Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Brachyurin.

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 g8136 g8136.t20 TTS g8136.t20 28746198 28746198
chr_2 g8136 g8136.t20 isoform g8136.t20 28746241 28747343
chr_2 g8136 g8136.t20 exon g8136.t20.exon1 28746241 28746298
chr_2 g8136 g8136.t20 cds g8136.t20.CDS1 28746241 28746298
chr_2 g8136 g8136.t20 exon g8136.t20.exon2 28746358 28746457
chr_2 g8136 g8136.t20 cds g8136.t20.CDS2 28746358 28746457
chr_2 g8136 g8136.t20 exon g8136.t20.exon3 28746533 28746625
chr_2 g8136 g8136.t20 cds g8136.t20.CDS3 28746533 28746625
chr_2 g8136 g8136.t20 exon g8136.t20.exon4 28746775 28747242
chr_2 g8136 g8136.t20 cds g8136.t20.CDS4 28746775 28747242
chr_2 g8136 g8136.t20 exon g8136.t20.exon5 28747310 28747343
chr_2 g8136 g8136.t20 cds g8136.t20.CDS5 28747310 28747343
chr_2 g8136 g8136.t20 TSS g8136.t20 28747477 28747477

Sequences

>g8136.t20 Gene=g8136 Length=753
ATGACTAATTTTCGTAGTGGAAGTAGAATTGCTGGTGGAACAGAAGCATCGCGAAATCAA
TTCCCATTTGCCACAATTTTCTTTATTTATGCTCCAAACGATGATCAATCAATTTGTTCT
GGATCAATTCTTTCAGCTCATTATGTTCTATCAGCAGCTCATTGCTTTACAAATTTAGCT
TCTGCCGATTTACTTGCAGGTGTGCACAATGTTGAAACAGAATTTCCCATATACGAGCTA
ACAATATTCAACTCTGACATTATCATTCATGAATCGTACGACAGAGTTCGTTATACAAAT
GATATTGCAGTTATAAGCACAAGACGATCACCATTTTCATTCACAAGAATTGAAATTCAA
CCAATTAATATCATCCCAAGATCATATGCAAATAGTAATCTTACTGGATATATGGCTAGA
ATTTCAGGATGGGGCCTAACCAGTGATACATCATCCATTAGTCCCGTGCCAAGATATATT
GATGCACCTATCATATCAAATGATGAGTGTGCGAGAACATTCGGTACATTGATAACGAGT
GGAAACATTTGTCTGAGTGGTAGCAATGGCAGATCGACATGTCCAGGGGACAGCGGTGGA
ATGACAATAGCTCATGGTAGTACACGAGTCCTTGCTGGAATTGTTAGTTTCGGAAGCGAT
AGAGGATGTACATTAGGCTATCCAACTGCCAAAACACGTATTACTGCATTTTATGATTGG
ATTACAAGTAAAACTGGAATTGTGATTTCATAA

>g8136.t20 Gene=g8136 Length=250
MTNFRSGSRIAGGTEASRNQFPFATIFFIYAPNDDQSICSGSILSAHYVLSAAHCFTNLA
SADLLAGVHNVETEFPIYELTIFNSDIIIHESYDRVRYTNDIAVISTRRSPFSFTRIEIQ
PINIIPRSYANSNLTGYMARISGWGLTSDTSSISPVPRYIDAPIISNDECARTFGTLITS
GNICLSGSNGRSTCPGDSGGMTIAHGSTRVLAGIVSFGSDRGCTLGYPTAKTRITAFYDW
ITSKTGIVIS

Protein features from InterProScan

Transcript Database ID Name Start End E.value
9 g8136.t20 CDD cd00190 Tryp_SPc 10 244 1.43335E-54
8 g8136.t20 Gene3D G3DSA:2.40.10.10 - 3 246 3.6E-51
2 g8136.t20 PANTHER PTHR24250:SF56 SERINE PROTEASE P96 5 245 2.1E-57
3 g8136.t20 PANTHER PTHR24250 CHYMOTRYPSIN-RELATED 5 245 2.1E-57
4 g8136.t20 PRINTS PR00722 Chymotrypsin serine protease family (S1) signature 40 55 6.4E-8
5 g8136.t20 PRINTS PR00722 Chymotrypsin serine protease family (S1) signature 97 111 6.4E-8
6 g8136.t20 PRINTS PR00722 Chymotrypsin serine protease family (S1) signature 191 203 6.4E-8
1 g8136.t20 Pfam PF00089 Trypsin 10 241 5.3E-39
10 g8136.t20 ProSitePatterns PS00134 Serine proteases, trypsin family, histidine active site. 50 55 -
12 g8136.t20 ProSiteProfiles PS50240 Serine proteases, trypsin domain profile. 10 246 24.829
11 g8136.t20 SMART SM00020 trypsin_2 9 241 1.1E-45
7 g8136.t20 SUPERFAMILY SSF50494 Trypsin-like serine proteases 7 246 4.95E-58

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: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