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.t7 TTS g618.t7 4531187 4531187
chr_3 g618 g618.t7 isoform g618.t7 4531392 4533851
chr_3 g618 g618.t7 exon g618.t7.exon1 4531392 4531453
chr_3 g618 g618.t7 cds g618.t7.CDS1 4531392 4531453
chr_3 g618 g618.t7 exon g618.t7.exon2 4531572 4531898
chr_3 g618 g618.t7 cds g618.t7.CDS2 4531572 4531898
chr_3 g618 g618.t7 exon g618.t7.exon3 4531981 4532214
chr_3 g618 g618.t7 cds g618.t7.CDS3 4531981 4532214
chr_3 g618 g618.t7 exon g618.t7.exon4 4532277 4532396
chr_3 g618 g618.t7 cds g618.t7.CDS4 4532277 4532396
chr_3 g618 g618.t7 exon g618.t7.exon5 4532820 4532854
chr_3 g618 g618.t7 cds g618.t7.CDS5 4532820 4532854
chr_3 g618 g618.t7 exon g618.t7.exon6 4533552 4533851
chr_3 g618 g618.t7 cds g618.t7.CDS6 4533552 4533622
chr_3 g618 g618.t7 TSS g618.t7 4534008 4534008

Sequences

>g618.t7 Gene=g618 Length=1078
ATGGCAAATCGTAAGTTAAAATATGAAAATTTAATAAAATATTTTTTTTAAAAATGCCGT
CAAAATGTGCCATTTTTATATTTTATTTTTAGAGGATTATAACAATTATCAAAGCTACGG
TGGTGGCCAACAAGACTATGGAAGTGGAAATAATTATGGTGGAGGTAATGGTAAGTAATT
TAATTTTAAAATAATAATTTTTCATTTCATTTCTAACAAAGTTTCTAATATGACGCTAGA
TTACCAAGGAAATGGAAACAATTATCGCGGTGGCAATTTCAACAAAGGAGGAAATTTTGG
CGGAAACAACAGAAGTGGTGGTTATAATAACAAAGGCGGTAGTGGTGGCGATATGGTCGT
TCAAGATGACACAATTTTCGTAAGTGGAATGGATCCTCAAATTACAGAATCAGAGATCAA
TAATCACTTTGGAAGTATTGGTATTATCAAGAAAGACAAACGTACCAATAAGCCAAAAAT
TTGGATCTACAAAGATAAAGCAACTGGTGAAGGCAAAGGTGAATGCACAATTACTTATGA
CGATCCTTGTACTGCATCAAGTGCAATAGAATGGTTCGATGGAAAGGAATTCAATGGTTA
TTCTATCAAAGTTCAATTGGCTCAACGAAACAACAGTTGGCAAAAAGGTGGACCAAAGAA
ATTTGGTGGTCAAGGCGGTGAAAGAGGAGGTCGAGGTGGATTTGGAGGAAGTGACAGAAA
TTTTTCACGACAAAATGACGATCGAGGTCCGCGAGGTGGAGGAAGTGGTGGAAACTCAGG
TGGACAACATCGAGAAGGAGATTGGATTTGTTCAGAATGCTCTAATAAGAATTTTGCATG
GCGAAATGAATGTAACCGATGTAAGGAACCAAAAGGTGACAATGCTGGAAGTGCACCAAG
TGGTGGCGGTGGAAACAGAGGCTATGGCTCAGGTGATCGAGGTGGTCCACGAAATTTTGG
AAATAGAGATGGAGGAAATGGTGGCAACCGTAATTTTAATCGCGGCGGAATGAAAGGTGG
CGATCGTCAATCATCAGGAGGAGGTGGTGGTGGTTTTAACAGACAAAGACCATATTAA

>g618.t7 Gene=g618 Length=282
MTLDYQGNGNNYRGGNFNKGGNFGGNNRSGGYNNKGGSGGDMVVQDDTIFVSGMDPQITE
SEINNHFGSIGIIKKDKRTNKPKIWIYKDKATGEGKGECTITYDDPCTASSAIEWFDGKE
FNGYSIKVQLAQRNNSWQKGGPKKFGGQGGERGGRGGFGGSDRNFSRQNDDRGPRGGGSG
GNSGGQHREGDWICSECSNKNFAWRNECNRCKEPKGDNAGSAPSGGGGNRGYGSGDRGGP
RNFGNRDGGNGGNRNFNRGGMKGGDRQSSGGGGGGFNRQRPY

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g618.t7 CDD cd12534 RRM_SARFH 49 131 1.2538E-48
7 g618.t7 Gene3D G3DSA:3.30.70.330 - 46 131 1.7E-21
6 g618.t7 Gene3D G3DSA:4.10.1060.10 Znf265 179 218 4.9E-11
13 g618.t7 MobiDBLite mobidb-lite consensus disorder prediction 135 188 -
12 g618.t7 MobiDBLite mobidb-lite consensus disorder prediction 215 282 -
3 g618.t7 PANTHER PTHR23238 RNA BINDING PROTEIN 32 275 8.7E-54
2 g618.t7 Pfam PF00076 RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) 49 127 3.8E-8
1 g618.t7 Pfam PF00641 Zn-finger in Ran binding protein and others 188 216 4.0E-11
9 g618.t7 ProSitePatterns PS01358 Zinc finger RanBP2-type signature. 192 211 -
15 g618.t7 ProSiteProfiles PS50102 Eukaryotic RNA Recognition Motif (RRM) profile. 47 133 12.953
14 g618.t7 ProSiteProfiles PS50199 Zinc finger RanBP2 type profile. 188 217 10.557
11 g618.t7 SMART SM00360 rrm1_1 48 129 1.3E-12
10 g618.t7 SMART SM00547 zf_4 190 214 4.8E-6
4 g618.t7 SUPERFAMILY SSF54928 RNA-binding domain, RBD 45 162 2.55E-21
5 g618.t7 SUPERFAMILY SSF90209 Ran binding protein zinc finger-like 180 218 4.71E-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

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