RetrogeneDB ID: retro_mmus_3646

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: X:78855410..78858281(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000083258
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Zc3h18
• Ensembl ID: ENSMUSG00000017478
• Aliases: Zc3h18, 1190001B23Rik, 5830416A07Rik, Nhn1
• Description: zinc finger CCCH-type containing 18 [Source:MGI Symbol;Acc:MGI:1923264]

Sequence

>retro_mmus_3646
ATGAATGTGGCCGAGAGCCCTGAACTGGATCCTCACTCCCCAGAGGATGAAGAGCAGCCGGCACTCTCAGATGATGACAT
TCTGAGAGAAAGTGGATCTGAACAAGATTTGGATGGAGCTGGGGAAAGGGCTTCTGATTTGGAGGAGGAGGAAAATGCAA
CCAGGGTACAAAGCCAGGAGGAAACTTGCTCGGATGAGAAAGACCGAGCCAGTGAGCCCAAGTCCCAAGATCAGGATTCA
GAGGCTCATGAGCTGAGCAGGGGCCCAGAGGGATCCCCATGCGAGGAGGGGGATGATGTTGAAGAAGATGGGACAAGTGA
CCTCAGGGACGAAGCCTCCTCAGTGACCCGGGAACTGGATGAGCATAAACTAGACTATGATGAGGGGGTCCTTGAGGAGC
CAGCTCCTGCTGCCCAGGAGGAGGAGGCTGAGAAGGCTGGGGCTGAGGAGAAGGAGGAGAAGGGGGAAGGGGCTCCCGGA
GAGGAAGGGAAGCCTGATGTCCAAAGTGTGGGAGAACAAGAACCCACAGAAGCTGCCAAGGAGAAGAAGAAAGAGGATGA
CGACGGGGAGATTGATGATGGCGAGATAGACGATGATGACTTGGAAGAAGGCGAAGTGAAGGACCCCAGTGACCAGAACG
TGAGGCCTCGCCCCACCTGCCGATTCTTCATGAAAGATGTTGTGACACCATTATCCACTCTTCTTCCACCAATACCAAAT
TCCATACCACTCAGAGGCCAGGTTAAAGGAAACTGCACGTGGGGAATGAGCTGTAGGTTTATCCACCCTGGAGTGAATGA
CAAGGGCAACTACTCCCTCATCACCAAAGCGGAACCTTTTCCAACAAACGGTGCCCCGCCTCTTGGACCTCACCCACTGA
TGCCTGCCAACCCTTGGCGTGGGCCAGTGGTTGATGAAATTTTGCCTCCACCCCCTCCAGAGCCCCCAACAGAGAGCGCC
TGGGAACGTGGACTCCGACATGCAAAAGAGGTTTTGAAAAAAGCAACCATTCGGAAAGAACAGGAGCCGGACTTTGAAGA
AAAAAAGTTCACAGTAACCATTGGTGAAGATGACCAGGAGTTTGAGAAGGAGAATGAAGTCTTCCGAGATTGGAATTCTC
GAGTCCCGAGAGATGTCAGAGACACAACACTTGAGCCTTATGCAGACCCTTATTATTACTATGAGATAGAGCAGTTTTGG
CGTGGTGGACAGTACGAGAATTTCAGGGTGCAGTATACAGAAGCAGAGCCATATCATAACTATCGCGAACGAGAGAGGGA
ACGAGAGCGAGAAAACAGACAACTAGAACGCGAGCAGGAACGAGAGCGTGACCGAGAGCGGGAGCGCAGGCAGAGAGAGC
GGGAGCGAAAACAGGAAAGAGAGCGGGACAAGGAGCGGCAGCGGAGGAAAGAGTGGGAAAGAGAGAGAGCCAAGCGAGAC
GAGAAGGACCGGGAGAAGGACAAGGAGAAGCTGAAGTCCCGGTCCCCACAGCCACCAAGCCGTCAAGCTGAACTACCAAA
GAAGAGCACCTCTGTGGGGCCCCAGGTGAAGCGAGCCTATGAGTGGAAGGACCCCTGGCGCCGATCCAAGTCTCCCAAGA
AGAAGCATGGCGTGTCAGTCTCCCCAAGCTGGGCACGAAGACGTCACAAAACCTCCGCCTCCTCAGCCTCTGCTTCCAAT
TCCTCCAGGTCATCTTCACGGTCTTCATCCTACTCTGGCTCGTCCTGGTCCCGGTCCCGATCCTCCTCCTACAGCTCCTA
TTCTAGCCGCTCTTTCAGACACAGCTCCTTCTCAGGCAGCCGATCCAGGTCCCGGTCCTTCTCGTCCCCATCCCCGTCTC
CCACACCTTCCCCACACAGACCTCCAGTCAGAACCAAGGGGGAGCCGACCCCACCTTCCAGCAAAGCAAGGGAGAAGTCA
ATAAAGAAGCCAGCCACTCCCCCAGCCCCATCACAGGCCACCAAAAGTACTGCTCCTGGTCCTGAGCCTGCCAAACCTGG
AGATCTCCAAGAAGCCAGGAGAAAGGAGAGGCAAACCAGGACTCCCCCAAGGAGGAGGACGCCCAGCAGCAGTGGTAGCG
GCAGTGGTAGCAGCTACAGTGGCTCCAGTTCCAGATCCAGGTCTCTGAGTGTGAGTAGCCTTTCCTCAGTGTCCAGCGCC
ACCTCGAGTAGCAGCTCAGTGCACAGTGTGGACTCAGATGACATGTATGCAGACCTGGCCAGTCCTGTGTCCTCAGCCAG
CTCTCGATCCCCAACTCCTGCCCAGACCAAGAAGGAGAGAGGGAAATCCAAGAAAGAAGACGGAGTGAGAGAGGAAAAGC
GGAAGCGGGATCCATCCACGCAGCCACCCAAGTCCTCTAAAGCTCCAGCAGGTGGGAAGGCCTCCCAGCAGGCAGCGGCA
CCTCAGCCGGCGGCCCCCGGACAGCCCCAACAGGGCTCCTTTGTTGCCCACAAGGAGATAAAGCTGACACTGCTGAACAA
GGCGGCTGATAAAGGAAGCCGGAAGCGCTATGAGCCATCAGACAAGGACCACCGGCAGAGCCCTCCTGCTAAGAAGGCCA
ACTTGTCCCCAGACCGAGGTTCTGGAGACCGGAAATCAGGTGGAAGAATGGGCTCCCCAAAACCAGAGATGCAGAGAGGC
CAGAACGCTAAAGCTCCTGCTGCCCCAGCGGACAGGAAGCGTCCACTGTCACCCCAGTCTAAGGGCTCCAGCAAGGTCAC
CATCGTGCCTGGCAAAGCCACAGATACTGCCACAGCAGGCACCAAGTCAGGGAAGGCCAGCACATTGTCACGGCGAGAGG
AGCTCCTTAAACAGCTCAAGAAGGTTGAGGAAGCCATCGCTCGCAAGCGGGCCAAGATCCCCGGGAAAATG

Alignment

ORF - retro_mmus_3646 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.41 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MDVAESPELDPHSPEDEEQPALSDDDILRESGSEQDLDGAGERASDLEEEENATRVQSQEETRSDEEDRA
          M.VAESPELDPHSPEDEEQPALSDDDILRESGSEQDLDGAGERASDLEEEENATRVQSQEET.SDE.DRA
Retrocopy MNVAESPELDPHSPEDEEQPALSDDDILRESGSEQDLDGAGERASDLEEEENATRVQSQEETCSDEKDRA

Parental  SEPKSQDQDSEAHELSRGPAGSPCEEGDDVEEDGTSDLRDEASSVTRELDEHELDYDEEVPEEPAPAAQE
          SEPKSQDQDSEAHELSRGP.GSPCEEGDDVEEDGTSDLRDEASSVTRELDEH.LDYDE.V.EEPAPAA..
Retrocopy SEPKSQDQDSEAHELSRGPEGSPCEEGDDVEEDGTSDLRDEASSVTRELDEHKLDYDEGVLEEPAPAAXX

Parental  EEAEKAGAEEEEEKGEGAPGEEGKPDVQSVGEQEPTEAAKEKKKEDDDGEIDDGEIDDDDLEEGEVKDPS
          ................GAPGEEGKPDVQSVGEQEPTEAAKEKKKEDDDGEIDDGEIDDDDLEEGEVKDPS
Retrocopy XXXXXXXXXXXXXXXXGAPGEEGKPDVQSVGEQEPTEAAKEKKKEDDDGEIDDGEIDDDDLEEGEVKDPS

Parental  DRKVRPRPTCRFFMKDVVTPLSTLLPPIPNSIPLRGQVKGNCTWGMSCRFIHPGVNDKGNYSLITKAEPF
          D..VRPRPTCRFFMKDVVTPLSTLLPPIPNSIPLRGQVKGNCTWGMSCRFIHPGVNDKGNYSLITKAEPF
Retrocopy DQNVRPRPTCRFFMKDVVTPLSTLLPPIPNSIPLRGQVKGNCTWGMSCRFIHPGVNDKGNYSLITKAEPF

Parental  PPNGAPPLGPHPLMPANPWGGPVVDEILPPPPPEPPTESAWERGLRHAKEVLKKATIRKEQEPDFEEKRF
          P.NGAPPLGPHPLMPANPW.GPVVDEILPPPPPEPPTESAWERGLRHAKEVLKKATIRKEQEPDFEEK.F
Retrocopy PTNGAPPLGPHPLMPANPWRGPVVDEILPPPPPEPPTESAWERGLRHAKEVLKKATIRKEQEPDFEEKKF

Parental  TVTIGEDDREFDKENEVFRDWNSRVPRDVRDTTLEPYADPYYDYEIERFWRGGQYENFRVQYTEAEPYHN
          TVTIGEDD.EF.KENEVFRDWNSRVPRDVRDTTLEPYADPYY.YEIE.FWRGGQYENFRVQYTEAEPYHN
Retrocopy TVTIGEDDQEFEKENEVFRDWNSRVPRDVRDTTLEPYADPYYYYEIEQFWRGGQYENFRVQYTEAEPYHN

Parental  YRERERERERENRQRERERERERDRERERRQRERERERERERDKERQRRKEEWERERAKRD----EKDRQ
          YRERERERERENRQ.ERE.ERERDRERERRQRERER..ERERDKERQRRKE.WERERAKRD....EKD..
Retrocopy YRERERERERENRQLEREQERERDRERERRQRERERKQERERDKERQRRKE-WERERAKRDEKDREKDKE

Parental  HRDRDRDKDREKDKEKPKPRSPQPPS--RQAEPPKKESTSVGPQVKRADEWKDPWRRSKSPKKKLGVSVS
          ..............E.PK......P...R..E.......S..P..K........W.R..........S.S
Retrocopy KLKSRSPQPPSRQAELPKKSTSVGPQVKRAYEWKDPWRRSKSPKKKHGVSVSPSWARRRHKTSASSASAS

Parental  PSRARRRRKTSASSASASNSSRSSSRS-SSYSGSGSSRSRSRSSSYSSYSSRSSRHSSFSGSRSRSRSFS
          .S.....R..S.S..S.S.S..SS..S.SS.S...SS.S.SRS.S.S..S...S...S......R.....
Retrocopy NSSRSSSRSSSYSGSSWSRSRSSSYSSYSSRSFRHSSFSGSRSRSRSFSSPSPSPTPSPHRPPVRTKGEP

Parental  SSPSPSPTPSPHRPPVRTKGEPAPPPGKAGEKSIKKPAPPPAPPQATKTTAPGPEPAKPGDLREARRKER
          ..PS..........P.............A......KP............T...P....P...........
Retrocopy TPPSSKAREKSIKKPATPPAPSQATKSTAPGPEPAKPGDLQEARRKERQTRTPPRRRTPSSSGSGSGSSY

Parental  QTRTPPRRSLSVSSVSSVSSATSSSSSVHSVDSDDMYADLASPVSSASSRSPTPAQTKKERGKSKKEDGV
          .......RSLSVSS.SSVSSATSSSSSVHSVDSDDMYADLASPVSSASSRSPTPAQTKKERGKSKKEDGV
Retrocopy SGSSSRSRSLSVSSLSSVSSATSSSSSVHSVDSDDMYADLASPVSSASSRSPTPAQTKKERGKSKKEDGV

Parental  REEKRRRDPSAQPPKSSKAPAGGKASQQAAAPQPAVPGQPQQGSFVAHKEIKLTLLNKAADKGSRKRYEP
          REEKR.RDPS.QPPKSSKAPAGGKASQQAAAPQPA.PGQPQQGSFVAHKEIKLTLLNKAADKGSRKRYEP
Retrocopy REEKRKRDPSTQPPKSSKAPAGGKASQQAAAPQPAAPGQPQQGSFVAHKEIKLTLLNKAADKGSRKRYEP

Parental  SDKD-RQSPPAKKANLSPDRGSRDRKSGGRMGSPKPERQRGQNAKAPAAPADRKRPLSPQSKGSSKVTSV
          SDKD.RQSPPAKKANLSPDRGS.DRKSGGRMGSPKPE.QRGQNAKAPAAPADRKRPLSPQSKGSSKVT.V
Retrocopy SDKDHRQSPPAKKANLSPDRGSGDRKSGGRMGSPKPEMQRGQNAKAPAAPADRKRPLSPQSKGSSKVTIV

Parental  PGKATDTATAGTKSGKASTLSRREELLKQLKAVEDAIARKRAKIPGKV
          PGKATDTATAGTKSGKASTLSRREELLKQLK.VE.AIARKRAKIPGK.
Retrocopy PGKATDTATAGTKSGKASTLSRREELLKQLKKVEEAIARKRAKIPGKM

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	0.05 RPM	39.09 RPM
SRP007412_cerebellum	0.09 RPM	66.74 RPM
SRP007412_heart	0.00 RPM	42.24 RPM
SRP007412_kidney	0.10 RPM	75.71 RPM
SRP007412_liver	0.03 RPM	64.72 RPM
SRP007412_testis	0.05 RPM	86.22 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_3646 was not detected

EST

No EST(s) were mapped for retro_mmus_3646 retrocopy.

TSS

No TSS is located nearby retro_mmus_3646 retrocopy 5' end.

Lab

retro_mmus_3646 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3646 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Mus musculus	ENSMUSG00000017478	1 retrocopy	retro_mmus_3646 ,