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.t4 TSS g15484.t4 5609001 5609001
chr_4 g15484 g15484.t4 isoform g15484.t4 5609032 5610514
chr_4 g15484 g15484.t4 exon g15484.t4.exon1 5609032 5609340
chr_4 g15484 g15484.t4 cds g15484.t4.CDS1 5609032 5609340
chr_4 g15484 g15484.t4 exon g15484.t4.exon2 5609674 5610112
chr_4 g15484 g15484.t4 cds g15484.t4.CDS2 5609674 5610112
chr_4 g15484 g15484.t4 exon g15484.t4.exon3 5610171 5610514
chr_4 g15484 g15484.t4 cds g15484.t4.CDS3 5610171 5610514
chr_4 g15484 g15484.t4 TTS g15484.t4 5610474 5610474

Sequences

>g15484.t4 Gene=g15484 Length=1092
ATGTCTCGAAAATTTTTTTTTATAATTTTAGTCACATTTTTTAAAATTTGTTTCTGTTAT
GTTGAAATTCCCTCACAATTTCGTGATGCAAAATCACCAATGGCATCAGAATTTAATTTG
GACATAATTCAAATGAATTTTCCTGGTTTATATGATGATGTTTTTGCTGGAATTGAAGGA
AGAATTGCTGGTGGTGTTGCAGCAGACGCACGTCAGTTTCCTTATCAAGGTTTGATGTAC
ATGGTGGATAATAAAAACGCAACATTCATTTGTGGTGGAAGTTTGATTACTCATAGCTTT
TTATTGACGGCAGCTCATTGTCTCTATCAATTTGAAGAAATTTCAGTCTTCCTTGGTGTT
ACAAATCGTGTTTCAGGTCCAGCAGCATTTAGTCAAGATATAACAGACAAAAGTCATATA
ATCATGCACAATCTTTACAATCCAACTGGTCACGTTAATGATATTGGTTTAATATATTTA
AGCACACTTACAGCTGAGCATTTTGACAATAAAAGAATTTCCTTAATTACTCTACCAACT
AGAAATGATATTGATGTAAATTTAGTTGGAATGGAAGCAACAGTTGCTGGATTCGGTTCA
ACTTCTGACACAAACAAAGCTTCTGAAATTCTTAGATACGTCACAATGCCAATCATAAAG
AATAGTATGTGTAAAATGACATTTGGAACTTTTATTAAAGCTACAAATTTGTGCATGAGT
GGTCAAGGTGGAAGAAGTGTTTGTTCGGGTGATTCCGGTAGTCCACTAACAGTCGAATTA
TTACCAGGAAAAATTGTCCAAGTAGGAATAGTTTCTTTTGGTCACAAACATGGATGCACT
TTAGGACATCCAGGAGTGTTTACACGAGGTAAAATTGAATATTTTTATAACATTAATAAT
TTTATAATTTTATTTTTTCAAATAGTGACAAGTTATCTTGATTGGATAGAAGGACATGTA
GGAAAGATGACAATTGAAGGAGCAATAAATAATTCACCAAATACAACTGACAGTAATAAA
AATAGTGCTAAATGTGTTCATAGTTTGAATATATTCTCAATTTTATTATTGATTATTTTT
AAATTTTTTTAG

>g15484.t4 Gene=g15484 Length=363
MSRKFFFIILVTFFKICFCYVEIPSQFRDAKSPMASEFNLDIIQMNFPGLYDDVFAGIEG
RIAGGVAADARQFPYQGLMYMVDNKNATFICGGSLITHSFLLTAAHCLYQFEEISVFLGV
TNRVSGPAAFSQDITDKSHIIMHNLYNPTGHVNDIGLIYLSTLTAEHFDNKRISLITLPT
RNDIDVNLVGMEATVAGFGSTSDTNKASEILRYVTMPIIKNSMCKMTFGTFIKATNLCMS
GQGGRSVCSGDSGSPLTVELLPGKIVQVGIVSFGHKHGCTLGHPGVFTRGKIEYFYNINN
FIILFFQIVTSYLDWIEGHVGKMTIEGAINNSPNTTDSNKNSAKCVHSLNIFSILLLIIF
KFF

Protein features from InterProScan

Transcript Database ID Name Start End E.value
18 g15484.t4 CDD cd00190 Tryp_SPc 62 319 1.13818E-58
9 g15484.t4 Gene3D G3DSA:2.40.10.10 - 71 289 2.3E-52
10 g15484.t4 Gene3D G3DSA:2.40.10.10 - 76 176 2.3E-52
2 g15484.t4 PANTHER PTHR24260 - 57 322 1.8E-57
3 g15484.t4 PANTHER PTHR24260:SF90 AT07769P-RELATED 57 322 1.8E-57
5 g15484.t4 PRINTS PR00722 Chymotrypsin serine protease family (S1) signature 92 107 2.8E-9
4 g15484.t4 PRINTS PR00722 Chymotrypsin serine protease family (S1) signature 150 164 2.8E-9
6 g15484.t4 PRINTS PR00722 Chymotrypsin serine protease family (S1) signature 245 257 2.8E-9
1 g15484.t4 Pfam PF00089 Trypsin 62 289 1.2E-38
13 g15484.t4 Phobius SIGNAL_PEPTIDE Signal peptide region 1 19 -
14 g15484.t4 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 4 -
15 g15484.t4 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 5 14 -
17 g15484.t4 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 15 19 -
12 g15484.t4 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 20 345 -
16 g15484.t4 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 346 362 -
11 g15484.t4 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 363 363 -
21 g15484.t4 ProSitePatterns PS00134 Serine proteases, trypsin family, histidine active site. 102 107 -
22 g15484.t4 ProSitePatterns PS00135 Serine proteases, trypsin family, serine active site. 246 257 -
23 g15484.t4 ProSiteProfiles PS50240 Serine proteases, trypsin domain profile. 62 321 25.623
20 g15484.t4 SMART SM00020 trypsin_2 61 316 2.5E-50
7 g15484.t4 SUPERFAMILY SSF50494 Trypsin-like serine proteases 54 321 3.21E-59
8 g15484.t4 SignalP_EUK SignalP-TM SignalP-TM 1 19 -
19 g15484.t4 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.

## Warning: Removed 1 row(s) containing missing values (geom_path).

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