RetrogeneDB ID: retro_mmul_1894

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 5:81495006..81495420(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.3989
• Ensembl ID: ENSMMUG00000000811
• Aliases: None
• Description: None

Sequence

>retro_mmul_1894
CTCATCGTGGGCTCCATTATCACAGTGGTTGCCTTCCTGGGCTGCGTAGGCTCTGTCAAGAAAAACAGGTGTCTGCTTAC
GTCCTTGTTCATTCTGCTGCTAATTATCCTCCTTGCTAAGGTGACTTTGGCCATCCTGCACTTTGTTTACGAACAGAAGC
TGAATGTATAGGTAGCTGAGGGCCTGATGGACAGCATCTGCCATTACCACAGGGACAACAGCACCAAGGCGATGTGGGAC
TCCATCCAGTCATTTCTGCACTGTTGTGGCCTAAATAGCAAGAGTGATTGGTCCAGTGGGCAACAAGCATCTTGCCCTTC
AGATCCAAAAGTGAAAGGTTGCTATGCAAAAGCGAGACTGTAATTTCATGACAATTTCTTGTATATCAGAATCATCACCA
TCTGTGTATATGTG

Alignment

ORF - retro_mmul_1894 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.09 %
• Parental protein coverage: 63.01 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VIVGSIIMVVAFLGCMGSIKENKCLLMSFFILLLIILLAEVILAFLLFVYEQKLNEYVAKGLTDSIHRYH
          .IVGSII.VVAFLGC.GS.K.N.CLL.S.FILLLIILLA.V.LA.L.FVYEQKLN..VA.GL.DSI..YH
Retrocopy LIVGSIITVVAFLGCVGSVKKNRCLLTSLFILLLIILLAKVTLAILHFVYEQKLNV*VAEGLMDSICHYH

Parental  SDNSTKAAWDSIQSFLQCCGINGTSDWTSGPPASCPSDPNVEGCYAKARLWFHSNFLYIGIITICVCV
          .DNSTKA.WDSIQSFL.CCG.N..SDW.SG..ASCPSDP.V.GCYAKARL.FH.NFLYI.IITICV.V
Retrocopy RDNSTKAMWDSIQSFLHCCGLNSKSDWSSGQQASCPSDPKVKGCYAKARL*FHDNFLYIRIITICVYV

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	0.34 RPM	20.62 RPM
SRP007412_brain_prefrontal_cortex	0.16 RPM	29.43 RPM
SRP007412_cerebellum	0.13 RPM	2.39 RPM
SRP007412_heart	0.06 RPM	4.59 RPM
SRP007412_kidney	0.47 RPM	5.16 RPM
SRP007412_liver	0.24 RPM	18.56 RPM
SRP007412_testis	0.00 RPM	1.28 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1894 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1894 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1894 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000010760	2 retrocopies	retro_chof_116, retro_chof_307,
Homo sapiens	ENSG00000143119	1 retrocopy	retro_hsap_2960,
Gorilla gorilla	ENSGGOG00000005468	1 retrocopy	retro_ggor_2050,
Macaca mulatta	ENSMMUG00000000811	1 retrocopy	retro_mmul_1894 ,
Nomascus leucogenys	ENSNLEG00000003649	1 retrocopy	retro_nleu_1643,
Otolemur garnettii	ENSOGAG00000016713	2 retrocopies	retro_ogar_2407, retro_ogar_469,
Pan troglodytes	ENSPTRG00000001085	1 retrocopy	retro_ptro_2004,