | SUPERFAMILY | SSF54928 | RNA-binding domain, RBD | 77 | 171 | 1.66E-13 |
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 transcript has been annotated with K14398 (cleavage and polyadenylation specificity factor subunit 6/7)
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.
