RetrogeneDB ID: retro_mmus_794

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 11:58688307..58689102(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000082495
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Strap
• Ensembl ID: ENSMUSG00000030224
• Aliases: Strap, AW557906, C78091, C79202, Unrip
• Description: serine/threonine kinase receptor associated protein [Source:MGI Symbol;Acc:MGI:1329037]

Sequence

>retro_mmus_794
GTGGCCATGAGGCAGACTCTGCTCACTTGCTCAGGCCGCATGCCGGCTGTGGTGGATTTGTCCTTCAGCAGCATCCCGCC
TAAAGGCTGCTTTCTGATCAGTGCTTGCAAAGATGGCCAACCTATGCTCCACCAGGGAGATACAGGAGACTAGATTGGAA
CATTTTTTGGGTCATAAAGGTGCTGTTTGGGGTACAACATTGACTAATAAAGATGCCACCAAAACTGCTACAGCAGCTGC
AGACATCACAGTGTGTGATGCTGTCTCAGGAGATGAATGGATGACCCTGGCTCATCAGCACATTGTCAAGACTGTGAAGT
TCACACAGGATAGCAGTTACCTGCTGACTGGGCACAGGATAAACTGTTGCACATACACGACTTGAAAAACCTGAAGCAGA
ACCTAAGGAAATTAATGCTCACACTTCCGGTATTAAAAAGGCTCTGTGGTGCAGTGAAGATAAATAGTTCCTTTCAGCTG
ATGATAAAACTGTTTGGCTCTGGCATCATACCACAGTGACAGAAGTGAAATCTTAAAATGTAATATGTCTTTAGCAGCAC
AAAATATATTCCTGAGGGAGAGATCTTGGTTATTGCTTTTCAATGTGCAGTAATTATTAATTGTCCGGAGCCAATTAAAT
CCTTTGAAGCTCCTGCGACCATCAATTCTGCATCTCTTCATCCAGAGAAGGAACTTTTTTGTTGCAGGTGGAGAAGCTTT
AAACTGTATAAGTACTTCTATAATGGTGGAGAAGAATTAGAATCCTACAAAGGTCACATTGGTCTCATTCAGTGT

Alignment

ORF - retro_mmus_794 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.46 %
• Parental protein coverage: 77.14 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  MAMRQTPLTCSGHTRPVVDLAFSGITPYGYFLISACKDGKPMLRQGDTGDWIGTF-LGHKGAVWGATL-N
          .AMRQT.LTCSG....VVDL.FS.I.P.G.FLISACKDG.PML.QGDTGD.IGTF.LGHKGAVWG.TL.N
Retrocopy VAMRQTLLTCSGRMPAVVDLSFSSIPPKGCFLISACKDGQPMLHQGDTGD*IGTF>LGHKGAVWGTTLTN

Parental  KDATKAATAAADFTAKVWDAVSGDELMTLAHKHIVKTVDFTQDSNYLLTG-GQDKLLRIYDLN-KPEAEP
          KDATK.ATAAAD.T..V.DAVSGDE.MTLAH.HIVKTV.FTQDS.YLLTG..QDKLL.I.DL..KPEAEP
Retrocopy KDATKTATAAADIT--VCDAVSGDEWMTLAHQHIVKTVKFTQDSSYLLTG<AQDKLLHIHDLK<KPEAEP

Parental  KEISGHTSGIKKALWCSDDKQILSADDKTVRLWDHATMTEVKS-LNFNMSV-SSMEYIPEGEILVITYGR
          KEI..HTSGIKKALWCS.DK..LSADDKTV.LW.H.T.TEVKS.L..NMS..SS..YIPEGEILVI....
Retrocopy KEINAHTSGIKKALWCSEDK*FLSADDKTVWLWHHTTVTEVKS<LKCNMSL<SSTKYIPEGEILVIAFQC

Parental  SIAFHSAVSLEPIKSFEAPATINSASLHPEKE-FLVAGGE-DFKLYKYDYNSGEELESYKGHFGPIHC
          ..........EPIKSFEAPATINSASLHPEKE.F.VAGGE..FKLYKY.YN.GEELESYKGH.G.I.C
Retrocopy AVIINCP---EPIKSFEAPATINSASLHPEKE>FFVAGGE<SFKLYKYFYNGGEELESYKGHIGLIQC

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	84.08 RPM
SRP007412_cerebellum	0.00 RPM	76.46 RPM
SRP007412_heart	0.00 RPM	73.59 RPM
SRP007412_kidney	0.00 RPM	78.44 RPM
SRP007412_liver	0.00 RPM	72.26 RPM
SRP007412_testis	0.00 RPM	132.96 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_794 was not detected

EST

No EST(s) were mapped for retro_mmus_794 retrocopy.

TSS

No TSS is located nearby retro_mmus_794 retrocopy 5' end.

Lab

retro_mmus_794 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_794 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000007422	2 retrocopies	retro_chof_1098, retro_chof_1620,
Callithrix jacchus	ENSCJAG00000021593	1 retrocopy	retro_cjac_2503,
Homo sapiens	ENSG00000023734	2 retrocopies	retro_hsap_2092, retro_hsap_3723,
Gorilla gorilla	ENSGGOG00000009939	1 retrocopy	retro_ggor_1633,
Macaca mulatta	ENSMMUG00000013307	2 retrocopies	retro_mmul_1695, retro_mmul_985,
Mus musculus	ENSMUSG00000028798	2 retrocopies	retro_mmus_1375, retro_mmus_607,
Mus musculus	ENSMUSG00000030224	1 retrocopy	retro_mmus_794 ,
Nomascus leucogenys	ENSNLEG00000004160	2 retrocopies	retro_nleu_1301, retro_nleu_1970,
Ochotona princeps	ENSOPRG00000015211	3 retrocopies	retro_opri_1029, retro_opri_217, retro_opri_541,
Pongo abelii	ENSPPYG00000004334	3 retrocopies	retro_pabe_2005, retro_pabe_3134, retro_pabe_3212,
Pan troglodytes	ENSPTRG00000004734	2 retrocopies	retro_ptro_1538, retro_ptro_2616,
Tursiops truncatus	ENSTTRG00000003466	2 retrocopies	retro_ttru_581, retro_ttru_974,