General information for g11294.t6
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as ATP-dependent zinc metalloprotease YME1L.
Parent gene
- The parent gene g11294 is located on chr_1: 15470804..15471390 (+ 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 | g11294 | g11294.t6 | isoform | g11294.t6 | 15469752 | 15471390 |
| chr_1 | g11294 | g11294.t6 | exon | g11294.t6.exon1 | 15469752 | 15469928 |
| chr_1 | g11294 | g11294.t6 | exon | g11294.t6.exon2 | 15469998 | 15470126 |
| chr_1 | g11294 | g11294.t6 | exon | g11294.t6.exon3 | 15470189 | 15470745 |
| chr_1 | g11294 | g11294.t6 | cds | g11294.t6.CDS1 | 15470314 | 15470745 |
| chr_1 | g11294 | g11294.t6 | exon | g11294.t6.exon4 | 15470804 | 15471390 |
| chr_1 | g11294 | g11294.t6 | cds | g11294.t6.CDS2 | 15470804 | 15471223 |
| chr_1 | g11294 | g11294.t6 | TTS | g11294.t6 | 15471628 | 15471628 |
| chr_1 | g11294 | g11294.t6 | TSS | g11294.t6 | NA | NA |
Sequences
>g11294.t6 Gene=g11294 Length=1450
TAGGAAATACTTCGGAGATTGATGCAGAGGATATTTCAGTTTCTTTTGATGATGTAAAAG
GATGCGATGAAGCTAAACAGGAGTTGAAAGAAGTCGTTGAATTTCTCAAAAACCCTGAAA
AGTTTAGCAATTTAGGAGGCAAATTGCCAAAAGGCGTACTCTTAGTCGGACCACCAGGTA
CCGGAAAAACTTTATTGGCTCGAGCTGTAGCAGGTGAAGCCGGAGTGCCATTCTTTCATG
CAGCTGGACCTGAGTTTGATGAAGTTCTTGTTGGTCAAGGAGCTAGACGAGTTCGCGATT
TATTTAAGGCTGCGAAGGAAAGGGCACCTTGTGTGATTTTTATCGACGAAATCGATTCAG
TTGGGGCAAAGAGAACTAATTCAGTTCTTCATCCATATGCAAATCAAACAATTAATCAAT
TACTCTCTGAAATGGATGGTTTTCAACAGAATGAGGGAGTAATCGTTCTAGGAGCAACAA
ATAGACGTGAAGATCTTGATCAGGCTTTATTACGACCGGGCAGATTTGATGTGGAAGTTG
TTGTACCTACACCTGATTACACAGGACGAAAGGAAATCATTAATCATTATCTTGGCAAGA
TTTTAAGTAAAGACATTAATACCGATCAATTGGCACGCGGAACAACTGGTTTTACTGGTG
CTGATTTGGAAAATATGATTAATCAAGCTGCATTAAAAGCAGCGATTGAAGGAGCTGAAG
TAGTTTCTATGCGACATCTTGAAAATGCACGTGATAAGGTGCTTATGGGTCCTGAAAGGA
AAAATAGATTACCAGATGAGGAAGCAAATAAAATCACAGCTTATCATGAAGGTGGTCATG
CAATTGTTGCTTATTACACTAAGGAATCACATCCGCTACATAAAGTGACTATCATGCCAC
GTGGTCCTAGTCTCGGACACACTGCGTATATTCCTGAAAAAGAGAGATATCATGTAACAA
AAACTCAATTGCTTGCTATGATGGACACAATGCTTGGTGGTCGTGCAGCAGAAGAATTAA
TTTTTGGAGCTGATAAAATTACATCAGGTGCAAGTAGTGATTTGAAACAAGCAACATCTA
TTGCTGCGCACATGGTTAAAGACTGGGGAATGTCCGAAAAAGTTGGACTTCGCACAATTG
AATCAGCAAAAGGATTGCAAGCTTCTGAAAATCTCTCAGCGACAACAATTGAATCAGTGA
GTATAGTAATAAAGTTTTCATTAAATGCAGTTATTAAAAGAAATATACTTCTTTTTTTGC
TATTCAGGTTGACTCTGAAATAAAGAAAATTTTAAATGACAGTTATGAACGTGCAAAAAG
TATTCTCAAGACACATTCAAAAGAACATAAAGCACTTGCTGAGGCATTATTGAAATATGA
AACATTAGATGCTGAAGATATTAAAGCTATTTTATCTGGTGACAAAATTGCAGCTGAATC
ATCACACTGA
>g11294.t6 Gene=g11294 Length=283
MDGFQQNEGVIVLGATNRREDLDQALLRPGRFDVEVVVPTPDYTGRKEIINHYLGKILSK
DINTDQLARGTTGFTGADLENMINQAALKAAIEGAEVVSMRHLENARDKVLMGPERKNRL
PDEEANKITAYHEGGHAIVAYYTKESHPLHKVTIMPRGPSLGHTAYIPEKERYHVTKTQL
LAMMDTMLGGRAAEELIFGADKITSGASSDLKQATSIAAHMVKDWGMSEKVGLRTIESAK
GLQASENLSATTIESVSIVIKFSLNAVIKRNILLFLLFRLTLK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g11294.t6 | Gene3D | G3DSA:3.40.50.300 | - | 1 | 41 | 3.0E-11 |
| 10 | g11294.t6 | Gene3D | G3DSA:1.10.8.60 | - | 42 | 114 | 6.5E-21 |
| 11 | g11294.t6 | Gene3D | G3DSA:1.20.58.760 | - | 115 | 271 | 1.6E-51 |
| 4 | g11294.t6 | PANTHER | PTHR43655:SF13 | MIP17311P | 1 | 270 | 2.8E-152 |
| 5 | g11294.t6 | PANTHER | PTHR43655 | ATP-DEPENDENT PROTEASE | 1 | 270 | 2.8E-152 |
| 1 | g11294.t6 | Pfam | PF00004 | ATPase family associated with various cellular activities (AAA) | 1 | 39 | 1.5E-6 |
| 2 | g11294.t6 | Pfam | PF17862 | AAA+ lid domain | 61 | 104 | 4.6E-10 |
| 3 | g11294.t6 | Pfam | PF01434 | Peptidase family M41 | 121 | 255 | 6.6E-50 |
| 8 | g11294.t6 | ProSitePatterns | PS00674 | AAA-protein family signature. | 10 | 28 | - |
| 7 | g11294.t6 | SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases | 1 | 133 | 3.0E-22 |
| 6 | g11294.t6 | SUPERFAMILY | SSF140990 | FtsH protease domain-like | 122 | 247 | 4.84E-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:0006508 | proteolysis | BP |
| GO:0005524 | ATP binding | MF |
| GO:0004222 | metalloendopeptidase activity | MF |
| GO:0004176 | ATP-dependent peptidase activity | MF |
| GO:0016887 | ATP hydrolysis 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.
