RetrogeneDB ID: retro_mmul_1959

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 5:91929435..91929922(-)
• Located in intron of: ENSMMUG00000011062

Retrocopy information

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

Parental gene information

• Parental gene symbol: ABT1
• Ensembl ID: ENSMMUG00000006914
• Aliases: None
• Description: None

Sequence

>retro_mmul_1959
TTGTCAGTCAACATGGAGGCAGAAGAATCGGAGAAGGCCGCAACAGAACAAAGGCACTGGAAGGGACAGACCAGACACTA
GATGCAGAGGAGGAACAGGAGGAATCCAAAGAAAAGGCCTGTGGCAACAAGAAGCAGGTAGTGCCAGGTATTGTGTACCT
GGGCCATATCCCACCACACTTCCAGCCCCTGCACATCAGCAACCTTCTTAGCACCTGTGGTGAGGTCAGACGCGTTTTCT
TTCAGGCTGAGGACTGGTTCATGAGATGTAAGAAGAAGGCAGCAGCAGCCATGGGAGGGAAAAAAAGCAGTCCTACAGCA
AGGACTACAACGAGGGATGGGTGGAGTTCCGTGACAAGCACAGAGCCAAGAGCGTGGCGGCCAGTCTACACAACACGCCT
ATGGGTGCCTGCAGGTGTAGCCCCTTCCATTATGACCTATGGAATCTGGAGTACTTGCACCATTTCACCTGGTCCCACCA
CAGCGAG

Alignment

ORF - retro_mmul_1959 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.76 %
• Parental protein coverage: 58.7 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MSVNMEAEESEKAATEH-EPLKGTEQTLDAEEEQEESEAAACGRNKRVMPGIVYLGHIPPRFRPLHVRNL
          .SVNMEAEESEKAATE....L.GT.QTLDAEEEQEES...ACG..K.V.PGIVYLGHIPP.F.PLH..NL
Retrocopy LSVNMEAEESEKAATEQ<KALEGTDQTLDAEEEQEESKEKACGNKKQVVPGIVYLGHIPPHFQPLHISNL

Parental  LSAYGEVGRVFFQAEDRFVRRKKKA-AAAAGGK-KRSYSKDYTEGWVEFRDKRIAKRVAASLHNTPMGAR
          LS..GEV.RVFFQAED.F.R.KKKA.AA..G.K.K.SYSKDY.EGWVEFRDK..AK.VAASLHNTPMGA.
Retrocopy LSTCGEVRRVFFQAEDWFMRCKKKAAAAMGGKK<KQSYSKDYNEGWVEFRDKHRAKSVAASLHNTPMGAC

Parental  RRSPFRYDLWNLKYLHRFTWSHLSE
          R.SPF.YDLWNL.YLH.FTWSH.SE
Retrocopy RCSPFHYDLWNLEYLHHFTWSHHSE

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	14.34 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	20.94 RPM
SRP007412_cerebellum	0.00 RPM	11.82 RPM
SRP007412_heart	0.06 RPM	8.24 RPM
SRP007412_kidney	0.12 RPM	9.74 RPM
SRP007412_liver	0.00 RPM	6.29 RPM
SRP007412_testis	1.55 RPM	10.33 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1959 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1959 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1959 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3066
Gorilla gorilla	retro_ggor_2106
Pongo abelii	retro_pabe_2541

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000005188	1 retrocopy	retro_chof_1748,
Cavia porcellus	ENSCPOG00000008937	1 retrocopy	retro_cpor_1386,
Gorilla gorilla	ENSGGOG00000024149	1 retrocopy	retro_ggor_2106,
Macaca mulatta	ENSMMUG00000006914	1 retrocopy	retro_mmul_1959 ,
Otolemur garnettii	ENSOGAG00000026316	1 retrocopy	retro_ogar_2895,
Pongo abelii	ENSPPYG00000016335	1 retrocopy	retro_pabe_2541,
Rattus norvegicus	ENSRNOG00000017585	1 retrocopy	retro_rnor_841,
Sarcophilus harrisii	ENSSHAG00000003493	1 retrocopy	retro_shar_97,