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 g1220 g1220.t1 TSS g1220.t1 8814104 8814104
chr_3 g1220 g1220.t1 isoform g1220.t1 8814195 8815392
chr_3 g1220 g1220.t1 exon g1220.t1.exon1 8814195 8814328
chr_3 g1220 g1220.t1 cds g1220.t1.CDS1 8814195 8814328
chr_3 g1220 g1220.t1 exon g1220.t1.exon2 8814382 8814667
chr_3 g1220 g1220.t1 cds g1220.t1.CDS2 8814382 8814667
chr_3 g1220 g1220.t1 exon g1220.t1.exon3 8814724 8815205
chr_3 g1220 g1220.t1 cds g1220.t1.CDS3 8814724 8815205
chr_3 g1220 g1220.t1 exon g1220.t1.exon4 8815269 8815392
chr_3 g1220 g1220.t1 cds g1220.t1.CDS4 8815269 8815392
chr_3 g1220 g1220.t1 TTS g1220.t1 NA NA

Sequences

>g1220.t1 Gene=g1220 Length=1026
ATGTCTGATGAAGATAAATATGTAGCTAATAGAAAGATTATTTGGAAAGTTAATAATATT
ACAAGTGAAAAGTTAAAGTATCTTAATTTTTACTCAAATTCGATTTCATTTCATTTTTCA
ACAAAAACTTCATGGGCTTTTTTGCTTCGTGGTTATGAGAATAAACTTGGATTCTTTTTT
GTGCGAAATTTTCCTGAAGGCAAAGGTATCGAAGATGAAGATGAATTTGATGTGAAATTG
GATTTAGAAATTAGAGGTGTAGATGGACAAGTGCTTGAAAAACGAGCATTTTCTAGAAAG
TCATACGAATTTACAGTCAAAACTGCTGATTGGGGATGGAAAAATATTTGCGAATATGCA
AAGATTTTCAGTGATACCAACTATTTATCGGACGGAAATACATTAACTTTCTTTATAGAC
GTAACATTGGAACAAACACAAAAAGAATTGAAAAAAAGAGATTTACATCCTTTATTGCTC
AACTATTCAAAGCATTTCAATAATAGTAATTTAAGTGACTTTATCATCACCTCATCAGAC
AACAGAAAGTTTTACGCACATCGTGTAATACTTGCTTCTCAGTCATCATTCTTTGATAAG
TTATTTGCTGGCGAGCCACTTGATAATAATAAGTTGAGAAATATGAGTATCCCAGATGCT
GATAGTGTAACACTTCAAGAATTACTCAGATTTATGTATACTGGACAAGTTGAAAAAATT
GATGAATATGCACGGGATTTGTTGTATGTTGCACACAAGTATAATGTGAAAGAACTAAAG
CAACAATGCATCTCAATTCTCGTGCAAAAAATCAAGTTTTCAAATATTTTCGATATACTT
AGTTTAGCAGAAAAATGCAGTGCTCAACGATTGATTTATGAATGCTTACAATTTATAGTG
AAGAACTACTTAAATATTATTACTCATAAAGATTGGAAAAAGTTAGGATTAGACATGATG
ATTCAAATTATAGATGCTATGGGACAGGAAGGTGGAAACGAAAAGATTCTATTCGGTTCA
CTCTAA

>g1220.t1 Gene=g1220 Length=341
MSDEDKYVANRKIIWKVNNITSEKLKYLNFYSNSISFHFSTKTSWAFLLRGYENKLGFFF
VRNFPEGKGIEDEDEFDVKLDLEIRGVDGQVLEKRAFSRKSYEFTVKTADWGWKNICEYA
KIFSDTNYLSDGNTLTFFIDVTLEQTQKELKKRDLHPLLLNYSKHFNNSNLSDFIITSSD
NRKFYAHRVILASQSSFFDKLFAGEPLDNNKLRNMSIPDADSVTLQELLRFMYTGQVEKI
DEYARDLLYVAHKYNVKELKQQCISILVQKIKFSNIFDILSLAEKCSAQRLIYECLQFIV
KNYLNIITHKDWKKLGLDMMIQIIDAMGQEGGNEKILFGSL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
11 g1220.t1 CDD cd18186 BTB_POZ_ZBTB_KLHL-like 171 254 0.000e+00
10 g1220.t1 CDD cd14733 BACK 274 325 3.000e-07
8 g1220.t1 Gene3D G3DSA:2.60.210.10 Apoptosis 1 149 3.100e-05
7 g1220.t1 Gene3D G3DSA:3.30.710.10 Potassium Channel Kv1.1; Chain A 161 309 0.000e+00
2 g1220.t1 PANTHER PTHR24413:SF213 FI01029P-RELATED 90 315 0.000e+00
3 g1220.t1 PANTHER PTHR24413 SPECKLE-TYPE POZ PROTEIN 90 315 0.000e+00
1 g1220.t1 Pfam PF00651 BTB/POZ domain 164 270 0.000e+00
9 g1220.t1 ProSiteProfiles PS50097 BTB domain profile. 172 241 1.781e+01
6 g1220.t1 SMART SM00225 BTB_4 172 271 0.000e+00
4 g1220.t1 SUPERFAMILY SSF49599 TRAF domain-like 9 143 2.090e-05
5 g1220.t1 SUPERFAMILY SSF54695 POZ domain 158 271 0.000e+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. There were no conditions that were differentially expressed