General information for g16976.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Matrix metalloproteinase-16.
Parent gene
- The parent gene g16976 is located on chr_4: 11938492..11943205 (- 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 | g16976 | g16976.t1 | isoform | g16976.t1 | 11938492 | 11943205 |
| chr_4 | g16976 | g16976.t1 | exon | g16976.t1.exon1 | 11938492 | 11938766 |
| chr_4 | g16976 | g16976.t1 | cds | g16976.t1.CDS1 | 11938492 | 11938766 |
| chr_4 | g16976 | g16976.t1 | exon | g16976.t1.exon2 | 11938823 | 11939177 |
| chr_4 | g16976 | g16976.t1 | cds | g16976.t1.CDS2 | 11938823 | 11939177 |
| chr_4 | g16976 | g16976.t1 | exon | g16976.t1.exon3 | 11939591 | 11939823 |
| chr_4 | g16976 | g16976.t1 | cds | g16976.t1.CDS3 | 11939591 | 11939823 |
| chr_4 | g16976 | g16976.t1 | exon | g16976.t1.exon4 | 11940132 | 11940580 |
| chr_4 | g16976 | g16976.t1 | cds | g16976.t1.CDS4 | 11940132 | 11940580 |
| chr_4 | g16976 | g16976.t1 | exon | g16976.t1.exon5 | 11940634 | 11940914 |
| chr_4 | g16976 | g16976.t1 | cds | g16976.t1.CDS5 | 11940634 | 11940914 |
| chr_4 | g16976 | g16976.t1 | exon | g16976.t1.exon6 | 11942231 | 11942389 |
| chr_4 | g16976 | g16976.t1 | cds | g16976.t1.CDS6 | 11942231 | 11942389 |
| chr_4 | g16976 | g16976.t1 | exon | g16976.t1.exon7 | 11942718 | 11942997 |
| chr_4 | g16976 | g16976.t1 | cds | g16976.t1.CDS7 | 11942718 | 11942997 |
| chr_4 | g16976 | g16976.t1 | exon | g16976.t1.exon8 | 11943090 | 11943205 |
| chr_4 | g16976 | g16976.t1 | cds | g16976.t1.CDS8 | 11943090 | 11943205 |
| chr_4 | g16976 | g16976.t1 | TSS | g16976.t1 | NA | NA |
| chr_4 | g16976 | g16976.t1 | TTS | g16976.t1 | NA | NA |
Sequences
>g16976.t1 Gene=g16976 Length=2148
ATGTGCTGTAGCAAATTAATTGGAGCAACAATCATAAGTTTTTCAGTTCTTAAATTTTGT
TTTCTTGTTGATTTTTTGAATTTACATTTGGGAAATCTAACAATTTTAACTGAAAGAACT
TTAAAATTTTCATCAATAAAAATCAACAGACTGCGCAAAATTTACATTGAAATTTATGAA
ATGAAAACTAAAATTAATGAATCAATGTCCTTTACTTTACCACTTATTATGGCAATCATC
ATTATGTGTCTCATTCGTCGTTGCTATCGATTTTATGCACTTTTCACAGGACAATTACAT
TTAAGTGCTTTCATTTTTACTCTTATGAATAATACAACAGAAGAAATTGCTTTTATTTTT
GCACTCTGCTATTGCAGTGATAAAAGTGAAATAATGATGGAAAATTTACTATCAAAATTT
CGTGAAATGGACTGTTTGAAAATTGAGAATGAAAAATTGAAAATAATTGGACAATTTTAT
GACCAAGTTTCACATCAACGAATTGAATTTCAACTTTTTAATTCTATCAATTTAAATGTG
GAATTAACAGCTAATATAACCTACATGCAAAATTTTGGCTATCTCGATAGTCCTGACATC
AATGCACCAGAAGGTCTTTTAGCAGAGTCACTTTATGCTGAAAATGCAATTGTTGAAGGA
ATAAAAAATCTTCAAAGATTTGGTGGTCTTGAACCAAATGGTATTGTTGATGGTCCAACG
ATGGAACTTTTAAATACACCAAGATGTGGCGTCAAAGATATTTTGAATGATCATGAACGA
AAAAAACGTTACATTATAGGATCGAAAAATTGGAAGAAAAAGAAAATTACTTATTTCATT
GCAAACTTTAGTCCAAAAGTTAATGAAACTTTAATGATAACTGCATTAGAAAAAGCATTT
CATGCTTGGTCAATTTATAGCAATTTAGTATTTAAAAGAATTTTTGATCCATCAGCGGAT
ATAATTATTGCTTTTGGTTCACATTATCATGGTGATCGTTATCCATTTGATGGTTCTGGA
AATATTTTAGCTCATGCATTTTATCCATATGAAGAAAATGCTTTTGGTGGTGACATTCAT
TTTGATAATGATGAAAATTGGAAAGAAGGTTCATTAAATTTAAATGAAGGTGTTGATTTT
TTGACTGTTGCATTTCATGAAATTGGTCATAGTTTAGGTTTGGCTCATAGTCCTGTTTAT
AGCTCAATTATGTTTCCTTATTACAAAGGAGTCACAGCGGCACAACTTGATTATGATGAT
ATTTTGGGAATGTATCAACTTTATATTCAAAGTCAATTAGAAGACAACACAAGTAAAGAA
GAAAATGATGATAAACAAACTGAAGAATCAACTACAAATTTACCTGAAACAACTTCAAAT
TCTTCTTCTGAAAATTCATCAAAAAGTAAAGAAATTGACAAAGAAAAAACAACTGAGAAA
CAAAATTTATCTAATGAAAATGAAGTTGATTCATCAGAAACTAATGAAGTTAGCAAAAAT
GAAGAAGAAGATGATGAGTCAATTTCAATTCCACAAGCAACGGAATCATTCTGCCTAGGT
TCATTTGATGCCATGGGAACAATCAATGATGAACTTTTAATAATAAAATCAGACATTGTT
TGGAAATTTACAAATAAATTTGAGCTTTTTGAAAATTTTCCAATGAAAATTTCAAAAGTT
TTTCCAAATTTACCACAAAGGTTTAAAAAAATCGATGCTTTTGTTCAATCAAGCGATGAA
AATGAAATTAATATTTTTTCTGGAAATGAATTTATAACTTATGATATTCGTGGACCAATT
TATACTGCTTATAATTTAACGAGATACACAAATGATCCTGACATTGAAAAAATTGATGCT
GCAATGATTTGGTCAAAGAACAAAAAAACTTATTTATTTTCTGAAGATCGTTTTTGGAGA
TTTTCAAATGATCGTTTAATGGATCCATTTTACCCAAGAATTATGAAAAGATGGAAAGGA
GTACCAAAAAATCTTACAGGTGCAATTTCATTTCCTCATAGTGGACCAACAGTTTTTTTT
AAAGATGATGAATTTATAATTTATGATGATGAAAATGTTAAACCCGAAGAAGGCTATCCA
AAGAAAATTTATGAAATTTTTGAATTTTGTGAAAATTTTGATGTATAA
>g16976.t1 Gene=g16976 Length=715
MCCSKLIGATIISFSVLKFCFLVDFLNLHLGNLTILTERTLKFSSIKINRLRKIYIEIYE
MKTKINESMSFTLPLIMAIIIMCLIRRCYRFYALFTGQLHLSAFIFTLMNNTTEEIAFIF
ALCYCSDKSEIMMENLLSKFREMDCLKIENEKLKIIGQFYDQVSHQRIEFQLFNSINLNV
ELTANITYMQNFGYLDSPDINAPEGLLAESLYAENAIVEGIKNLQRFGGLEPNGIVDGPT
MELLNTPRCGVKDILNDHERKKRYIIGSKNWKKKKITYFIANFSPKVNETLMITALEKAF
HAWSIYSNLVFKRIFDPSADIIIAFGSHYHGDRYPFDGSGNILAHAFYPYEENAFGGDIH
FDNDENWKEGSLNLNEGVDFLTVAFHEIGHSLGLAHSPVYSSIMFPYYKGVTAAQLDYDD
ILGMYQLYIQSQLEDNTSKEENDDKQTEESTTNLPETTSNSSSENSSKSKEIDKEKTTEK
QNLSNENEVDSSETNEVSKNEEEDDESISIPQATESFCLGSFDAMGTINDELLIIKSDIV
WKFTNKFELFENFPMKISKVFPNLPQRFKKIDAFVQSSDENEINIFSGNEFITYDIRGPI
YTAYNLTRYTNDPDIEKIDAAMIWSKNKKTYLFSEDRFWRFSNDRLMDPFYPRIMKRWKG
VPKNLTGAISFPHSGPTVFFKDDEFIIYDDENVKPEEGYPKKIYEIFEFCENFDV
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 23 | g16976.t1 | CDD | cd04278 | ZnMc_MMP | 271 | 428 | 6.30508E-67 |
| 22 | g16976.t1 | CDD | cd00094 | HX | 521 | 703 | 6.82316E-31 |
| 13 | g16976.t1 | Gene3D | G3DSA:3.40.390.10 | Collagenase (Catalytic Domain) | 176 | 435 | 1.0E-74 |
| 14 | g16976.t1 | Gene3D | G3DSA:2.110.10.10 | Hemopexin | 516 | 712 | 1.3E-39 |
| 33 | g16976.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 435 | 510 | - |
| 32 | g16976.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 436 | 450 | - |
| 31 | g16976.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 451 | 466 | - |
| 34 | g16976.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 467 | 483 | - |
| 3 | g16976.t1 | PANTHER | PTHR10201 | MATRIX METALLOPROTEINASE | 186 | 670 | 1.3E-157 |
| 4 | g16976.t1 | PANTHER | PTHR10201:SF169 | MATRIX METALLOPROTEINASE-16-LIKE PROTEIN | 186 | 670 | 1.3E-157 |
| 7 | g16976.t1 | PRINTS | PR00138 | Matrixin signature | 244 | 257 | 1.1E-32 |
| 6 | g16976.t1 | PRINTS | PR00138 | Matrixin signature | 296 | 311 | 1.1E-32 |
| 5 | g16976.t1 | PRINTS | PR00138 | Matrixin signature | 319 | 347 | 1.1E-32 |
| 9 | g16976.t1 | PRINTS | PR00138 | Matrixin signature | 383 | 408 | 1.1E-32 |
| 8 | g16976.t1 | PRINTS | PR00138 | Matrixin signature | 416 | 429 | 1.1E-32 |
| 1 | g16976.t1 | Pfam | PF00413 | Matrixin | 270 | 428 | 1.0E-48 |
| 2 | g16976.t1 | Pfam | PF00045 | Hemopexin | 618 | 662 | 1.1E-7 |
| 15 | g16976.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 6 | - |
| 20 | g16976.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 7 | 26 | - |
| 17 | g16976.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 27 | 67 | - |
| 19 | g16976.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 68 | 85 | - |
| 16 | g16976.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 86 | 91 | - |
| 21 | g16976.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 92 | 109 | - |
| 18 | g16976.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 110 | 715 | - |
| 35 | g16976.t1 | ProSiteProfiles | PS51642 | Hemopexin repeat profile. | 515 | 564 | 7.758 |
| 36 | g16976.t1 | ProSiteProfiles | PS51642 | Hemopexin repeat profile. | 615 | 662 | 12.688 |
| 37 | g16976.t1 | ProSiteProfiles | PS51642 | Hemopexin repeat profile. | 663 | 710 | 7.135 |
| 30 | g16976.t1 | SMART | SM00235 | col_5 | 267 | 430 | 1.1E-29 |
| 29 | g16976.t1 | SMART | SM00120 | HX_rpt_3 | 522 | 566 | 0.018 |
| 28 | g16976.t1 | SMART | SM00120 | HX_rpt_3 | 618 | 663 | 6.2E-9 |
| 27 | g16976.t1 | SMART | SM00120 | HX_rpt_3 | 665 | 712 | 0.28 |
| 10 | g16976.t1 | SUPERFAMILY | SSF47090 | PGBD-like | 187 | 254 | 1.48E-12 |
| 12 | g16976.t1 | SUPERFAMILY | SSF55486 | Metalloproteases (zincins), catalytic domain | 263 | 428 | 1.75E-43 |
| 11 | g16976.t1 | SUPERFAMILY | SSF50923 | Hemopexin-like domain | 517 | 711 | 5.49E-36 |
| 25 | g16976.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 7 | 26 | - |
| 24 | g16976.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 69 | 86 | - |
| 26 | g16976.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 91 | 113 | - |
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. There were no conditions that were differentially expressed