RetrogeneDB ID: retro_mmul_1709

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 3:108183772..108184725(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.13619
• Ensembl ID: ENSMMUG00000011423
• Aliases: None
• Description: None

Sequence

>retro_mmul_1709
AGAACCTGCAGTGTAATGACAACAGTTAAGTCCAGGCCATTTTGGGAAAAGCAAGGGAAGATACTGCTGAAAGGTCGCAG
GCTCCTTATAGACGCTCTCAAGGCTGGAGCTGTGCCAACAGTTTTCTTCTCTAGCCATCTATAATACATAAAGAAGCTGC
TCATCGATAAGCCGAAGGGTGTCAGCCTCATTAAGATGAAATTCGAGGACATGAGGGATTGGTCCAACCTAGTAATGCCA
CAAAAATAATGGGGATTTTTGCCAAACCTGACCATGTTAACATGACATATCCAAAGACTCAGCTTTAGCACTCACTGCCT
TTGTTATTGATTTGTGACAATCTCTGTGACCCTGGGAATCTGGGGACAATTCTGAGATCTCCAGCTGGGGCGGGCTGCAG
CAAAGTGTTAGTCATTTTGAAATGTGTGGATGCCTAGGAGCCCAAAGTGCTACGGGTGGTTATGGGTGTACTTTTCCCGG
TGCCCATTATCAGTAGTCTGAAAACAAAAACAGTGGCAAATTACCTGCCCCCTGACACCCAGGTCTGTTTGGCTGACAAC
CGAAGCCTTTATGCTGAGGCTCAGATGTCTAATAAAGACAGTGACTATGGCTGGGTGTGTGATTGGCGATTCCTGAAGTT
TCACAAGTACGAAGAAAAGGAAGGTCTAGAAACTGGAGCCAGTAAAGGTTTGCTACCTGTTATTGAGGTTCAGAGTTATG
GCTTCGACTGGACAGAGGCACCAGCAGCTGCAGTGGTTGGCAGCGAGACCTACGGCATGAACCTGGATTCTCTGTAGTTG
GCCGAGAGCCCTGGGGGCAACAGGCTGCTGATCCCTGTTGCACCTGGTGTGGACAGCCTCAACTCAGCCATGGCTGCACG
CATCCCGCTTTTTGAAGGGAAAAGACAACTGTGGGTGAGGGCGGAACACTTGAGCAGGGACAGGAGTTACCAC

Alignment

ORF - retro_mmul_1709 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.04 %
• Parental protein coverage: 75.71 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RLSSVMTIVKSRPFREKQGKILLEGRRLITDALKAGAVPKMFFFSRLEYLKELPVDKLKGVSLIKVKFED
          R..SVMT.VKSRPF.EKQGKILL.GRRL..DALKAGAVP..FF.S.L.Y.K.L..DK.KGVSLIK.KFED
Retrocopy RTCSVMTTVKSRPFWEKQGKILLKGRRLLIDALKAGAVPTVFFSSHL*YIKKLLIDKPKGVSLIKMKFED

Parental  IKDWSNLVTPQG-IMGIFAKPDHVKMAYPKTQLQHSLPLSLICDNLRDPGNLGTILRSAAGAGCSKVLLT
          ..DWSNLV.PQ..IMGIFAKPDHV.M.YPKTQL.HSLPL.LICDNL.DPGNLGTILRS.AGAGCSKVL..
Retrocopy MRDWSNLVMPQK<IMGIFAKPDHVNMTYPKTQL*HSLPLLLICDNLCDPGNLGTILRSPAGAGCSKVLVI

Parental  KGCVDPWEPKVLRAGMGAHFQVPIINNLEWETVPNYLPPDTRVYVADNCGLYAQAQMSNKASDHGWVSNQ
          ..CVD..EPKVLR..MG..F.VPII..L...TV.NYLPPDT.V..ADN..LYA.AQMSNK.SD.GWV...
Retrocopy LKCVDA*EPKVLRVVMGVLFPVPIISSLKTKTVANYLPPDTQVCLADNRSLYAEAQMSNKDSDYGWVCDW

Parental  RLLKFQKYEEEEDVETGASQDWLPDVEVQSYDSDWTEAPAAVVIGGETDGVSVESLQLAESTGGKRLLIP
          R.LKF.KYEE.E..ETGAS...LP..EVQSY..DWTEAPAA.V.G.ET.G....SL.LAES.GG.RLLIP
Retrocopy RFLKFHKYEEKEGLETGASKGLLPVIEVQSYGFDWTEAPAAAVVGSETYGMNLDSL*LAESPGGNRLLIP

Parental  VVPGVDSLNSAMAASILLFEGKRQLRGRAEHLSRDRSHH
          V.PGVDSLNSAMAA.I.LFEGKRQL..RAEHLSRDRS.H
Retrocopy VAPGVDSLNSAMAARIPLFEGKRQLWVRAEHLSRDRSYH

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	5.15 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	18.25 RPM
SRP007412_cerebellum	0.00 RPM	6.52 RPM
SRP007412_heart	0.00 RPM	5.71 RPM
SRP007412_kidney	0.00 RPM	6.57 RPM
SRP007412_liver	0.00 RPM	8.95 RPM
SRP007412_testis	0.08 RPM	11.16 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1709 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1709 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1709 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3704
Gorilla gorilla	retro_ggor_2505
Pongo abelii	retro_pabe_3149
Callithrix jacchus	retro_cjac_3130

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000021701	1 retrocopy	retro_cjac_3130,
Homo sapiens	ENSG00000171861	1 retrocopy	retro_hsap_3704,
Gorilla gorilla	ENSGGOG00000015518	1 retrocopy	retro_ggor_2505,
Macaca mulatta	ENSMMUG00000011423	1 retrocopy	retro_mmul_1709 ,
Nomascus leucogenys	ENSNLEG00000000570	1 retrocopy	retro_nleu_180,
Pongo abelii	ENSPPYG00000007762	1 retrocopy	retro_pabe_3149,