RetrogeneDB ID: retro_mmul_1142

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 15:38959993..38961180(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.13406
• Ensembl ID: ENSMMUG00000021285
• Aliases: None
• Description: armadillo repeat-containing protein 8 [Source:RefSeq peptide;Acc:NP_001247943]

Sequence

>retro_mmul_1142
GTATTAAGGACATTGCCTTATTTGGTTTAAATGTGCAGTAAGAAGAGACTACTAGAGGAGAGAGTTAAAGGAGCTGAGAC
ACTTGCCTATCTGATTGAACCAGATATTGAGGTACAGAGAATCGCTAGCATAACTGATCACCTCATTGCCATGTTTGCTG
ACTATTCCAAGTATCCCAACTCGTTGAGTGCCATCACTGATATTAAAAGGCTTGATCATGATTTAAAACATGCTCATGAA
CTCTGCCAGGCTGCATTCAATCTCTACAACTCTCATGGAGCAAATGATGAAGACATTCAGAAGAAAAGTCTTGAGACTGA
AAATATGATGGACTGAACTGTGACTGGCTTGTCTGAGTCTAGTGTCAAGGTGCAGTTACCTGCTGTCAGATGTATGCACC
ATTTATCGAGATCTATGCAGCAGCTTCAAAACAGTTTCTAGGATCACGTTCTGTAAAAACCTTTAATGAAGGTTTTACAA
AACGTACCAGATGAAATCCTAGTAGTAGCATCTTCCATGGTATGTAATCTTCTTGAATTATCTCCAAGGAAAGAGTCAAT
TTTAAAATCAGAAGTTGTAAAGCTACTTTGTGGATTAACCCAGAGTGAAAATCCTGCTTTGTGAGTGAGCAGAATTTGGG
CTTTAATGAATATGGCATTTCAGGCTGAACAAAAAATAAAAGCAGACATGTTACAAACCTTGAGTACTGAACAGCTATTC
TGGTTATTATCAGATTCAGATTTTAATGTGCTGATGAAGACATTGGGACTTCTTAGAAATCTCCTCTTGACCTGGCCTCA
TATAATAAAATAATGAGTACTCATGGAAAGCAAATTATGCAAGCTGTCATCCTTATTTTAGAAGGGGAACCTAACTTTAA
GATCAAAGAGTAGATATTGTGCATCTTAGCCAACATAGAACATGAGACAACAGCAAAATAATCTATTATGACCAATGATG
ATATCCTTCAGAAAATCAAATATTACATGGACCATTCACATGTCAAACTGCAGCTTCCAGTGATGTTTTGTATATCAAAC
CTCTTATGGAATGAAGAGGAAGGTTCACAAGAATGCCAGGATAAATTATGAGACATGGGCATCATAGATATTCTACACAA
ACTGAGTCGGCCACCAGATTCAGACCTTTGTGACAAGGCAAAAATGGCCCTGCAGCAGTACCTAGCA

Alignment

ORF - retro_mmul_1142 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.16 %
• Parental protein coverage: 60.33 %
• Number of stop codons detected: 8
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VLKTLPCLVRMCSKERLLEERVEGAETLAYLIEPDVELQRIASITDHLIAMLADYFKYPSSVSAITDIKR
          VL.TLP.LV.MCSK.RLLEERV.GAETLAYLIEPD.E.QRIASITDHLIAM.ADY.KYP.S.SAITDIKR
Retrocopy VLRTLPYLV*MCSKKRLLEERVKGAETLAYLIEPDIEVQRIASITDHLIAMFADYSKYPNSLSAITDIKR

Parental  LDHDLKHAHELRQAAFKLYASLGANDEDIRKKIIETENMMDRIVTGLSESSVKVRLAAVRCLHSLSRSVQ
          LDHDLKHAHEL.QAAF.LY.S.GANDEDI.KK..ETENMMD..VTGLSESSVKV.L.AVRC.H.LSRS.Q
Retrocopy LDHDLKHAHELCQAAFNLYNSHGANDEDIQKKSLETENMMD*TVTGLSESSVKVQLPAVRCMHHLSRSMQ

Parental  QLRTSFQDHAVWKPLMKVLQNAPDEILVVASSMLCNLLLEFSPSKEPILESGAVELLCGLTQSENPALRV
          QL..SF.DH...KPLMKVLQN.PDEILVVASSM.CN.LLE.SP.KE.IL.S..V.LLCGLTQSENPAL.V
Retrocopy QLQNSF*DHVL*KPLMKVLQNVPDEILVVASSMVCN-LLELSPRKESILKSEVVKLLCGLTQSENPAL*V

Parental  NGIWALMNMAFQAEQKIKADILRSLSTEQLFRLLSDSDLNVLMKTLGLLRNLLSTRPHI-DKIMSTHGKQ
          ..IWALMNMAFQAEQKIKAD.L..LSTEQLF.LLSDSD.NVLMKTLGLLRNLL.T.PHI..KIMSTHGKQ
Retrocopy SRIWALMNMAFQAEQKIKADMLQTLSTEQLFWLLSDSDFNVLMKTLGLLRNLLLTWPHI<NKIMSTHGKQ

Parental  IMQAVTLILEGEHNIEVKEQTLCILANIADGTTAKDLIMTNDDILQKIKYYMGHSHVKLQLAAMFCISNL
          IMQAV.LILEGE.N...KE..LCILANI...TTAK..IMTNDDILQKIKYYM.HSHVKLQL..MFCISNL
Retrocopy IMQAVILILEGEPNFKIKE*ILCILANIEHETTAK*SIMTNDDILQKIKYYMDHSHVKLQLPVMFCISNL

Parental  IWNEEEGSQERQDKLRDMGIVDILHKLSQSPDSNLCDKAKMALQQYLA
          .WNEEEGSQE.QDKL.DMGI.DILHKLS..PDS.LCDKAKMALQQYLA
Retrocopy LWNEEEGSQECQDKL*DMGIIDILHKLSRPPDSDLCDKAKMALQQYLA

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	0.34 RPM	49.08 RPM
SRP007412_brain_prefrontal_cortex	0.08 RPM	35.94 RPM
SRP007412_cerebellum	0.00 RPM	60.64 RPM
SRP007412_heart	0.00 RPM	14.31 RPM
SRP007412_kidney	0.12 RPM	22.65 RPM
SRP007412_liver	0.00 RPM	10.17 RPM
SRP007412_testis	0.11 RPM	29.25 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1142 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1142 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1142 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000114098	1 retrocopy	retro_hsap_4253,
Gorilla gorilla	ENSGGOG00000023535	1 retrocopy	retro_ggor_2851,
Macaca mulatta	ENSMMUG00000021285	1 retrocopy	retro_mmul_1142 ,
Pongo abelii	ENSPPYG00000014140	2 retrocopies	retro_pabe_3384, retro_pabe_3385,