RetrogeneDB ID: retro_mmus_3684

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: X:106641383..106642734(-)
• Located in intron of: ENSMUSG00000073010

Retrocopy information

• Ensembl ID: ENSMUSG00000083595
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Zfp277
• Ensembl ID: ENSMUSG00000055917
• Aliases: Zfp277, 2410017E24Rik, NIRF4
• Description: zinc finger protein 277 [Source:MGI Symbol;Acc:MGI:1890393]

Sequence

>retro_mmus_3684
GGGCTTCCTGTGGATCCCCAGGAGGCTGGGGTCCGCGGTGGAATCGAGCACAAGTATTATGAAGACAGTAAAGACTATAT
CCTAGAGCCGCTTTCCCTGCCAGAGAGTCCAGGTGGCACCGCCGCTTTAGAGGGGTCTTTACCTGTGCCTTGTATTTTCT
GTGAAGAACATTTTTCCATGGCTGAACAATACAAACGTTTGAAGCCCATGATTATCGAGCATAAGATTGTCATAGCTGAT
GTATAGCTCGTTGCAGGTTTCCGAAGGTACATTTTATACTGGAGGAAATGGTTCACTGAACAGTCCATCACTAATTTTTG
CAGTGTGATAAGAATCAATGCCAAGGTTCCATTTGAAGAACAAGACAACTATTATTTGTTATACGATGCATTACCAGAAT
ATAGAATCCCCAGAGAAGAGCTTCAAACACAGAAACTGAAAGAAGTTCTGGATCAGCAACAGGGAGAGGGAAATGATACA
AGCTTTCATGGCGTGTGCATGTTTTGCAGTGAGGAATTTCGCTGAAACAGATCTGTTCTGTTGAACCACATGGTCAGACA
GCATGCTTTCAACATTGGTTTGCCAGACAACATTGTAAATTGCACTGAATTCCTATGCACATTACAAAAGAAACTGGACA
ATTTACAGTGTTTGTACTGTGAGAAGACCTTCAGAGACAAAAACACCCTTAAAGATCACATGAGAAAAAAAGCAGCATTG
TAGGATCAATCCAAAAAAAAAAAAAGAGAGAGAATATGACTGATTCTATGCCATCAATTACTTGGAACTTGGGAAGTAAT
GGGAAGAGGTGCAGTCAGAAGATGGCCTCAAGCTTCTGGACCTTCAGGAAGATGACTGGTCTGATTGGCAGGAGTACCCA
GTCTCTGCTGTCTGTCTATTTTGTGAAAAGCAAGAGGAAGACGATAGATAAACTGTATGTGCACATGAAGGACACACATG
AGTTTGATCTCCTCAGAATAAAGTCAGAGCTTGGATTAAATTTCTATCAGCAAGTGAAGCTGATCAATTTCATTAGAAGG
CAAGTTCACCAATGCAAGTGCTTCAGTTGCCATGTAAAGTTCAAATCCAAAGCAGATTTAAGGACTCACACGGAAGACAC
TAAACACACTTCACTGCTTCCTGACAGGAGACATGGGATCAACTGGAGTATTATTTCCCCACCTATGAGAATGACACTCT
CCTGTGTACACTGTCTGACAGTGAAAGTGACCTAACAGCTCAAGAGCAAACTTTAAATGTTCCCACCATCAGTGAAGACA
CGTCCAGACTGTGTGCTTTAAAACAGAGCAGTGTCCTCAACCAATTGCTACTCCAGGGATACCTGGAAAAC

Alignment

ORF - retro_mmus_3684 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.28 %
• Parental protein coverage: 98.47 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  GLPVDPREAGVRGVRGGIGHTDHEDSKDCILEPLSLPESPGGTTALEGSPSVPCIFCEEHFPMAEQDKLL
          GLPVDP.EA...GVRGGI.H...EDSKD.ILEPLSLPESPGGT.ALEGS..VPCIFCEEHF.MAEQ.K.L
Retrocopy GLPVDPQEA---GVRGGIEHKYYEDSKDYILEPLSLPESPGGTAALEGSLPVPCIFCEEHFSMAEQYKRL

Parental  KHMIIEHKIVIADVKLVADFRRYILYWRKRFTEQPITDFCSVIRINSTAPFEEQDNYYLLCDALPEDRIL
          K.MIIEHKIVIADV.LVA.FRRYILYWRK.FTEQ.IT.FCSVIRIN...PFEEQDNYYLL.DALPE.RI.
Retrocopy KPMIIEHKIVIADV*LVAGFRRYILYWRKWFTEQSITNFCSVIRINAKVPFEEQDNYYLLYDALPEYRIP

Parental  REELQKHKLKEVLDQQQRERNDTSFHGVCMFCSEEFRGNRSVLLNHMAREHAFNIGLPDNIVNCAEFLCT
          REELQ..KLKEVLDQQQ.E.NDTSFHGVCMFCSEEFR.NRSVLLNHM.R.HAFNIGLPDNIVNC.EFLCT
Retrocopy REELQTQKLKEVLDQQQGEGNDTSFHGVCMFCSEEFR*NRSVLLNHMVRQHAFNIGLPDNIVNCTEFLCT

Parental  LQKKLDNLQCLYCEKTFRDKNTLKDHMRKK-QHRRIN---PKNREYDRFYVINYLELGKSWEEVQSEDDR
          LQKKLDNLQCLYCEKTFRDKNTLKDHMRKK.QH.RIN......REYD.FY.INYLELGK.WEEVQSED..
Retrocopy LQKKLDNLQCLYCEKTFRDKNTLKDHMRKK>QHCRINXXXXXEREYD*FYAINYLELGK*WEEVQSEDGL

Parental  ELLDLQEDDWSDWQEYPVSAVCLFCEKQEE-TIDKLYVHMKDTHEFDLLRIKSELGLNFYQQVKLVNFIR
          .LLDLQEDDWSDWQEYPVSAVCLFCEKQEE.TIDKLYVHMKDTHEFDLLRIKSELGLNFYQQVKL.NFIR
Retrocopy KLLDLQEDDWSDWQEYPVSAVCLFCEKQEE>TIDKLYVHMKDTHEFDLLRIKSELGLNFYQQVKLINFIR

Parental  RQVHQCKCYSCHVKFKSKADLRTHMEDTKHTSLLPDRK-TWDQLEYYFPTYENDTLLCTLSDSESDLTAQ
          RQVHQCKC.SCHVKFKSKADLRTH.EDTKHTSLLPDR..TWDQLEYYFPTYENDTLLCTLSDSESDLTAQ
Retrocopy RQVHQCKCFSCHVKFKSKADLRTHTEDTKHTSLLPDRR<TWDQLEYYFPTYENDTLLCTLSDSESDLTAQ

Parental  EQTENVPVISEDTSRLCALKQSSVLNQLLLQGCLEN
          EQT.NVP.ISEDTSRLCALKQSSVLNQLLLQG.LEN
Retrocopy EQTLNVPTISEDTSRLCALKQSSVLNQLLLQGYLEN

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	15.23 RPM
SRP007412_cerebellum	0.04 RPM	7.95 RPM
SRP007412_heart	0.00 RPM	7.16 RPM
SRP007412_kidney	0.06 RPM	11.67 RPM
SRP007412_liver	0.03 RPM	6.39 RPM
SRP007412_testis	0.05 RPM	4.07 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_3684 was not detected

EST

No EST(s) were mapped for retro_mmus_3684 retrocopy.

TSS

No TSS is located nearby retro_mmus_3684 retrocopy 5' end.

Lab

retro_mmus_3684 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3684 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000016891	2 retrocopies	retro_cjac_558, retro_cjac_698,
Mus musculus	ENSMUSG00000055917	1 retrocopy	retro_mmus_3684 ,
Otolemur garnettii	ENSOGAG00000005326	1 retrocopy	retro_ogar_1774,