RetrogeneDB ID: retro_mmul_751

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 1099214801624:522..1217(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.11950
• Ensembl ID: ENSMMUG00000023012
• Aliases: None
• Description: vacuolar protein sorting-associated protein VTA1 homolog [Source:RefSeq peptide;Acc:NP_001248449]

Sequence

>retro_mmul_751
ATTGCTCTACTTTCCCCACTTCCTCCCCAGTTTAAGAGCATACAGCATCATATGAGAACAGCTCAGGAGCATGACAAGCA
GGACCCTGCGGTGCTCTATTGCTGTTGTTTCTATGCAATGCAAACCAAAATGAAGACTGATAGTAAAACTCCTGAGTGTT
GTACATTTTTATCAAAGCTAAAGGATCAGTTAGAAATGCTTATGAAACAGCTGGGTGATAATGAAGCTATTAGGCAAGAA
AATACTTGGTCCTGCCCATTTGGAGAATTGTACTTAGAAAATGTTTTTATATTCAGACAATGAAGATCATGCTGGGTGAT
TTCACAAGATGATCAAGTCCCTTTCATACTCCACAGTTTTAAATAGATGTCATAATAATATTTGGACAACTCATTGATGA
AAATGTGAAACACAGAAAGTATGTAAAGTGAAAGGCAAAATATACTCATATTTATTTAAAGAATAGGAAGCTGTCTCAAC
TAGTATCTGTTGGAATTGAGGAAGACAACAATATTGCAGAAAATGAAGATGCTGGATCAACCTATCTGTCCACTGAGCCA
TGTCAGCCACCATCTTCAACTTATGACCCAAGCCACATGCCACAAAGAAGCTATATTAGAATACAGATTCCTCCCAGTGC
ACACACTCCAGCTAATACATCAGTAGAAGCACATCACAATACAGTTGTAACAAAT

Alignment

ORF - retro_mmul_751 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.96 %
• Parental protein coverage: 75.9 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LASLPPLPAQFKSIQHHLRTAQEHDKRDPVVAYYCRLYAMQTGMKIDSKTPECRKFLSKLMDQLEALKKQ
          .A.L.PLP.QFKSIQHH.RTAQEHDK.DP.V.Y.C..YAMQT.MK.DSKTPEC..FLSKL.DQLE.L.KQ
Retrocopy IALLSPLPPQFKSIQHHMRTAQEHDKQDPAVLYCCCFYAMQTKMKTDSKTPECCTFLSKLKDQLEMLMKQ

Parental  LGDNEAITQE-IVGCAHLENYALKMFLYADNEDRAGRFHKNMIKS-FYTASLLIDVITVFGELTDENVKH
          LGDNEAI.QE.I.G.AHLEN...KMFLY.DNED.AG.FHK.MIKS.F.T....IDVI..FG.L.DENVKH
Retrocopy LGDNEAIRQE>ILGPAHLENCT*KMFLYSDNEDHAG*FHK-MIKS>FHTPQF*IDVIIIFGQLIDENVKH

Parental  RKYARWKATYIHNCLKNGETPQAGPVGIEEDNDVEENEDAGAASLPTQPTQPSSSSTYDPSNMPSGNYTG
          RKY...KA.Y.H..LKN....Q...VGIEEDN...ENEDAG...L.T.P.QP..SSTYDPS.MP...Y..
Retrocopy RKYVK*KAKYTHIYLKNRKLSQLVSVGIEEDNNIAENEDAGSTYLSTEPCQP-PSSTYDPSHMPQRSYIR

Parental  IQIPPGAHAPANTPAEVPHSTGVAS
          IQIPP.AH.PANT..E..H.T.V..
Retrocopy IQIPPSAHTPANTSVEAHHNTVVTN

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	29.58 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	23.64 RPM
SRP007412_cerebellum	0.00 RPM	26.15 RPM
SRP007412_heart	0.00 RPM	10.89 RPM
SRP007412_kidney	0.00 RPM	14.32 RPM
SRP007412_liver	0.00 RPM	6.33 RPM
SRP007412_testis	0.00 RPM	11.16 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_751 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_751 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_751 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000009844	1 retrocopy	retro_hsap_4088,
Gorilla gorilla	ENSGGOG00000015524	1 retrocopy	retro_ggor_2742,
Microcebus murinus	ENSMICG00000004420	2 retrocopies	retro_mmur_1290, retro_mmur_290,
Macaca mulatta	ENSMMUG00000023012	1 retrocopy	retro_mmul_751 ,
Nomascus leucogenys	ENSNLEG00000015053	1 retrocopy	retro_nleu_1911,
Oryctolagus cuniculus	ENSOCUG00000002554	10 retrocopies	retro_ocun_1543, retro_ocun_1689, retro_ocun_1790, retro_ocun_1810, retro_ocun_1821, retro_ocun_1832, retro_ocun_1848, retro_ocun_1853, retro_ocun_1864, retro_ocun_965,
Pan troglodytes	ENSPTRG00000018662	1 retrocopy	retro_ptro_2773,
Rattus norvegicus	ENSRNOG00000011540	1 retrocopy	retro_rnor_799,
Tursiops truncatus	ENSTTRG00000014998	1 retrocopy	retro_ttru_1825,