General information for g13359.t3
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.t3 | isoform | g13359.t3 | 29509740 | 29511391 |
| chr_1 | g13359 | g13359.t3 | exon | g13359.t3.exon1 | 29509740 | 29509991 |
| chr_1 | g13359 | g13359.t3 | exon | g13359.t3.exon2 | 29510057 | 29510194 |
| chr_1 | g13359 | g13359.t3 | cds | g13359.t3.CDS1 | 29510087 | 29510194 |
| chr_1 | g13359 | g13359.t3 | exon | g13359.t3.exon3 | 29510255 | 29510417 |
| chr_1 | g13359 | g13359.t3 | cds | g13359.t3.CDS2 | 29510255 | 29510417 |
| chr_1 | g13359 | g13359.t3 | exon | g13359.t3.exon4 | 29510487 | 29511391 |
| chr_1 | g13359 | g13359.t3 | cds | g13359.t3.CDS3 | 29510487 | 29511391 |
| chr_1 | g13359 | g13359.t3 | TTS | g13359.t3 | 29511462 | 29511462 |
| chr_1 | g13359 | g13359.t3 | TSS | g13359.t3 | NA | NA |
Sequences
>g13359.t3 Gene=g13359 Length=1458
TTGTTATTATCCTTTAACAACTTGTATTTATCGTTGAATTTAAATTTTATTAAATTTTCA
GGAACAACAGAGCGTGTTTTAACCTTTGTTGAAGCTAAGAGGGTTTGAGGAAATTTTTCA
GCAGTAATGCGCCTAAAATTATATTCATTCCCCTTTAGGAAACTTTTTTTTATTTCAATA
TTTTGTCATATTAATTTTCAATTTTATAAAGCATATTAAAATCTATTTTAGATTTATTTA
AATCATCGTGAGAAAAGTCAATAAAACTTATTTTGCTTCAAAATGGCTATGAGCAAAACA
ACATCTACTTATAATCGAACGAATTGGGAAGATTCAGAGTTTCCTATATTGTGTCAAACA
TGTCTAGGAGATAATCCTTATCTTCGAATGATTAAAGAGAAATATGGCAAAGAATGTAAA
ATTTGCAGTCGTCCATTCACAATATTTCGTTGGTGTCCAGGAGCAAGAATGCGCTTTAAG
AAGACAGAAATTTGTCAAACATGCTCAAAATTGAAGAACGTTTGTCAAACATGTCTACTG
GATCTTGAATATGGATTACCGACTCAAGTGCGAGATACAGCACTCAAAATTCAAGATGAA
ATCCCACAAAGTGATGTAAATAAAGAATATTATTTGCAAAATGTTGAAAAGCAAATGGCA
ATGAATGATGGACAAATGCCTGGTGGTGGAAAAGCTCAACAAGCTTCAGATGTTTTATCT
AAATTAGCTCGCACTACACCATATTACAAACGAAATCTTCCTCACATTTGCTCATTTTGG
GTAAAAGGAGAATGTAAAAGAGGTGAAGAGTGTCCATATAGACATGAAAAACCAAACGAT
GTAGACGATCCTCTCTCAGAACAAAATATTCGTGATCGATATTATGGTGTTAACGATCCA
GTAGCTGAAAAGTTACTTAAAAGAGCTGCTTCATTACCTGTCCTTGAAACTCCTAGTGAC
AAGACAATAACTACATTATATTGTGGTAATGTCGGTGAACATTTGACCGAAGTTGATATA
AGAGATCAATTTTATCAATATGGAGAAATTAGAAATGTAACACTTGTGCCGAAACAACAG
TGTGCTTTCGTACAGTTTACCAAACGTTCTTCAGCTGAATTGGCAGCAGAGAAGACCTTC
AATAAATTGGTTCTTGGTGGTAAAAAATTGAGCATACGATGGGCATACTCACAAGCAAAA
CAAGCCACAGCCACATCATCATCATCACAATTGCGGCCTCGTATTGATCCCCGTTTAGAT
CCTGTACCTGGACTCCCCGATTTACCAACACCAAACGATTATTTCAATTTGAATGCAAAT
GATATGATGGTTCTACCAGCGGGCGTTAAACTTGCACAAATTCCACAACAATTTTTGCCA
CCCTCATTACCAAATACATCATCTGGAATACATTATCCTTCTATGGATCCAAGTCGATTA
GGCGCACTACAAAAATAA
>g13359.t3 Gene=g13359 Length=391
MAMSKTTSTYNRTNWEDSEFPILCQTCLGDNPYLRMIKEKYGKECKICSRPFTIFRWCPG
ARMRFKKTEICQTCSKLKNVCQTCLLDLEYGLPTQVRDTALKIQDEIPQSDVNKEYYLQN
VEKQMAMNDGQMPGGGKAQQASDVLSKLARTTPYYKRNLPHICSFWVKGECKRGEECPYR
HEKPNDVDDPLSEQNIRDRYYGVNDPVAEKLLKRAASLPVLETPSDKTITTLYCGNVGEH
LTEVDIRDQFYQYGEIRNVTLVPKQQCAFVQFTKRSSAELAAEKTFNKLVLGGKKLSIRW
AYSQAKQATATSSSSQLRPRIDPRLDPVPGLPDLPTPNDYFNLNANDMMVLPAGVKLAQI
PQQFLPPSLPNTSSGIHYPSMDPSRLGALQK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g13359.t3 | CDD | cd12224 | RRM_RBM22 | 229 | 301 | 1.58266E-40 |
| 6 | g13359.t3 | Gene3D | G3DSA:4.10.1000.10 | CCCH zinc finger | 149 | 197 | 6.8E-7 |
| 7 | g13359.t3 | Gene3D | G3DSA:3.30.70.330 | - | 222 | 320 | 1.1E-17 |
| 11 | g13359.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 372 | 391 | - |
| 2 | g13359.t3 | PANTHER | PTHR14089 | PRE-MRNA-SPLICING FACTOR RBM22 | 3 | 388 | 3.7E-160 |
| 3 | g13359.t3 | PANTHER | PTHR14089:SF6 | PRE-MRNA-SPLICING FACTOR RBM22 | 3 | 388 | 3.7E-160 |
| 1 | g13359.t3 | Pfam | PF00076 | RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) | 232 | 296 | 5.7E-10 |
| 12 | g13359.t3 | ProSiteProfiles | PS50103 | Zinc finger C3H1-type profile. | 162 | 184 | 14.774 |
| 13 | g13359.t3 | ProSiteProfiles | PS50102 | Eukaryotic RNA Recognition Motif (RRM) profile. | 230 | 303 | 13.72 |
| 9 | g13359.t3 | SMART | SM00356 | c3hfinal6 | 157 | 183 | 3.0E-5 |
| 10 | g13359.t3 | SMART | SM00360 | rrm1_1 | 231 | 299 | 3.3E-14 |
| 5 | g13359.t3 | SUPERFAMILY | SSF90229 | CCCH zinc finger | 161 | 182 | 3.14E-6 |
| 4 | g13359.t3 | SUPERFAMILY | SSF54928 | RNA-binding domain, RBD | 224 | 307 | 3.12E-18 |
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 transcript has been annotated with K12872 (pre-mRNA-splicing factor RBM22/SLT11)
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.
