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_4 g16398 g16398.t16 TSS g16398.t16 9340829 9340829
chr_4 g16398 g16398.t16 isoform g16398.t16 9340865 9342001
chr_4 g16398 g16398.t16 exon g16398.t16.exon1 9340865 9341132
chr_4 g16398 g16398.t16 cds g16398.t16.CDS1 9341101 9341132
chr_4 g16398 g16398.t16 exon g16398.t16.exon2 9341273 9341364
chr_4 g16398 g16398.t16 cds g16398.t16.CDS2 9341273 9341364
chr_4 g16398 g16398.t16 exon g16398.t16.exon3 9341430 9341554
chr_4 g16398 g16398.t16 cds g16398.t16.CDS3 9341430 9341554
chr_4 g16398 g16398.t16 exon g16398.t16.exon4 9341613 9341767
chr_4 g16398 g16398.t16 cds g16398.t16.CDS4 9341613 9341767
chr_4 g16398 g16398.t16 exon g16398.t16.exon5 9341830 9342001
chr_4 g16398 g16398.t16 cds g16398.t16.CDS5 9341830 9342001
chr_4 g16398 g16398.t16 TTS g16398.t16 9342130 9342130

Sequences

>g16398.t16 Gene=g16398 Length=812
ATGAAACTCTTGCTTCTCGCACTTTTCGCTGCTGTGGCACTTGCCCAGGAAAACTATGAT
GGACCAGAATACGCTCCATTTGATGCCTCAGAAATCATCCCAGTTGAAGATTTCCCAGGT
TTCTGGACAATCGTGAATTCCCAAAAGAAGTTTTCACACCAAATCCACGTGCCTCAAGAA
TTGTCGGTGGTGTTGAAGTTGTTCCACACAGCCATCCATACCAAGTTGCCCTTCACATGC
AATTCGGTACTGGCACTGGTCTCTGCCGAAATGTCGTTGAACCAAATCAACAACGTCGTA
CTGTTCCATCATCAGGCTACCGCATCCACGCCAACTACAACCCATCAAACTTGAACAATG
ATATCGCTATCCTCATCACACCAACACCAAACTTTGCCTTCGGTGCACATGTTCAAGCCG
CTCGTATGCCAACTGCTTTTGCTAGTGAACTTTTCGTCGGTGAAACTGCCCGCTCAACTG
GATGGGGAAGAACAACTAACACTGGTGCAACCTCAGCTGTCCTTCGTAAGGCTTACAATC
CAGTCATTACTAATGCTGCTTGCTCAGCTGTCTATGGTGGATCAGTTGTAATTGCTTCAG
TCATTTGCATTGCTACAAGCGGTGTCAACCAAGGAACATGCAACGGTGACTCAGGCGGTG
TCCTTTCAGTTCCAAGAGCTGGAGATACTCGTCCAATCCAAATTGGTGTTACATCATTCG
TCGCTGCAGCTGGTTGCGTTGCTGGATTCCCATCAGGCTTCGCAAGAGTTACATCATTCC
TTACCTGGATTAACAACAACCAAAATCCATAA

>g16398.t16 Gene=g16398 Length=191
MQFGTGTGLCRNVVEPNQQRRTVPSSGYRIHANYNPSNLNNDIAILITPTPNFAFGAHVQ
AARMPTAFASELFVGETARSTGWGRTTNTGATSAVLRKAYNPVITNAACSAVYGGSVVIA
SVICIATSGVNQGTCNGDSGGVLSVPRAGDTRPIQIGVTSFVAAAGCVAGFPSGFARVTS
FLTWINNNQNP

Protein features from InterProScan

Transcript Database ID Name Start End E.value
7 g16398.t16 CDD cd00190 Tryp_SPc 11 188 2.37491E-42
6 g16398.t16 Gene3D G3DSA:2.40.10.10 - 17 186 6.3E-35
5 g16398.t16 Gene3D G3DSA:2.40.10.10 - 63 181 6.3E-35
2 g16398.t16 PANTHER PTHR24250:SF56 SERINE PROTEASE P96 11 187 1.6E-45
3 g16398.t16 PANTHER PTHR24250 CHYMOTRYPSIN-RELATED 11 187 1.6E-45
1 g16398.t16 Pfam PF00089 Trypsin 14 185 2.3E-27
8 g16398.t16 ProSitePatterns PS00135 Serine proteases, trypsin family, serine active site. 133 144 -
10 g16398.t16 ProSiteProfiles PS50240 Serine proteases, trypsin domain profile. 1 190 16.633
9 g16398.t16 SMART SM00020 trypsin_2 3 185 2.3E-17
4 g16398.t16 SUPERFAMILY SSF50494 Trypsin-like serine proteases 16 189 1.94E-39

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. There were no conditions that were differentially expressed