RetrogeneDB ID: retro_mmul_299

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 18:52833707..52834832(+)
• Located in intron of: ENSMMUG00000010402

Retrocopy information

• Ensembl ID: ENSMMUG00000014993
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: MMU.2546
• Ensembl ID: ENSMMUG00000003552
• Aliases: None
• Description: None

Sequence

>retro_mmul_299
ATGGCGAACCAGGTTATCAAGTGCAAGGCTGCAGTTGCTTGGGAGGCTGGAAAGCCTCTCTCCATAGAGGAGATAGAGGT
GGCACCCCCAAAGGCTCATGAAGTTCGAATCAAGATCATTGCCACTGCAGTTTGCCACACTGATGCCTATACCCTGAGCG
GAGCTGAGCCTGAGGGTTGTTTTCCAGTGATCTTGGGACATGAAGGTGCTGGAATTGTGGAAAGTGTTGGCGAGGGAGTT
ACTAAACTGAAGGCGGGTGACACTGTCATCCCACTTTACATCCCACAGTGTGGAGAATGCAAATTTTGTCTAAATCATAA
AACTAACCTTTGCCAGAAGATAAGAGTCACTCAAGGGAAAGGATTAATGCCAGATGGTACCAGCAGATTTACTTGCAAAG
GAAAGACAATTTTGCATTACATGGGAACCAGCACATTTTCTGAATACACAGTTGTGGCTGATATCTCTGTTGCTAAAATA
GATCCTTTAGCACCTTTGGATAAAGTCTGCCTTCTAGGTTGTGGCATTTCAACTGGTTATGGTGCTGCTGTGAACACTGC
CAAGGTGGAGCCTGGCTCTGTTTGTGCGGTCTTTGGCCTGGGAGGAGTTGGACTGGCAGTTATCATGGGCTGTAAAGTGG
CTGGTGCATCCCGGATCATTGGTGTGGACATCAATAAAGATAAATTTGCAAGGGCCAAAGAGTTTGGAGCCACTGAATGT
ATTAACCCTCAGGATTTTAGTAAACCCATCCAGGAAGTGCTCATTGAGATGACTGATGGAGGAGTAGACTATTCCTTTGA
ATGTACTGGTAATGTGAAGGTCATGAGAGCAGCACTTGAGGCGTGTCACAAGGGCTGGGGCATCAGCGTGGTGGTTGGAA
TAGCTGCTTCAGGTGAAGAAATTGCCACTCGTCCATTCCAGCTGGTAACAGGTCGCACATGGAAAGGCACTGCCTTTGGA
GGATGGAAGAGTGTTGAAAGTGTCCCAAAGTTGGTGTCTGAATATATGTCCAAAAAGATAAAAGTTGATGAATTTGTGAC
TCACAATCTGTCTTTTGATGAAATTAACAAAGCCTTTGAACTGATGCATTCTGGAAAGAGCATTCGAACTGTTGTAAAGA
TTTAA

Alignment

ORF - retro_mmul_299 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.38 %
• Parental protein coverage: 99.46 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QVIKCKAAVAWEAGKPLSIEEIEVAPPKAHEVRIKIIATAVCHTDAYTLSGADPEGCFPVILGHEGAGVV
          QVIKCKAAVAWEAGKPLSIEEIEVAPPKAHEVRIKIIATAVCHTDAYTLSGA.PEGCFPVILGHEGAG.V
Retrocopy QVIKCKAAVAWEAGKPLSIEEIEVAPPKAHEVRIKIIATAVCHTDAYTLSGAEPEGCFPVILGHEGAGIV

Parental  ESVGEGVTKLKAGDTVIPLYIPQCGECKFCLNPKTNLCQKIRVTQGKGLMPDGTSRFTCKGKTILHYMGT
          ESVGEGVTKLKAGDTVIPLYIPQCGECKFCLN.KTNLCQKIRVTQGKGLMPDGTSRFTCKGKTILHYMGT
Retrocopy ESVGEGVTKLKAGDTVIPLYIPQCGECKFCLNHKTNLCQKIRVTQGKGLMPDGTSRFTCKGKTILHYMGT

Parental  STFSEYTVVADISVAKIDPLAPLDKVCLLGCGISTGYGAAVNTAKVEPGSVCAVFGLGGVGLAVIMGCKV
          STFSEYTVVADISVAKIDPLAPLDKVCLLGCGISTGYGAAVNTAKVEPGSVCAVFGLGGVGLAVIMGCKV
Retrocopy STFSEYTVVADISVAKIDPLAPLDKVCLLGCGISTGYGAAVNTAKVEPGSVCAVFGLGGVGLAVIMGCKV

Parental  AGASRIIGVDINKDKFARAKEFGATECINPQDFSKPIQEVLIEMTDGGVDYSFECIGNVKVMRAALEACH
          AGASRIIGVDINKDKFARAKEFGATECINPQDFSKPIQEVLIEMTDGGVDYSFEC.GNVKVMRAALEACH
Retrocopy AGASRIIGVDINKDKFARAKEFGATECINPQDFSKPIQEVLIEMTDGGVDYSFECTGNVKVMRAALEACH

Parental  KGWGVSVVVGVAASGEEIATRPFQLVTGRTWKGTAFGGWKSVESVPKLVSEYMSKKIKVDEFVTHNLSFD
          KGWG.SVVVG.AASGEEIATRPFQLVTGRTWKGTAFGGWKSVESVPKLVSEYMSKKIKVDEFVTHNLSFD
Retrocopy KGWGISVVVGIAASGEEIATRPFQLVTGRTWKGTAFGGWKSVESVPKLVSEYMSKKIKVDEFVTHNLSFD

Parental  EINKAFELMHSGKSIRTVVKI
          EINKAFELMHSGKSIRTVVKI
Retrocopy EINKAFELMHSGKSIRTVVKI

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	0.45 RPM	20.84 RPM
SRP007412_brain_prefrontal_cortex	1.11 RPM	36.17 RPM
SRP007412_cerebellum	0.65 RPM	19.63 RPM
SRP007412_heart	1.35 RPM	47.34 RPM
SRP007412_kidney	2.00 RPM	67.60 RPM
SRP007412_liver	5.42 RPM	132.65 RPM
SRP007412_testis	1.13 RPM	16.47 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_299 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_299 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_299 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 12 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000013007	1 retrocopy	retro_cfam_14,
Callithrix jacchus	ENSCJAG00000007198	2 retrocopies	retro_cjac_1029, retro_cjac_2933,
Homo sapiens	ENSG00000197894	3 retrocopies	retro_hsap_175, retro_hsap_330, retro_hsap_3607,
Gorilla gorilla	ENSGGOG00000028244	2 retrocopies	retro_ggor_2434, retro_ggor_354,
Myotis lucifugus	ENSMLUG00000002722	1 retrocopy	retro_mluc_1702,
Macaca mulatta	ENSMMUG00000003552	1 retrocopy	retro_mmul_299 ,
Mustela putorius furo	ENSMPUG00000009642	1 retrocopy	retro_mputfur_1625,
Nomascus leucogenys	ENSNLEG00000013946	3 retrocopies	retro_nleu_1772, retro_nleu_2636, retro_nleu_983,
Pongo abelii	ENSPPYG00000014946	3 retrocopies	retro_pabe_176, retro_pabe_359, retro_pabe_453,
Pan troglodytes	ENSPTRG00000016303	3 retrocopies	retro_ptro_166, retro_ptro_2438, retro_ptro_266,
Sus scrofa	ENSSSCG00000009185	1 retrocopy	retro_sscr_659,
Xenopus tropicalis	ENSXETG00000009304	1 retrocopy	retro_xtro_57,