RetrogeneDB ID: retro_mmul_1505

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 2:39571015..39571473(-)
• Located in intron of: ENSMMUG00000016367

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.11177
• Ensembl ID: ENSMMUG00000020772
• Aliases: None
• Description: cysteine and glycine-rich protein 1 [Source:RefSeq peptide;Acc:NP_001244214]

Sequence

>retro_mmul_1505
ATGGTTTGCAGGAAAAATTTAGAGAGCACAACAGTGGCAATTCACAATGAAGAGATCTACTGCAAATCCTGCTATGGAAA
GGAATATGGGCCAAAAGGCTATGGTTATGGCCAGGGCGCTGGCATGCTTAACATGGCGAGAGGCTGGGCATCAAGCCAGA
GTGTTCAGCCTCACAGGCCTACAACAAATCCAAACACTTCTAAATTTGCTCAGAAATCTGGAGGTGCTGAGAACTGTTCC
AGATGTGGGGACTTGGTATATGCTGCCGAGAAGATAATTGGAGCTGGAAAGCCCTGGCACAAAAACTGTTTCTGATGTGC
AAAGTGTGGGAAGAGTCTTGAATCAACAACTCCACTGAAAAAGAAGGTGAAATCTATTGTAAAGGATGCTATGCAAAGAA
CTCTGGGCCCAAGGGATTTGGCTATGGCCAAGGAGCAGGGGCTCTTGTTCACGCCCAG

Alignment

ORF - retro_mmul_1505 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.79 %
• Parental protein coverage: 80.83 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MVCKKNLDSTTVAVHGEEIYCKSCYGKKYGPKGYGYGQGAGTLSTDKGESLGIKHEEAPGHRPTTNPNAS
          MVC.KNL.STTVA.H.EEIYCKSCYGK.YGPKGY..G.G.G.................P.HRPTTNPN.S
Retrocopy MVCRKNLESTTVAIHNEEIYCKSCYGKEYGPKGY--GYGQGAGMLNMARGWASSQSVQP-HRPTTNPNTS

Parental  KFAQKIGGSERCPRCSQAVYAAEKVIGAGKSWHKSCFRCAKCGKGLESTT-LADKDGEIYCKGCYAKNFG
          KFAQK.GG.E.C.RC...VYAAEK.IGAGK.WHK.CF.CAKCGK.LESTT....K.GEIYCKGCYAKN.G
Retrocopy KFAQKSGGAENCSRCGDLVYAAEKIIGAGKPWHKNCF*CAKCGKSLESTT<STEKEGEIYCKGCYAKNSG

Parental  PKGFGFGQGAGALVHSE
          PKGFG.GQGAGALVH..
Retrocopy PKGFGYGQGAGALVHAQ

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	134.91 RPM
SRP007412_brain_prefrontal_cortex	0.32 RPM	199.99 RPM
SRP007412_cerebellum	0.39 RPM	92.60 RPM
SRP007412_heart	1.06 RPM	280.06 RPM
SRP007412_kidney	0.35 RPM	121.36 RPM
SRP007412_liver	2.14 RPM	124.25 RPM
SRP007412_testis	0.26 RPM	16.85 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1505 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1505 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1505 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2833
Pan troglodytes	retro_ptro_1920
Gorilla gorilla	retro_ggor_1967
Pongo abelii	retro_pabe_2199

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012114	1 retrocopy	retro_amel_1294,
Echinops telfairi	ENSETEG00000017067	1 retrocopy	retro_etel_417,
Macaca mulatta	ENSMMUG00000007158	2 retrocopies	retro_mmul_1479, retro_mmul_553,
Macaca mulatta	ENSMMUG00000018257	1 retrocopy	retro_mmul_1474,
Macaca mulatta	ENSMMUG00000020772	1 retrocopy	retro_mmul_1505 ,
Mus musculus	ENSMUSG00000026421	1 retrocopy	retro_mmus_2226,
Pan troglodytes	ENSPTRG00000001836	2 retrocopies	retro_ptro_1920, retro_ptro_1922,
Tupaia belangeri	ENSTBEG00000008991	1 retrocopy	retro_tbel_2176,
Drosophila melanogaster	FBgn0259209	1 retrocopy	retro_dmel_71,