Gene loci information

Transcript annotation

  • This transcript has been annotated as Pre-mRNA-splicing factor RBM22.

Parent gene

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.t11 TSS g13359.t11 29509895 29509895
chr_1 g13359 g13359.t11 isoform g13359.t11 29510417 29511391
chr_1 g13359 g13359.t11 exon g13359.t11.exon1 29510417 29511067
chr_1 g13359 g13359.t11 cds g13359.t11.CDS1 29510588 29511067
chr_1 g13359 g13359.t11 exon g13359.t11.exon2 29511124 29511391
chr_1 g13359 g13359.t11 cds g13359.t11.CDS2 29511124 29511180
chr_1 g13359 g13359.t11 TTS g13359.t11 29511462 29511462

Sequences

>g13359.t11 Gene=g13359 Length=919
GGTAAAACATTTTTGAAATTTGAAAAACCTTTTATTTGTTCATTTAAAATTACAATTTAT
TAAATTTCAGGATTACCGACTCAAGTGCGAGATACAGCACTCAAAATTCAAGATGAAATC
CCACAAAGTGATGTAAATAAAGAATATTATTTGCAAAATGTTGAAAAGCAAATGGCAATG
AATGATGGACAAATGCCTGGTGGTGGAAAAGCTCAACAAGCTTCAGATGTTTTATCTAAA
TTAGCTCGCACTACACCATATTACAAACGAAATCTTCCTCACATTTGCTCATTTTGGGTA
AAAGGAGAATGTAAAAGAGGTGAAGAGTGTCCATATAGACATGAAAAACCAAACGATGTA
GACGATCCTCTCTCAGAACAAAATATTCGTGATCGATATTATGGTGTTAACGATCCAGTA
GCTGAAAAGTTACTTAAAAGAGCTGCTTCATTACCTGTCCTTGAAACTCCTAGTGACAAG
ACAATAACTACATTATATTGTGGTAATGTCGGTGAACATTTGACCGAAGTTGATATAAGA
GATCAATTTTATCAATATGGAGAAATTAGAAATGTAACACTTGTGCCGAAACAACAGTGT
GCTTTCGTACAGTTTACCAAACGTTCTTCAGCTGAATTGGCAGCAGAGAAGACAAGCAAA
ACAAGCCACAGCCACATCATCATCATCACAATTGCGGCCTCGTATTGATCCCCGTTTAGA
TCCTGTACCTGGACTCCCCGATTTACCAACACCAAACGATTATTTCAATTTGAATGCAAA
TGATATGATGGTTCTACCAGCGGGCGTTAAACTTGCACAAATTCCACAACAATTTTTGCC
ACCCTCATTACCAAATACATCATCTGGAATACATTATCCTTCTATGGATCCAAGTCGATT
AGGCGCACTACAAAAATAA

>g13359.t11 Gene=g13359 Length=178
MAMNDGQMPGGGKAQQASDVLSKLARTTPYYKRNLPHICSFWVKGECKRGEECPYRHEKP
NDVDDPLSEQNIRDRYYGVNDPVAEKLLKRAASLPVLETPSDKTITTLYCGNVGEHLTEV
DIRDQFYQYGEIRNVTLVPKQQCAFVQFTKRSSAELAAEKTSKTSHSHIIIITIAASY

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g13359.t11 Gene3D G3DSA:4.10.1000.10 CCCH zinc finger 24 74 0.0000002
9 g13359.t11 Gene3D G3DSA:3.30.70.330 - 101 176 0.0000000
2 g13359.t11 PANTHER PTHR14089 PRE-MRNA-SPLICING FACTOR RBM22 12 164 0.0000000
3 g13359.t11 PANTHER PTHR14089:SF6 PRE-MRNA-SPLICING FACTOR RBM22 12 164 0.0000000
1 g13359.t11 Pfam PF00076 RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) 108 162 0.0000000
10 g13359.t11 ProSiteProfiles PS50103 Zinc finger C3H1-type profile. 38 60 14.7740000
11 g13359.t11 ProSiteProfiles PS50102 Eukaryotic RNA Recognition Motif (RRM) profile. 106 177 11.1790000
6 g13359.t11 SMART SM00356 c3hfinal6 33 59 0.0000300
7 g13359.t11 SMART SM00360 rrm1_1 107 173 0.0000000
5 g13359.t11 SUPERFAMILY SSF90229 CCCH zinc finger 36 58 0.0000012
4 g13359.t11 SUPERFAMILY SSF54928 RNA-binding domain, RBD 100 169 0.0000000

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.

Raw TPM values