RetrogeneDB ID: retro_mmus_2860

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 6:97729262..97730018(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Akr1b7
• Ensembl ID: ENSMUSG00000052131
• Aliases: Akr1b7, AR, Avdp, MVDP
• Description: aldo-keto reductase family 1, member B7 [Source:MGI Symbol;Acc:MGI:101918]

Sequence

>retro_mmus_2860
ATGGCCACCTCTGTGGAGCTCAGTACCAGAGCTACAATGATCATATAGGCCTGGACACCTGGACTTTTTCCCTAGGCAAA
ATTGAAGAAGCTGAGAAGGTGACCATTGATGCTGGATAGCACCACATTGACTATGCCCATGTGTATCGGAATGAGAAAGA
GATGGGAGAAGCCATTCAAGAGAAGATCCAGGAGAAAGCTATGAAGCAAGAGGACCTCTTCAGTGTCTGCAAGCTATGCT
CCACATGCTTTGAGAGAAAGTTAATGAAGGAAGCCTTTTGGAAGCCTCATGAATCCCAGACTGGACTATCTGGACTTTTG
GCTTATTCACTGGCCACAGGGACATTAGCAGGGAAAGTGTTAGTCCCCAAAGACAATAAAGGCAATGCTTTCACCATTCA
AACAACATTCTTGGATGCCTAGGAGGTCATGAAAGCCTTGATGAATGAAGAGGTAGAGGCAACCCTGAGTGTCTGCAAAC
ACTTCTGGATTGAGAGGTGGTTGAGGAAGCCAGGACTGAAATATAAAGCAGTGGCTAGTCAAGTCAAGTGCCACCCATAC
TCTACCCAGGACAAACTGATCCAAGACTGTTGCTCTCAGGATATCAGCATCATGGTCTACAGCCTTCCTGAACTCTCTGA
ATAGTCCTTGAGCCAACCCAGAAGAGTCTTTGCTATTACAGGATCTCAAGGTTACATAGATTACTGCAAAGTACAAGAAA
ACCTCAGATTGGGCTCTGACTCAGTTTAATATCCAG

Alignment

ORF - retro_mmus_2860 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 50.58 %
• Parental protein coverage: 80.7 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MATFVELSTKAKMPL-VGLGTWKSSPGQVKEAVKAAIDAGYRHIDCAYVYHNENEVGEAIQEKIKENAVK
          MAT.VELST.A.M....GL.TW..S.G...EA.K..IDAG..HID.A.VY.NE.E.GEAIQEKI.E.A.K
Retrocopy MATSVELSTRATMII<IGLDTWTFSLGKIEEAEKVTIDAG*HHIDYAHVYRNEKEMGEAIQEKIQEKAMK

Parental  REDLFIVSKLWATFFEKSLVK-KAFQNTLSDLKLDYLDLYLVHWPQGF-QAGNALLPKDNKGKVLLSKST
          .EDLF.V.KL..T.FE..L.K.K.F...L....LDYLD..L.HWPQG...AG..L.PKDNKG.......T
Retrocopy QEDLFSVCKLCSTCFERKLMK>KPF-GSLMNPRLDYLDFWLIHWPQGH<LAGKVLVPKDNKGNAFTIQTT

Parental  FLDAWEAMEELVDQGLVKALGISNFNHFQIERLLNKPGLKHKPVTNQIESHPYLTQEKLIQYCQSKGIAV
          FLDA.E.M..L........L......HF.IER.L.KPGLK.K.V..Q...HPY.TQ.KLIQ.C.S..I..
Retrocopy FLDA*EVMKALMNEEVEATLSVC--KHFWIERWLRKPGLKYKAVASQVKCHPYSTQDKLIQDCCSQDISI

Parental  TAYSP-LGSPDRPYAKPEDPVVMEIPKIKEIAAKHKKTVAQVLIRFHVQ
          ..YS..L.S...P.A.PE........K...I.AK.KKT....L..F..Q
Retrocopy MVYSL>LNSLNSP*ANPEESLLLQDLKVT*ITAKYKKTSDWALTQFNIQ

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	0.17 RPM
SRP007412_heart	0.00 RPM	0.03 RPM
SRP007412_kidney	0.00 RPM	6.26 RPM
SRP007412_liver	0.00 RPM	1.45 RPM
SRP007412_testis	0.00 RPM	0.37 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_2860 was not detected

EST

No EST(s) were mapped for retro_mmus_2860 retrocopy.

TSS

No TSS is located nearby retro_mmus_2860 retrocopy 5' end.

Lab

retro_mmus_2860 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2860 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000166	1 retrocopy	retro_chof_400,
Callithrix jacchus	ENSCJAG00000012250	1 retrocopy	retro_cjac_3038,
Erinaceus europaeus	ENSEEUG00000004422	1 retrocopy	retro_eeur_681,
Echinops telfairi	ENSETEG00000006005	3 retrocopies	retro_etel_1055, retro_etel_1643, retro_etel_748,
Homo sapiens	ENSG00000198074	1 retrocopy	retro_hsap_581,
Macaca mulatta	ENSMMUG00000013098	2 retrocopies	retro_mmul_1357, retro_mmul_2455,
Mus musculus	ENSMUSG00000001642	10 retrocopies	retro_mmus_1252, retro_mmus_2082, retro_mmus_2678, retro_mmus_3242, retro_mmus_3488, retro_mmus_444, retro_mmus_534, retro_mmus_764, retro_mmus_784, retro_mmus_920,
Mus musculus	ENSMUSG00000029762	1 retrocopy	retro_mmus_627,
Mus musculus	ENSMUSG00000052131	1 retrocopy	retro_mmus_2860 ,
Mus musculus	ENSMUSG00000061758	1 retrocopy	retro_mmus_1490,
Nomascus leucogenys	ENSNLEG00000013088	1 retrocopy	retro_nleu_801,
Pongo abelii	ENSPPYG00000018018	1 retrocopy	retro_pabe_606,
Pan troglodytes	ENSPTRG00000019718	1 retrocopy	retro_ptro_428,
Sorex araneus	ENSSARG00000001396	1 retrocopy	retro_sara_608,