Gene loci information

Transcript annotation

  • This transcript has been annotated as 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 g743 g743.t1 isoform g743.t1 5684907 5686958
chr_3 g743 g743.t1 exon g743.t1.exon1 5684907 5685054
chr_3 g743 g743.t1 cds g743.t1.CDS1 5684907 5685054
chr_3 g743 g743.t1 exon g743.t1.exon2 5685190 5685332
chr_3 g743 g743.t1 cds g743.t1.CDS2 5685190 5685332
chr_3 g743 g743.t1 exon g743.t1.exon3 5685392 5685570
chr_3 g743 g743.t1 cds g743.t1.CDS3 5685392 5685570
chr_3 g743 g743.t1 exon g743.t1.exon4 5685681 5685858
chr_3 g743 g743.t1 cds g743.t1.CDS4 5685681 5685858
chr_3 g743 g743.t1 exon g743.t1.exon5 5686555 5686834
chr_3 g743 g743.t1 cds g743.t1.CDS5 5686555 5686834
chr_3 g743 g743.t1 exon g743.t1.exon6 5686900 5686958
chr_3 g743 g743.t1 cds g743.t1.CDS6 5686900 5686958
chr_3 g743 g743.t1 TSS g743.t1 NA NA
chr_3 g743 g743.t1 TTS g743.t1 NA NA

Sequences

>g743.t1 Gene=g743 Length=987
ATGGGAGAAGTATTAAAATCATCCACATTTTCAGCAGGAGCAAATGACAAACTCAAATGG
TGTTTACGAGTCAATCCAAAAGGACTTGATGAAGAAAGTAAAGATTATCTCTCCCTGTAC
TTGTTACTCGTTTCCTGCAACAAATCGGAAGTTCGAGCCAAATTTAAATTCTCAATATTG
AATGCGAAACGTGAAGAGACCAAAGCAATGGAATCACAACGTGCATACCGTTTCGTACAA
GGAAAAGATTGGGGATTCAAAAAATTCATTCGACGTGATTTTCTTCTAGATGAAGCAAAT
GGTCTATTGCCCGAGGACAAATTAACAATTTTCTGTGAGGTCAGTGTTGTTGCTGACAGT
GTTAATATATCAGGACAAAGTAACATAATCCAATTCAAAGTGCCAGAATGTAAGCTGTCT
GAGGATTTGGGCAATTTATTTGATAATGAAAAGTTTAGCGATGTGACATTATCGGTAGGC
GGACGAGAGTTTCAGGCGCACAAAGCTATTCTTGCTGCACGAAGTCCTGTCTTTGCCGCC
ATGTTTGAGCATGAAATGGAAGAGCGAAAGCAAAATCGCGTAGCAATCACCGATGTAGAC
CACGAAGTACTCAAAGAAATGCTCCGATTTATATATACCGGAAAAGCACCCAACTTGGAA
AAAATGGCTGATGATTTATTAGCTGCAGCTGATAAGTATGCTCTTGAAAAGCTTAAAGTG
ATGTGTGAAGAAGCACTTTGTGTGAATCTATCAGTAGAAACAGCTGCCGAGACATTGATA
CTTGCAGATTTACATAGTGCGGATCAATTGAAGGCACAAACAATTGATTTCATTAACACC
AGTCATGCAACTGATGTGATGGAAACCGTTGGATGGAAAAATATGGTAACAACACATCCG
CATCTAATAAATGAGGCATTTCGCGCATTAGCTACTCAACAAATACCACCTATCGGTCCA
CCAAGGAAGCGAGTTAAAATGAGCTGA

>g743.t1 Gene=g743 Length=328
MGEVLKSSTFSAGANDKLKWCLRVNPKGLDEESKDYLSLYLLLVSCNKSEVRAKFKFSIL
NAKREETKAMESQRAYRFVQGKDWGFKKFIRRDFLLDEANGLLPEDKLTIFCEVSVVADS
VNISGQSNIIQFKVPECKLSEDLGNLFDNEKFSDVTLSVGGREFQAHKAILAARSPVFAA
MFEHEMEERKQNRVAITDVDHEVLKEMLRFIYTGKAPNLEKMADDLLAAADKYALEKLKV
MCEEALCVNLSVETAAETLILADLHSADQLKAQTIDFINTSHATDVMETVGWKNMVTTHP
HLINEAFRALATQQIPPIGPPRKRVKMS

Protein features from InterProScan

Transcript Database ID Name Start End E.value
14 g743.t1 CDD cd18345 BTB_POZ_roadkill-like 135 255 0.0000000
11 g743.t1 Gene3D G3DSA:2.60.210.10 Apoptosis 1 119 0.0000000
10 g743.t1 Gene3D G3DSA:3.30.710.10 Potassium Channel Kv1.1; Chain A 129 245 0.0000000
9 g743.t1 Gene3D G3DSA:1.25.40.420 - 249 328 0.0000000
3 g743.t1 PANTHER PTHR24413 SPECKLE-TYPE POZ PROTEIN 1 326 0.0000000
4 g743.t1 PANTHER PTHR24413:SF91 SPECKLE-TYPE POZ PROTEIN-LIKE 1 326 0.0000000
1 g743.t1 Pfam PF00917 MATH domain 18 115 0.0000016
2 g743.t1 Pfam PF00651 BTB/POZ domain 144 249 0.0000000
12 g743.t1 ProSiteProfiles PS50144 MATH/TRAF domain profile. 1 114 23.4080000
13 g743.t1 ProSiteProfiles PS50097 BTB domain profile. 153 220 21.2230000
8 g743.t1 SMART SM00061 math_3 1 95 0.0000001
7 g743.t1 SMART SM00225 BTB_4 153 250 0.0000000
5 g743.t1 SUPERFAMILY SSF49599 TRAF domain-like 2 123 0.0000000
6 g743.t1 SUPERFAMILY SSF54695 POZ domain 130 247 0.0000000

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

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