RetrogeneDB ID: retro_mmus_557

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 10:44153469..44154879(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: Pramel7
• Ensembl ID: ENSMUSG00000025839
• Aliases: Pramel7, AA675346, C81180
• Description: preferentially expressed antigen in melanoma like 7 [Source:MGI Symbol;Acc:MGI:2156391]

Sequence

>retro_mmus_557
ATGGTCCGTGCCCCACCCACACTCCAGAATCAGGCTTCACTGAGCCTGGTGAGGAATGAAGTATTGACCGTCTCTGATAC
GGAGTACCTAACAAGGGAATTCTTCCCACCTCTGTTCAAGGAGGCCAAAGCATAGACAATTACGATCCTGGTGGAGTACT
GGCTCTATGCTTGCCTTCATGTTGGGTTGCTGATTAATAAACCCAACTTTCAGACCTTCCAGGCTATACTGGATAGAGTA
GACACATGGCTGAAATGGAAGTATCGCCCCCGGATGTGCAGGCTTAAAAACGTTGACTTCAGGGATGAACAACACCATGC
TTCCTCAGATATGCAGGATGGGAGAGAGGGTAGAGACCACTTAGTAGGAACTATGCCTAAGAAGCCAATAGTGGAGGGCC
ACTCAAGAACAAGGAAACAGTGTCTGAGGCTGTTCCATGACCTTTCCTTTATGTCTTCTCTGCATGAAGATAAACACTAA
ACACTGTTGTTGGAGTGGGCAAAGGAGAGGAAGAACTTCCTGCATCTGTGCTGTGAGAAGTTGGAGATCAGAGCAGTAAA
AGTGTCCAAGGTCAGGAATGCATTAAAATTTCTACAGCCAGAGTTCATCAAGAAGTTGGAACTGAATACAGTGGGGAATT
TGTCCAAACTGGCAAACTTTGTACCTTTCATTAGAAAGAGGAGAAACCTTCGGAAACCCATGCTAGTACGCACCTTTGGA
ACAAGGACTTTCACTCAAGAGGAGAGGCAGAACATCAGCAAGATCATTTCTCTATTCTGCAAACTCAGCGGTCTCCGGCA
TCTCACTATTGATGATGTCTATTTTCTCACAGACCACATGAAAGAGTTGCTCGGGTGTCTGGAGGCCCCATTGGTGTCCT
TCAAGATCACCCTGTGTCAACTCTCTCAGTCAGACTTGGAGTCATTTGCCCAGCGTTGGAACTACAGTCAGCTTAAACAC
CTGTGCTTGAGAGGAGCCACTTTAACTAACCTGGATGTCAAGCCTCTAAGAGATTTCTTAAAGCAGGTTGCAGCTAACCT
GCAGACTCTGGACTTAGAAGACTGTAGGATGGATGATTCTCACCTCAGTACCCTTCTGCCTGCCCTGATCAAATGCTCCC
AGCCTACTAGCATCAATTTGTATGACAATGACATCTCCAAGGATGTCCTGGAGAACTTTTTGCACCGCACTACCAATCTG
AGCCAGCTAGCAGTAGAAATGTATCCTGCTCCATCAGAGGTCTATAATGAGTTGAAATATGTTGTAGTAGAGATATTTAT
TCAGCTTTGTGCTGAACTCATGGACAAACTCATGGATGTAAGGCAGCCCAATTCAGTGTGCTTTGGTTCCTCTTCCTGTT
ATGACTGTGAGGATCATTATTTATATGAAGATGGGGACGACACACTTTGT

Alignment

ORF - retro_mmus_557 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.42 %
• Parental protein coverage: 99.16 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MVSAPPTLQDQAFRSLVRNEVLTVSDAECLIREFFPPLFKEASTQKKPKTIMILVEHWPYPCLHVGLLID
          MV.APPTLQ.QA..SLVRNEVLTVSD.E.L.REFFPPLFKEA....K..TI.ILVE.W.Y.CLHVGLLI.
Retrocopy MVRAPPTLQNQASLSLVRNEVLTVSDTEYLTREFFPPLFKEA----KA*TITILVEYWLYACLHVGLLIN

Parental  KPNFQIFQAILDGVDTWLKRKYRPRMGRLKKVDFRDAQHHASLDMQDEREGRDYLVGTLPKKQIVEDHSR
          KPNFQ.FQAILD.VDTWLK.KYRPRM.RLK.VDFRD.QHHAS.DMQD.REGRD.LVGT.PKK.IVE.HSR
Retrocopy KPNFQTFQAILDRVDTWLKWKYRPRMCRLKNVDFRDEQHHASSDMQDGREGRDHLVGTMPKKPIVEGHSR

Parental  TRKERLKLFHDLSFMSSLHEDKHQTLLLEWAKERTSFLHLCCEKLEIGAVEVSKVRNVLKFLQPELIKEL
          TRK..L.LFHDLSFMSSLHEDKH.TLLLEWAKER..FLHLCCEKLEI.AV.VSKVRN.LKFLQPE.IK.L
Retrocopy TRKQCLRLFHDLSFMSSLHEDKH*TLLLEWAKERKNFLHLCCEKLEIRAVKVSKVRNALKFLQPEFIKKL

Parental  KLNTVGNLSKLAKFVPFIRKMRNLQKLMLVRTFGTRTFTQEEKQNISKIISLFCKLSCLRHLTIDDVYFL
          .LNTVGNLSKLA.FVPFIRK.RNL.K.MLVRTFGTRTFTQEE.QNISKIISLFCKLS.LRHLTIDDVYFL
Retrocopy ELNTVGNLSKLANFVPFIRKRRNLRKPMLVRTFGTRTFTQEERQNISKIISLFCKLSGLRHLTIDDVYFL

Parental  TDQMKELLRCLEAPLVSLKITLCQLSQSDLESFAQRWNYSQLKHLCLRGVTLTNLDVTPLRDFLKRVAAN
          TD.MKELL.CLEAPLVS.KITLCQLSQSDLESFAQRWNYSQLKHLCLRG.TLTNLDV.PLRDFLK.VAAN
Retrocopy TDHMKELLGCLEAPLVSFKITLCQLSQSDLESFAQRWNYSQLKHLCLRGATLTNLDVKPLRDFLKQVAAN

Parental  LQTLDLEDCRMDDSHFRTLLPALIKCTQLTSINLYDNDISEDVLENFLHRTTNLSQLTTEMYPAPSEVYN
          LQTLDLEDCRMDDSH..TLLPALIKC.Q.TSINLYDNDIS.DVLENFLHRTTNLSQL..EMYPAPSEVYN
Retrocopy LQTLDLEDCRMDDSHLSTLLPALIKCSQPTSINLYDNDISKDVLENFLHRTTNLSQLAVEMYPAPSEVYN

Parental  ESNYVIVEIFIQICSELMNKLMEVRQANSVCFGSSSCYDCDNRYLYEDDGDVTLC
          E..YV.VEIFIQ.C.ELM.KLM.VRQ.NSVCFGSSSCYDC...YLYE.DGD.TLC
Retrocopy ELKYVVVEIFIQLCAELMDKLMDVRQPNSVCFGSSSCYDCEDHYLYE-DGDDTLC

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain	0.00 RPM	0.00 RPM
SRP007412_cerebellum	0.00 RPM	0.00 RPM
SRP007412_heart	0.00 RPM	0.06 RPM
SRP007412_kidney	0.00 RPM	0.02 RPM
SRP007412_liver	0.00 RPM	0.00 RPM
SRP007412_testis	0.05 RPM	0.50 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_557 was not detected

EST

No EST(s) were mapped for retro_mmus_557 retrocopy.

TSS

No TSS is located nearby retro_mmus_557 retrocopy 5' end.

Lab

retro_mmus_557 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_557 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Dipodomys ordii	ENSDORG00000013324	1 retrocopy	retro_dord_231,
Homo sapiens	ENSG00000187545	1 retrocopy	retro_hsap_220,
Mus musculus	ENSMUSG00000025839	1 retrocopy	retro_mmus_557 ,
Otolemur garnettii	ENSOGAG00000000273	2 retrocopies	retro_ogar_1100, retro_ogar_1238,
Ochotona princeps	ENSOPRG00000009716	1 retrocopy	retro_opri_661,
Pan troglodytes	ENSPTRG00000029629	1 retrocopy	retro_ptro_330,