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.t1 TTS g2443.t1 18010963 18010963
chr_3 g2443 g2443.t1 isoform g2443.t1 18011014 18012961
chr_3 g2443 g2443.t1 exon g2443.t1.exon1 18011014 18011712
chr_3 g2443 g2443.t1 cds g2443.t1.CDS1 18011014 18011712
chr_3 g2443 g2443.t1 exon g2443.t1.exon2 18011770 18012890
chr_3 g2443 g2443.t1 cds g2443.t1.CDS2 18011770 18012890
chr_3 g2443 g2443.t1 exon g2443.t1.exon3 18012946 18012961
chr_3 g2443 g2443.t1 cds g2443.t1.CDS3 18012946 18012961
chr_3 g2443 g2443.t1 TSS g2443.t1 18013020 18013020

Sequences

>g2443.t1 Gene=g2443 Length=1836
ATGGATTCAAATGAAGATTATATAAAAATTGAGCAATCATCCAGGAAAGTAGACAATATT
ACTAAAAAAGCAAAATTTCGAAGGAAAATTGAAAATATCAAAAAAGGACGAATTATTGTT
CGCAATCTTTCATTTAAAGTTACAGAAGAATTACTTAGAGAAGAATTTGAGAAATATGGC
GAAATATCTGAAGTGAATATATTGAAAAAACCAGATGGAAAACTTGTGGGATGTGCATTT
TTGCAGTATTTTAATTATAATGATTCTACAAAAGCAATCAAGGCAATGAATGGAAAGGAT
TTTCTTAAACGTAAAATTACTGTTGACTTTGCTGTTAGTAAAAACCGCTACAAAAATGCT
CATAAGAGCGAATTTGATGATTCGATAAAAGATAATCTGGATACAGTTGAAATGAAAGAA
GAACAAGAAACCAAAATTGAAAAAGAAAATAAGGCGAAATCAGAACATAGCAATGGTGAA
GAAGAGGAAGAAAATGACGATAATAATTCAAATATTACAGACGATGATAAAAAGATTGAA
TCAGAAGTAAAAGAAAAAAAATCTGATATCAAAAAAGAAAAGAAGTATAATGAAAAGGAT
AATGAGTATACAGTTTTTGTTAAAAATCTAAATTTTGATACAACAAATGAAGATTTGCAT
GAGTGTTTCAAGAAATTCGGCCCCATTAAATATGCACTTATTGTTAAAGACTCAATTTCT
GGTCACTCCAAAGGAACTGCATTTGTAAAATTTCTTAGAAAGGAATCTGTTGAGATCTGT
CTTGCACAATCTGGAAAAATAAATCTACAAGATTTTGTGCTTGAAGTTTTACCTACTCTT
TCAAAGCAAACTGTCAAAAATATTGAGAAACAGAAAGAAATAACAAAGAAAGAACCAAAA
GACTCAAGAAATCTCTATTTAATACGTGAAGGAATGATTGCGGCTGGCTCAACTGCTTCT
GAAGGCGTATCAGCAACCGATATGGCAAAAAGACTGCGATTAGAACAAATCAAATCTTCA
ATGTTAAAAAATTTAACACGTTTCATTTCTCGTGAACGTCTGACAATTCATAATCTACCA
GAAAATTATGATGATGCAAAGTTGCGAAAAATGGTTGAGTCGAGAACTAAAATAAAGCCA
ATCGAATGTCGTGTGATGAGGGAAAATAAGCCATCAGCACTACATCCAAATGGAAAATCT
AAGGGTTTTGGATTTTTATCATTTAAAAAGCACGAAGATGCGTTACTTGTTCTTAGAAAA
CTCAATAATAATCCAGAAGTTTTTAGTGCCAAACATCGACCCATTGTAAGTTTCAGCATT
GAAGATATGAATGTATTGAAAATCAAAGAAAAACGTAAACAGCGTTCAATGCTCAATAAT
CCAACGTATCAAAAGAAACTAGAGAAATTAAAAGTTAAGAAACTTAAAAAACAAATGGAG
AAAAAAGATAACAAATCAAATACGTTAATAATGAAAAAGAAGCAACGAAAAGTTAAATCT
GATGAGCATGTTGAGTTATACACAGGCTTTGCGTCGAAACCAGGAGCTTTTGTGAAACTT
CGTGGTACGTTTAAACTTAAAGAGCAATCTAGAATTCATGAAAAAACTATGAAAGAACGT
AACAAAAAAGTGAGACGAGAAAAACAACTGGCAGAAGTTCGTCAGGAGAAACAAGAGAAA
AAATTTGATCGAATATCCAATAAAAGGAAGATTAAAGACACTAATGACACTTTAGCATCG
AAAATAAATAAATACAAAAGTTTAATTGGTGCAAACGAAGAAGCAGATAGCAAACGACAG
AAAATAGGAGCAAGAGGAAAATGGTTTATGGATTGA

>g2443.t1 Gene=g2443 Length=611
MDSNEDYIKIEQSSRKVDNITKKAKFRRKIENIKKGRIIVRNLSFKVTEELLREEFEKYG
EISEVNILKKPDGKLVGCAFLQYFNYNDSTKAIKAMNGKDFLKRKITVDFAVSKNRYKNA
HKSEFDDSIKDNLDTVEMKEEQETKIEKENKAKSEHSNGEEEEENDDNNSNITDDDKKIE
SEVKEKKSDIKKEKKYNEKDNEYTVFVKNLNFDTTNEDLHECFKKFGPIKYALIVKDSIS
GHSKGTAFVKFLRKESVEICLAQSGKINLQDFVLEVLPTLSKQTVKNIEKQKEITKKEPK
DSRNLYLIREGMIAAGSTASEGVSATDMAKRLRLEQIKSSMLKNLTRFISRERLTIHNLP
ENYDDAKLRKMVESRTKIKPIECRVMRENKPSALHPNGKSKGFGFLSFKKHEDALLVLRK
LNNNPEVFSAKHRPIVSFSIEDMNVLKIKEKRKQRSMLNNPTYQKKLEKLKVKKLKKQME
KKDNKSNTLIMKKKQRKVKSDEHVELYTGFASKPGAFVKLRGTFKLKEQSRIHEKTMKER
NKKVRREKQLAEVRQEKQEKKFDRISNKRKIKDTNDTLASKINKYKSLIGANEEADSKRQ
KIGARGKWFMD

Protein features from InterProScan

Transcript Database ID Name Start End E.value
14 g2443.t1 CDD cd12415 RRM3_RBM28_like 204 275 8.94388E-25
13 g2443.t1 CDD cd12416 RRM4_RBM28_like 353 442 2.86012E-31
11 g2443.t1 Coils Coil Coil 465 492 -
12 g2443.t1 Coils Coil Coil 541 561 -
10 g2443.t1 Gene3D G3DSA:3.30.70.330 - 2 124 5.3E-23
9 g2443.t1 Gene3D G3DSA:3.30.70.330 - 127 293 9.8E-25
8 g2443.t1 Gene3D G3DSA:3.30.70.330 - 354 445 2.4E-14
18 g2443.t1 MobiDBLite mobidb-lite consensus disorder prediction 138 159 -
19 g2443.t1 MobiDBLite mobidb-lite consensus disorder prediction 138 184 -
4 g2443.t1 PANTHER PTHR48039 RNA-BINDING MOTIF PROTEIN 14B 18 562 5.7E-114
5 g2443.t1 PANTHER PTHR48039:SF2 RNA-BINDING PROTEIN 28 18 562 5.7E-114
3 g2443.t1 Pfam PF00076 RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) 38 106 5.5E-17
2 g2443.t1 Pfam PF00076 RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) 205 270 4.8E-16
1 g2443.t1 Pfam PF00076 RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) 354 423 1.0E-6
22 g2443.t1 ProSiteProfiles PS50102 Eukaryotic RNA Recognition Motif (RRM) profile. 36 113 16.875
21 g2443.t1 ProSiteProfiles PS50102 Eukaryotic RNA Recognition Motif (RRM) profile. 203 281 14.215
20 g2443.t1 ProSiteProfiles PS50102 Eukaryotic RNA Recognition Motif (RRM) profile. 352 435 10.224
16 g2443.t1 SMART SM00360 rrm1_1 37 109 1.8E-22
17 g2443.t1 SMART SM00360 rrm1_1 204 277 3.9E-19
15 g2443.t1 SMART SM00360 rrm1_1 353 437 2.0E-5
6 g2443.t1 SUPERFAMILY SSF54928 RNA-binding domain, RBD 28 119 9.67E-25
7 g2443.t1 SUPERFAMILY SSF54928 RNA-binding domain, RBD 201 423 1.89E-30

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

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.

Raw TPM values