General information for g13359.t6
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Pre-mRNA-splicing factor RBM22.
Parent gene
- The parent gene g13359 is located on chr_1: 29510425..29511391 (+ 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 | g13359 | g13359.t6 | TSS | g13359.t6 | 29509895 | 29509895 |
| chr_1 | g13359 | g13359.t6 | isoform | g13359.t6 | 29510087 | 29511391 |
| chr_1 | g13359 | g13359.t6 | exon | g13359.t6.exon1 | 29510087 | 29511056 |
| chr_1 | g13359 | g13359.t6 | cds | g13359.t6.CDS1 | 29510588 | 29511056 |
| chr_1 | g13359 | g13359.t6 | exon | g13359.t6.exon2 | 29511114 | 29511391 |
| chr_1 | g13359 | g13359.t6 | cds | g13359.t6.CDS2 | 29511114 | 29511391 |
| chr_1 | g13359 | g13359.t6 | TTS | g13359.t6 | 29511462 | 29511462 |
Sequences
>g13359.t6 Gene=g13359 Length=1248
ATGGCTATGAGCAAAACAACATCTACTTATAATCGAACGAATTGGGAAGATTCAGAGTTT
CCTATATTGTGTCAAACATGTCTAGGAGATAATCCTTATCTTCGAATGGTAAGTAATAAT
GAAATTTCTACAAAAATTATTTCTCATGAAAATCGATCATTTTTTCAGATTAAAGAGAAA
TATGGCAAAGAATGTAAAATTTGCAGTCGTCCATTCACAATATTTCGTTGGTGTCCAGGA
GCAAGAATGCGCTTTAAGAAGACAGAAATTTGTCAAACATGCTCAAAATTGAAGAACGTT
TGTCAAACATGTCTACTGGATCTTGAATATGGTAAAACATTTTTGAAATTTGAAAAACCT
TTTATTTGTTCATTTAAAATTACAATTTATTAAATTTCAGGATTACCGACTCAAGTGCGA
GATACAGCACTCAAAATTCAAGATGAAATCCCACAAAGTGATGTAAATAAAGAATATTAT
TTGCAAAATGTTGAAAAGCAAATGGCAATGAATGATGGACAAATGCCTGGTGGTGGAAAA
GCTCAACAAGCTTCAGATGTTTTATCTAAATTAGCTCGCACTACACCATATTACAAACGA
AATCTTCCTCACATTTGCTCATTTTGGGTAAAAGGAGAATGTAAAAGAGGTGAAGAGTGT
CCATATAGACATGAAAAACCAAACGATGTAGACGATCCTCTCTCAGAACAAAATATTCGT
GATCGATATTATGGTGTTAACGATCCAGTAGCTGAAAAGTTACTTAAAAGAGCTGCTTCA
TTACCTGTCCTTGAAACTCCTAGTGACAAGACAATAACTACATTATATTGTGGTAATGTC
GGTGAACATTTGACCGAAGTTGATATAAGAGATCAATTTTATCAATATGGAGAAATTAGA
AATGTAACACTTGTGCCGAAACAACAGTGTGCTTTCGTACAGTTTACCAAACGTTCTTCA
GCTGAATTGGGGGCATACTCACAAGCAAAACAAGCCACAGCCACATCATCATCATCACAA
TTGCGGCCTCGTATTGATCCCCGTTTAGATCCTGTACCTGGACTCCCCGATTTACCAACA
CCAAACGATTATTTCAATTTGAATGCAAATGATATGATGGTTCTACCAGCGGGCGTTAAA
CTTGCACAAATTCCACAACAATTTTTGCCACCCTCATTACCAAATACATCATCTGGAATA
CATTATCCTTCTATGGATCCAAGTCGATTAGGCGCACTACAAAAATAA
>g13359.t6 Gene=g13359 Length=248
MAMNDGQMPGGGKAQQASDVLSKLARTTPYYKRNLPHICSFWVKGECKRGEECPYRHEKP
NDVDDPLSEQNIRDRYYGVNDPVAEKLLKRAASLPVLETPSDKTITTLYCGNVGEHLTEV
DIRDQFYQYGEIRNVTLVPKQQCAFVQFTKRSSAELGAYSQAKQATATSSSSQLRPRIDP
RLDPVPGLPDLPTPNDYFNLNANDMMVLPAGVKLAQIPQQFLPPSLPNTSSGIHYPSMDP
SRLGALQK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g13359.t6 | Gene3D | G3DSA:4.10.1000.10 | CCCH zinc finger | 25 | 74 | 3.5E-7 |
| 10 | g13359.t6 | Gene3D | G3DSA:3.30.70.330 | - | 101 | 177 | 3.2E-13 |
| 8 | g13359.t6 | MobiDBLite | mobidb-lite | consensus disorder prediction | 229 | 248 | - |
| 2 | g13359.t6 | PANTHER | PTHR14089 | PRE-MRNA-SPLICING FACTOR RBM22 | 12 | 245 | 1.9E-68 |
| 3 | g13359.t6 | PANTHER | PTHR14089:SF6 | PRE-MRNA-SPLICING FACTOR RBM22 | 12 | 245 | 1.9E-68 |
| 1 | g13359.t6 | Pfam | PF00076 | RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) | 108 | 155 | 2.7E-8 |
| 11 | g13359.t6 | ProSiteProfiles | PS50103 | Zinc finger C3H1-type profile. | 38 | 60 | 14.774 |
| 12 | g13359.t6 | ProSiteProfiles | PS50102 | Eukaryotic RNA Recognition Motif (RRM) profile. | 106 | 155 | 10.036 |
| 6 | g13359.t6 | SMART | SM00356 | c3hfinal6 | 33 | 59 | 3.0E-5 |
| 7 | g13359.t6 | SMART | SM00360 | rrm1_1 | 107 | 177 | 4.2E-5 |
| 5 | g13359.t6 | SUPERFAMILY | SSF90229 | CCCH zinc finger | 36 | 58 | 1.96E-6 |
| 4 | g13359.t6 | SUPERFAMILY | SSF54928 | RNA-binding domain, RBD | 100 | 155 | 2.17E-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:0046872 | metal ion binding | MF |
| GO:0003723 | RNA binding | MF |
| 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.
