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_3 g1464 g1464.t1 TTS g1464.t1 11058577 11058577
chr_3 g1464 g1464.t1 isoform g1464.t1 11058703 11059664
chr_3 g1464 g1464.t1 exon g1464.t1.exon1 11058703 11058851
chr_3 g1464 g1464.t1 cds g1464.t1.CDS1 11058703 11058851
chr_3 g1464 g1464.t1 exon g1464.t1.exon2 11058913 11058932
chr_3 g1464 g1464.t1 cds g1464.t1.CDS2 11058913 11058932
chr_3 g1464 g1464.t1 exon g1464.t1.exon3 11058992 11059274
chr_3 g1464 g1464.t1 cds g1464.t1.CDS3 11058992 11059274
chr_3 g1464 g1464.t1 exon g1464.t1.exon4 11059334 11059664
chr_3 g1464 g1464.t1 cds g1464.t1.CDS4 11059334 11059664
chr_3 g1464 g1464.t1 TSS g1464.t1 11059694 11059694

Sequences

>g1464.t1 Gene=g1464 Length=783
ATGAAGTTCTTTATTTTAATAGTTTCCTTATTTGCTGCAGTGTCAGCTTTTCCCAATAGA
GAAGAAAGGATCGTTGGTGGCTCAGTCGCTAAACCTAATTCGCATCCTTTTGTTGTACTT
CTTGTTGTCAATTTACCAAATCATAATGATGCAATGTGCGGAGGCTCAATAATCAGCAAA
ACAGTCATTTTAACTGCTGCACATTGCCTGCAAGGTTCAATTTCAACAGAAGTTGCAGCT
GGTGTTCACGACATCACACATGAAGAACCAACACAACAACATATGACTGTTATGCCTCCT
CAATATCGCGTTCATAGCCAATTCAATCCAAAAAATTTTAATAATGATGTGGCTACTTTA
ATTTTACCCCATCAATTGACTCTCAATAAGTATGTCGCAACAATAACATTGGCAAAAGCA
AATATAGGATTACTTGAAGGTGTAAATGCGATGTCGTTGGGTTGGGGAGACACAGTCAAT
GGTGGACCTCATTCGAATGTCTTAAAAGAGGTTACGAATAAAATTATCAAAAATTCTGAA
TGTGTTCCACATTATACAGGTGGAATTGTTAATGCTGCTGCTATGTGTGTTGCTTCGACC
AATAGAAATGGAATATGTGATGGTGATTCTGGAGGTCCTTTGGTAATTGCCCAAGGCAGC
AATCTTATACAAGTTGGTATTGCAAGCTTCATTCCAACTCGTCCGAATACTTGTGGTGTA
GTTCCTGCTGGTTACGCTCGAGTCAGTTCTTTTATTGCATGGATTGAAAGTCATATGAAA
TAA

>g1464.t1 Gene=g1464 Length=260
MKFFILIVSLFAAVSAFPNREERIVGGSVAKPNSHPFVVLLVVNLPNHNDAMCGGSIISK
TVILTAAHCLQGSISTEVAAGVHDITHEEPTQQHMTVMPPQYRVHSQFNPKNFNNDVATL
ILPHQLTLNKYVATITLAKANIGLLEGVNAMSLGWGDTVNGGPHSNVLKEVTNKIIKNSE
CVPHYTGGIVNAAAMCVASTNRNGICDGDSGGPLVIAQGSNLIQVGIASFIPTRPNTCGV
VPAGYARVSSFIAWIESHMK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
16 g1464.t1 CDD cd00190 Tryp_SPc 24 258 1.93682E-62
9 g1464.t1 Gene3D G3DSA:2.40.10.10 - 25 249 5.9E-56
10 g1464.t1 Gene3D G3DSA:2.40.10.10 - 36 256 5.9E-56
2 g1464.t1 PANTHER PTHR24260 - 3 260 7.3E-56
3 g1464.t1 PANTHER PTHR24260:SF90 AT07769P-RELATED 3 260 7.3E-56
6 g1464.t1 PRINTS PR00722 Chymotrypsin serine protease family (S1) signature 54 69 8.2E-11
5 g1464.t1 PRINTS PR00722 Chymotrypsin serine protease family (S1) signature 112 126 8.2E-11
4 g1464.t1 PRINTS PR00722 Chymotrypsin serine protease family (S1) signature 203 215 8.2E-11
1 g1464.t1 Pfam PF00089 Trypsin 24 255 1.5E-44
12 g1464.t1 Phobius SIGNAL_PEPTIDE Signal peptide region 1 16 -
13 g1464.t1 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 2 -
14 g1464.t1 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 3 11 -
15 g1464.t1 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 12 16 -
11 g1464.t1 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 17 260 -
18 g1464.t1 ProSitePatterns PS00134 Serine proteases, trypsin family, histidine active site. 64 69 -
19 g1464.t1 ProSitePatterns PS00135 Serine proteases, trypsin family, serine active site. 204 215 -
20 g1464.t1 ProSiteProfiles PS50240 Serine proteases, trypsin domain profile. 24 260 25.974
17 g1464.t1 SMART SM00020 trypsin_2 23 255 4.6E-53
7 g1464.t1 SUPERFAMILY SSF50494 Trypsin-like serine proteases 6 260 1.36E-61
8 g1464.t1 SignalP_EUK SignalP-noTM SignalP-noTM 1 16 -

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

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