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.t4 isoform g2443.t4 18012113 18012961
chr_3 g2443 g2443.t4 exon g2443.t4.exon1 18012113 18012890
chr_3 g2443 g2443.t4 cds g2443.t4.CDS1 18012115 18012890
chr_3 g2443 g2443.t4 exon g2443.t4.exon2 18012946 18012961
chr_3 g2443 g2443.t4 cds g2443.t4.CDS2 18012946 18012961
chr_3 g2443 g2443.t4 TSS g2443.t4 18013020 18013020
chr_3 g2443 g2443.t4 TTS g2443.t4 NA NA

Sequences

>g2443.t4 Gene=g2443 Length=794
ATGGATTCAAATGAAGATTATATAAAAATTGAGCAATCATCCAGGAAAGTAGACAATATT
ACTAAAAAAGCAAAATTTCGAAGGAAAATTGAAAATATCAAAAAAGGACGAATTATTGTT
CGCAATCTTTCATTTAAAGTTACAGAAGAATTACTTAGAGAAGAATTTGAGAAATATGGC
GAAATATCTGAAGTGAATATATTGAAAAAACCAGATGGAAAACTTGTGGGATGTGCATTT
TTGCAGTATTTTAATTATAATGATTCTACAAAAGCAATCAAGGCAATGAATGGAAAGGAT
TTTCTTAAACGTAAAATTACTGTTGACTTTGCTGTTAGTAAAAACCGCTACAAAAATGCT
CATAAGAGCGAATTTGATGATTCGATAAAAGATAATCTGGATACAGTTGAAATGAAAGAA
GAACAAGAAACCAAAATTGAAAAAGAAAATAAGGCGAAATCAGAACATAGCAATGGTGAA
GAAGAGGAAGAAAATGACGATAATAATTCAAATATTACAGACGATGATAAAAAGATTGAA
TCAGAAGTAAAAGAAAAAAAATCTGATATCAAAAAAGAAAAGAAGTATAATGAAAAGGAT
AATGAGTATACAGTTTTTGTTAAAAATCTAAATTTTGATACAACAAATGAAGATTTGCAT
GAGTGTTTCAAGAAATTCGGCCCCATTAAATATGCACTTATTGTTAAAGACTCAATTTCT
GGTCACTCCAAAGGAACTGCATTTGTAAAATTTCTTAGAAAGGAATCTGTTGAGATCTGT
CTTGCACAATCTGG

>g2443.t4 Gene=g2443 Length=264
MDSNEDYIKIEQSSRKVDNITKKAKFRRKIENIKKGRIIVRNLSFKVTEELLREEFEKYG
EISEVNILKKPDGKLVGCAFLQYFNYNDSTKAIKAMNGKDFLKRKITVDFAVSKNRYKNA
HKSEFDDSIKDNLDTVEMKEEQETKIEKENKAKSEHSNGEEEEENDDNNSNITDDDKKIE
SEVKEKKSDIKKEKKYNEKDNEYTVFVKNLNFDTTNEDLHECFKKFGPIKYALIVKDSIS
GHSKGTAFVKFLRKESVEICLAQS

Protein features from InterProScan

Transcript Database ID Name Start End E.value
9 g2443.t4 CDD cd12415 RRM3_RBM28_like 204 264 7.53444E-25
8 g2443.t4 Gene3D G3DSA:3.30.70.330 - 2 124 1.1E-23
7 g2443.t4 Gene3D G3DSA:3.30.70.330 - 126 264 4.9E-24
12 g2443.t4 MobiDBLite mobidb-lite consensus disorder prediction 138 191 -
13 g2443.t4 MobiDBLite mobidb-lite consensus disorder prediction 138 159 -
14 g2443.t4 MobiDBLite mobidb-lite consensus disorder prediction 171 191 -
3 g2443.t4 PANTHER PTHR48039 RNA-BINDING MOTIF PROTEIN 14B 18 263 9.6E-53
4 g2443.t4 PANTHER PTHR48039:SF2 RNA-BINDING PROTEIN 28 18 263 9.6E-53
1 g2443.t4 Pfam PF00076 RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) 38 106 1.5E-17
2 g2443.t4 Pfam PF00076 RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) 205 262 5.1E-16
16 g2443.t4 ProSiteProfiles PS50102 Eukaryotic RNA Recognition Motif (RRM) profile. 36 113 16.875
15 g2443.t4 ProSiteProfiles PS50102 Eukaryotic RNA Recognition Motif (RRM) profile. 203 264 14.385
10 g2443.t4 SMART SM00360 rrm1_1 37 109 1.8E-22
11 g2443.t4 SMART SM00360 rrm1_1 204 263 7.1E-10
6 g2443.t4 SUPERFAMILY SSF54928 RNA-binding domain, RBD 28 119 2.01E-25
5 g2443.t4 SUPERFAMILY SSF54928 RNA-binding domain, RBD 182 262 1.2E-20

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