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 g1128 g1128.t1 TTS g1128.t1 8337214 8337214
chr_3 g1128 g1128.t1 isoform g1128.t1 8337327 8338549
chr_3 g1128 g1128.t1 exon g1128.t1.exon1 8337327 8337435
chr_3 g1128 g1128.t1 cds g1128.t1.CDS1 8337327 8337435
chr_3 g1128 g1128.t1 exon g1128.t1.exon2 8337495 8337967
chr_3 g1128 g1128.t1 cds g1128.t1.CDS2 8337495 8337967
chr_3 g1128 g1128.t1 exon g1128.t1.exon3 8338027 8338064
chr_3 g1128 g1128.t1 cds g1128.t1.CDS3 8338027 8338064
chr_3 g1128 g1128.t1 exon g1128.t1.exon4 8338126 8338340
chr_3 g1128 g1128.t1 cds g1128.t1.CDS4 8338126 8338340
chr_3 g1128 g1128.t1 exon g1128.t1.exon5 8338396 8338484
chr_3 g1128 g1128.t1 cds g1128.t1.CDS5 8338396 8338484
chr_3 g1128 g1128.t1 exon g1128.t1.exon6 8338547 8338549
chr_3 g1128 g1128.t1 cds g1128.t1.CDS6 8338547 8338549
chr_3 g1128 g1128.t1 TSS g1128.t1 8338570 8338570

Sequences

>g1128.t1 Gene=g1128 Length=927
ATGAACGACAAATTTAAGTTTTTTTTGTCATTTAATCAATCCAAGTTGGGATTAGGAAAA
TTTGGAAATTTTAAAAACGATTATGGACTTTGGTTTATTCGTACTAATGGAAATCCTCAA
TCATTCACTGGTACAATAGGTCTTGATCCTGCTTTTGACAAAAATTTAGTTGATTGGAAG
CAAATTGAAATTAATGTAAGATTGATTAAAAGTGCATTCAATCGTCACTCGGATACAATT
GCCTCTGTAACTGCCCGTTATCTGGAAAAAAATATCTTTAAGTTCGGATTAACTAAATCA
ATGACAGGTGACTTGACTCAAATAAATTTTTCTTGTATTGTCGAGATCAATATGCCAATC
ATTTTAAACAATAAAAAAAATAGCAAACGTGATGGTGCAAAAAATCATTTAAAGTCTATG
TTTGAATCAGGAAATGATGCTGATATCACAATTATGTCAGAAGGAAAAGAGCTCAAAGTT
CATAATTTCATTTTAAAACGATCAGAAGTTTTTTCGAAAATGTTTAGTGGTGAAATGAAG
GAATCTCGAAATAGAATCGTAGTTATTGAAGACATCAAACACGAAGTGATTGTTGAAATG
TGCCGATATTTATATTACGATGAAATTCCTAAAATTAAATCACTTGCTCTTCCTTTATTA
GTTGCTGCTTCAAAATATTTAATCGATGATTTAGTTGAAGAATGTGAAGATTTTTTGATG
ACAAACATTACTCTTGACAATTATCATGAGGTTATAGTAATTGCTGATCAACTTAATAAG
GAAAAGTTGCGAGAAGCTGCTATTGATTATATTATTACCAATTGTAAATCAATTTTCCCG
TCTACTGCTTGGAAGGAATTAAAAACTAGTCACGTGCAACTTGCATTGACTGTCATGGAA
AAATTTATGTTAACTTTTCAACTATGA

>g1128.t1 Gene=g1128 Length=308
MNDKFKFFLSFNQSKLGLGKFGNFKNDYGLWFIRTNGNPQSFTGTIGLDPAFDKNLVDWK
QIEINVRLIKSAFNRHSDTIASVTARYLEKNIFKFGLTKSMTGDLTQINFSCIVEINMPI
ILNNKKNSKRDGAKNHLKSMFESGNDADITIMSEGKELKVHNFILKRSEVFSKMFSGEMK
ESRNRIVVIEDIKHEVIVEMCRYLYYDEIPKIKSLALPLLVAASKYLIDDLVEECEDFLM
TNITLDNYHEVIVIADQLNKEKLREAAIDYIITNCKSIFPSTAWKELKTSHVQLALTVME
KFMLTFQL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
7 g1128.t1 Gene3D G3DSA:3.30.710.10 Potassium Channel Kv1.1; Chain A 125 237 0.00
6 g1128.t1 Gene3D G3DSA:1.25.40.420 - 242 306 0.00
2 g1128.t1 PANTHER PTHR24413:SF213 FI01029P-RELATED 107 302 0.00
3 g1128.t1 PANTHER PTHR24413 SPECKLE-TYPE POZ PROTEIN 107 302 0.00
1 g1128.t1 Pfam PF00651 BTB/POZ domain 137 241 0.00
8 g1128.t1 ProSiteProfiles PS50097 BTB domain profile. 147 213 13.86
5 g1128.t1 SMART SM00225 BTB_4 147 243 0.00
4 g1128.t1 SUPERFAMILY SSF54695 POZ domain 133 241 0.00

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