RetrogeneDB ID: retro_mmul_621

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 10:14654021..14654951(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: N-PAC
• Ensembl ID: ENSMMUG00000009567
• Aliases: GLYR1, N-PAC
• Description: None

Sequence

>retro_mmul_621
AAAGAGGAAACTGGTTCCACCTCCATCCGGGCAGCTGACAGCAGGGCTGTGAATGGCAGCATCACAACAAAAAGATAGGA
TTTGGGGGCCTTGGTCTCATGGGAAGTGGCATCGTCTCCAGCTTGCTAAAAATGGGTCACACGGTGACTGTCTGGAACTG
CACTGCCAAGAAATGTGATTTGTTCATCTAGGAGGGGGCCTACTTGGGAAGAACGCCTGCTGAAGTCCTGTCAACCTGTG
GCACCACTTTCGCCCATGTGTTGGATCCCAAGGCAGCCAAGGACCTGGTGCTGGGCCCCAGTGGTATGCTGCAAGGGATC
CACCTGGAGAGTGCTATGTGGACATGTCAACATTGGACGCTGACATAGTCACTGAGCTGGCCCAGGTGATTGTGTCCAGG
TCAGGGAGCGGGGGCGCTTTCCAGAAGCCTCCATCTCAGGGAATCAGCAGCTTTCTAATCAAGGGATGTTGGTGATCTTA
GCAGCTGGAGACAGGGGCCTATATGAGGACTGCAGCAGCTGCATCCAGACAATGGGGAAGACCTCCTTTTTCCTAGGTGA
AGTTGGCAGCGCAGCCAAGATGATGCTGATCATGAACATGGTCCAAGGGAGCTTCATGGCCATGATCACTGAGGTGCTGA
CCCTGGCCCAGGTGACATATCAGTCCCAGCAGACACTCTTGGACATCCTCAATCAGGGACAGTTGGCCAGCATCTTGCTA
GACCAGAAGTGCCAAAATATCCTGCAAGGAAACTTTAAGCCTGATTTCTACCTGAAATACATGCAGAAGGATCTCTGCTT
AGCCATTGTACTGGGCAACGCGGTTAACCATCCGACTCCCATGGCAGCTGCAGCCAACAAGGTGTACAAAAGAGCCAAGG
CACTAGACCAGTCCGACAATATGTCCACCGTGTCCCAAGCCTACATACAC

Alignment

ORF - retro_mmul_621 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.7 %
• Parental protein coverage: 66.6 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  EKETGSTSIQAADSTAVNGSITPTDKKIGF-LGLGLMGSGIVSNLLKMGHTVTVWNRTAEKCDLFIQEGA
          ..ETGSTSI.AADS.AVNGSIT......G..LGL..MGSGIVS.LLKMGHTVTVWN.TA.KCDLFI.EGA
Retrocopy KEETGSTSIRAADSRAVNGSITTKR*DLGA<LGL--MGSGIVSSLLKMGHTVTVWNCTAKKCDLFI*EGA

Parental  RLGRTPAEVVSTCDITFACVSDPKAAKDLVLGPSGVLQGIR-PGKCYVDMSTVDADTVTELAQVIVSR--
          .LGRTPAEV.STC..TFA.V.DPKAAKDLVLGPSG.LQGI..PG.CYVDMST.DAD.VTELAQVIVSR..
Retrocopy YLGRTPAEVLSTCGTTFAHVLDPKAAKDLVLGPSGMLQGIH<PGECYVDMSTLDADIVTELAQVIVSRSG

Parental  -GGRFLEAP-VSGNQQLSNDGMLVILAAGDRGLYEDCSSCFQAMGKTSFFLGEVGNAAKMMLIVNMVQGS
          .GG.F...P..SGNQQLSN.GMLVILAAGDRGLYEDCSSC.Q.MGKTSFFLGEVG.AAKMMLI.NMVQGS
Retrocopy SGGAFQKPP<ISGNQQLSNQGMLVILAAGDRGLYEDCSSCIQTMGKTSFFLGEVGSAAKMMLIMNMVQGS

Parental  FMATIAEGLTLAQVTGQSQQTLLDILNQGQLASIFLDQKCQNILQGNFKPDFYLKYIQKDLRLAIALGDA
          FMA.I.E.LTLAQVT.QSQQTLLDILNQGQLASI.LDQKCQNILQGNFKPDFYLKY.QKDL.LAI.LG.A
Retrocopy FMAMITEVLTLAQVTYQSQQTLLDILNQGQLASILLDQKCQNILQGNFKPDFYLKYMQKDLCLAIVLGNA

Parental  VNHPTPMAAAANEVYKRAKALDQSDNDMSAVYRAYIH
          VNHPTPMAAAAN.VYKRAKALDQSDN.MS.V..AYIH
Retrocopy VNHPTPMAAAANKVYKRAKALDQSDN-MSTVSQAYIH

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	0.22 RPM	45.38 RPM
SRP007412_brain_prefrontal_cortex	0.16 RPM	68.30 RPM
SRP007412_cerebellum	0.13 RPM	36.16 RPM
SRP007412_heart	0.06 RPM	22.61 RPM
SRP007412_kidney	0.23 RPM	36.38 RPM
SRP007412_liver	0.08 RPM	21.77 RPM
SRP007412_testis	0.04 RPM	27.33 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_621 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_621 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_621 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000019912	1 retrocopy	retro_cjac_2514,
Erinaceus europaeus	ENSEEUG00000011783	1 retrocopy	retro_eeur_477,
Homo sapiens	ENSG00000140632	1 retrocopy	retro_hsap_2432,
Gorilla gorilla	ENSGGOG00000016258	1 retrocopy	retro_ggor_1512,
Macaca mulatta	ENSMMUG00000009567	1 retrocopy	retro_mmul_621 ,
Nomascus leucogenys	ENSNLEG00000009950	1 retrocopy	retro_nleu_240,
Oryctolagus cuniculus	ENSOCUG00000010486	1 retrocopy	retro_ocun_680,
Pongo abelii	ENSPPYG00000007072	1 retrocopy	retro_pabe_1791,
Pan troglodytes	ENSPTRG00000007730	1 retrocopy	retro_ptro_1404,