Gene loci information

Transcript annotation

  • This transcript has been annotated as ATP-dependent zinc metalloprotease YME1L.

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_1 g11294 g11294.t5 TSS g11294.t5 15468534 15468534
chr_1 g11294 g11294.t5 isoform g11294.t5 15469515 15470804
chr_1 g11294 g11294.t5 exon g11294.t5.exon1 15469515 15470804
chr_1 g11294 g11294.t5 cds g11294.t5.CDS1 15470314 15470769
chr_1 g11294 g11294.t5 TTS g11294.t5 15471628 15471628

Sequences

>g11294.t5 Gene=g11294 Length=1290
AGTATGATGACATTATAAATAGTATAAATTTACTTATTTTTCTTATTTTTTTAGATTGTC
CAACAGTTGTTAATGATTATAATAATCACGGCAATTATGGTTAGCTTATTTACTTCAAAT
AATGGATCTGTTTTCAGGTAGTTTTACTTTTCTTATTAATAAACCATTCCTTCAATTACA
TTGAAAAATTTGACTTGATAAAATTTTTAAGAAATAATTTTGATAACAGAATTCAACTAG
GAAATACTTCGGAGATTGATGCAGAGGATATTTCAGTTTCTTTTGATGATGTAAAAGGAT
GCGATGAAGCTAAACAGGAGTTGAAAGAAGTCGTTGAATTTCTCAAAAACCCTGAAAAGT
TTAGCAATTTAGGAGGCAAATTGCCAAAAGGCGTACTCTTAGTCGGACCACCAGGTTTGT
TATTCTCATTTAACAATGTTATAAAGTTATTTTCATGCCAATACATTGTGTATATCTTTA
TAGGTACCGGAAAAACTTTATTGGCTCGAGCTGTAGCAGGTGAAGCCGGAGTGCCATTCT
TTCATGCAGCTGGACCTGAGTTTGATGAAGTTCTTGTTGGTCAAGGAGCTAGACGAGTTC
GCGATTTATTTAGTAAGTCTAATTATAGATTTTAAATCAATAGAAAAGAAATTAATTTAG
TGAATGAATTGCAGAGGCTGCGAAGGAAAGGGCACCTTGTGTGATTTTTATCGACGAAAT
CGATTCAGTTGGGGCAAAGAGAACTAATTCAGTTCTTCATCCATATGCAAATCAAACAAT
TAATCAATTACTCTCTGAAATGGATGGTTTTCAACAGAATGAGGGAGTAATCGTTCTAGG
AGCAACAAATAGACGTGAAGATCTTGATCAGGCTTTATTACGACCGGGCAGATTTGATGT
GGAAGTTGTTGTACCTACACCTGATTACACAGGACGAAAGGAAATCATTAATCATTATCT
TGGCAAGATTTTAAGTAAAGACATTAATACCGATCAATTGGCACGCGGAACAACTGGTTT
TACTGGTGCTGATTTGGAAAATATGATTAATCAAGCTGCATTAAAAGCAGCGATTGAAGG
AGCTGAAGTAGTTTCTATGCGACATCTTGAAAATGCACGTGATAAGGTGCTTATGGGTCC
TGAAAGGAAAAATAGATTACCAGATGAGGAAGCAAATAAAATCACAGCTTATCATGAAGG
TGGTCATGCAATTGTTGCTTATTACACTAAGGTAAGAAAAATTTTAATTATTTAAAATTA
GTTTATCTAATATTTAAATATTTTATCAGG

>g11294.t5 Gene=g11294 Length=151
MDGFQQNEGVIVLGATNRREDLDQALLRPGRFDVEVVVPTPDYTGRKEIINHYLGKILSK
DINTDQLARGTTGFTGADLENMINQAALKAAIEGAEVVSMRHLENARDKVLMGPERKNRL
PDEEANKITAYHEGGHAIVAYYTKVRKILII

Protein features from InterProScan

Transcript Database ID Name Start End E.value
7 g11294.t5 Gene3D G3DSA:3.40.50.300 - 1 41 1.1E-11
8 g11294.t5 Gene3D G3DSA:1.10.8.60 - 42 114 1.6E-21
9 g11294.t5 Gene3D G3DSA:1.20.58.760 - 115 151 6.3E-6
3 g11294.t5 PANTHER PTHR43655:SF13 MIP17311P 1 145 5.3E-85
4 g11294.t5 PANTHER PTHR43655 ATP-DEPENDENT PROTEASE 1 145 5.3E-85
1 g11294.t5 Pfam PF00004 ATPase family associated with various cellular activities (AAA) 1 39 5.5E-7
2 g11294.t5 Pfam PF17862 AAA+ lid domain 61 104 1.6E-10
6 g11294.t5 ProSitePatterns PS00674 AAA-protein family signature. 10 28 -
5 g11294.t5 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 1 133 7.81E-23

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.

Raw TPM values