RetrogeneDB ID: retro_mmus_1953

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 2:87871315..87872202(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000082056
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Zscan5b
• Ensembl ID: ENSMUSG00000058028
• Aliases: Zscan5b, Zfg1, Zfp371
• Description: zinc finger and SCAN domain containing 5B [Source:MGI Symbol;Acc:MGI:2159640]

Sequence

>retro_mmus_1953
AGCCGGGAGCTACAGAACTTCTCAGAGACTGAAGAGCCATCCACTAACCAGGAAGAGGACATTTTTCTGGGAGTAATTAC
TGAGAGGAGACAGCCAGACTACCTGAGATCAGACCAGAGACTGAGGAGTGACTCAGTTCCTGACTGGGAAGAGGCAGAGG
CTTCTTTGTTTGTTGGTCAGGACCATCCAACACTGGGGCCTGCTGGTTCTCTCAGAGTAAAGGGTGCTGTGCTGTCCGAG
GAAGATACTGTTTTGGATGCTGCACCATCATTATTCACCCATATTCTGGAAAGAGATTTAGCCTTGAATAGGGATCTTCA
GGGTCTTCGTGGTTTCAACTTACTTCCCAAAGAGTGGCGTTTTATATGCACAATACAGAAGATGGGCTAGAGGCTGCTAA
TCTTGAGCCTGCTTACCCATAGCCTGTAGAGCAAGTTGACAGTCTTGCTGGCCAGACTCGGTTTCAGTGTACTGAATGCA
AGAAGAGCTTTCTTTACAGGTCTCACTTTGACCTCCGTCAGAGTTTACACACAGAAGAGAGACCCTTCAAGTGCAACTTG
TGCAGCAAGGCCTTTCTACAGTCCTCTGACCTGAGAGTCTACCAGCATGTCCATACTCGGGAGAAGCCTTACATGTATGC
AGTCTGCGGAATGGAGTTTACCCACAGGTCCACCTTGCAGGGCCACATTCTGGTTCACATGAAGGATAATCCTTATGTGT
GCAAGGATTGTGGGCAACGATTCAGCCACAAGGGCAACCTCATTGTCCATTTCCGCATCCATTGCGACTTGAGACCCTGC
ATCATTAAGAAGTGTAGCATGGCTTTCTGACAGCAGGGAACTTGGAAACAACACATGAAAACCTGCTCAAGAAATATAAA
GGCATCT

Alignment

ORF - retro_mmus_1953 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.92 %
• Parental protein coverage: 63.46 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SRELQNLSETEEPSTSQEEGILLGVIPERRQPDYLRPEMSPGSDSVPDLEEAEASVFVGQDPLPALGPAG
          SRELQN.SETEEPST.QEE.I.LGVI.ERRQPDYLR......SDSVPD.EEAEAS.FVGQD..P.LGPAG
Retrocopy SRELQNFSETEEPSTNQEEDIFLGVITERRQPDYLRSDQRLRSDSVPDWEEAEASLFVGQDH-PTLGPAG

Parental  SLGVKGAVQPQEDTVVDAVPS-FTHILERDLALNRDLQSLSG-FNLPTSQGVASYMGNTEDGLEAANPEP
          SL.VKGAV...EDTV.DA.PS.FTHILERDLALNRDLQ.L.G.F.L.TSQ.VA.YM.NTEDGLEAAN.EP
Retrocopy SLRVKGAVLSEEDTVLDAAPSLFTHILERDLALNRDLQGLRG<FQL-TSQRVAFYMHNTEDGLEAANLEP

Parental  ANPQPEKQVDSLAGQARFQCTECKKSFLYKSRFDLHQRSHTGERPFKCILCNKAFVQSSDLRVHQRVHTG
          A.P.P..QVDSLAGQ.RFQCTECKKSFLY.S.FDL.Q..HT.ERPFKC.LC.KAF.QSSDLRV.Q.VHT.
Retrocopy AYP*PVEQVDSLAGQTRFQCTECKKSFLYRSHFDLRQSLHTEERPFKCNLCSKAFLQSSDLRVYQHVHTR

Parental  EKPYMCEVCGMEFAHGSTLQGHSRVHTKEKPFVCKDCGQRFCHKGNLNVHFRIHCNLRPYVCKKCNKTFR
          EKPYM..VCGMEF.H.STLQGH..VH.K..P.VCKDCGQRF.HKGNL.VHFRIHC.LRP...KKC...F.
Retrocopy EKPYMYAVCGMEFTHRSTLQGHILVHMKDNPYVCKDCGQRFSHKGNLIVHFRIHCDLRPCIIKKCSMAF*

Parental  QQGTWKRHMKTHLRKRKVS
          QQGTWK.HMKT..R..K.S
Retrocopy QQGTWKQHMKTCSRNIKAS

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	0.00 RPM
SRP007412_kidney	0.04 RPM	0.02 RPM
SRP007412_liver	0.00 RPM	0.00 RPM
SRP007412_testis	0.00 RPM	3.38 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1953 was not detected

EST

No EST(s) were mapped for retro_mmus_1953 retrocopy.

TSS

No TSS is located nearby retro_mmus_1953 retrocopy 5' end.

Lab

retro_mmus_1953 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1953 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000047236	1 retrocopy	retro_btau_975,
Myotis lucifugus	ENSMLUG00000012011	1 retrocopy	retro_mluc_30,
Mus musculus	ENSMUSG00000058028	3 retrocopies	retro_mmus_1078, retro_mmus_1953 , retro_mmus_2723,