General information for g15484.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Collagenase.
Parent gene
- The parent gene g15484 is located on chr_4: 5609690..5610514 (+ strand)
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.t1 | TSS | g15484.t1 | 5609001 | 5609001 |
| chr_4 | g15484 | g15484.t1 | isoform | g15484.t1 | 5609032 | 5610514 |
| chr_4 | g15484 | g15484.t1 | exon | g15484.t1.exon1 | 5609032 | 5609340 |
| chr_4 | g15484 | g15484.t1 | cds | g15484.t1.CDS1 | 5609032 | 5609340 |
| chr_4 | g15484 | g15484.t1 | exon | g15484.t1.exon2 | 5609674 | 5610112 |
| chr_4 | g15484 | g15484.t1 | cds | g15484.t1.CDS2 | 5609674 | 5610112 |
| chr_4 | g15484 | g15484.t1 | exon | g15484.t1.exon3 | 5610171 | 5610290 |
| chr_4 | g15484 | g15484.t1 | cds | g15484.t1.CDS3 | 5610171 | 5610290 |
| chr_4 | g15484 | g15484.t1 | exon | g15484.t1.exon4 | 5610348 | 5610514 |
| chr_4 | g15484 | g15484.t1 | cds | g15484.t1.CDS4 | 5610348 | 5610514 |
| chr_4 | g15484 | g15484.t1 | TTS | g15484.t1 | 5610474 | 5610474 |
Sequences
>g15484.t1 Gene=g15484 Length=1035
ATGTCTCGAAAATTTTTTTTTATAATTTTAGTCACATTTTTTAAAATTTGTTTCTGTTAT
GTTGAAATTCCCTCACAATTTCGTGATGCAAAATCACCAATGGCATCAGAATTTAATTTG
GACATAATTCAAATGAATTTTCCTGGTTTATATGATGATGTTTTTGCTGGAATTGAAGGA
AGAATTGCTGGTGGTGTTGCAGCAGACGCACGTCAGTTTCCTTATCAAGGTTTGATGTAC
ATGGTGGATAATAAAAACGCAACATTCATTTGTGGTGGAAGTTTGATTACTCATAGCTTT
TTATTGACGGCAGCTCATTGTCTCTATCAATTTGAAGAAATTTCAGTCTTCCTTGGTGTT
ACAAATCGTGTTTCAGGTCCAGCAGCATTTAGTCAAGATATAACAGACAAAAGTCATATA
ATCATGCACAATCTTTACAATCCAACTGGTCACGTTAATGATATTGGTTTAATATATTTA
AGCACACTTACAGCTGAGCATTTTGACAATAAAAGAATTTCCTTAATTACTCTACCAACT
AGAAATGATATTGATGTAAATTTAGTTGGAATGGAAGCAACAGTTGCTGGATTCGGTTCA
ACTTCTGACACAAACAAAGCTTCTGAAATTCTTAGATACGTCACAATGCCAATCATAAAG
AATAGTATGTGTAAAATGACATTTGGAACTTTTATTAAAGCTACAAATTTGTGCATGAGT
GGTCAAGGTGGAAGAAGTGTTTGTTCGGGTGATTCCGGTAGTCCACTAACAGTCGAATTA
TTACCAGGAAAAATTGTCCAAGTAGGAATAGTTTCTTTTGGTCACAAACATGGATGCACT
TTAGGACATCCAGGAGTGTTTACACGAGTGACAAGTTATCTTGATTGGATAGAAGGACAT
GTAGGAAAGATGACAATTGAAGGAGCAATAAATAATTCACCAAATACAACTGACAGTAAT
AAAAATAGTGCTAAATGTGTTCATAGTTTGAATATATTCTCAATTTTATTATTGATTATT
TTTAAATTTTTTTAG
>g15484.t1 Gene=g15484 Length=344
MSRKFFFIILVTFFKICFCYVEIPSQFRDAKSPMASEFNLDIIQMNFPGLYDDVFAGIEG
RIAGGVAADARQFPYQGLMYMVDNKNATFICGGSLITHSFLLTAAHCLYQFEEISVFLGV
TNRVSGPAAFSQDITDKSHIIMHNLYNPTGHVNDIGLIYLSTLTAEHFDNKRISLITLPT
RNDIDVNLVGMEATVAGFGSTSDTNKASEILRYVTMPIIKNSMCKMTFGTFIKATNLCMS
GQGGRSVCSGDSGSPLTVELLPGKIVQVGIVSFGHKHGCTLGHPGVFTRVTSYLDWIEGH
VGKMTIEGAINNSPNTTDSNKNSAKCVHSLNIFSILLLIIFKFF
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 18 | g15484.t1 | CDD | cd00190 | Tryp_SPc | 62 | 300 | 4.08497E-63 |
| 10 | g15484.t1 | Gene3D | G3DSA:2.40.10.10 | - | 71 | 293 | 1.2E-58 |
| 9 | g15484.t1 | Gene3D | G3DSA:2.40.10.10 | - | 76 | 298 | 1.2E-58 |
| 2 | g15484.t1 | PANTHER | PTHR24260 | - | 57 | 303 | 1.5E-61 |
| 3 | g15484.t1 | PANTHER | PTHR24260:SF90 | AT07769P-RELATED | 57 | 303 | 1.5E-61 |
| 5 | g15484.t1 | PRINTS | PR00722 | Chymotrypsin serine protease family (S1) signature | 92 | 107 | 2.4E-9 |
| 4 | g15484.t1 | PRINTS | PR00722 | Chymotrypsin serine protease family (S1) signature | 150 | 164 | 2.4E-9 |
| 6 | g15484.t1 | PRINTS | PR00722 | Chymotrypsin serine protease family (S1) signature | 245 | 257 | 2.4E-9 |
| 1 | g15484.t1 | Pfam | PF00089 | Trypsin | 62 | 297 | 2.7E-43 |
| 13 | g15484.t1 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 19 | - |
| 14 | g15484.t1 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 4 | - |
| 15 | g15484.t1 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 5 | 14 | - |
| 17 | g15484.t1 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 15 | 19 | - |
| 12 | g15484.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 20 | 326 | - |
| 16 | g15484.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 327 | 343 | - |
| 11 | g15484.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 344 | 344 | - |
| 21 | g15484.t1 | ProSitePatterns | PS00134 | Serine proteases, trypsin family, histidine active site. | 102 | 107 | - |
| 22 | g15484.t1 | ProSitePatterns | PS00135 | Serine proteases, trypsin family, serine active site. | 246 | 257 | - |
| 23 | g15484.t1 | ProSiteProfiles | PS50240 | Serine proteases, trypsin domain profile. | 62 | 302 | 26.719 |
| 20 | g15484.t1 | SMART | SM00020 | trypsin_2 | 61 | 297 | 1.3E-61 |
| 7 | g15484.t1 | SUPERFAMILY | SSF50494 | Trypsin-like serine proteases | 54 | 302 | 2.04E-66 |
| 8 | g15484.t1 | SignalP_EUK | SignalP-TM | SignalP-TM | 1 | 19 | - |
| 19 | g15484.t1 | 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