Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative RNA-binding protein 28.

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_3 g2443 g2443.t3 TTS g2443.t3 18010963 18010963
chr_3 g2443 g2443.t3 isoform g2443.t3 18011014 18012433
chr_3 g2443 g2443.t3 exon g2443.t3.exon1 18011014 18011712
chr_3 g2443 g2443.t3 cds g2443.t3.CDS1 18011014 18011712
chr_3 g2443 g2443.t3 exon g2443.t3.exon2 18011770 18012433
chr_3 g2443 g2443.t3 cds g2443.t3.CDS2 18011770 18011973
chr_3 g2443 g2443.t3 TSS g2443.t3 18013020 18013020

Sequences

>g2443.t3 Gene=g2443 Length=1363
TGGTGAAGAAGAGGAAGAAAATGACGATAATAATTCAAATATTACAGACGATGATAAAAA
GATTGAATCAGAAGTAAAAGAAAAAAAATCTGATATCAAAAAAGAAAAGAAGTATAATGA
AAAGGATAATGAGTATACAGTTTTTGTTAAAAATCTAAATTTTGATACAACAAATGAAGA
TTTGCATGAGTGTTTCAAGAAATTCGGCCCCATTAAATATGCACTTATTGTTAAAGACTC
AATTTCTGGTCACTCCAAAGGAACTGCATTTGTAAAATTTCTTAGAAAGGAATCTGTTGA
GATCTGTCTTGCACAATCTGGAAAAATAAATCTACAAGATTTTGTGCTTGAAGTTTTACC
TACTCTTTCAAAGCAAACTGTCAAAAATATTGAGAAACAGAAAGAAATAACAAAGAAAGA
ACCAAAAGACTCAAGAAATCTCTATTTAATACGTGAAGGAATGATTGCGGCTGGCTCAAC
TGCTTCTGAAGGCGTATCAGCAACCGATATGGCAAAAAGACTGCGATTAGAACAAATCAA
ATCTTCAATGTTAAAAAATTTAACACGTTTCATTTCTCGTGAACGTCTGACAATTCATAA
TCTACCAGAAAATTATGATGATGCAAAGTTGCGAAAAATGGTTGAGTCGAGAACTAAAAT
AAAGCCAATCGAATGTCGTGTGATGAGGGAAAATAAGCCATCAGCACTACATCCAAATGG
AAAATCTAAGGGTTTTGGATTTTTATCATTTAAAAAGCACGAAGATGCGTTACTTGTTCT
TAGAAAACTCAATAATAATCCAGAAGTTTTTAGTGCCAAACATCGACCCATTGTAAGTTT
CAGCATTGAAGATATGAATGTATTGAAAATCAAAGAAAAACGTAAACAGCGTTCAATGCT
CAATAATCCAACGTATCAAAAGAAACTAGAGAAATTAAAAGTTAAGAAACTTAAAAAACA
AATGGAGAAAAAAGATAACAAATCAAATACGTTAATAATGAAAAAGAAGCAACGAAAAGT
TAAATCTGATGAGCATGTTGAGTTATACACAGGCTTTGCGTCGAAACCAGGAGCTTTTGT
GAAACTTCGTGGTACGTTTAAACTTAAAGAGCAATCTAGAATTCATGAAAAAACTATGAA
AGAACGTAACAAAAAAGTGAGACGAGAAAAACAACTGGCAGAAGTTCGTCAGGAGAAACA
AGAGAAAAAATTTGATCGAATATCCAATAAAAGGAAGATTAAAGACACTAATGACACTTT
AGCATCGAAAATAAATAAATACAAAAGTTTAATTGGTGCAAACGAAGAAGCAGATAGCAA
ACGACAGAAAATAGGAGCAAGAGGAAAATGGTTTATGGATTGA

>g2443.t3 Gene=g2443 Length=300
MIAAGSTASEGVSATDMAKRLRLEQIKSSMLKNLTRFISRERLTIHNLPENYDDAKLRKM
VESRTKIKPIECRVMRENKPSALHPNGKSKGFGFLSFKKHEDALLVLRKLNNNPEVFSAK
HRPIVSFSIEDMNVLKIKEKRKQRSMLNNPTYQKKLEKLKVKKLKKQMEKKDNKSNTLIM
KKKQRKVKSDEHVELYTGFASKPGAFVKLRGTFKLKEQSRIHEKTMKERNKKVRREKQLA
EVRQEKQEKKFDRISNKRKIKDTNDTLASKINKYKSLIGANEEADSKRQKIGARGKWFMD

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g2443.t3 CDD cd12416 RRM4_RBM28_like 42 131 1.72469E-32
7 g2443.t3 Coils Coil Coil 154 181 -
6 g2443.t3 Coils Coil Coil 230 250 -
5 g2443.t3 Gene3D G3DSA:3.30.70.330 - 43 135 7.0E-15
2 g2443.t3 PANTHER PTHR48039 RNA-BINDING MOTIF PROTEIN 14B 1 259 2.1E-42
3 g2443.t3 PANTHER PTHR48039:SF2 RNA-BINDING PROTEIN 28 1 259 2.1E-42
1 g2443.t3 Pfam PF00076 RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) 43 112 3.4E-7
10 g2443.t3 ProSiteProfiles PS50102 Eukaryotic RNA Recognition Motif (RRM) profile. 41 124 10.224
9 g2443.t3 SMART SM00360 rrm1_1 42 126 2.0E-5
4 g2443.t3 SUPERFAMILY SSF54928 RNA-binding domain, RBD 39 113 1.03E-10

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 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