Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Protein roadkill.

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 g938 g938.t1 TTS g938.t1 6978505 6978505
chr_3 g938 g938.t1 isoform g938.t1 6978587 6980792
chr_3 g938 g938.t1 exon g938.t1.exon1 6978587 6978692
chr_3 g938 g938.t1 cds g938.t1.CDS1 6978587 6978692
chr_3 g938 g938.t1 exon g938.t1.exon2 6978751 6979217
chr_3 g938 g938.t1 cds g938.t1.CDS2 6978751 6979217
chr_3 g938 g938.t1 exon g938.t1.exon3 6979276 6979313
chr_3 g938 g938.t1 cds g938.t1.CDS3 6979276 6979313
chr_3 g938 g938.t1 exon g938.t1.exon4 6979382 6979584
chr_3 g938 g938.t1 cds g938.t1.CDS4 6979382 6979584
chr_3 g938 g938.t1 exon g938.t1.exon5 6979643 6979690
chr_3 g938 g938.t1 cds g938.t1.CDS5 6979643 6979690
chr_3 g938 g938.t1 exon g938.t1.exon6 6980692 6980792
chr_3 g938 g938.t1 cds g938.t1.CDS6 6980692 6980792
chr_3 g938 g938.t1 TSS g938.t1 NA NA

Sequences

>g938.t1 Gene=g938 Length=963
ATGAATGTTCTTGAGCCTCGTAATTTATGCATCTTCTGGTGTAATGATCATTTATATGTA
AAATCAGTGACTGTTGATATGATGGAGATGCCAAGTAGAGATAATGGTTCGAAGAACACA
AAGATTTTCACAAATGTATATGGAAAATGGACTGTTACTATTCTTAGTGTTGGTTATTAT
CCATCGTTGATTGGTATAATATTTTTAGATCCTGTTTTTAAAAAAAAATTGGTCGATTGG
AAACAAGTTAATATTGAAGTTGATTGCAAAAATTCCAATGGATACAATGAGTCTGTTACA
GCTGAGAATCTTGAGAAAACGACATTTGTCTTCCAAACGAGTTCCAACCAAGGGAGCTAT
TGTACATTAAGTTATCAAATCAATATTAAGATTAAGATGCCAGAAATTTCAATTATTGAA
GACAAACGATTTGGAACAAAAAATCATTTGAAATCTTTATTTGATTCTGGAAAAGATTCT
GATATCACAATCAAAGCAGAAGAAAAAGAAATCAAAGTTCATAAGCTTATTTTGAAACGA
TCGGAAGTTTTTGCAAAAATGTTGAATGGTACATCAAAAGAGACTCAAAGTAAAATCATA
GAAATTAAGGATATCAAATATGAAGTGATCGTTGAAATGTGCCGATTTTTGTATTATGAT
GAAATTCCAAAAATTGATTCACTTGCTCTTCCTTTATTAATTGCTGCTGATAAATATATG
ATCAATGATTTAGCTAACAAATGTGAAAAATTTTTGATGTTAAACATAACTATTGGGAAT
TTTCATGAAGTCTTGGTAACTGCTGATCAACTAAATAAAAATAAATTGCGTGAAGCCACA
ATTGATTACATCATTGCAAACCGTAAATCGATTTTCCCATCTGTAACATGGAAAACTTTA
AAGACAAATCACATGCAACTTGCTATGCTTGTCATGGAAAAATTTATGTTAAAAGATGCT
TAA

>g938.t1 Gene=g938 Length=320
MNVLEPRNLCIFWCNDHLYVKSVTVDMMEMPSRDNGSKNTKIFTNVYGKWTVTILSVGYY
PSLIGIIFLDPVFKKKLVDWKQVNIEVDCKNSNGYNESVTAENLEKTTFVFQTSSNQGSY
CTLSYQINIKIKMPEISIIEDKRFGTKNHLKSLFDSGKDSDITIKAEEKEIKVHKLILKR
SEVFAKMLNGTSKETQSKIIEIKDIKYEVIVEMCRFLYYDEIPKIDSLALPLLIAADKYM
INDLANKCEKFLMLNITIGNFHEVLVTADQLNKNKLREATIDYIIANRKSIFPSVTWKTL
KTNHMQLAMLVMEKFMLKDA

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g938.t1 Gene3D G3DSA:3.30.710.10 Potassium Channel Kv1.1; Chain A 138 250 3.7E-27
7 g938.t1 Gene3D G3DSA:1.25.40.420 - 255 319 2.0E-10
2 g938.t1 PANTHER PTHR24413:SF213 FI01029P-RELATED 97 314 3.5E-36
3 g938.t1 PANTHER PTHR24413 SPECKLE-TYPE POZ PROTEIN 97 314 3.5E-36
1 g938.t1 Pfam PF00651 BTB/POZ domain 150 252 1.1E-20
9 g938.t1 ProSiteProfiles PS50097 BTB domain profile. 160 226 13.612
6 g938.t1 SMART SM00225 BTB_4 160 256 6.7E-17
5 g938.t1 SUPERFAMILY SSF54695 POZ domain 147 253 4.97E-22
4 g938.t1 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 46 68 -

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:0005515 protein 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