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.t6 TTS g1128.t6 8337214 8337214
chr_3 g1128 g1128.t6 isoform g1128.t6 8337327 8338549
chr_3 g1128 g1128.t6 exon g1128.t6.exon1 8337327 8337435
chr_3 g1128 g1128.t6 cds g1128.t6.CDS1 8337327 8337435
chr_3 g1128 g1128.t6 exon g1128.t6.exon2 8337495 8338001
chr_3 g1128 g1128.t6 cds g1128.t6.CDS2 8337495 8337961
chr_3 g1128 g1128.t6 exon g1128.t6.exon3 8338123 8338549
chr_3 g1128 g1128.t6 TSS g1128.t6 8338570 8338570

Sequences

>g1128.t6 Gene=g1128 Length=1043
ATGGTAAATATTGCTTTGCATTTTATAATGTTAATAATAAAAAAAGAAATTAAATATCAT
TGCAGAACGACAAATTTAAGTTTTTTTTGTCATTTAATCAATCCAAGTTGGGATTAGGAA
AATTTGGAAATTTTAAAAACGATTATGGACTTTGGTAAAATATTTGATTTTGTTAGCTAT
TTCAATTTTAAAAATTCTCTTTTAAAAAGGTTTATTCGTACTAATGGAAATCCTCAATCA
TTCACTGGTACAATAGGTCTTGATCCTGCTTTTGACAAAAATTTAGTTGATTGGAAGCAA
ATTGAAATTAATGTAAGATTGATTAAAAGTGCATTCAATCGTCACTCGGATACAATTGCC
TCTGTAACTGCCCGTTATCTGGAAAAAAATATCTTTAAGTTCGGATTAACTAAATCAATG
ACAGGTAAAATTTGATTTAAAGTATTAAAATTCTATTATAGATCAATATGCCAATCATTT
TAAACAATAAAAAAAATAGCAAACGTGATGGTGCAAAAAATCATTTAAAGTCTATGTTTG
AATCAGGAAATGATGCTGATATCACAATTATGTCAGAAGGAAAAGAGCTCAAAGTTCATA
ATTTCATTTTAAAACGATCAGAAGTTTTTTCGAAAATGTTTAGTGGTGAAATGAAGGAAT
CTCGAAATAGAATCGTAGTTATTGAAGACATCAAACACGAAGTGATTGTTGAAATGTGCC
GATATTTATATTACGATGAAATTCCTAAAATTAAATCACTTGCTCTTCCTTTATTAGTTG
CTGCTTCAAAATATTTAATCGATGATTTAGTTGAAGAATGTGAAGATTTTTTGATGACAA
ACATTACTCTTGACAATTATCATGAGGTTATAGTAATTGCTGATCAACTTAATAAGGAAA
AGTTGCGAGAAGCTGCTATTGATTATATTATTACCAATTGTAAATCAATTTTCCCGTCTA
CTGCTTGGAAGGAATTAAAAACTAGTCACGTGCAACTTGCATTGACTGTCATGGAAAAAT
TTATGTTAACTTTTCAACTATGA

>g1128.t6 Gene=g1128 Length=191
MPIILNNKKNSKRDGAKNHLKSMFESGNDADITIMSEGKELKVHNFILKRSEVFSKMFSG
EMKESRNRIVVIEDIKHEVIVEMCRYLYYDEIPKIKSLALPLLVAASKYLIDDLVEECED
FLMTNITLDNYHEVIVIADQLNKEKLREAAIDYIITNCKSIFPSTAWKELKTSHVQLALT
VMEKFMLTFQL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g1128.t6 Coils Coil Coil 191 191 -
7 g1128.t6 Gene3D G3DSA:3.30.710.10 Potassium Channel Kv1.1; Chain A 8 120 7.5E-27
6 g1128.t6 Gene3D G3DSA:1.25.40.420 - 125 189 1.2E-11
2 g1128.t6 PANTHER PTHR24413:SF213 FI01029P-RELATED 10 185 1.7E-37
3 g1128.t6 PANTHER PTHR24413 SPECKLE-TYPE POZ PROTEIN 10 185 1.7E-37
1 g1128.t6 Pfam PF00651 BTB/POZ domain 20 124 8.1E-20
9 g1128.t6 ProSiteProfiles PS50097 BTB domain profile. 30 96 13.86
5 g1128.t6 SMART SM00225 BTB_4 30 126 7.2E-14
4 g1128.t6 SUPERFAMILY SSF54695 POZ domain 16 124 1.96E-22

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