General information for g2439.t6
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.t6 | TSS | g2439.t6 | 18004318 | 18004318 |
| chr_3 | g2439 | g2439.t6 | isoform | g2439.t6 | 18005366 | 18007019 |
| chr_3 | g2439 | g2439.t6 | exon | g2439.t6.exon1 | 18005366 | 18005555 |
| chr_3 | g2439 | g2439.t6 | exon | g2439.t6.exon2 | 18005722 | 18005790 |
| chr_3 | g2439 | g2439.t6 | exon | g2439.t6.exon3 | 18005856 | 18006761 |
| chr_3 | g2439 | g2439.t6 | cds | g2439.t6.CDS1 | 18006050 | 18006761 |
| chr_3 | g2439 | g2439.t6 | exon | g2439.t6.exon4 | 18006820 | 18007019 |
| chr_3 | g2439 | g2439.t6 | cds | g2439.t6.CDS2 | 18006820 | 18007019 |
| chr_3 | g2439 | g2439.t6 | TTS | g2439.t6 | 18007090 | 18007090 |
Sequences
>g2439.t6 Gene=g2439 Length=1365
AAGTCTAATTGATCGTGTTCATAAAATTTATAATGACACAATCTGGCAAGATCGAGATGT
AGATGGATTTCGCGGAATGGGTTTTGTCATCAAAAAAATTTTAGTTCATAGTGAGCCAAC
AAAAGTTAGAGGTGGTGAAGCTCATTACAACATGATCCGAGAAAAATGGGATGTAAGAAA
TTTGCTTGAGGCGGTATTTTAGGTTTAGCTTATGTTGGTTCACCGCGAAGAAATTCTGTT
GGTGGAATTTGTACTCCTGAATATTTTAAAAATGGCTACACTCTCTATCTGAATTCTGGT
CTTAGTTCATCAAGAAATCATTATGGTCAACGTGTGATCACAAGAGAAGCTGATTTAGTC
ACAGCACATGAATTTGGGCACAATTGGGGAAGTGAACATGATCCTGACATTGCTGAATGT
TCTCCTTCAGCTTCACAAGGAGGAAGTTTCTTGATGTATACATATTCAGTTAGTGGTTAT
GATGTCAATAACAAGAAATTTTCACCATGTTCGTTACGTTCAATAAGAAAAGTATTACAA
GCAAAAAGTGGACGTTGTTTCTCAGAACCTGAAGAATCATTTTGTGGAAATTTGCGTGTT
GAGGGTGATGAGCAGTGTGATGCTGGTTTATTAGGCACAGAAGATAATGATCAATGCTGC
GATAAAAACTGTAAATTACGAAAAAATCAGGGAGCAGTTTGCAGTGATAAAAATTCTCCA
TGTTGTCAAAATTGTCAATTTATGCCAGCTGGAGTTAAGTGTCGAGAGGCAGCATATAGT
ACTTGTGAACAAGAAGCGCGATGTACTGGAAACAGTGCTGATTGCCCTAAATCTCCTGCA
ATGCAAGATGGAACAATTTGTCAGGAACGTGGACAATGTCGAAGTGGAAAATGTGTTCCT
TTCTGCGAAACTCAAGGACTACAAAGTTGTATGTGCGATGTTATTGCAGATGCATGCAAA
CGATGCTGCCGAATGTCCATTAATGAGACATGCTTTGCCGTTGAACCACCTGATATTTTG
CCAGATGGTACACCTTGCATTCAAGGCTTCTGTAATAAAGGTGTTTGTGAAAAAACAATT
CAAGATGTTGTTGAACGCTTCTGGGATATCATTGAAGAAATTAATATTAACAAAGTATTG
AGATTTTTACGTGACAACATAGTTATCGTTGTTATTACGATCACAACATTATTTTGGGTA
CCAACCAGTTGTTTAATAAGTTATTTTGATAGACGTTCAAGGCATGCAGAGTTAAAAGAA
TATAATTGGAAGCAACAATTAGATCTGATTCATCCAAGCGATCGTCGACGCGTCATTCAT
ATTCGTGTCCCACGGCAAAAAATTACTTTACCTACAAGAATGTAA
>g2439.t6 Gene=g2439 Length=303
MYTYSVSGYDVNNKKFSPCSLRSIRKVLQAKSGRCFSEPEESFCGNLRVEGDEQCDAGLL
GTEDNDQCCDKNCKLRKNQGAVCSDKNSPCCQNCQFMPAGVKCREAAYSTCEQEARCTGN
SADCPKSPAMQDGTICQERGQCRSGKCVPFCETQGLQSCMCDVIADACKRCCRMSINETC
FAVEPPDILPDGTPCIQGFCNKGVCEKTIQDVVERFWDIIEEININKVLRFLRDNIVIVV
ITITTLFWVPTSCLISYFDRRSRHAELKEYNWKQQLDLIHPSDRRRVIHIRVPRQKITLP
TRM
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 12 | g2439.t6 | CDD | cd14246 | ADAM17_MPD | 149 | 206 | 4.20998E-19 |
| 8 | g2439.t6 | Gene3D | G3DSA:3.40.390.10 | Collagenase (Catalytic Domain) | 1 | 39 | 4.1E-9 |
| 7 | g2439.t6 | Gene3D | G3DSA:4.10.70.10 | Echistatin | 40 | 127 | 1.1E-14 |
| 3 | g2439.t6 | PANTHER | PTHR45702:SF6 | DISINTEGRIN AND METALLOPROTEINASE DOMAIN-CONTAINING PROTEIN 17 | 1 | 292 | 3.7E-109 |
| 4 | g2439.t6 | PANTHER | PTHR45702 | ADAM10/ADAM17 METALLOPEPTIDASE FAMILY MEMBER | 1 | 292 | 3.7E-109 |
| 2 | g2439.t6 | Pfam | PF00200 | Disintegrin | 50 | 126 | 4.1E-14 |
| 1 | g2439.t6 | Pfam | PF16698 | Membrane-proximal domain, switch, for ADAM17 | 150 | 206 | 4.0E-17 |
| 10 | g2439.t6 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 235 | - |
| 11 | g2439.t6 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 236 | 258 | - |
| 9 | g2439.t6 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 259 | 303 | - |
| 15 | g2439.t6 | ProSiteProfiles | PS50214 | Disintegrin domain profile. | 41 | 132 | 13.611 |
| 14 | g2439.t6 | SMART | SM00050 | DISIN_2 | 50 | 131 | 3.2E-9 |
| 6 | g2439.t6 | SUPERFAMILY | SSF55486 | Metalloproteases (zincins), catalytic domain | 1 | 38 | 6.02E-6 |
| 5 | g2439.t6 | SUPERFAMILY | SSF57552 | Blood coagulation inhibitor (disintegrin) | 50 | 129 | 3.96E-13 |
| 13 | g2439.t6 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 236 | 258 | - |
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 |
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.
