General information for g2439.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as ADAM 17-like protease.
Parent gene
- The parent gene g2439 is located on chr_3: 18005856..18007019 (+ 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_3 | g2439 | g2439.t1 | TSS | g2439.t1 | 18004318 | 18004318 |
| chr_3 | g2439 | g2439.t1 | isoform | g2439.t1 | 18004381 | 18007019 |
| chr_3 | g2439 | g2439.t1 | exon | g2439.t1.exon1 | 18004381 | 18004438 |
| chr_3 | g2439 | g2439.t1 | cds | g2439.t1.CDS1 | 18004381 | 18004438 |
| chr_3 | g2439 | g2439.t1 | exon | g2439.t1.exon2 | 18004556 | 18005307 |
| chr_3 | g2439 | g2439.t1 | cds | g2439.t1.CDS2 | 18004556 | 18005307 |
| chr_3 | g2439 | g2439.t1 | exon | g2439.t1.exon3 | 18005364 | 18005555 |
| chr_3 | g2439 | g2439.t1 | cds | g2439.t1.CDS3 | 18005364 | 18005555 |
| chr_3 | g2439 | g2439.t1 | exon | g2439.t1.exon4 | 18005652 | 18005790 |
| chr_3 | g2439 | g2439.t1 | cds | g2439.t1.CDS4 | 18005652 | 18005790 |
| chr_3 | g2439 | g2439.t1 | exon | g2439.t1.exon5 | 18005856 | 18006761 |
| chr_3 | g2439 | g2439.t1 | cds | g2439.t1.CDS5 | 18005856 | 18006761 |
| chr_3 | g2439 | g2439.t1 | exon | g2439.t1.exon6 | 18006820 | 18007019 |
| chr_3 | g2439 | g2439.t1 | cds | g2439.t1.CDS6 | 18006820 | 18007019 |
| chr_3 | g2439 | g2439.t1 | TTS | g2439.t1 | 18007090 | 18007090 |
Sequences
>g2439.t1 Gene=g2439 Length=2247
ATGGCGAAAATTTTCTTTGCTACATTTCTTGTATTTCTTCACTTATTTGAAGCTCAAACC
CAATTGCATAAAAATTTAAAATACTATGAAACATTACATGCAGATGAAATTACACATAAA
ATTGTCAAAAGGGGAATAAAACCAAGTATCAATTTGCACAATAAAATTAGAGAAGTGGAA
TTTACTGCATTAGGAAAAAAATTCAAATTGATTCTTCATCCACACAGGGATGTTTTGCAT
CAAAATTTTCGTGCAGTTACAGTAAATTCGGAAGGTAATGAAACAGTCGTTCATCTCGAT
CAAGATAGCTTTTTCAGAGGTCGTGTATTTGGAGAGAGTACATCACATGTTTCTGCTCAT
ATTGATGAGAAAAATGTACTCACTGCTACAATAATTTTACCTGATGAAACTTATCATATT
GAACCATCTTGGAGACATCTTGAGAAAAAACTCCCAGAAAGTAGCAACAAACATATGGTT
GCTTATAAAGCGTCAGACGTTAAATTGAGTTGGGAGCATCACAATGAAAATAAAAATGAT
GGAGAGAATCATTTTGTTCCTGGCAGATGTGGATATGTTAAAGAAGGTGCTGAACTTGAA
ACAGATGATGATGATGATGAAATTGAAGAACCAGAAGTTGAAGCATATGGTGGAAACGAA
ACACCGCATAGTGAAAGAAGATCAAAAAGACAAGCTGATCAATATGAATACACTCCAACA
AAAACACGATGTCCTCTTTTACTCGTTGCTGATTATCGTTTTTTCCAAGAAATGGGAAGT
TCAAATACAAAAACTACAATTTCTTATTTGATAAGTCTAATTGATCGTGTTCATAAAATT
TATAATGACACAATCTGGCAAGATCGAGATGTAGATGGATTTCGCGGAATGGGTTTTGTC
ATCAAAAAAATTTTAGTTCATAGTGAGCCAACAAAAGTTAGAGGTGGTGAAGCTCATTAC
AACATGATCCGAGAAAAATGGGATGTAAGAAATTTGCTTGAGGTTTTTTCACGCGAATAT
TCACATAAAGATTTTTGTCTTGCACATTTATTTACTGATTTAAAATTTGAAGGCGGTATT
TTAGGTTTAGCTTATGTTGGTTCACCGCGAAGAAATTCTGTTGGTGGAATTTGTACTCCT
GAATATTTTAAAAATGGCTACACTCTCTATCTGAATTCTGGTCTTAGTTCATCAAGAAAT
CATTATGGTCAACGTGTGATCACAAGAGAAGCTGATTTAGTCACAGCACATGAATTTGGG
CACAATTGGGGAAGTGAACATGATCCTGACATTGCTGAATGTTCTCCTTCAGCTTCACAA
GGAGGAAGTTTCTTGATGTATACATATTCAGTTAGTGGTTATGATGTCAATAACAAGAAA
TTTTCACCATGTTCGTTACGTTCAATAAGAAAAGTATTACAAGCAAAAAGTGGACGTTGT
TTCTCAGAACCTGAAGAATCATTTTGTGGAAATTTGCGTGTTGAGGGTGATGAGCAGTGT
GATGCTGGTTTATTAGGCACAGAAGATAATGATCAATGCTGCGATAAAAACTGTAAATTA
CGAAAAAATCAGGGAGCAGTTTGCAGTGATAAAAATTCTCCATGTTGTCAAAATTGTCAA
TTTATGCCAGCTGGAGTTAAGTGTCGAGAGGCAGCATATAGTACTTGTGAACAAGAAGCG
CGATGTACTGGAAACAGTGCTGATTGCCCTAAATCTCCTGCAATGCAAGATGGAACAATT
TGTCAGGAACGTGGACAATGTCGAAGTGGAAAATGTGTTCCTTTCTGCGAAACTCAAGGA
CTACAAAGTTGTATGTGCGATGTTATTGCAGATGCATGCAAACGATGCTGCCGAATGTCC
ATTAATGAGACATGCTTTGCCGTTGAACCACCTGATATTTTGCCAGATGGTACACCTTGC
ATTCAAGGCTTCTGTAATAAAGGTGTTTGTGAAAAAACAATTCAAGATGTTGTTGAACGC
TTCTGGGATATCATTGAAGAAATTAATATTAACAAAGTATTGAGATTTTTACGTGACAAC
ATAGTTATCGTTGTTATTACGATCACAACATTATTTTGGGTACCAACCAGTTGTTTAATA
AGTTATTTTGATAGACGTTCAAGGCATGCAGAGTTAAAAGAATATAATTGGAAGCAACAA
TTAGATCTGATTCATCCAAGCGATCGTCGACGCGTCATTCATATTCGTGTCCCACGGCAA
AAAATTACTTTACCTACAAGAATGTAA
>g2439.t1 Gene=g2439 Length=748
MAKIFFATFLVFLHLFEAQTQLHKNLKYYETLHADEITHKIVKRGIKPSINLHNKIREVE
FTALGKKFKLILHPHRDVLHQNFRAVTVNSEGNETVVHLDQDSFFRGRVFGESTSHVSAH
IDEKNVLTATIILPDETYHIEPSWRHLEKKLPESSNKHMVAYKASDVKLSWEHHNENKND
GENHFVPGRCGYVKEGAELETDDDDDEIEEPEVEAYGGNETPHSERRSKRQADQYEYTPT
KTRCPLLLVADYRFFQEMGSSNTKTTISYLISLIDRVHKIYNDTIWQDRDVDGFRGMGFV
IKKILVHSEPTKVRGGEAHYNMIREKWDVRNLLEVFSREYSHKDFCLAHLFTDLKFEGGI
LGLAYVGSPRRNSVGGICTPEYFKNGYTLYLNSGLSSSRNHYGQRVITREADLVTAHEFG
HNWGSEHDPDIAECSPSASQGGSFLMYTYSVSGYDVNNKKFSPCSLRSIRKVLQAKSGRC
FSEPEESFCGNLRVEGDEQCDAGLLGTEDNDQCCDKNCKLRKNQGAVCSDKNSPCCQNCQ
FMPAGVKCREAAYSTCEQEARCTGNSADCPKSPAMQDGTICQERGQCRSGKCVPFCETQG
LQSCMCDVIADACKRCCRMSINETCFAVEPPDILPDGTPCIQGFCNKGVCEKTIQDVVER
FWDIIEEININKVLRFLRDNIVIVVITITTLFWVPTSCLISYFDRRSRHAELKEYNWKQQ
LDLIHPSDRRRVIHIRVPRQKITLPTRM
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 20 | g2439.t1 | CDD | cd04270 | ZnMc_TACE_like | 242 | 488 | 7.91975E-133 |
| 19 | g2439.t1 | CDD | cd14246 | ADAM17_MPD | 594 | 651 | 2.4183E-24 |
| 11 | g2439.t1 | Gene3D | G3DSA:3.40.390.10 | Collagenase (Catalytic Domain) | 238 | 484 | 6.9E-84 |
| 10 | g2439.t1 | Gene3D | G3DSA:4.10.70.10 | Echistatin | 485 | 572 | 4.7E-14 |
| 24 | g2439.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 198 | 214 | - |
| 25 | g2439.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 198 | 235 | - |
| 23 | g2439.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 219 | 235 | - |
| 5 | g2439.t1 | PANTHER | PTHR45702:SF6 | DISINTEGRIN AND METALLOPROTEINASE DOMAIN-CONTAINING PROTEIN 17 | 25 | 737 | 8.9E-250 |
| 6 | g2439.t1 | PANTHER | PTHR45702 | ADAM10/ADAM17 METALLOPEPTIDASE FAMILY MEMBER | 25 | 737 | 8.9E-250 |
| 4 | g2439.t1 | Pfam | PF01562 | Reprolysin family propeptide | 39 | 160 | 2.9E-8 |
| 2 | g2439.t1 | Pfam | PF13688 | Metallo-peptidase family M12 | 241 | 462 | 5.0E-36 |
| 3 | g2439.t1 | Pfam | PF00200 | Disintegrin | 495 | 571 | 1.7E-13 |
| 1 | g2439.t1 | Pfam | PF16698 | Membrane-proximal domain, switch, for ADAM17 | 595 | 651 | 1.4E-16 |
| 14 | g2439.t1 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 18 | - |
| 15 | g2439.t1 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 3 | - |
| 16 | g2439.t1 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 4 | 13 | - |
| 18 | g2439.t1 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 14 | 18 | - |
| 13 | g2439.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 19 | 680 | - |
| 17 | g2439.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 681 | 703 | - |
| 12 | g2439.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 704 | 748 | - |
| 27 | g2439.t1 | ProSiteProfiles | PS50215 | ADAM type metalloprotease domain profile. | 242 | 485 | 21.358 |
| 26 | g2439.t1 | ProSiteProfiles | PS50214 | Disintegrin domain profile. | 486 | 577 | 13.611 |
| 22 | g2439.t1 | SMART | SM00050 | DISIN_2 | 495 | 576 | 3.2E-9 |
| 8 | g2439.t1 | SUPERFAMILY | SSF55486 | Metalloproteases (zincins), catalytic domain | 239 | 483 | 3.26E-51 |
| 7 | g2439.t1 | SUPERFAMILY | SSF57552 | Blood coagulation inhibitor (disintegrin) | 495 | 574 | 1.5E-12 |
| 9 | g2439.t1 | SignalP_EUK | SignalP-noTM | SignalP-noTM | 1 | 18 | - |
| 21 | g2439.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 681 | 703 | - |
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:0008237 | metallopeptidase activity | MF |
| GO:0006508 | proteolysis | BP |
| GO:0004222 | metalloendopeptidase activity | MF |
KEGG
Orthology
- This transcript has been annotated with K06059 (disintegrin and metalloproteinase domain-containing protein 17)
Pathway
- This transcript belongs to the following pathways
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.
