Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Serine protease snake.

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_2 g5463 g5463.t4 TTS g5463.t4 9725568 9725568
chr_2 g5463 g5463.t4 isoform g5463.t4 9725593 9726995
chr_2 g5463 g5463.t4 exon g5463.t4.exon1 9725593 9725775
chr_2 g5463 g5463.t4 cds g5463.t4.CDS1 9725593 9725775
chr_2 g5463 g5463.t4 exon g5463.t4.exon2 9726028 9726335
chr_2 g5463 g5463.t4 cds g5463.t4.CDS2 9726028 9726335
chr_2 g5463 g5463.t4 exon g5463.t4.exon3 9726393 9726434
chr_2 g5463 g5463.t4 cds g5463.t4.CDS3 9726393 9726434
chr_2 g5463 g5463.t4 exon g5463.t4.exon4 9726502 9726579
chr_2 g5463 g5463.t4 cds g5463.t4.CDS4 9726502 9726579
chr_2 g5463 g5463.t4 exon g5463.t4.exon5 9726651 9726773
chr_2 g5463 g5463.t4 cds g5463.t4.CDS5 9726651 9726773
chr_2 g5463 g5463.t4 exon g5463.t4.exon6 9726836 9726995
chr_2 g5463 g5463.t4 cds g5463.t4.CDS6 9726836 9726995
chr_2 g5463 g5463.t4 TSS g5463.t4 9727169 9727169

Sequences

>g5463.t4 Gene=g5463 Length=894
ATGGAACAAGTGAGACTAAAGTTAGTTCGTACAAATCCTCCAACTATCTGTAGTCAAACA
GACCGATCAGTTTGTTGTCCGCTTCCTTCAACAACTACAACTACGACTTCAACAACAAAA
CCATCGCCATCACGTTCAATGCAAAGAATAAGTGAACAAAAATGCAGGGAATATGGAAAA
AGTGTTATTCAAATTACTAAAGTGGCATCTCTCATGCTGGGAGAACCACATGTAGATATA
GTAGTAGACAAGTGCAAACATAAAAGTGTTTCGTTGATTGTTGGCGGGACAGAAGCTTCG
TTAGCTGAATTTCCTCATCAAGCACTTCTCGGTTATAATAATGGAGAGCCAAGTGAATGG
GGCTGTGGAGGATCGCTTATTTCACCGAAATTTGTCTTAACTGCTGCTCATTGTTTATCA
CCACGTGGATTTGGTAATGTAAAATTTGTTAGACTTGGAATGAGCAGTAGATCACAAAAT
GACAATTCAACATTAACATTTGGTGTGACGGAAATTATTCAACATCCTAATTATAATTCA
AAAACATTTAATGAAGACATTGGTTTGCTGAGACTGAATGCAACAGTTCCAATTAATGAA
TATATTTTACCCATTTGCATGCCAACGAAACTTTATAATCCAAATAAAGCGATTGCATCA
GGATTTGGTAGAACAGGCTATCAACGATCAACTTCAGATAAATTATTGAAAGGGGATTCT
GGCGGACCATTACAAATTTATAATGATAATGAAGTCAAGTGCACATATACGCAAATAGGA
GTCGTCAGTTTTGGTTTAAAACAATGTGGAACTGTTGGAACACCTGGGGTTTATGTTAAT
GTTTATAATTATCTCGATTGGATCGAAAAAATTGTTTGGGCAGGTGAAAGTTAA

>g5463.t4 Gene=g5463 Length=297
MEQVRLKLVRTNPPTICSQTDRSVCCPLPSTTTTTTSTTKPSPSRSMQRISEQKCREYGK
SVIQITKVASLMLGEPHVDIVVDKCKHKSVSLIVGGTEASLAEFPHQALLGYNNGEPSEW
GCGGSLISPKFVLTAAHCLSPRGFGNVKFVRLGMSSRSQNDNSTLTFGVTEIIQHPNYNS
KTFNEDIGLLRLNATVPINEYILPICMPTKLYNPNKAIASGFGRTGYQRSTSDKLLKGDS
GGPLQIYNDNEVKCTYTQIGVVSFGLKQCGTVGTPGVYVNVYNYLDWIEKIVWAGES

Protein features from InterProScan

Transcript Database ID Name Start End E.value
12 g5463.t4 CDD cd00190 Tryp_SPc 93 291 5.12106E-67
10 g5463.t4 Gene3D G3DSA:2.40.10.10 - 84 235 2.5E-38
11 g5463.t4 Gene3D G3DSA:2.40.10.10 - 236 291 9.6E-16
4 g5463.t4 PANTHER PTHR24260:SF107 EG:BACR7A4.3 PROTEIN-RELATED 16 236 7.9E-53
6 g5463.t4 PANTHER PTHR24260 - 16 236 7.9E-53
3 g5463.t4 PANTHER PTHR24260:SF107 EG:BACR7A4.3 PROTEIN-RELATED 235 294 7.9E-53
5 g5463.t4 PANTHER PTHR24260 - 235 294 7.9E-53
8 g5463.t4 PRINTS PR00722 Chymotrypsin serine protease family (S1) signature 123 138 8.2E-7
7 g5463.t4 PRINTS PR00722 Chymotrypsin serine protease family (S1) signature 233 245 8.2E-7
2 g5463.t4 Pfam PF00089 Trypsin 93 235 1.9E-30
1 g5463.t4 Pfam PF00089 Trypsin 237 288 3.3E-10
13 g5463.t4 ProSitePatterns PS00134 Serine proteases, trypsin family, histidine active site. 133 138 -
15 g5463.t4 ProSiteProfiles PS50240 Serine proteases, trypsin domain profile. 93 293 22.621
14 g5463.t4 SMART SM00020 trypsin_2 92 288 8.1E-54
9 g5463.t4 SUPERFAMILY SSF50494 Trypsin-like serine proteases 77 293 8.01E-64

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g5463/g5463.t4; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5463.t4.fa.iupred3.txt does not exist

GO terms from InterProScan

GOID TERM ONTOLOGY
GO:0004252 serine-type endopeptidase activity MF
GO:0006508 proteolysis BP

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