RetrogeneDB ID: retro_mmul_1826

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 4:29100198..29101199(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DDX6
• Ensembl ID: ENSMMUG00000018651
• Aliases: None
• Description: None

Sequence

>retro_mmul_1826
AACCAACCCGATAATAGCACTCAGCAGCAAGCACAGAGTATGACCACCACAGTTAAGCCTGGTGATAACTGGAAAAAGAC
TTTAAAACTCCTTCCAAAGGATCTAAGAACCAAAACATTAGATGTGACCTCCACAAGAGGAAATGAGTTTGAAGATTACT
GTTTGAAACGGGAGTTACTGATGAGAATTTTTGAAATCAGATGGAAAAAGCCATCTCCTTTTCAAGAAGAGAGCATTCCC
ATTGCTTTATCTTGTAGGGATATCTTAGCTAGAGCAAAAAAATGGAACAGGCAAGAGCAGTGCCTATGACATTCCCTTAC
TTGAAAGGCTACACCTGAAGAAGGACACTATACAAACAGTGGTGATTTTTCCCACTGGAGAACCTGCTCTACAGGTCAGT
CAAATTTGCATCCAGGTCAGCAAACACATGGGAGGAGCCAAAGTGATGACAACCACAGGAGGAACCAATTTAGATGATGT
AATGAGGATTCATGATACAGTGCACGTGGTAATTGCTGCCCCTGGGAGAATCCTGAATCTTATCAAGAAAGTAGTAGCAA
AGGTCAATCATGTCCAGGTGATACTATTGGATGAGGCAGATAAGTTCCTGTCATAGGATTTTGTGCAGATAATGGAAGAT
ATTATTCTCGTGCTGCCTGAAGACAGGCAGATTTTACTATATTCTGCTACTTTCCCCCCTAGTATACAGAAGTTTGTGAA
TTCCCATTTTCAGAAATCCTGAGACTAACCTGATGGAAAAACTAACTCTGAAGGACATAACCCAGTATTACACATATGTA
ACTGAACACCGAAAAGCACACAGCCTCAACACACTTTTCTCCAGGCTTCAGCTAAACCAGTCGATCATTTTCTTTAACTG
CTCTCAGCGAGTTGAATGGCAAGCCAAAATTTCTCAACTGGTTTATTTTTGTTTCTACATTCATGCTAAAATGAGGCAGG
AACATCAAAACTGTGTATTTTATTATTTCTGAAATGGTTTA

Alignment

ORF - retro_mmul_1826 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.26 %
• Parental protein coverage: 69.75 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  NTINNGTQQQAQSMTTTIKPGDDWKKTLKLPPKDLRIKTSYSCPSVSGGNWFQDHNTAATLLLQPSKIDI
          N...N.TQQQAQSMTTT.KPGD.WKKTLKL.PKDL...T.........GN.F.D......LL.....I..
Retrocopy NQPDNSTQQQAQSMTTTVKPGDNWKKTLKLLPKDL--RTKTLDVTSTRGNEFEDYCLKRELLMRIFEIRW

Parental  QAIPKVVDEESIPIALSGRDILARAK-NGTGKSGAYLIPLLERLDLKKDNIQAMVIVPTRELALQVSQIC
          ...P....EESIPIALS.RDILARAK.NGTGKS.AY.IPLLERL.LKKD.IQ..VI.PT.E.ALQVSQIC
Retrocopy KK-PSPFQEESIPIALSCRDILARAK>NGTGKSSAYDIPLLERLHLKKDTIQTVVIFPTGEPALQVSQIC

Parental  IQVSKHMGGAKVMATTGGTNLRDDIMRLDDTVHVVIATPGRILDLIKKGVAKVDHVQMIVLDEADKLLSQ
          IQVSKHMGGAKVM.TTGGTNL.DD.MR..DTVHVVIA.PGRIL.LIKK.VAKV.HVQ.I.LDEADK.LS.
Retrocopy IQVSKHMGGAKVMTTTGGTNL-DDVMRIHDTVHVVIAAPGRILNLIKKVVAKVNHVQVILLDEADKFLS*

Parental  DFVQIMEDIILTLPKNRQILLYSATFPLSVQKFMNSHL-QKPYEINLMEELTLKGVTQYYAYVTERQKVH
          DFVQIMEDIIL.LP..RQILLYSATFP.S.QKF.NSH....P.E.NLME.LTLK..TQYY.YVTE..K.H
Retrocopy DFVQIMEDIILVLPEDRQILLYSATFPPSIQKFVNSHF>RNP-ETNLMEKLTLKDITQYYTYVTEHRKAH

Parental  CLNTLFSRLQINQSIIFCNSSQRVELLAKKISQLGYSCFYIHAKMRQEHRNRVFHDFRNGL
          .LNTLFSRLQ.NQSIIF.N.SQRVE..A.KISQL.Y.CFYIHAKMRQEH.N.VF..F.NGL
Retrocopy SLNTLFSRLQLNQSIIFFNCSQRVEWQA-KISQLVYFCFYIHAKMRQEHQNCVFYYF*NGL

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	47.17 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	33.40 RPM
SRP007412_cerebellum	0.06 RPM	56.31 RPM
SRP007412_heart	0.00 RPM	14.54 RPM
SRP007412_kidney	0.00 RPM	23.71 RPM
SRP007412_liver	0.00 RPM	8.15 RPM
SRP007412_testis	0.00 RPM	27.21 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1826 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1826 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1826 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3569
Pan troglodytes	retro_ptro_2424
Pongo abelii	retro_pabe_2941

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000012442	1 retrocopy	retro_cfam_1347,
Callithrix jacchus	ENSCJAG00000013591	3 retrocopies	retro_cjac_1427, retro_cjac_1924, retro_cjac_379,
Gorilla gorilla	ENSGGOG00000016751	1 retrocopy	retro_ggor_955,
Macaca mulatta	ENSMMUG00000018651	2 retrocopies	retro_mmul_1300, retro_mmul_1826 ,
Mus musculus	ENSMUSG00000032097	1 retrocopy	retro_mmus_1896,
Nomascus leucogenys	ENSNLEG00000007372	1 retrocopy	retro_nleu_695,
Otolemur garnettii	ENSOGAG00000007978	1 retrocopy	retro_ogar_2861,
Pongo abelii	ENSPPYG00000003942	2 retrocopies	retro_pabe_1018, retro_pabe_2941,
Pan troglodytes	ENSPTRG00000004353	2 retrocopies	retro_ptro_2424, retro_ptro_838,
Rattus norvegicus	ENSRNOG00000012453	4 retrocopies	retro_rnor_2546, retro_rnor_2613, retro_rnor_900, retro_rnor_901,