RetrogeneDB ID: retro_mmul_2333

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 8:38191429..38191936(-)
• Located in intron of: ENSMMUG00000000943

Retrocopy information

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

Parental gene information

• Parental gene symbol: CXorf56
• Ensembl ID: ENSMMUG00000022665
• Aliases: None
• Description: chromosome X open reading frame 56 [Source:HGNC Symbol;Acc:26239]

Sequence

>retro_mmul_2333
GACCGGTCCCGTGTGATTGATGCTGCCAAACATGCCCATAAGTTTTGTAACACAGAAGATGAAGAGACTATGTATCTGCG
GAGACCTGGAGGCATTGAACGACAGTACAGAAAGAAATGTGCAAAGTGTGGACTGCCGCTCTTCTACCAATTCCAGCCGA
AGAATGCTCCTGTTACCTTCATTGTGGATGGAGCTGTAGTTAAGTTTGGCCAGGGCTTTGGGAAAACGAACATATATACT
CAGAAACAAGAGCCTCCTAAGAAGGTGATGATGACCAAACGGACCAAAGACATGGGCAAGTTCAGTTCTGTCACTGTGTC
TACCATTGATGAAGAGGAAGAGGAGATTGAGGCTAGGGAAGTTGCTGACTCGTATGCACAGAACGCCAAAGTGATTGAAA
AACAGCTAGAGCGCAAAGGCATGAGCAAGAGACGACTACAAGAGCTGGCTGAACGGGAAGCCAAGAAAGCGAAAATGAAG
GGGACCTTGATTGACAACCAGTTCAAA

Alignment

ORF - retro_mmul_2333 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.22 %
• Parental protein coverage: 76.82 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DRSRVIDAAKHAHKFCNTEDEETMYLRRPEGIERQYRKKCAKCGLPLFYQSQPKNAPVTFIVDGAVVKFG
          DRSRVIDAAKHAHKFCNTEDEETMYLRRP.GIERQYRKKCAKCGLPLFYQ.QPKNAPVTFIVDGAVVKFG
Retrocopy DRSRVIDAAKHAHKFCNTEDEETMYLRRPGGIERQYRKKCAKCGLPLFYQFQPKNAPVTFIVDGAVVKFG

Parental  QGFGKTNIYTQKQEPPKKVMMTKRTKDMGKFSSVTVSTIDEEEEEIEAREVADSYAQNAKVIEKQLERKG
          QGFGKTNIYTQKQEPPKKVMMTKRTKDMGKFSSVTVSTIDEEEEEIEAREVADSYAQNAKVIEKQLERKG
Retrocopy QGFGKTNIYTQKQEPPKKVMMTKRTKDMGKFSSVTVSTIDEEEEEIEAREVADSYAQNAKVIEKQLERKG

Parental  MSKRRLQELAELEAKKAKMKGTLIDNQFK
          MSKRRLQELAE.EAKKAKMKGTLIDNQFK
Retrocopy MSKRRLQELAEREAKKAKMKGTLIDNQFK

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	0.67 RPM	10.98 RPM
SRP007412_brain_prefrontal_cortex	0.32 RPM	8.65 RPM
SRP007412_cerebellum	0.45 RPM	5.49 RPM
SRP007412_heart	0.18 RPM	6.54 RPM
SRP007412_kidney	0.70 RPM	5.05 RPM
SRP007412_liver	0.00 RPM	3.29 RPM
SRP007412_testis	18.58 RPM	8.03 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2333 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2333 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2333 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Callithrix jacchus	retro_cjac_311

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000005111	1 retrocopy	retro_cjac_311,
Homo sapiens	ENSG00000018610	1 retrocopy	retro_hsap_4044,
Gorilla gorilla	ENSGGOG00000013324	1 retrocopy	retro_ggor_2711,
Latimeria chalumnae	ENSLACG00000012468	1 retrocopy	retro_lcha_59,
Myotis lucifugus	ENSMLUG00000015751	1 retrocopy	retro_mluc_72,
Macaca mulatta	ENSMMUG00000022665	1 retrocopy	retro_mmul_2333 ,
Mus musculus	ENSMUSG00000006423	1 retrocopy	retro_mmus_1715,
Nomascus leucogenys	ENSNLEG00000014862	1 retrocopy	retro_nleu_2057,
Otolemur garnettii	ENSOGAG00000012474	1 retrocopy	retro_ogar_145,
Pongo abelii	ENSPPYG00000020670	1 retrocopy	retro_pabe_177,
Pan troglodytes	ENSPTRG00000022224	1 retrocopy	retro_ptro_104,
Sorex araneus	ENSSARG00000003163	1 retrocopy	retro_sara_5,
Sarcophilus harrisii	ENSSHAG00000006319	1 retrocopy	retro_shar_16,
Ictidomys tridecemlineatus	ENSSTOG00000011579	1 retrocopy	retro_itri_103,
Tursiops truncatus	ENSTTRG00000013101	2 retrocopies	retro_ttru_231, retro_ttru_77,