RetrogeneDB ID: retro_mmul_1640

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 3:145052978..145053492(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.2042
• Ensembl ID: ENSMMUG00000017596
• Aliases: WBP1L, C10orf26, C9H10orf26
• Description: outcome predictor in acute leukemia 1 precursor [Source:RefSeq peptide;Acc:NP_001181516]

Sequence

>retro_mmul_1640
GATAAGGAAGCCTGCATGGATACCAATAATCAAAGCTACATCTGTGACACAGGACACTGCTGTGGACAGTCTCAGTGCTA
CAACTACTACTAGGAACTCTAGTAGCTCTGGCTGGTGTGGACCATCATCATCATCCTTAGCTGCTGCTGCAATGGCCACC
ACCGCCAAGCCAAGCACCGCCTTCAGGCCCAGCATCGGCAACATGAAATCAACCTGATCCCCTGCCGAGAAGCCTTCAAT
CACTCAGTGCTGCCTTTTTATTTCAGATTTTTGCTAAACTACTTAACTCCTCCTTATGAGGAAGTGGTGAGCCAGCCTCC
AACTCCTCCCCCAGCATACAGTGCCTTCCAGCTATGCAGCAGCAGCAGCTCCTGCCTGCACAGTGCGGCCCGGCAGATGG
CAGTCCCCCGGCGCCAATCCCACCAGGGGATCCAAGGGAATCCCCTTGTCTGAGCCCAGCAGAAGCATCACAAGACCCCC
AAGCATCGCTGATCCTGAGCCCTCTGACCTACCA

Alignment

ORF - retro_mmul_1640 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.66 %
• Parental protein coverage: 52.25 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  DKEACVGTNNQSYICDTGHCCGQSQCCNYYYELWWFWLVWTIIIILSCCCVCHHRRAKHRLQAQQRQHEI
          DKEAC..TNNQSYICDTGHCCGQSQC.NYY.EL...WLVWTIIIILSCCC..HHR.AKHRLQAQ.RQHEI
Retrocopy DKEACMDTNNQSYICDTGHCCGQSQCYNYY*EL**LWLVWTIIIILSCCCNGHHRQAKHRLQAQHRQHEI

Parental  NLIAYREAHNYSALPFYFRFLPNYLLPPYEEVVNRPPTPPPPYSAFQL-QQQ-QLLPPQCGPAGGSP-PG
          NLI..REA.N.S.LPFYFRFL.NYL.PPYEEVV..PPTPPP.YSAFQL..QQ.QLLP.QCGPA.GSP.PG
Retrocopy NLIPCREAFNHSVLPFYFRFLLNYLTPPYEEVVSQPPTPPPAYSAFQL<MQQQQLLPAQCGPADGSP<PG

Parental  VDPTRGSQGAQSSPLSGPSRSSTRPPSIADPEPSDLP
          ..PTRGS.G....PLS.PSRS.TRPPSIADPEPSDLP
Retrocopy ANPTRGSKGI---PLSEPSRSITRPPSIADPEPSDLP

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	4.82 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	9.04 RPM
SRP007412_cerebellum	0.00 RPM	3.10 RPM
SRP007412_heart	0.06 RPM	5.18 RPM
SRP007412_kidney	0.00 RPM	11.97 RPM
SRP007412_liver	0.00 RPM	8.95 RPM
SRP007412_testis	0.04 RPM	3.66 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1640 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1640 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1640 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3774
Pongo abelii	retro_pabe_3084

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000014336	1 retrocopy	retro_btau_855,
Choloepus hoffmanni	ENSCHOG00000007532	1 retrocopy	retro_chof_1174,
Callithrix jacchus	ENSCJAG00000018079	1 retrocopy	retro_cjac_2235,
Homo sapiens	ENSG00000166272	1 retrocopy	retro_hsap_3774,
Macaca mulatta	ENSMMUG00000017596	1 retrocopy	retro_mmul_1640 ,
Pongo abelii	ENSPPYG00000002610	1 retrocopy	retro_pabe_3084,
Tupaia belangeri	ENSTBEG00000005555	1 retrocopy	retro_tbel_3660,
Tursiops truncatus	ENSTTRG00000012618	2 retrocopies	retro_ttru_138, retro_ttru_437,