Gene loci information

Transcript annotation

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

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 g618 g618.t9 TTS g618.t9 4531187 4531187
chr_3 g618 g618.t9 isoform g618.t9 4531392 4533851
chr_3 g618 g618.t9 exon g618.t9.exon1 4531392 4531453
chr_3 g618 g618.t9 cds g618.t9.CDS1 4531392 4531453
chr_3 g618 g618.t9 exon g618.t9.exon2 4531572 4531898
chr_3 g618 g618.t9 cds g618.t9.CDS2 4531572 4531898
chr_3 g618 g618.t9 exon g618.t9.exon3 4531981 4532214
chr_3 g618 g618.t9 cds g618.t9.CDS3 4531981 4532214
chr_3 g618 g618.t9 exon g618.t9.exon4 4532277 4532389
chr_3 g618 g618.t9 cds g618.t9.CDS4 4532277 4532379
chr_3 g618 g618.t9 exon g618.t9.exon5 4532820 4532854
chr_3 g618 g618.t9 exon g618.t9.exon6 4533552 4533612
chr_3 g618 g618.t9 exon g618.t9.exon7 4533682 4533851
chr_3 g618 g618.t9 TSS g618.t9 4534008 4534008

Sequences

>g618.t9 Gene=g618 Length=1002
ATGGCAAATCGTAAGTTAAAATATGAAAATTTAATAAAATATTTTTTTTAAAAATGCCGT
CAAAATGTGCCATTTTTATATTTTATTTTTAGAGGATTATAACAATTATCAAAGCTACGG
TGGTGGCCAACAAGACTATGGAAGTGGAAATAATTATGGTGGAGGTAATGATTACCAAGG
AAATGGAAACAATTATCGCGGTGGCAATTTCAACAAAGGAGGAAATTTTGGCGGAAACAA
CAGAAGTGGTGGTTATAATAACAAAGTGGTGGCGATATGGTCGTTCAAGATGACACAATT
TTCGTAAGTGGAATGGATCCTCAAATTACAGAATCAGAGATCAATAATCACTTTGGAAGT
ATTGGTATTATCAAGAAAGACAAACGTACCAATAAGCCAAAAATTTGGATCTACAAAGAT
AAAGCAACTGGTGAAGGCAAAGGTGAATGCACAATTACTTATGACGATCCTTGTACTGCA
TCAAGTGCAATAGAATGGTTCGATGGAAAGGAATTCAATGGTTATTCTATCAAAGTTCAA
TTGGCTCAACGAAACAACAGTTGGCAAAAAGGTGGACCAAAGAAATTTGGTGGTCAAGGC
GGTGAAAGAGGAGGTCGAGGTGGATTTGGAGGAAGTGACAGAAATTTTTCACGACAAAAT
GACGATCGAGGTCCGCGAGGTGGAGGAAGTGGTGGAAACTCAGGTGGACAACATCGAGAA
GGAGATTGGATTTGTTCAGAATGCTCTAATAAGAATTTTGCATGGCGAAATGAATGTAAC
CGATGTAAGGAACCAAAAGGTGACAATGCTGGAAGTGCACCAAGTGGTGGCGGTGGAAAC
AGAGGCTATGGCTCAGGTGATCGAGGTGGTCCACGAAATTTTGGAAATAGAGATGGAGGA
AATGGTGGCAACCGTAATTTTAATCGCGGCGGAATGAAAGGTGGCGATCGTCAATCATCA
GGAGGAGGTGGTGGTGGTTTTAACAGACAAAGACCATATTAA

>g618.t9 Gene=g618 Length=241
MVVQDDTIFVSGMDPQITESEINNHFGSIGIIKKDKRTNKPKIWIYKDKATGEGKGECTI
TYDDPCTASSAIEWFDGKEFNGYSIKVQLAQRNNSWQKGGPKKFGGQGGERGGRGGFGGS
DRNFSRQNDDRGPRGGGSGGNSGGQHREGDWICSECSNKNFAWRNECNRCKEPKGDNAGS
APSGGGGNRGYGSGDRGGPRNFGNRDGGNGGNRNFNRGGMKGGDRQSSGGGGGGFNRQRP
Y

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g618.t9 CDD cd12534 RRM_SARFH 8 90 3.81388E-49
7 g618.t9 Gene3D G3DSA:3.30.70.330 - 5 90 1.2E-21
6 g618.t9 Gene3D G3DSA:4.10.1060.10 Znf265 138 177 3.9E-11
13 g618.t9 MobiDBLite mobidb-lite consensus disorder prediction 94 147 -
12 g618.t9 MobiDBLite mobidb-lite consensus disorder prediction 174 241 -
3 g618.t9 PANTHER PTHR23238 RNA BINDING PROTEIN 5 234 1.7E-61
2 g618.t9 Pfam PF00076 RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) 8 86 2.8E-8
1 g618.t9 Pfam PF00641 Zn-finger in Ran binding protein and others 147 175 3.2E-11
9 g618.t9 ProSitePatterns PS01358 Zinc finger RanBP2-type signature. 151 170 -
15 g618.t9 ProSiteProfiles PS50102 Eukaryotic RNA Recognition Motif (RRM) profile. 6 92 12.953
14 g618.t9 ProSiteProfiles PS50199 Zinc finger RanBP2 type profile. 147 176 10.557
11 g618.t9 SMART SM00360 rrm1_1 7 88 1.3E-12
10 g618.t9 SMART SM00547 zf_4 149 173 4.8E-6
4 g618.t9 SUPERFAMILY SSF54928 RNA-binding domain, RBD 6 121 2.01E-21
5 g618.t9 SUPERFAMILY SSF90209 Ran binding protein zinc finger-like 139 177 3.61E-11

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:0003723 RNA binding MF
GO:0006355 regulation of transcription, DNA-templated BP
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