RetrogeneDB ID: retro_mmul_2088

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 6:69178262..69178846(-)
• Located in intron of: ENSMMUG00000015422

Retrocopy information

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

Parental gene information

• Parental gene symbol: CHP
• Ensembl ID: ENSMMUG00000017092
• Aliases: None
• Description: calcium-binding protein p22 [Source:RefSeq peptide;Acc:NP_001253300]

Sequence

>retro_mmul_2088
ATGGGTTCTCAGCCCTCCATGTTACCGTGGGACAAAGAGCTCGAGGAGATCAAGAAGGAGATCAGCTTTTCCCACAGTCA
AATCACTTGCTCTATAGCCGGTTCACCAGCCTGGACAAAGAAGAGACTGGCACTCTCAGCCAGGAAGATTTCCTGAGGAT
TCCAGAACTTGTCATCGACCCACTGGGGGACCAAATCATCAATGCCTTCTTTCCAGAGGGAGAGGACCAGGTAAACTTCC
GTGGATTCACGCAAACTTTGGCTCATCTCCTCCTCATTGAGGATAACGAAAAGAGCAAAGATGTGAATGGACCCGAACCA
CTCAACAGCCGAAGCAACAAACTGCACTTTGCTTTTTGACTATATGAGTTCGATAAAGATGATAAGCTCTCCCGTGATGA
GCTGATACAGGTGCTATGCTTGATGGCTGGAGTAAATATCTCAGATGAGCAGCTGGGCAGCATCGCAGACAGGACCATTC
CGGAGGCTGATCAGGATGGAGACAGTGCCATATCTTTCACAGAATTTGTTAAGGTTTTGGAGAAGGTGGATGTAGAACAG
AAAATGAGCATCTGATTTCTTCAC

Alignment

ORF - retro_mmul_2088 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.16 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MGSRASTLLRDEELEEIKKETGFSHSQIT-RLYSRFTSLDKGENGTLSREDFQRIPELAINPLGDRIINA
          MGS..S.L..D.ELEEIKKE..FSHSQIT..LYSRFTSLDK.E.GTLS.EDF.RIPEL.I.PLGD.IINA
Retrocopy MGSQPSMLPWDKELEEIKKEISFSHSQIT<LLYSRFTSLDKEETGTLSQEDFLRIPELVIDPLGDQIINA

Parental  FFPEGEDQVNFRGFMRTLAHFRPIEDNEKSKDVNGPEPLNSRSNKLHFAFRLYDLDKDEKISRDELLQVL
          FFPEGEDQVNFRGF..TLAH...IEDNEKSKDVNGPEPLNSRSNKLHFAF.LY..DKD.K.SRDEL.QVL
Retrocopy FFPEGEDQVNFRGFTQTLAHLLLIEDNEKSKDVNGPEPLNSRSNKLHFAF*LYEFDKDDKLSRDELIQVL

Parental  RMMVGVNISDEQLGSIADRTIQEADQDGDSAISFTEFVKVLEKVDVEQKMSIRFLH
          ..M.GVNISDEQLGSIADRTI.EADQDGDSAISFTEFVKVLEKVDVEQKMSI.FLH
Retrocopy CLMAGVNISDEQLGSIADRTIPEADQDGDSAISFTEFVKVLEKVDVEQKMSI*FLH

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	54.34 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	61.80 RPM
SRP007412_cerebellum	0.00 RPM	20.53 RPM
SRP007412_heart	0.12 RPM	23.79 RPM
SRP007412_kidney	0.35 RPM	30.40 RPM
SRP007412_liver	0.04 RPM	25.53 RPM
SRP007412_testis	0.00 RPM	19.00 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2088 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2088 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2088 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3334
Pan troglodytes	retro_ptro_2144
Gorilla gorilla	retro_ggor_1293
Pongo abelii	retro_pabe_2749

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000009525	1 retrocopy	retro_cfam_2136,
Cavia porcellus	ENSCPOG00000010577	2 retrocopies	retro_cpor_1224, retro_cpor_726,
Homo sapiens	ENSG00000187446	2 retrocopies	retro_hsap_3334, retro_hsap_3541,
Gorilla gorilla	ENSGGOG00000007312	2 retrocopies	retro_ggor_1293, retro_ggor_2392,
Macaca mulatta	ENSMMUG00000017092	2 retrocopies	retro_mmul_1809, retro_mmul_2088 ,
Macaca mulatta	ENSMMUG00000017460	1 retrocopy	retro_mmul_1141,
Mus musculus	ENSMUSG00000014077	4 retrocopies	retro_mmus_1458, retro_mmus_2094, retro_mmus_3133, retro_mmus_3469,
Nomascus leucogenys	ENSNLEG00000003465	4 retrocopies	retro_nleu_1678, retro_nleu_2269, retro_nleu_2608, retro_nleu_2609,
Procavia capensis	ENSPCAG00000005419	1 retrocopy	retro_pcap_240,
Pongo abelii	ENSPPYG00000006370	2 retrocopies	retro_pabe_2749, retro_pabe_2925,
Pan troglodytes	ENSPTRG00000006942	2 retrocopies	retro_ptro_2144, retro_ptro_2407,
Rattus norvegicus	ENSRNOG00000004742	2 retrocopies	retro_rnor_2034, retro_rnor_2223,
Ictidomys tridecemlineatus	ENSSTOG00000014503	1 retrocopy	retro_itri_227,