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.t15 TTS g618.t15 4531187 4531187
chr_3 g618 g618.t15 isoform g618.t15 4531767 4533851
chr_3 g618 g618.t15 exon g618.t15.exon1 4531767 4531898
chr_3 g618 g618.t15 cds g618.t15.CDS1 4531768 4531898
chr_3 g618 g618.t15 exon g618.t15.exon2 4531981 4532214
chr_3 g618 g618.t15 cds g618.t15.CDS2 4531981 4532214
chr_3 g618 g618.t15 exon g618.t15.exon3 4532277 4532396
chr_3 g618 g618.t15 cds g618.t15.CDS3 4532277 4532396
chr_3 g618 g618.t15 exon g618.t15.exon4 4533552 4533612
chr_3 g618 g618.t15 cds g618.t15.CDS4 4533552 4533612
chr_3 g618 g618.t15 exon g618.t15.exon5 4533682 4533759
chr_3 g618 g618.t15 cds g618.t15.CDS5 4533682 4533684
chr_3 g618 g618.t15 exon g618.t15.exon6 4533842 4533851
chr_3 g618 g618.t15 TSS g618.t15 4534008 4534008

Sequences

>g618.t15 Gene=g618 Length=635
ATGGCAAATCAGGATTATAACAATTATCAAAGCTACGGTGGTGGCCAACAAGACTATGGA
AGTGGAAATAATTATGGTGGAGGTAATGATTACCAAGGAAATGGAAACAATTATCGCGGT
GGCAATTTCAACAAAGGAGGAAATTTTGGGCGGTAGTGGTGGCGATATGGTCGTTCAAGA
TGACACAATTTTCGTAAGTGGAATGGATCCTCAAATTACAGAATCAGAGATCAATAATCA
CTTTGGAAGTATTGGTATTATCAAGAAAGACAAACGTACCAATAAGCCAAAAATTTGGAT
CTACAAAGATAAAGCAACTGGTGAAGGCAAAGGTGAATGCACAATTACTTATGACGATCC
TTGTACTGCATCAAGTGCAATAGAATGGTTCGATGGAAAGGAATTCAATGGTTATTCTAT
CAAAGTTCAATTGGCTCAACGAAACAACAGTTGGCAAAAAGGTGGACCAAAGAAATTTGG
TGGTCAAGGCGGTGAAAGAGGAGGTCGAGGTGGATTTGGAGGAAGTGACAGAAATTTTTC
ACGACAAAATGACGATCGAGGTCCGCGAGGTGGAGGAAGTGGTGGAAACTCAGGTGGACA
ACATCGAGAAGGAGATTGGATTTGTTCAGAATGCT

>g618.t15 Gene=g618 Length=183
MITKEMETIIAVAISTKEEILGGSGGDMVVQDDTIFVSGMDPQITESEINNHFGSIGIIK
KDKRTNKPKIWIYKDKATGEGKGECTITYDDPCTASSAIEWFDGKEFNGYSIKVQLAQRN
NSWQKGGPKKFGGQGGERGGRGGFGGSDRNFSRQNDDRGPRGGGSGGNSGGQHREGDWIC
SEC

Protein features from InterProScan

Transcript Database ID Name Start End E.value
5 g618.t15 CDD cd12534 RRM_SARFH 35 117 1.05823E-48
4 g618.t15 Gene3D G3DSA:3.30.70.330 - 32 117 6.5E-22
7 g618.t15 MobiDBLite mobidb-lite consensus disorder prediction 121 183 -
2 g618.t15 PANTHER PTHR23238 RNA BINDING PROTEIN 31 183 1.6E-47
1 g618.t15 Pfam PF00076 RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) 35 113 1.5E-8
8 g618.t15 ProSiteProfiles PS50102 Eukaryotic RNA Recognition Motif (RRM) profile. 33 119 12.953
6 g618.t15 SMART SM00360 rrm1_1 34 115 1.3E-12
3 g618.t15 SUPERFAMILY SSF54928 RNA-binding domain, RBD 33 122 9.54E-21

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

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