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 g16397 g16397.t32 TTS g16397.t32 9326087 9326087
chr_4 g16397 g16397.t32 isoform g16397.t32 9336191 9337367
chr_4 g16397 g16397.t32 exon g16397.t32.exon1 9336191 9336380
chr_4 g16397 g16397.t32 cds g16397.t32.CDS1 9336209 9336380
chr_4 g16397 g16397.t32 exon g16397.t32.exon2 9336435 9336558
chr_4 g16397 g16397.t32 cds g16397.t32.CDS2 9336435 9336558
chr_4 g16397 g16397.t32 exon g16397.t32.exon3 9336663 9336776
chr_4 g16397 g16397.t32 cds g16397.t32.CDS3 9336663 9336776
chr_4 g16397 g16397.t32 exon g16397.t32.exon4 9336840 9336990
chr_4 g16397 g16397.t32 cds g16397.t32.CDS4 9336840 9336990
chr_4 g16397 g16397.t32 exon g16397.t32.exon5 9337059 9337367
chr_4 g16397 g16397.t32 cds g16397.t32.CDS5 9337059 9337367
chr_4 g16397 g16397.t32 TSS g16397.t32 9337406 9337406

Sequences

>g16397.t32 Gene=g16397 Length=888
ATGAAACTTTTCCTTCTCGCGATCCTCGCCGTTGGCGCTCTTGCCCAGGAGAACTATGAG
GGCCCAGAGTACGCTCCAATTGATCCATCATCAATCATTCCTGTTCAGGAAATGCCCGGT
TTCTGGGATGACAAGACCGAATTCCCAGCATGGATGAAGTCACCAGTCAATGTCCGTGAT
CGTCGTATTGTCGGTGGTGTTGAAGTTGTTCCACACAGCCATCCATACCAAGTTGCCCTT
CACATTCAATTCGGTGGTGGTACTGGTCTCTGCGGTGGTTCAGTTTTGACAATCCGTTCA
GTTTTGACTGCTGCTCATTGTCCAATTGGTTCAAGCTCAACCTTGGTCATTGCTGGTGCT
CACAACAGAAATGTCGTTGAAGCCAATCAACAACGTCGTACTGTTCCATCATCAGGCTAC
CGCATCCACGCCAACTACAATCCATCAAACTTGAACAATGATATTGCTGTTCTCATCACA
CCAACACCAAACTTTGCATGGACCACAGCTGTTCAACCAACACGTCGTCCAACTGGTGCT
CAACTTAGCGATCTTTTCGTTGGAGATAGATCACCTGTCCTCCGTAAGGCTTACAATACA
ATCATCACTAATGCTGCTTGCGCTCAAGTTTATGGAACAAGCGTCGTAAATGCTGGAGTT
ATTTGCAAGGAAACAGCTCAATCAAATCAAGGAACATGCAACGGAGATTCAGGCGGTGTG
CTTTCAGTTGAACGTCCTGGACACGCTCAATGGGTCCAAGTTGGTGTTACCTCATTTGGT
GCTGCTGCTGGTTGTGTTGCTGGATTCCCATCAGGCTTCGCTCGTATGACTCATTTCGAT
GCATGGATTAATGCCAACCAAAATCCATAAAAAGTGAACATTCATTTT

>g16397.t32 Gene=g16397 Length=289
MKLFLLAILAVGALAQENYEGPEYAPIDPSSIIPVQEMPGFWDDKTEFPAWMKSPVNVRD
RRIVGGVEVVPHSHPYQVALHIQFGGGTGLCGGSVLTIRSVLTAAHCPIGSSSTLVIAGA
HNRNVVEANQQRRTVPSSGYRIHANYNPSNLNNDIAVLITPTPNFAWTTAVQPTRRPTGA
QLSDLFVGDRSPVLRKAYNTIITNAACAQVYGTSVVNAGVICKETAQSNQGTCNGDSGGV
LSVERPGHAQWVQVGVTSFGAAAGCVAGFPSGFARMTHFDAWINANQNP

Protein features from InterProScan

Transcript Database ID Name Start End E.value
17 g16397.t32 CDD cd00190 Tryp_SPc 63 286 1.85388E-45
9 g16397.t32 Gene3D G3DSA:2.40.10.10 - 63 108 1.7E-12
11 g16397.t32 Gene3D G3DSA:2.40.10.10 - 113 189 2.1E-8
10 g16397.t32 Gene3D G3DSA:2.40.10.10 - 190 288 8.4E-19
2 g16397.t32 PANTHER PTHR24250:SF56 SERINE PROTEASE P96 58 285 9.0E-59
3 g16397.t32 PANTHER PTHR24250 CHYMOTRYPSIN-RELATED 58 285 9.0E-59
6 g16397.t32 PRINTS PR00722 Chymotrypsin serine protease family (S1) signature 92 107 4.4E-8
4 g16397.t32 PRINTS PR00722 Chymotrypsin serine protease family (S1) signature 150 164 4.4E-8
5 g16397.t32 PRINTS PR00722 Chymotrypsin serine protease family (S1) signature 230 242 4.4E-8
1 g16397.t32 Pfam PF00089 Trypsin 63 283 6.8E-34
13 g16397.t32 Phobius SIGNAL_PEPTIDE Signal peptide region 1 15 -
14 g16397.t32 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 2 -
15 g16397.t32 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 3 11 -
16 g16397.t32 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 12 15 -
12 g16397.t32 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 16 289 -
19 g16397.t32 ProSitePatterns PS00134 Serine proteases, trypsin family, histidine active site. 102 107 -
20 g16397.t32 ProSitePatterns PS00135 Serine proteases, trypsin family, serine active site. 231 242 -
21 g16397.t32 ProSiteProfiles PS50240 Serine proteases, trypsin domain profile. 63 288 22.437
18 g16397.t32 SMART SM00020 trypsin_2 62 283 1.8E-40
7 g16397.t32 SUPERFAMILY SSF50494 Trypsin-like serine proteases 55 286 1.75E-52
8 g16397.t32 SignalP_EUK SignalP-noTM SignalP-noTM 1 15 -

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