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.t2 TSS g11294.t2 15468534 15468534
chr_1 g11294 g11294.t2 isoform g11294.t2 15468654 15471390
chr_1 g11294 g11294.t2 exon g11294.t2.exon1 15468654 15468695
chr_1 g11294 g11294.t2 cds g11294.t2.CDS1 15468654 15468695
chr_1 g11294 g11294.t2 exon g11294.t2.exon2 15468781 15469515
chr_1 g11294 g11294.t2 cds g11294.t2.CDS2 15468781 15469515
chr_1 g11294 g11294.t2 exon g11294.t2.exon3 15469569 15469651
chr_1 g11294 g11294.t2 cds g11294.t2.CDS3 15469569 15469651
chr_1 g11294 g11294.t2 exon g11294.t2.exon4 15469726 15469928
chr_1 g11294 g11294.t2 cds g11294.t2.CDS4 15469726 15469928
chr_1 g11294 g11294.t2 exon g11294.t2.exon5 15469998 15470126
chr_1 g11294 g11294.t2 cds g11294.t2.CDS5 15469998 15470126
chr_1 g11294 g11294.t2 exon g11294.t2.exon6 15470189 15470745
chr_1 g11294 g11294.t2 cds g11294.t2.CDS6 15470189 15470745
chr_1 g11294 g11294.t2 exon g11294.t2.exon7 15470804 15471136
chr_1 g11294 g11294.t2 cds g11294.t2.CDS7 15470804 15471136
chr_1 g11294 g11294.t2 exon g11294.t2.exon8 15471208 15471390
chr_1 g11294 g11294.t2 cds g11294.t2.CDS8 15471208 15471390
chr_1 g11294 g11294.t2 TTS g11294.t2 15471628 15471628

Sequences

>g11294.t2 Gene=g11294 Length=2265
ATGTTCACAGTGCAAAATATAAATCATTCAATACACAATCAGCAAGCAGTACTTTTTCAT
TTGTCAAGTTTAACGCCGAGGTTAAATAAAGTATGTAAACATCAAAAGGCAACCGGCAAA
ACTAAAAGGATTAATGATTTAGAAACTTCAACTTATATCACATTCAAAGATGACCTATTT
GAGATTATCAAAAAGGAATTCAAAGATTCGATTGAACACAATAGAAAGTTGACATTCAAC
TTAAGTCTTAAAAGTTCAATAGAAAATCTTTTTTGTAAATCTGCACCTATTTTATCAAAT
GCAAAAAATGCACCGTTTATATCAACTGGATCTTTTGACATGAACAAAAACACTACTTAC
TGCAGTGATAGAGAGTTGCCTCATCAAAAATTTTTTAAGACTAATTTCTTCACGAAATCC
AATAATTTTGAATTTAATCTACAACAAAAGAGATATTTTAAAACATTTCGAGCTGTAATT
GCGGAAAATCAGAGAAATCCAACATTATTGAGTCGTCTGAAAGAAGCTTATAATCAACCT
GCAGGAGCGGCAAAAAGAATCGACAGCTTCAATCAAACATCGACAGGAGGAACACAATCA
ACAACTAAACAAACAATTCAACACGAGTCTTTATCAAAACTCTTAAGTCAATATGAATCA
AGTCTCACTCCAGAACAAAAACAACAACTCAAAGTGGCGTTTGCTGAAGGTTATCTTGCA
GCATCTCATCCTGAAAATGCAGAGAAGAAAGGTGGAAGAGCTATTAAATACTTAAAAATT
GTCCAACAGTTGTTAATGATTATAATAATCACGGCAATTATGGTTAGCTTATTTACTTCA
AATAATGGATCTGTTTTCAGAAATAATTTTGATAACAGAATTCAACTAGGAAATACTTCG
GAGATTGATGCAGAGGATATTTCAGTTTCTTTTGATGATGTAAAAGGATGCGATGAAGCT
AAACAGGAGTTGAAAGAAGTCGTTGAATTTCTCAAAAACCCTGAAAAGTTTAGCAATTTA
GGAGGCAAATTGCCAAAAGGCGTACTCTTAGTCGGACCACCAGGTACCGGAAAAACTTTA
TTGGCTCGAGCTGTAGCAGGTGAAGCCGGAGTGCCATTCTTTCATGCAGCTGGACCTGAG
TTTGATGAAGTTCTTGTTGGTCAAGGAGCTAGACGAGTTCGCGATTTATTTAAGGCTGCG
AAGGAAAGGGCACCTTGTGTGATTTTTATCGACGAAATCGATTCAGTTGGGGCAAAGAGA
ACTAATTCAGTTCTTCATCCATATGCAAATCAAACAATTAATCAATTACTCTCTGAAATG
GATGGTTTTCAACAGAATGAGGGAGTAATCGTTCTAGGAGCAACAAATAGACGTGAAGAT
CTTGATCAGGCTTTATTACGACCGGGCAGATTTGATGTGGAAGTTGTTGTACCTACACCT
GATTACACAGGACGAAAGGAAATCATTAATCATTATCTTGGCAAGATTTTAAGTAAAGAC
ATTAATACCGATCAATTGGCACGCGGAACAACTGGTTTTACTGGTGCTGATTTGGAAAAT
ATGATTAATCAAGCTGCATTAAAAGCAGCGATTGAAGGAGCTGAAGTAGTTTCTATGCGA
CATCTTGAAAATGCACGTGATAAGGTGCTTATGGGTCCTGAAAGGAAAAATAGATTACCA
GATGAGGAAGCAAATAAAATCACAGCTTATCATGAAGGTGGTCATGCAATTGTTGCTTAT
TACACTAAGGAATCACATCCGCTACATAAAGTGACTATCATGCCACGTGGTCCTAGTCTC
GGACACACTGCGTATATTCCTGAAAAAGAGAGATATCATGTAACAAAAACTCAATTGCTT
GCTATGATGGACACAATGCTTGGTGGTCGTGCAGCAGAAGAATTAATTTTTGGAGCTGAT
AAAATTACATCAGGTGCAAGTAGTGATTTGAAACAAGCAACATCTATTGCTGCGCACATG
GTTAAAGACTGGGGAATGTCCGAAAAAGTTGGACTTCGCACAATTGAATCAGCAAAAGGA
TTGCAAGCTTCTGAAAATCTCTCAGCGACAACAATTGAATCAGTTGACTCTGAAATAAAG
AAAATTTTAAATGACAGTTATGAACGTGCAAAAAGTATTCTCAAGACACATTCAAAAGAA
CATAAAGCACTTGCTGAGGCATTATTGAAATATGAAACATTAGATGCTGAAGATATTAAA
GCTATTTTATCTGGTGACAAAATTGCAGCTGAATCATCACACTGA

>g11294.t2 Gene=g11294 Length=754
MFTVQNINHSIHNQQAVLFHLSSLTPRLNKVCKHQKATGKTKRINDLETSTYITFKDDLF
EIIKKEFKDSIEHNRKLTFNLSLKSSIENLFCKSAPILSNAKNAPFISTGSFDMNKNTTY
CSDRELPHQKFFKTNFFTKSNNFEFNLQQKRYFKTFRAVIAENQRNPTLLSRLKEAYNQP
AGAAKRIDSFNQTSTGGTQSTTKQTIQHESLSKLLSQYESSLTPEQKQQLKVAFAEGYLA
ASHPENAEKKGGRAIKYLKIVQQLLMIIIITAIMVSLFTSNNGSVFRNNFDNRIQLGNTS
EIDAEDISVSFDDVKGCDEAKQELKEVVEFLKNPEKFSNLGGKLPKGVLLVGPPGTGKTL
LARAVAGEAGVPFFHAAGPEFDEVLVGQGARRVRDLFKAAKERAPCVIFIDEIDSVGAKR
TNSVLHPYANQTINQLLSEMDGFQQNEGVIVLGATNRREDLDQALLRPGRFDVEVVVPTP
DYTGRKEIINHYLGKILSKDINTDQLARGTTGFTGADLENMINQAALKAAIEGAEVVSMR
HLENARDKVLMGPERKNRLPDEEANKITAYHEGGHAIVAYYTKESHPLHKVTIMPRGPSL
GHTAYIPEKERYHVTKTQLLAMMDTMLGGRAAEELIFGADKITSGASSDLKQATSIAAHM
VKDWGMSEKVGLRTIESAKGLQASENLSATTIESVDSEIKKILNDSYERAKSILKTHSKE
HKALAEALLKYETLDAEDIKAILSGDKIAAESSH

Protein features from InterProScan

Transcript Database ID Name Start End E.value
15 g11294.t2 CDD cd00009 AAA 315 478 2.00722E-27
9 g11294.t2 Gene3D G3DSA:3.40.50.300 - 298 480 2.6E-65
10 g11294.t2 Gene3D G3DSA:1.10.8.60 - 481 553 3.0E-20
11 g11294.t2 Gene3D G3DSA:1.20.58.760 - 554 752 7.2E-70
6 g11294.t2 Hamap MF_01458 ATP-dependent zinc metalloprotease FtsH [ftsH]. 1 753 30.998615
19 g11294.t2 MobiDBLite mobidb-lite consensus disorder prediction 187 206 -
4 g11294.t2 PANTHER PTHR43655:SF13 MIP17311P 99 751 0.0
5 g11294.t2 PANTHER PTHR43655 ATP-DEPENDENT PROTEASE 99 751 0.0
1 g11294.t2 Pfam PF00004 ATPase family associated with various cellular activities (AAA) 348 478 1.5E-42
2 g11294.t2 Pfam PF17862 AAA+ lid domain 500 543 1.7E-9
3 g11294.t2 Pfam PF01434 Peptidase family M41 561 742 2.3E-66
12 g11294.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 259 -
14 g11294.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 260 279 -
13 g11294.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 280 754 -
18 g11294.t2 ProSitePatterns PS00674 AAA-protein family signature. 449 467 -
17 g11294.t2 SMART SM00382 AAA_5 344 481 1.1E-22
8 g11294.t2 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 307 548 1.17E-64
7 g11294.t2 SUPERFAMILY SSF140990 FtsH protease domain-like 561 747 4.19E-64
20 g11294.t2 TIGRFAM TIGR01241 FtsH_fam: ATP-dependent metallopeptidase HflB 258 743 3.1E-179
16 g11294.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 264 286 -

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