RetrogeneDB ID: retro_mmul_248

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 19:11607269..11609150(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMMUG00000008817
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMMUG00000013571
• Aliases: None
• Description: None

Sequence

>retro_mmul_248
ATGGTAGAGAGATCCTGTGAAATTAAAGATAATAGTCAATGTGGAGGACCCTTTACCCAGATTCAAGACAGTATTGTGAA
CGAGAAAATACCTGGAGTAGATCCATGGGAAAGCAGTGCGTGTGCAGAAGTCCTCATGGGTCGTTCATCTCTTAATTGCT
ACATTAGAGTTGACAGTGAACACAAACCATGTGAGTATCAAGAATATGGAGAGAAGCCATATACACATACACAATGTGGG
ACAACTTTCAGTTATCAGCCCTCCTTTCAAATACGTGAAAGGCCTCAGCATGGAAAGAAACTCTATGATTGTAAGGAATG
TGCAACCTTCAGTTCTCTTGAAAACCTCCAAAGACACATGGCAGTACACCATGGAGATGGACGTTGTATGTGTAAGTTGT
GTGGAAATGCCTTTATTTGGCCTAGTTTATTTCATATGCTTGGAAGAACTCACACTGAAGAGAAACCATATGAATATGAG
CAGTGTTCTACAGCGTTTCCTGCTTATAGTTCCTCTCTAAGACATGAAAGAACACACAGTGGAGAGAAACCCTATCAATG
TAATCTATGTGGGAACGCCTTCAGTTGTTCCTGTTACACTCAACTATATGAAATGAGTCACACTGGAGAACAATCCTATG
AATGTCAGCAATGTGGGAAAACATTTTATCATCTTGGAAGCTTTCAAAGACACATGATAATGCACACTGGAGATGGACCT
CATAAATGTAAGATATGTGGAAAAGGCTTTCTTTCTCCCAGTTCAGTTCGAAGACATAAAAGAACTCACACTGGAGAGAA
ACCCTATGAATGTAAGTATTGTGGGAAAGCATTCTCTGATTGCACAGGTTTTCGAAGACACATGATAACGCACACTGGAG
ATGGACCTCATAAATGCAAGGTATGTGGGAAAGCCTTTGATTCTCCCAGTTTATGTCGAAGGCATGAAAAAACTCATACT
GGGGAGAAACCCTATAAATGTGAATGTGGGAAAGCCTTTAGTGATTTCTATTACTTTCGAAATCATGAAACTACTCACAC
TGGAGAGAAGCCATATAAATGTAAACAATGTGGAAAAGCCTTCATTTGTTGCACTTACCTTCAAATACATGAAAGAATTC
ACACTGGGGAGAGACCCTATAAATGTAAACAATGTGGAAAAGCCTTCAGGTCTTCCAATTACATTCGAGTACATGAAAAG
ACTCACACTGGAGAAAAGCCCTATGAATGTAAGCAGTGTGGAAAAGCACTTTCTCATCTGAAAAGCTTTCAGAGACACAT
GATAATGCACACTGGAGACGGACCTCATAAATGTAAGGTATGTGGGAAAAGCTTTGATTCTCCCAGTTCATTTCGAAGAC
ATGAAAGAATTCACACTGGGGAGAGACCCTATAAGTGTAAACTATGTGGGAAAGGCTTCAGGTCTTCCAGTTACATTCAA
CTACATGAAAGGACCCACACTGGAGAGAAACCCTATGGTTGTCAGCAATGTGGGAAAGCATTATCTGATCTCTCAAGCTT
TCGAAGACACATGATAACGCATACTGGAAATGGACCTCATAAATGTAAGATATGTGGGAAAGGCTTTGATTATCCTAGTT
CAGTGCAAAGACATGAAAGAACTCACACTGGAGAGAAACCCTATGAATGCAAGGAATGTGGGAAAGCCTTCAGTCATTCA
AGTTACTTACGGATACATGTAAGAGTTCATACTGGGGAGAAGCCCTATAAATGTAAGGAATGTGGGAAACCATTCCATTG
TCCCAGTGCCTTTCATAAACATGAAAGGACCCACAGTGTAGAGAAACCCTATAAGTGTAAAGAAGGTGGGGAAACATTTC
ATTGTATCAGTTCCTTTCATAAGCATGAAGGGACCCACTAG

Alignment

ORF - retro_mmul_248 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.72 %
• Parental protein coverage: 82.21 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QIPDDALNKKTSPGVKSCESSVCGEVFLGHSSLNRHIRADAAHKPSEYQEYGQKPYKCQQRKKAFRCHPS
          QI.D...N.K..PGV...ESS.C.EV..G.SSLN..IR.D..HKP.EYQEYG.KPY...Q....F...PS
Retrocopy QIQDSIVNEKI-PGVDPWESSACAEVLMGRSSLNCYIRVDSEHKPCEYQEYGEKPYTHTQCGTTFSYQPS

Parental  FQTEEKAHTGEKLYDCKECGKTFISRSSIRRHMIMHNGDGPYKCKFCGKACPCLRVCLIHERVHTGEKPY
          FQ..E....G.KLYDCKEC..TF.S.....RHM..H.GDG...CK.CG.A...........R.HT.EKPY
Retrocopy FQIRERPQHGKKLYDCKECA-TFSSLENLQRHMAVHHGDGRCMCKLCGNAFIWPSLFHMLGRTHTEEKPY

Parental  ECKQCGKAF-SYSNSLQIHERTHTGEKPYECKECGKAFGSPNSFYEHKRIHTGEKPYECKQCGKAFRWFH
          E..QC..AF..YS.SL..HERTH.GEKPY.C..CG.AF............HTGE..YEC.QCGK.F....
Retrocopy EYEQCSTAFPAYSSSLR-HERTHSGEKPYQCNLCGNAFSCSCYTQLYEMSHTGEQSYECQQCGKTFYHLG

Parental  SFQIHERTHSEEKPYECTKCGKAFKCPSYLCRHEVTHSGKKPYECKQCGKALS-YLNFQRHMKMHTRMRP
          SFQ.H...H....P..C..CGK.F..PS...RH..TH.G.KPYECK.CGKA.S....F.RHM..HT...P
Retrocopy SFQRHMIMHTGDGPHKCKICGKGFLSPSSVRRHKRTHTGEKPYECKYCGKAFSDCTGFRRHMITHTGDGP

Parental  YKCKTCGKDFDSPSSFLRHYHERTHTGEKPYECKQCGKAFISSTSFRYHERTHTGEKPYACKQCGKAFRS
          .KCK.CGK.FDSPS..L...HE.THTGEKPY.C..CGKAF.....FR.HE.THTGEKPY.CKQCGKAF..
Retrocopy HKCKVCGKAFDSPS--LCRRHEKTHTGEKPYKC-ECGKAFSDFYYFRNHETTHTGEKPYKCKQCGKAFIC

Parental  ASHLQYHERTHTGEKPYECKQCGKAFRSASHLQMHERTHTGKQLYESKQCEKTFGSVRNLQIHEKTHTGE
          ...LQ.HER.HTGE.PY.CKQCGKAFRS......HE.THTG...YE.KQC.K........Q.H...HTG.
Retrocopy CTYLQIHERIHTGERPYKCKQCGKAFRSSNYIRVHEKTHTGEKPYECKQCGKALSHLKSFQRHMIMHTGD

Parental  KPY--KECGKAFNNFSSFQIHATMTHTGEKPYECKECGKAFNYFSSLHIHKRVHTGEKPYECKDCGKAFG
          .P...K.CGK.F...SSF..H....HTGE.PY.CK.CGK.F...S....H.R.HTGEKPY.C..CGKA..
Retrocopy GPHKCKVCGKSFDSPSSFRRHERI-HTGERPYKCKLCGKGFRSSSYIQLHERTHTGEKPYGCQQCGKALS

Parental  LPGSFRRHKRAHTGVKPYECKQCGKAFTSSGSFQCHKRIHTGEKPYECKQCGKAFISSTAIRRHERTHTG
          ...SFRRH...HTG..P..CK.CGK.F....S.Q.H.R.HTGEKPYECK.CGKAF..S...R.H.R.HTG
Retrocopy DLSSFRRHMITHTGNGPHKCKICGKGFDYPSSVQRHERTHTGEKPYECKECGKAFSHSSYLRIHVRVHTG

Parental  EKPYECKQCGKAFISFSSVRYHERTHTGEKQYECKQCGKAFMSSTAFQYHEKTH
          EKPY.CK.CGK.F...S....HERTH..EK.Y.CK..G..F.....F..HE.TH
Retrocopy EKPYKCKECGKPFHCPSAFHKHERTHSVEKPYKCKEGGETFHCISSFHKHEGTH

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	4.48 RPM	0.56 RPM
SRP007412_brain_prefrontal_cortex	2.70 RPM	0.24 RPM
SRP007412_cerebellum	7.75 RPM	0.52 RPM
SRP007412_heart	2.59 RPM	1.35 RPM
SRP007412_kidney	6.34 RPM	3.05 RPM
SRP007412_liver	1.27 RPM	0.51 RPM
SRP007412_testis	1.06 RPM	4.15 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_248 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_248 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_248 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000008838	1 retrocopy	retro_acar_51,
Anolis carolinensis	ENSACAG00000023302	2 retrocopies	retro_acar_3, retro_acar_34,
Anolis carolinensis	ENSACAG00000026389	2 retrocopies	retro_acar_13, retro_acar_4,
Anolis carolinensis	ENSACAG00000026721	1 retrocopy	retro_acar_23,
Anolis carolinensis	ENSACAG00000026996	1 retrocopy	retro_acar_22,
Anolis carolinensis	ENSACAG00000027062	1 retrocopy	retro_acar_29,
Ciona savignyi	ENSCSAVG00000007589	2 retrocopies	retro_csav_30, retro_csav_31,
Equus caballus	ENSECAG00000010608	1 retrocopy	retro_ecab_68,
Equus caballus	ENSECAG00000021667	1 retrocopy	retro_ecab_560,
Macaca mulatta	ENSMMUG00000013571	1 retrocopy	retro_mmul_248 ,