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.t1 TSS g11294.t1 15468534 15468534
chr_1 g11294 g11294.t1 isoform g11294.t1 15468654 15471390
chr_1 g11294 g11294.t1 exon g11294.t1.exon1 15468654 15468695
chr_1 g11294 g11294.t1 cds g11294.t1.CDS1 15468654 15468695
chr_1 g11294 g11294.t1 exon g11294.t1.exon2 15468781 15469515
chr_1 g11294 g11294.t1 cds g11294.t1.CDS2 15468781 15469515
chr_1 g11294 g11294.t1 exon g11294.t1.exon3 15469569 15469651
chr_1 g11294 g11294.t1 cds g11294.t1.CDS3 15469569 15469651
chr_1 g11294 g11294.t1 exon g11294.t1.exon4 15469744 15469928
chr_1 g11294 g11294.t1 cds g11294.t1.CDS4 15469744 15469928
chr_1 g11294 g11294.t1 exon g11294.t1.exon5 15469998 15470126
chr_1 g11294 g11294.t1 cds g11294.t1.CDS5 15469998 15470126
chr_1 g11294 g11294.t1 exon g11294.t1.exon6 15470189 15470745
chr_1 g11294 g11294.t1 cds g11294.t1.CDS6 15470189 15470745
chr_1 g11294 g11294.t1 exon g11294.t1.exon7 15470804 15471136
chr_1 g11294 g11294.t1 cds g11294.t1.CDS7 15470804 15471136
chr_1 g11294 g11294.t1 exon g11294.t1.exon8 15471208 15471390
chr_1 g11294 g11294.t1 cds g11294.t1.CDS8 15471208 15471390
chr_1 g11294 g11294.t1 TTS g11294.t1 15471628 15471628

Sequences

>g11294.t1 Gene=g11294 Length=2247
ATGTTCACAGTGCAAAATATAAATCATTCAATACACAATCAGCAAGCAGTACTTTTTCAT
TTGTCAAGTTTAACGCCGAGGTTAAATAAAGTATGTAAACATCAAAAGGCAACCGGCAAA
ACTAAAAGGATTAATGATTTAGAAACTTCAACTTATATCACATTCAAAGATGACCTATTT
GAGATTATCAAAAAGGAATTCAAAGATTCGATTGAACACAATAGAAAGTTGACATTCAAC
TTAAGTCTTAAAAGTTCAATAGAAAATCTTTTTTGTAAATCTGCACCTATTTTATCAAAT
GCAAAAAATGCACCGTTTATATCAACTGGATCTTTTGACATGAACAAAAACACTACTTAC
TGCAGTGATAGAGAGTTGCCTCATCAAAAATTTTTTAAGACTAATTTCTTCACGAAATCC
AATAATTTTGAATTTAATCTACAACAAAAGAGATATTTTAAAACATTTCGAGCTGTAATT
GCGGAAAATCAGAGAAATCCAACATTATTGAGTCGTCTGAAAGAAGCTTATAATCAACCT
GCAGGAGCGGCAAAAAGAATCGACAGCTTCAATCAAACATCGACAGGAGGAACACAATCA
ACAACTAAACAAACAATTCAACACGAGTCTTTATCAAAACTCTTAAGTCAATATGAATCA
AGTCTCACTCCAGAACAAAAACAACAACTCAAAGTGGCGTTTGCTGAAGGTTATCTTGCA
GCATCTCATCCTGAAAATGCAGAGAAGAAAGGTGGAAGAGCTATTAAATACTTAAAAATT
GTCCAACAGTTGTTAATGATTATAATAATCACGGCAATTATGGTTAGCTTATTTACTTCA
AATAATGGATCTGTTTTCAGAATTCAACTAGGAAATACTTCGGAGATTGATGCAGAGGAT
ATTTCAGTTTCTTTTGATGATGTAAAAGGATGCGATGAAGCTAAACAGGAGTTGAAAGAA
GTCGTTGAATTTCTCAAAAACCCTGAAAAGTTTAGCAATTTAGGAGGCAAATTGCCAAAA
GGCGTACTCTTAGTCGGACCACCAGGTACCGGAAAAACTTTATTGGCTCGAGCTGTAGCA
GGTGAAGCCGGAGTGCCATTCTTTCATGCAGCTGGACCTGAGTTTGATGAAGTTCTTGTT
GGTCAAGGAGCTAGACGAGTTCGCGATTTATTTAAGGCTGCGAAGGAAAGGGCACCTTGT
GTGATTTTTATCGACGAAATCGATTCAGTTGGGGCAAAGAGAACTAATTCAGTTCTTCAT
CCATATGCAAATCAAACAATTAATCAATTACTCTCTGAAATGGATGGTTTTCAACAGAAT
GAGGGAGTAATCGTTCTAGGAGCAACAAATAGACGTGAAGATCTTGATCAGGCTTTATTA
CGACCGGGCAGATTTGATGTGGAAGTTGTTGTACCTACACCTGATTACACAGGACGAAAG
GAAATCATTAATCATTATCTTGGCAAGATTTTAAGTAAAGACATTAATACCGATCAATTG
GCACGCGGAACAACTGGTTTTACTGGTGCTGATTTGGAAAATATGATTAATCAAGCTGCA
TTAAAAGCAGCGATTGAAGGAGCTGAAGTAGTTTCTATGCGACATCTTGAAAATGCACGT
GATAAGGTGCTTATGGGTCCTGAAAGGAAAAATAGATTACCAGATGAGGAAGCAAATAAA
ATCACAGCTTATCATGAAGGTGGTCATGCAATTGTTGCTTATTACACTAAGGAATCACAT
CCGCTACATAAAGTGACTATCATGCCACGTGGTCCTAGTCTCGGACACACTGCGTATATT
CCTGAAAAAGAGAGATATCATGTAACAAAAACTCAATTGCTTGCTATGATGGACACAATG
CTTGGTGGTCGTGCAGCAGAAGAATTAATTTTTGGAGCTGATAAAATTACATCAGGTGCA
AGTAGTGATTTGAAACAAGCAACATCTATTGCTGCGCACATGGTTAAAGACTGGGGAATG
TCCGAAAAAGTTGGACTTCGCACAATTGAATCAGCAAAAGGATTGCAAGCTTCTGAAAAT
CTCTCAGCGACAACAATTGAATCAGTTGACTCTGAAATAAAGAAAATTTTAAATGACAGT
TATGAACGTGCAAAAAGTATTCTCAAGACACATTCAAAAGAACATAAAGCACTTGCTGAG
GCATTATTGAAATATGAAACATTAGATGCTGAAGATATTAAAGCTATTTTATCTGGTGAC
AAAATTGCAGCTGAATCATCACACTGA

>g11294.t1 Gene=g11294 Length=748
MFTVQNINHSIHNQQAVLFHLSSLTPRLNKVCKHQKATGKTKRINDLETSTYITFKDDLF
EIIKKEFKDSIEHNRKLTFNLSLKSSIENLFCKSAPILSNAKNAPFISTGSFDMNKNTTY
CSDRELPHQKFFKTNFFTKSNNFEFNLQQKRYFKTFRAVIAENQRNPTLLSRLKEAYNQP
AGAAKRIDSFNQTSTGGTQSTTKQTIQHESLSKLLSQYESSLTPEQKQQLKVAFAEGYLA
ASHPENAEKKGGRAIKYLKIVQQLLMIIIITAIMVSLFTSNNGSVFRIQLGNTSEIDAED
ISVSFDDVKGCDEAKQELKEVVEFLKNPEKFSNLGGKLPKGVLLVGPPGTGKTLLARAVA
GEAGVPFFHAAGPEFDEVLVGQGARRVRDLFKAAKERAPCVIFIDEIDSVGAKRTNSVLH
PYANQTINQLLSEMDGFQQNEGVIVLGATNRREDLDQALLRPGRFDVEVVVPTPDYTGRK
EIINHYLGKILSKDINTDQLARGTTGFTGADLENMINQAALKAAIEGAEVVSMRHLENAR
DKVLMGPERKNRLPDEEANKITAYHEGGHAIVAYYTKESHPLHKVTIMPRGPSLGHTAYI
PEKERYHVTKTQLLAMMDTMLGGRAAEELIFGADKITSGASSDLKQATSIAAHMVKDWGM
SEKVGLRTIESAKGLQASENLSATTIESVDSEIKKILNDSYERAKSILKTHSKEHKALAE
ALLKYETLDAEDIKAILSGDKIAAESSH

Protein features from InterProScan

Transcript Database ID Name Start End E.value
15 g11294.t1 CDD cd00009 AAA 309 472 1.95017E-27
9 g11294.t1 Gene3D G3DSA:3.40.50.300 - 292 474 2.6E-65
10 g11294.t1 Gene3D G3DSA:1.10.8.60 - 475 547 3.0E-20
11 g11294.t1 Gene3D G3DSA:1.20.58.760 - 548 746 7.1E-70
6 g11294.t1 Hamap MF_01458 ATP-dependent zinc metalloprotease FtsH [ftsH]. 1 747 30.96883
19 g11294.t1 MobiDBLite mobidb-lite consensus disorder prediction 187 206 -
4 g11294.t1 PANTHER PTHR43655:SF13 MIP17311P 99 745 0.0
5 g11294.t1 PANTHER PTHR43655 ATP-DEPENDENT PROTEASE 99 745 0.0
1 g11294.t1 Pfam PF00004 ATPase family associated with various cellular activities (AAA) 342 472 1.5E-42
2 g11294.t1 Pfam PF17862 AAA+ lid domain 494 537 1.7E-9
3 g11294.t1 Pfam PF01434 Peptidase family M41 555 736 2.3E-66
12 g11294.t1 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 259 -
14 g11294.t1 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 260 279 -
13 g11294.t1 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 280 748 -
18 g11294.t1 ProSitePatterns PS00674 AAA-protein family signature. 443 461 -
17 g11294.t1 SMART SM00382 AAA_5 338 475 1.1E-22
8 g11294.t1 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 301 542 1.26E-64
7 g11294.t1 SUPERFAMILY SSF140990 FtsH protease domain-like 555 741 4.05E-64
20 g11294.t1 TIGRFAM TIGR01241 FtsH_fam: ATP-dependent metallopeptidase HflB 259 737 4.3E-180
16 g11294.t1 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 257 279 -

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:0016020 membrane CC
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

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.

Raw TPM values