General information for g1641.t12
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as RNA-binding protein 8A.
Parent gene
- The parent gene g1641 is located on chr_3: 12271182..12271799 (- 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 | g1641 | g1641.t12 | TTS | g1641.t12 | 12271065 | 12271065 |
| chr_3 | g1641 | g1641.t12 | isoform | g1641.t12 | 12271182 | 12271799 |
| chr_3 | g1641 | g1641.t12 | exon | g1641.t12.exon1 | 12271182 | 12271474 |
| chr_3 | g1641 | g1641.t12 | cds | g1641.t12.CDS1 | 12271182 | 12271474 |
| chr_3 | g1641 | g1641.t12 | exon | g1641.t12.exon2 | 12271581 | 12271679 |
| chr_3 | g1641 | g1641.t12 | cds | g1641.t12.CDS2 | 12271581 | 12271679 |
| chr_3 | g1641 | g1641.t12 | exon | g1641.t12.exon3 | 12271739 | 12271799 |
| chr_3 | g1641 | g1641.t12 | cds | g1641.t12.CDS3 | 12271739 | 12271799 |
| chr_3 | g1641 | g1641.t12 | TSS | g1641.t12 | 12271884 | 12271884 |
Sequences
>g1641.t12 Gene=g1641 Length=453
ATGGCTGACGTTTTAGATATTGATAATGCTGAAGATTTTGAGGTTGATGATGATGGTGAT
CAGGGAATTTTGCGATTAAAAGAAAAAGCAAAGAAGAAAAAAGGTCGTGGATTTGGAGCT
GATACAATCCATCGTGAAACAATTGATTATGAAAGTGTACAAGGCTGGATCTTGTTTATT
ACATCAATACATGAAGAGGCACATGAGGATGATATTCAAGAGAAATTCTGTGAATTTGGA
GATATCAAAAACATTCATCTTAATCTCGATCGAAGAACTGGCTTTCTTAAAGGATATGCT
CTAGTCGAATATGAGACTTATAAGCAAGCACTTGCAGCTAAAGAAGCAATGGATGGTGCA
GAAATTTTGGGACAAAAAATCAGTGTCGATTGGTGTTTCGTGAAAGGTCCGAAAAGATCG
AGAAAAGGTGCTGATCGCAAAAAGAAGCAGTAA
>g1641.t12 Gene=g1641 Length=150
MADVLDIDNAEDFEVDDDGDQGILRLKEKAKKKKGRGFGADTIHRETIDYESVQGWILFI
TSIHEEAHEDDIQEKFCEFGDIKNIHLNLDRRTGFLKGYALVEYETYKQALAAKEAMDGA
EILGQKISVDWCFVKGPKRSRKGADRKKKQ
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g1641.t12 | CDD | cd12324 | RRM_RBM8 | 52 | 137 | 0.000 |
| 6 | g1641.t12 | Gene3D | G3DSA:3.30.70.330 | - | 1 | 148 | 0.000 |
| 2 | g1641.t12 | PANTHER | PTHR45894:SF1 | RNA-BINDING PROTEIN 8A | 2 | 146 | 0.000 |
| 3 | g1641.t12 | PANTHER | PTHR45894 | RNA-BINDING PROTEIN 8A | 2 | 146 | 0.000 |
| 1 | g1641.t12 | Pfam | PF00076 | RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) | 58 | 127 | 0.000 |
| 7 | g1641.t12 | ProSiteProfiles | PS50102 | Eukaryotic RNA Recognition Motif (RRM) profile. | 56 | 134 | 14.266 |
| 5 | g1641.t12 | SMART | SM00360 | rrm1_1 | 57 | 130 | 0.000 |
| 4 | g1641.t12 | SUPERFAMILY | SSF54928 | RNA-binding domain, RBD | 48 | 143 | 0.000 |
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:0003676 | nucleic acid binding | MF |
KEGG
Orthology
- This transcript has been annotated with K12876 (RNA-binding protein 8A)
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