RetrogeneDB ID: retro_mmul_1479

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 2:168166398..168166628(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CRIP1
• Ensembl ID: ENSMMUG00000007158
• Aliases: None
• Description: cysteine-rich protein 1 [Source:RefSeq peptide;Acc:NP_001253775]

Sequence

>retro_mmul_1479
ATACCTAAGTGCCTCAAGTACGACAAGGAGGTGTACTTCGCCGAGAGGGTGACCTCTCTGGGCAAGGACTGGCATCGGCC
CTGCCTGAAGTGCCAGAAGGTGGGAAGACGCTGACCTCGGGGGGCCGCGCTGAGCAGGAAGGCAGGCCCTGCTGCAACCA
CCCTTGCTACGCCGCCATGTTTGAGCAGAAAGGCTTTGGTCGGGGTGGAGCCGACAGCCACACTTTCAAG

Alignment

ORF - retro_mmul_1479 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.05 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MPKCPKCNKEVYFAERVTSLGKDWHRPCLKCEKCG-KTLTSGGHAEHEGKPYCNHPCYAAMFGPKGFGRG
          .PKC.K..KEVYFAERVTSLGKDWHRPCLKC.K.G.KTLTSGG.AE.EG.P.CNHPCYAAMF..KGFGRG
Retrocopy IPKCLKYDKEVYFAERVTSLGKDWHRPCLKCQKVG<KTLTSGGRAEQEGRPCCNHPCYAAMFEQKGFGRG

Parental  GAESHTFK
          GA.SHTFK
Retrocopy GADSHTFK

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	1.79 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	3.01 RPM
SRP007412_cerebellum	0.00 RPM	0.97 RPM
SRP007412_heart	0.00 RPM	26.20 RPM
SRP007412_kidney	0.00 RPM	10.21 RPM
SRP007412_liver	0.00 RPM	8.75 RPM
SRP007412_testis	0.04 RPM	1.02 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1479 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1479 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1479 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000047229	1 retrocopy	retro_btau_488,
Callithrix jacchus	ENSCJAG00000019788	1 retrocopy	retro_cjac_163,
Dipodomys ordii	ENSDORG00000001365	1 retrocopy	retro_dord_70,
Homo sapiens	ENSG00000213145	1 retrocopy	retro_hsap_2550,
Gorilla gorilla	ENSGGOG00000027381	1 retrocopy	retro_ggor_3,
Macropus eugenii	ENSMEUG00000001631	1 retrocopy	retro_meug_93,
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,
Pongo abelii	ENSPPYG00000006209	1 retrocopy	retro_pabe_114,
Pan troglodytes	ENSPTRG00000033768	1 retrocopy	retro_ptro_43,
Pteropus vampyrus	ENSPVAG00000014240	1 retrocopy	retro_pvam_1304,
Rattus norvegicus	ENSRNOG00000027990	2 retrocopies	retro_rnor_2590, retro_rnor_2599,
Sarcophilus harrisii	ENSSHAG00000000807	1 retrocopy	retro_shar_341,
Tursiops truncatus	ENSTTRG00000004063	1 retrocopy	retro_ttru_1367,