Gene loci information

Transcript annotation

  • This transcript has been annotated as Matrix metalloproteinase-16.

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 g16976 g16976.t2 isoform g16976.t2 11938103 11941688
chr_4 g16976 g16976.t2 exon g16976.t2.exon1 11938103 11938766
chr_4 g16976 g16976.t2 cds g16976.t2.CDS1 11938492 11938766
chr_4 g16976 g16976.t2 exon g16976.t2.exon2 11938823 11939177
chr_4 g16976 g16976.t2 cds g16976.t2.CDS2 11938823 11939177
chr_4 g16976 g16976.t2 exon g16976.t2.exon3 11939591 11939823
chr_4 g16976 g16976.t2 cds g16976.t2.CDS3 11939591 11939823
chr_4 g16976 g16976.t2 exon g16976.t2.exon4 11940132 11940580
chr_4 g16976 g16976.t2 cds g16976.t2.CDS4 11940132 11940580
chr_4 g16976 g16976.t2 exon g16976.t2.exon5 11940634 11940914
chr_4 g16976 g16976.t2 cds g16976.t2.CDS5 11940634 11940914
chr_4 g16976 g16976.t2 exon g16976.t2.exon6 11941555 11941688
chr_4 g16976 g16976.t2 cds g16976.t2.CDS6 11941555 11941677
chr_4 g16976 g16976.t2 TSS g16976.t2 NA NA
chr_4 g16976 g16976.t2 TTS g16976.t2 NA NA

Sequences

>g16976.t2 Gene=g16976 Length=2116
GACTTAAAAAAATGGAAAATTTAAATTTTGTGATATTTTTAATATTTTGTAAATTTATTT
TTGTGTCATCTTCACCAATAAATTCATTCATTATCAAAACAGAATACAATAAAAATTTCA
ATGCTGACAAATTGATAACCTACATGCAAAATTTTGGCTATCTCGATAGTCCTGACATCA
ATGCACCAGAAGGTCTTTTAGCAGAGTCACTTTATGCTGAAAATGCAATTGTTGAAGGAA
TAAAAAATCTTCAAAGATTTGGTGGTCTTGAACCAAATGGTATTGTTGATGGTCCAACGA
TGGAACTTTTAAATACACCAAGATGTGGCGTCAAAGATATTTTGAATGATCATGAACGAA
AAAAACGTTACATTATAGGATCGAAAAATTGGAAGAAAAAGAAAATTACTTATTTCATTG
CAAACTTTAGTCCAAAAGTTAATGAAACTTTAATGATAACTGCATTAGAAAAAGCATTTC
ATGCTTGGTCAATTTATAGCAATTTAGTATTTAAAAGAATTTTTGATCCATCAGCGGATA
TAATTATTGCTTTTGGTTCACATTATCATGGTGATCGTTATCCATTTGATGGTTCTGGAA
ATATTTTAGCTCATGCATTTTATCCATATGAAGAAAATGCTTTTGGTGGTGACATTCATT
TTGATAATGATGAAAATTGGAAAGAAGGTTCATTAAATTTAAATGAAGGTGTTGATTTTT
TGACTGTTGCATTTCATGAAATTGGTCATAGTTTAGGTTTGGCTCATAGTCCTGTTTATA
GCTCAATTATGTTTCCTTATTACAAAGGAGTCACAGCGGCACAACTTGATTATGATGATA
TTTTGGGAATGTATCAACTTTATATTCAAAGTCAATTAGAAGACAACACAAGTAAAGAAG
AAAATGATGATAAACAAACTGAAGAATCAACTACAAATTTACCTGAAACAACTTCAAATT
CTTCTTCTGAAAATTCATCAAAAAGTAAAGAAATTGACAAAGAAAAAACAACTGAGAAAC
AAAATTTATCTAATGAAAATGAAGTTGATTCATCAGAAACTAATGAAGTTAGCAAAAATG
AAGAAGAAGATGATGAGTCAATTTCAATTCCACAAGCAACGGAATCATTCTGCCTAGGTT
CATTTGATGCCATGGGAACAATCAATGATGAACTTTTAATAATAAAATCAGACATTGTTT
GGAAATTTACAAATAAATTTGAGCTTTTTGAAAATTTTCCAATGAAAATTTCAAAAGTTT
TTCCAAATTTACCACAAAGGTTTAAAAAAATCGATGCTTTTGTTCAATCAAGCGATGAAA
ATGAAATTAATATTTTTTCTGGAAATGAATTTATAACTTATGATATTCGTGGACCAATTT
ATACTGCTTATAATTTAACGAGATACACAAATGATCCTGACATTGAAAAAATTGATGCTG
CAATGATTTGGTCAAAGAACAAAAAAACTTATTTATTTTCTGAAGATCGTTTTTGGAGAT
TTTCAAATGATCGTTTAATGGATCCATTTTACCCAAGAATTATGAAAAGATGGAAAGGAG
TACCAAAAAATCTTACAGGTGCAATTTCATTTCCTCATAGTGGACCAACAGTTTTTTTTA
AAGATGATGAATTTATAATTTATGATGATGAAAATGTTAAACCCGAAGAAGGCTATCCAA
AGAAAATTTATGAAATTTTTGAATTTTGTGAAAATTTTGATGTATAAAAATTTATTGAAA
ACTTTTGTTCTGTTTTGACAGTATTAAAGGTAGGGTTCGGCACTTGCATGCATACTTGAC
TAGTATGAGCATAGTGACTTGAATATATTCATGCAAGTTGACTTATGAAAAATTTCATTT
GATTTGATCGAAAATTTCCATATTTGTATAAAAATCGATGGTTCTTTAGTTTACAAAGTT
TTGACCAAATTGAATAAATTTTAAATAAAAAATACACTTTTTTAAAGCCAACTTGCATGC
ATTTAGTCAAGTCACCAGTCTAGTATGAATGCAAGTGACGAACACTAAGAAATAAAAATT
TGATAAAATCATAGTTATTTTTTTAAACTTTTCTTTATTTATTATCAAAAAAATTTTACA
ATTTTTTAAATATTTT

>g16976.t2 Gene=g16976 Length=571
MENLNFVIFLIFCKFIFVSSSPINSFIIKTEYNKNFNADKLITYMQNFGYLDSPDINAPE
GLLAESLYAENAIVEGIKNLQRFGGLEPNGIVDGPTMELLNTPRCGVKDILNDHERKKRY
IIGSKNWKKKKITYFIANFSPKVNETLMITALEKAFHAWSIYSNLVFKRIFDPSADIIIA
FGSHYHGDRYPFDGSGNILAHAFYPYEENAFGGDIHFDNDENWKEGSLNLNEGVDFLTVA
FHEIGHSLGLAHSPVYSSIMFPYYKGVTAAQLDYDDILGMYQLYIQSQLEDNTSKEENDD
KQTEESTTNLPETTSNSSSENSSKSKEIDKEKTTEKQNLSNENEVDSSETNEVSKNEEED
DESISIPQATESFCLGSFDAMGTINDELLIIKSDIVWKFTNKFELFENFPMKISKVFPNL
PQRFKKIDAFVQSSDENEINIFSGNEFITYDIRGPIYTAYNLTRYTNDPDIEKIDAAMIW
SKNKKTYLFSEDRFWRFSNDRLMDPFYPRIMKRWKGVPKNLTGAISFPHSGPTVFFKDDE
FIIYDDENVKPEEGYPKKIYEIFEFCENFDV

Protein features from InterProScan

Transcript Database ID Name Start End E.value
24 g16976.t2 CDD cd04278 ZnMc_MMP 127 284 1.1615E-66
23 g16976.t2 CDD cd00094 HX 377 559 9.30517E-30
15 g16976.t2 Gene3D G3DSA:3.40.390.10 Collagenase (Catalytic Domain) 27 291 1.5E-75
16 g16976.t2 Gene3D G3DSA:2.110.10.10 Hemopexin 372 568 8.3E-40
32 g16976.t2 MobiDBLite mobidb-lite consensus disorder prediction 291 366 -
31 g16976.t2 MobiDBLite mobidb-lite consensus disorder prediction 292 306 -
29 g16976.t2 MobiDBLite mobidb-lite consensus disorder prediction 307 322 -
30 g16976.t2 MobiDBLite mobidb-lite consensus disorder prediction 323 339 -
4 g16976.t2 PANTHER PTHR10201 MATRIX METALLOPROTEINASE 37 526 3.6E-159
5 g16976.t2 PANTHER PTHR10201:SF169 MATRIX METALLOPROTEINASE-16-LIKE PROTEIN 37 526 3.6E-159
22 g16976.t2 PIRSF PIRSF001191 MMP_stromelysin 9 570 2.1E-114
8 g16976.t2 PRINTS PR00138 Matrixin signature 100 113 4.7E-33
7 g16976.t2 PRINTS PR00138 Matrixin signature 152 167 4.7E-33
10 g16976.t2 PRINTS PR00138 Matrixin signature 175 203 4.7E-33
9 g16976.t2 PRINTS PR00138 Matrixin signature 239 264 4.7E-33
6 g16976.t2 PRINTS PR00138 Matrixin signature 272 285 4.7E-33
1 g16976.t2 Pfam PF00413 Matrixin 126 284 6.9E-49
3 g16976.t2 Pfam PF00045 Hemopexin 474 518 8.4E-8
2 g16976.t2 Pfam PF00045 Hemopexin 524 563 1.5E-4
18 g16976.t2 Phobius SIGNAL_PEPTIDE Signal peptide region 1 25 -
19 g16976.t2 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 5 -
20 g16976.t2 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 6 17 -
21 g16976.t2 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 18 25 -
17 g16976.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 26 571 -
35 g16976.t2 ProSiteProfiles PS51642 Hemopexin repeat profile. 371 420 7.758
34 g16976.t2 ProSiteProfiles PS51642 Hemopexin repeat profile. 471 518 12.688
33 g16976.t2 ProSiteProfiles PS51642 Hemopexin repeat profile. 519 566 7.135
28 g16976.t2 SMART SM00235 col_5 123 286 1.1E-29
25 g16976.t2 SMART SM00120 HX_rpt_3 378 422 0.018
26 g16976.t2 SMART SM00120 HX_rpt_3 474 519 6.2E-9
27 g16976.t2 SMART SM00120 HX_rpt_3 521 568 0.28
11 g16976.t2 SUPERFAMILY SSF47090 PGBD-like 41 110 6.28E-13
13 g16976.t2 SUPERFAMILY SSF55486 Metalloproteases (zincins), catalytic domain 119 284 1.16E-43
12 g16976.t2 SUPERFAMILY SSF50923 Hemopexin-like domain 373 567 3.53E-36
14 g16976.t2 SignalP_EUK SignalP-noTM SignalP-noTM 1 20 -

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