General information for g14112.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Matrix metalloproteinase-2.
Parent gene
- The parent gene g14112 is located on chr_1: 34749015..34764841 (- 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_1 | g14112 | g14112.t3 | isoform | g14112.t3 | 34749015 | 34755796 |
| chr_1 | g14112 | g14112.t3 | exon | g14112.t3.exon1 | 34749015 | 34749450 |
| chr_1 | g14112 | g14112.t3 | cds | g14112.t3.CDS1 | 34749017 | 34749450 |
| chr_1 | g14112 | g14112.t3 | exon | g14112.t3.exon2 | 34749510 | 34749660 |
| chr_1 | g14112 | g14112.t3 | cds | g14112.t3.CDS2 | 34749510 | 34749660 |
| chr_1 | g14112 | g14112.t3 | exon | g14112.t3.exon3 | 34749717 | 34749783 |
| chr_1 | g14112 | g14112.t3 | cds | g14112.t3.CDS3 | 34749717 | 34749783 |
| chr_1 | g14112 | g14112.t3 | exon | g14112.t3.exon4 | 34751167 | 34751313 |
| chr_1 | g14112 | g14112.t3 | cds | g14112.t3.CDS4 | 34751167 | 34751313 |
| chr_1 | g14112 | g14112.t3 | exon | g14112.t3.exon5 | 34755510 | 34755796 |
| chr_1 | g14112 | g14112.t3 | cds | g14112.t3.CDS5 | 34755510 | 34755784 |
| chr_1 | g14112 | g14112.t3 | TSS | g14112.t3 | NA | NA |
| chr_1 | g14112 | g14112.t3 | TTS | g14112.t3 | NA | NA |
Sequences
>g14112.t3 Gene=g14112 Length=1088
CAAAACTATTTAATGGAATTCGGTTATTTGCCGAAATCAAACAGTGAGACTGGAAATTTG
CGCATTGAAGAGCAACTTAGAAATGCAATTAGAAGACTTCAAGCATTTGCTGGAATTCCA
CAGACAGGTAAAATGGATGCAAAAACAAACCTGTTGATGAAATCGCCACGTTGCGGTGTG
CCTGATGATTTTGATTCAAGTGATTTCAAACAACGACAGCGAACGCGATTCAAACGTTTT
GTTATCAACAATGGACAGAAATGGGAAAACACAAATCTCACGTGGAGCTTTGTGAATCAA
ACTATGACAAATATTGACGCTGGAATGGCGCGAAGAATATTTCATGAAGCACTAGCAATA
TGGTCAAAAGATTCAAAATTAAATTTCCGTGAGGTCTATGATCCAAATGCTGACATACAG
ATAATGTTCGCACAAGAAGATCATGGAGATGGTTTTAGATTTGATGGTCCAGGCAATGTT
TTAGCTCATGCCTTTTATCCAGGAAGTGGTAGAGGTGGTGATGCACATTTTGATCAAGAT
GAAGCTTGGCATTTAGATGATAGAACAATAGAACATAGTGGAACAAGTTTGAAAAATGTT
GCAATTCATGAATTTGGTCACAGTTTGGGTCTTGGACATTCAAGTGTAAAAGGAGCTGTG
ATGTTTCCATGGTATCATGGTTATAGAGGTGATGGTGATTTACCAGAAGATGACAGACTT
GCAATTCAAACACTTTATGGTGTACGTGATGGAGCAAGGCAATGGGGACCAAATCCAAGG
CGGCATCATTACACTTCATCAACGCCTAGAACGACAACAACAAGAACAACAACAACTTAT
AGACCTCGTCATTATACACCAGATCAACGACATTATCCAGATCAGCCTAGAAGAAATCCA
AATGAATATCCATCACGTTATCCAAGTTATTCAACTACAACTACAACAACAACAAGAAGA
CCAACATATCATCACAATAATAGAAATAATCATCATCATCAGCATCATAATAAACAACAT
ACAAATCATGGACATGACAAAAAGCCAGACACATGCAGCACATCTTATGACGCAATTACA
ATGATTCG
>g14112.t3 Gene=g14112 Length=358
MEFGYLPKSNSETGNLRIEEQLRNAIRRLQAFAGIPQTGKMDAKTNLLMKSPRCGVPDDF
DSSDFKQRQRTRFKRFVINNGQKWENTNLTWSFVNQTMTNIDAGMARRIFHEALAIWSKD
SKLNFREVYDPNADIQIMFAQEDHGDGFRFDGPGNVLAHAFYPGSGRGGDAHFDQDEAWH
LDDRTIEHSGTSLKNVAIHEFGHSLGLGHSSVKGAVMFPWYHGYRGDGDLPEDDRLAIQT
LYGVRDGARQWGPNPRRHHYTSSTPRTTTTRTTTTYRPRHYTPDQRHYPDQPRRNPNEYP
SRYPSYSTTTTTTTRRPTYHHNNRNNHHHQHHNKQHTNHGHDKKPDTCSTSYDAITMI
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 13 | g14112.t3 | CDD | cd04278 | ZnMc_MMP | 83 | 243 | 1.10754E-69 |
| 12 | g14112.t3 | Gene3D | G3DSA:3.40.390.10 | Collagenase (Catalytic Domain) | 1 | 250 | 9.7E-83 |
| 16 | g14112.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 247 | 347 | - |
| 15 | g14112.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 256 | 279 | - |
| 17 | g14112.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 298 | 319 | - |
| 18 | g14112.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 320 | 338 | - |
| 3 | g14112.t3 | PANTHER | PTHR10201 | MATRIX METALLOPROTEINASE | 4 | 336 | 1.5E-71 |
| 4 | g14112.t3 | PANTHER | PTHR10201:SF237 | MATRIX METALLOPROTEINASE-28 | 4 | 336 | 1.5E-71 |
| 6 | g14112.t3 | PRINTS | PR00138 | Matrixin signature | 49 | 62 | 1.9E-38 |
| 9 | g14112.t3 | PRINTS | PR00138 | Matrixin signature | 110 | 125 | 1.9E-38 |
| 5 | g14112.t3 | PRINTS | PR00138 | Matrixin signature | 133 | 161 | 1.9E-38 |
| 7 | g14112.t3 | PRINTS | PR00138 | Matrixin signature | 196 | 221 | 1.9E-38 |
| 8 | g14112.t3 | PRINTS | PR00138 | Matrixin signature | 230 | 243 | 1.9E-38 |
| 1 | g14112.t3 | Pfam | PF01471 | Putative peptidoglycan binding domain | 3 | 45 | 7.4E-6 |
| 2 | g14112.t3 | Pfam | PF00413 | Matrixin | 83 | 243 | 2.3E-52 |
| 14 | g14112.t3 | SMART | SM00235 | col_5 | 80 | 244 | 6.2E-36 |
| 10 | g14112.t3 | SUPERFAMILY | SSF47090 | PGBD-like | 2 | 58 | 4.08E-15 |
| 11 | g14112.t3 | SUPERFAMILY | SSF55486 | Metalloproteases (zincins), catalytic domain | 76 | 245 | 8.76E-47 |
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:0031012 | extracellular matrix | CC |
| GO:0008237 | metallopeptidase activity | MF |
| GO:0006508 | proteolysis | BP |
| GO:0004222 | metalloendopeptidase activity | MF |
| GO:0008270 | zinc ion binding | MF |
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.
