Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Collagenase.

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 g15484 g15484.t2 TSS g15484.t2 5609001 5609001
chr_4 g15484 g15484.t2 isoform g15484.t2 5609032 5610102
chr_4 g15484 g15484.t2 exon g15484.t2.exon1 5609032 5609340
chr_4 g15484 g15484.t2 cds g15484.t2.CDS1 5609032 5609340
chr_4 g15484 g15484.t2 exon g15484.t2.exon2 5609674 5610102
chr_4 g15484 g15484.t2 cds g15484.t2.CDS2 5609674 5610102
chr_4 g15484 g15484.t2 TTS g15484.t2 5610474 5610474

Sequences

>g15484.t2 Gene=g15484 Length=738
ATGTCTCGAAAATTTTTTTTTATAATTTTAGTCACATTTTTTAAAATTTGTTTCTGTTAT
GTTGAAATTCCCTCACAATTTCGTGATGCAAAATCACCAATGGCATCAGAATTTAATTTG
GACATAATTCAAATGAATTTTCCTGGTTTATATGATGATGTTTTTGCTGGAATTGAAGGA
AGAATTGCTGGTGGTGTTGCAGCAGACGCACGTCAGTTTCCTTATCAAGGTTTGATGTAC
ATGGTGGATAATAAAAACGCAACATTCATTTGTGGTGGAAGTTTGATTACTCATAGCTTT
TTATTGACGGCAGCTCATTGTCTCTATCAATTTGAAGAAATTTCAGTCTTCCTTGGTGTT
ACAAATCGTGTTTCAGGTCCAGCAGCATTTAGTCAAGATATAACAGACAAAAGTCATATA
ATCATGCACAATCTTTACAATCCAACTGGTCACGTTAATGATATTGGTTTAATATATTTA
AGCACACTTACAGCTGAGCATTTTGACAATAAAAGAATTTCCTTAATTACTCTACCAACT
AGAAATGATATTGATGTAAATTTAGTTGGAATGGAAGCAACAGTTGCTGGATTCGGTTCA
ACTTCTGACACAAACAAAGCTTCTGAAATTCTTAGATACGTCACAATGCCAATCATAAAG
AATAGTATGTGTAAAATGACATTTGGAACTTTTATTAAAGCTACAAATTTGTGCATGAGT
GGTCAAGGTGGAAGAAGT

>g15484.t2 Gene=g15484 Length=246
MSRKFFFIILVTFFKICFCYVEIPSQFRDAKSPMASEFNLDIIQMNFPGLYDDVFAGIEG
RIAGGVAADARQFPYQGLMYMVDNKNATFICGGSLITHSFLLTAAHCLYQFEEISVFLGV
TNRVSGPAAFSQDITDKSHIIMHNLYNPTGHVNDIGLIYLSTLTAEHFDNKRISLITLPT
RNDIDVNLVGMEATVAGFGSTSDTNKASEILRYVTMPIIKNSMCKMTFGTFIKATNLCMS
GQGGRS

Protein features from InterProScan

Transcript Database ID Name Start End E.value
12 g15484.t2 CDD cd00190 Tryp_SPc 62 245 4.10833E-38
6 g15484.t2 Gene3D G3DSA:2.40.10.10 - 55 246 1.2E-35
2 g15484.t2 PANTHER PTHR24260 - 57 243 2.6E-38
3 g15484.t2 PANTHER PTHR24260:SF90 AT07769P-RELATED 57 243 2.6E-38
1 g15484.t2 Pfam PF00089 Trypsin 62 243 1.1E-25
8 g15484.t2 Phobius SIGNAL_PEPTIDE Signal peptide region 1 19 -
9 g15484.t2 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 4 -
10 g15484.t2 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 5 14 -
11 g15484.t2 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 15 19 -
7 g15484.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 20 246 -
14 g15484.t2 ProSitePatterns PS00134 Serine proteases, trypsin family, histidine active site. 102 107 -
16 g15484.t2 ProSiteProfiles PS50240 Serine proteases, trypsin domain profile. 62 246 16.909
15 g15484.t2 SMART SM00020 trypsin_2 61 246 2.2E-13
4 g15484.t2 SUPERFAMILY SSF50494 Trypsin-like serine proteases 53 244 2.5E-42
5 g15484.t2 SignalP_EUK SignalP-TM SignalP-TM 1 19 -
13 g15484.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 5 24 -

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