RetrogeneDB ID: retro_mmul_917

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 12:51884365..51885204(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: C18H18ORF25
• Ensembl ID: ENSMMUG00000011473
• Aliases: None
• Description: None

Sequence

>retro_mmul_917
GCATCCACAGAGAGTGACAAGCCTATAACCGGCCGAGTTTATGAGAGTGACTCCTCTAATCACTGCATGCTTTCCCCTTC
CTCTAGTGATCACCTGGCTGATTCAGACACGTTGTCTTCCGCAGAAGAGAATGAACCCTCTCAGGCAGAAACGGCGGTAG
AAGGAGACCCTTCAGGAGTGTCTGGTGCCACAGTTGGGCGCAAGTCTAGGCGGTCCCATTTCGAAAGTGAAATATCCACT
ATGGCTGCCAAGAAAAACTAGCAATCCAGTGATAAACAGAATGGGTTAAAGGTCATGGGAGCCAAAAGCACAAGGAGAGG
ATCAGGCTACTGAGGCACAAACAGGAGGTTGCTGCAAGGAAGAAATACAACCTGCTGTAGGACAGTAAGTAGTACCAGTG
ATAGTGACCTGACTTGTGACTCAAGCACGAGCTCATCAGGTGATGATGAAGAGGTTTCAGGGAGCAGCAAGACAATCACT
GCAGAGATACCAGATGGACCTCCAGTTGTAGCTCATTATGATATGCCTGACACCAGCTCTGATCCAAAAGTGGTAAATGT
GTTGGCAATTTATTGGCAGCTGCAGTAGTTCAAGAGCACAATAATTCTATATGCAGCCAGGACACGGGAGCTACCTGGAG
GACCAGCCAGCTTCTACAGGAGCTGAATGCAGAAGCAGGTCATTTGCATCCAGGATTCCTAGCAAGTGATAAAACATCTG
CCGGCAATGCACCGCTCAATTAAGAAATTAATATTGCCTCTTCAGATAGTGAAGCAGAGATTGGGGGAGTTCAGGAACAT
GCAAGTTGTGTTCATCCTCGAGGTGGTGTGATTCTGAGT

Alignment

ORF - retro_mmul_917 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.05 %
• Parental protein coverage: 69.8 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  ASTESDKPTTGRVYESDSSNHCMLSPSSSGHLADSDTLSSVEENEPSQAETAVEGDPSGVSGATVGRKSR
          ASTESDKP.TGRVYESDSSNHCMLSPSSS.HLADSDTLSS.EENEPSQAETAVEGDPSGVSGATVGRKSR
Retrocopy ASTESDKPITGRVYESDSSNHCMLSPSSSDHLADSDTLSSAEENEPSQAETAVEGDPSGVSGATVGRKSR

Parental  RSRSESETSTMAAKKNRQSSDKQNGRVAKVKGHRS-QKHKERIRLLRQKREAAARKKYNLLQDS-STSDS
          RS..ESE.STMAAKKN.QSSDKQNG...KV.G..S..K...R...LR.K.E.AARKKYNLL.DS.S....
Retrocopy RSHFESEISTMAAKKN*QSSDKQNG--LKVMGAKS<HKERIRL--LRHKQEVAARKKYNLL*DS>SSTSD

Parental  DLTCDSSTSSSD-DDEEVSGSSKTITAEIPDGPPVVAHYDMSDTNSEPEVVNVDNL-LAAAVV-QEHNNS
          ......S..SS..DDEEVSGSSKTITAEIPDGPPVVAHYDM.DT.S.P.VVNV....L.AA.V.QEHNNS
Retrocopy SDLTCDSSTSSSGDDEEVSGSSKTITAEIPDGPPVVAHYDMPDTSSDPKVVNVLAI<LLAAAVVQEHNNS

Parental  VGGQDTGATWRTTGLLEELNAEAGHLDPGFLASDKTSAGNAPLNEEINIASSDSEVEIVGVQEHARCVHP
          ...QDTGATWRT..LL.ELNAEAGHL.PGFLASDKTSAGNAPLN.EINIASSDSE.EI.GVQEHA.CVHP
Retrocopy ICSQDTGATWRTSQLLQELNAEAGHLHPGFLASDKTSAGNAPLN*EINIASSDSEAEIGGVQEHASCVHP

Parental  RGGVIQS
          RGGVI.S
Retrocopy RGGVILS

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	11.88 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	11.82 RPM
SRP007412_cerebellum	0.00 RPM	15.43 RPM
SRP007412_heart	0.12 RPM	10.78 RPM
SRP007412_kidney	0.12 RPM	11.15 RPM
SRP007412_liver	0.00 RPM	4.08 RPM
SRP007412_testis	0.00 RPM	7.24 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_917 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_917 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_917 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2190
Callithrix jacchus	retro_cjac_2748

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000008285	1 retrocopy	retro_cjac_2748,
Homo sapiens	ENSG00000152242	1 retrocopy	retro_hsap_2190,
Macaca mulatta	ENSMMUG00000011473	1 retrocopy	retro_mmul_917 ,
Nomascus leucogenys	ENSNLEG00000011251	1 retrocopy	retro_nleu_320,