RetrogeneDB ID: retro_mmus_564

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 10:58757269..58758943(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Zc3h11a
• Ensembl ID: ENSMUSG00000026464
• Aliases: Zc3h11a, 1110003F06Rik, 5730454B08Rik, G630041M05Rik, Zc3hdc11a, Zc3hh11a, mKIAA0663
• Description: zinc finger CCCH type containing 11A [Source:MGI Symbol;Acc:MGI:1917829]

Sequence

>retro_mmus_564
ATGCCTGATCAGGGAGAAGACTGCTACTTTTATTTCTATTCTACATGCACCAGAGGTGACAACTGCCCATTCCGCCACTG
TGAAGCTGCACTAGGAAATGAAACTGTTTGCACACTATGGCAAGAAGGTCGTTGTTTTCGACAGGTGTGCAGATTTCGCC
ACATGGAAATTGCCAAAAAACGAAGTGAAATTCCTTGTTATTGGGAAAATCAGCCAATGGGATGTCGGAAACTAAATTGC
GCTTTCCACCACAACAGAAGTCGTTATGTTGATGGACTGTTCCTACCTCCAAGCAAAACTATGTTACCCACTGTGCCTGA
GTCGCAAGAAGAAATAAAGGCTAGCCAGCTCAGGGTCCAACAGGACAAATTGTCAATTCAGTATAACCCCTCCCCTCAGC
TCCGGAGTGTAATGAAAGTAGAGAGTTCAAATAAAGTTCTCATTCCCACACATCCGCGTGTTGTAATCAATATTACAGCT
GATGATGACAATGATCAGTCTTCTGAGGAGGAGGATGAAAGCAAAACACCTGCCCTGAAACCAACTCCTGAAGTCCATGA
TGGATTCCCAGTGGCTTCTGCCTGCAAACCTGGGGTCAGTTTAAAGCAAGGTGAATGCTTGGATTTTGGAATAAGAACTC
TTGAGGAAATGAAAGCAACGAAAATGAAGGAAAAATTCATGAAGCAAGGTGACTCCTCGGGAGAATCTCCAGTAGGAGAT
TCTCAGCCCAATCCAGGCCCTGAGAAGGAGAATGTTGGGACTGTGGTGGGAACAGTAACTCCATCAAGCAAACAAGAAGA
GTCCTTGGTTAGACTGAGTCTTAGTGAGAGACTGGGAAAACGAAAACTTTCAGTAGGTGGTGACAGTGAACCCCCATTAA
AGAGAAGACTTGCACAGAGGTTAGGGAAAAAAGTGGAAGCCCCAGAAGCTAACATTGATAAAGCACCAAAGAAAAAGAGA
GTTCATAACGCTGGTGAGATTCACGTGAAGACATTGGAAGAAATTCTTCTTGAAAAAGTCTGCCGGCAATGTGGAGACTT
GCAACCTAAACCCAAGAGAGAAGAACCTTCAGGAGCCGACAATTCTCCATCAGGAACAAAAACTTCCTCAGTGTGGATCA
AAACCTTCTCTGAGGTCCTGGCTGAAAAGAGACATCGGCAGCAGGAAATGGAAAGACAGAAGTCCAAAAACGATACAAAT
TGCCGGGTGCTAACAGAAGACACTGAACTGAAAAAGATTGTGAGTCTTCGGACTGTTGCTGTTGGCAATGGACAACCGGA
GGAGCCTGCAGGAAGAGCCAGGTCTATGCAGGAGGTGCATATTAAGACGCTAGAGGAAATTAAACTGGAGAAGGCCCTGA
GGGTGCAGCAAAGCTCTAAGAGTAGTGGCAACTCCCGACCTCAAGCTGAGGCTGTCCCGGTGGCAAAGAGGCTGTTCCGC
ATCAACAGGAGAGCAGTTACAAAAGAAGAGAAAAAACTTGAAGACAGTGGTAATGCTTCTCAGAGCAGTGTGATGAAGAT
GGAGGCTAGTGAGACTTCAGAAAAGAGCATAAGTGATCCCACAAAACTTCCAGTCAACAAATGTGACACTGTCAACGAGA
AACACACACCGAGACAGCAGGAGAGAGGAGTGTCACAAAAGGAGAAAGCAACCTTGTCATCTGTGCGTGGAGAT

Alignment

ORF - retro_mmus_564 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.68 %
• Parental protein coverage: 71.46 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MPNQGEDCYFYFYSTCAKGDSCPFRHCEAALGNETVCTLWQEGRCFRQVCRFRHMEIDKKRSEIPCYWEN
          MP.QGEDCYFYFYSTC..GD.CPFRHCEAALGNETVCTLWQEGRCFRQVCRFRHMEI.KKRSEIPCYWEN
Retrocopy MPDQGEDCYFYFYSTCTRGDNCPFRHCEAALGNETVCTLWQEGRCFRQVCRFRHMEIAKKRSEIPCYWEN

Parental  QPVGCQKLNCAFHHTRSRYVDGLFLPPSKTVLPTVPESQEEEVKTSQLTVQQSKLSVQSNPSPQLRSVMK
          QP.GC.KLNCAFHH.RSRYVDGLFLPPSKT.LPTVPESQ.EE.K.SQL.VQQ.KLS.Q.NPSPQLRSVMK
Retrocopy QPMGCRKLNCAFHHNRSRYVDGLFLPPSKTMLPTVPESQ-EEIKASQLRVQQDKLSIQYNPSPQLRSVMK

Parental  VESSENVPSPTHPPVVINAADDDEDDDDQFSEEGDESKTPALQPSPDVHNGLRVASARKPGVSLKQGECL
          VESS..V..PTHP.VVIN...D..DD.DQ.SEE.DESKTPAL.P.P.VH.G..VASA.KPGVSLKQGECL
Retrocopy VESSNKVLIPTHPRVVINITAD--DDNDQSSEEEDESKTPALKPTPEVHDGFPVASACKPGVSLKQGECL

Parental  NFGIKTLEEIKSKKMKEKSKKQGEGSSGVSSVLQQPQPNPGPEKENVRTVVRMVTLSSKPEEPLVRLSLS
          .FGI.TLEE.K..KMKEK..KQG..SSG.S.V....QPNPGPEKENV.TVV..VT.SSK.EE.LVRLSLS
Retrocopy DFGIRTLEEMKATKMKEKFMKQGD-SSGESPV-GDSQPNPGPEKENVGTVVGTVTPSSKQEESLVRLSLS

Parental  ERLGKRKLSVGGDSDPPLKRSLAQRLGKKVESPETNIDKAPKKERGHKAGEIHVKTLEEILLERASQKRG
          ERLGKRKLSVGGDS.PPLKR.LAQRLGKKVE.PE.NIDKAPKK.R.H.AGEIHVKTLEEILLE......G
Retrocopy ERLGKRKLSVGGDSEPPLKRRLAQRLGKKVEAPEANIDKAPKKKRVHNAGEIHVKTLEEILLEKVCRQCG

Parental  ELQTKLKAEEPSGADDSPSGTKSSSSVRIKTFSEVLAEKKHRQQEMERQKSKKDTSCLTLTDDTEMKKTV
          .LQ.K.K.EEPSGAD.SPSGTK..SSV.IKTFSEVLAEK.HRQQEMERQKSK.DT.C..LT.DTE.KK.V
Retrocopy DLQPKPKREEPSGADNSPSGTK-TSSVWIKTFSEVLAEKRHRQQEMERQKSKNDTNCRVLTEDTELKKIV

Parental  SLPTVAVSKGQPEEPAGRARSMQEVHIKTLEEIKLEKALRVQQSSESSGNSRPQAEAAPGTKRLLRITKR
          SL.TVAV..GQPEEPAGRARSMQEVHIKTLEEIKLEKALRVQQSS.SSGNSRPQAEA.P..KRL.RI..R
Retrocopy SLRTVAVGNGQPEEPAGRARSMQEVHIKTLEEIKLEKALRVQQSSKSSGNSRPQAEAVPVAKRLFRINRR

Parental  AGVKEEKKCGLEDSGDPPQSSVTKMEANETSDETISDPTKLAVNRCDTVKEKHTQRLQERGASQKEKAAL
          A..KEEKK..LEDSG...QSSV.KMEA.ETS...ISDPTKL.VN.CDTV.EKHT.R.QERG.SQKEKA.L
Retrocopy AVTKEEKK--LEDSGNASQSSVMKMEASETSEKSISDPTKLPVNKCDTVNEKHTPRQQERGVSQKEKATL

Parental  SSVRGD
          SSVRGD
Retrocopy SSVRGD

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	0.02 RPM	0.02 RPM
SRP007412_cerebellum	0.17 RPM	0.04 RPM
SRP007412_heart	0.03 RPM	0.00 RPM
SRP007412_kidney	0.10 RPM	0.02 RPM
SRP007412_liver	0.11 RPM	0.03 RPM
SRP007412_testis	0.05 RPM	0.09 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_564 was not detected

EST

No EST(s) were mapped for retro_mmus_564 retrocopy.

TSS

No TSS is located nearby retro_mmus_564 retrocopy 5' end.

Lab

retro_mmus_564 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_564 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000058673	2 retrocopies	retro_hsap_3481, retro_hsap_508,
Monodelphis domestica	ENSMODG00000001184	1 retrocopy	retro_mdom_1449,
Mus musculus	ENSMUSG00000026464	2 retrocopies	retro_mmus_3323, retro_mmus_564 ,
Otolemur garnettii	ENSOGAG00000000243	1 retrocopy	retro_ogar_3250,
Pan troglodytes	ENSPTRG00000001876	5 retrocopies	retro_ptro_2980, retro_ptro_2981, retro_ptro_2991, retro_ptro_380, retro_ptro_382,
Rattus norvegicus	ENSRNOG00000002993	3 retrocopies	retro_rnor_1570, retro_rnor_1673, retro_rnor_602,