RetrogeneDB ID: retro_mmul_1302

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 17:76976714..76977345(+)
• Located in intron of: ENSMMUG00000005847

Retrocopy information

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

Parental gene information

• Parental gene symbol: AMMECR1L
• Ensembl ID: ENSMMUG00000001987
• Aliases: None
• Description: None

Sequence

>retro_mmul_1302
GGAAAAATATATCATGTTCCTCCACTGGACCCCAAGTTGACAGCAGGCTGTTGTGGGAGCAAGAAGCCCAAATTATCTGG
AAGTGAAACACACAGTCACGAGAAGGAGTCCACAGCCGTCCCCGGCCCTAGGTCAGGACCTCTTCAAAACTGCCAGCATG
TAGACAGCAGCAGCAGATAGGAGAGTGTGTTGGACTTAACTCTGGGACCTGGAAGCTCTCCCATCACATGAATGAATCCG
GCATCAGGAACACTGAGCCCTCTCCCCCAGTCTAATGGAACGGCAGCTCCACAAAGAATCTGGAGGTGACTGCACAGATG
TGCTGCTATTGCTTTACTGAACTCTACTGTCAGCTCTATGGCTTTCCACAGCCACAACTTCCTAGATTCACCAATGACCC
CTGTCCGCTCTTTGTGACATGGAAGACAGGGAGTGACAAGTGGCTTCATGGCTGCATTGGGACCTTCTCAGCCATGAATC
TTTATTCAGGACTCAGGGAATACATGTTAGCCATTGCATTTAAGGACAGCTGATTTCCCCTCCAGTCTGAGAGGAGCTGC
CTAAGCTTTTCTGCTCTGTCTCCCTCCATACTAACTTTGAGGATGCTAGTGATTACCTGGACTGGGAGATA

Alignment

ORF - retro_mmul_1302 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.46 %
• Parental protein coverage: 68.06 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  GKRRCVPPLEPKLAAGCCGVKKPKLSGSGTHSHGNQSTTVPGSSSGPLQNHQHVDSSSGRENVSDLTLGP
          GK...VPPL.PKL.AGCCG.KKPKLSGS.THSH...ST.VPG..SGPLQN.QHVDSSS..E.V.DLTLGP
Retrocopy GKIYHVPPLDPKLTAGCCGSKKPKLSGSETHSHEKESTAVPGPRSGPLQNCQHVDSSSR*ESVLDLTLGP

Parental  GNSPITRMNPASGALSPLPRPNGTA-NTTKNLVVTAEMCCYCFDVLYCHLYGFPQPRLPRFTNDPYPLFV
          G.SPIT.MNPASG.LSPLP..NGTA...TKNL.VTA.MCCYCF..LYC.LYGFPQP.LPRFTNDP.PLFV
Retrocopy GSSPIT*MNPASGTLSPLPQSNGTA<SSTKNLEVTAQMCCYCFTELYCQLYGFPQPQLPRFTNDPCPLFV

Parental  TWKTGRDKRLRGCIGTFSAMNLHSGLREYTLTSALKDSRFP-PLTREELPKLFCSVSLLTNFEDASDYLD
          TWKTG.DK.L.GCIGTFSAMNL.SGLREY.L..A.KDS.FP.P...EELPKLFCSVSL.TNFEDASDYLD
Retrocopy TWKTGSDKWLHGCIGTFSAMNLYSGLREYMLAIAFKDS*FP<PPV*EELPKLFCSVSLHTNFEDASDYLD

Parental  WEV
          WE.
Retrocopy WEI

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	9.97 RPM
SRP007412_brain_prefrontal_cortex	0.08 RPM	15.07 RPM
SRP007412_cerebellum	0.00 RPM	14.53 RPM
SRP007412_heart	0.06 RPM	8.01 RPM
SRP007412_kidney	0.00 RPM	19.37 RPM
SRP007412_liver	0.00 RPM	9.70 RPM
SRP007412_testis	0.00 RPM	38.90 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1302 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1302 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1302 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1227
Pan troglodytes	retro_ptro_843
Gorilla gorilla	retro_ggor_961

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000009373	1 retrocopy	retro_chof_1566,
Callithrix jacchus	ENSCJAG00000010743	1 retrocopy	retro_cjac_383,
Equus caballus	ENSECAG00000023095	1 retrocopy	retro_ecab_1085,
Echinops telfairi	ENSETEG00000000510	1 retrocopy	retro_etel_9,
Homo sapiens	ENSG00000144233	1 retrocopy	retro_hsap_1227,
Gorilla gorilla	ENSGGOG00000014448	1 retrocopy	retro_ggor_961,
Myotis lucifugus	ENSMLUG00000006871	1 retrocopy	retro_mluc_684,
Macaca mulatta	ENSMMUG00000001987	1 retrocopy	retro_mmul_1302 ,
Mus musculus	ENSMUSG00000041915	2 retrocopies	retro_mmus_1330, retro_mmus_352,
Nomascus leucogenys	ENSNLEG00000015793	1 retrocopy	retro_nleu_700,
Pan troglodytes	ENSPTRG00000012437	1 retrocopy	retro_ptro_843,
Sarcophilus harrisii	ENSSHAG00000014762	1 retrocopy	retro_shar_86,