RetrogeneDB ID: retro_mmul_2580

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: X:54570718..54571138(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCDC117
• Ensembl ID: ENSMMUG00000007214
• Aliases: None
• Description: coiled-coil domain containing 117 [Source:HGNC Symbol;Acc:26599]

Sequence

>retro_mmul_2580
GAGAACCAGTGTGAAGTTGCCTGAAGTAAGCTTCAGGAGATTGAAGACAGGATAATTGATGAAGAAGTTGAAGCTCACAG
AAATGTTAACCACCTCCGTAGTCTTCTCCTTTCTGATACTATGAAAACAGGTTTGAAGAAGGAATTTGATGAACTTTACA
AAAACAAAAAAAAAATTGAGTCTATGAGCCATCCTTCCATGGAGCTTGTTCTCTAGAAACCCCTCACTGAACTCCTTCCC
AATGAGCCAAAGCCATCCTCTAATGCTAAGAACTATACAGGAGAGAGCCAAGCTAAGCATGCAGCTGCTGGCATTGCCTT
CTCTCAGAGAACTGAACTGTTCTGGGAACTTCGGCACACAGGGATGTCTCCTTATAATGGTTTGGAGATAGCTACTAGCA
CAGAAGCAGAGATGGAACTC

Alignment

ORF - retro_mmul_2580 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.06 %
• Parental protein coverage: 50.54 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EPQCEVARRKLQEIEDRIIDEDEEVEADRNVNHLPSLVLSDTMKTGLKREFDEVFTKKMI-ESMSRPSME
          E.QCEVA..KLQEIEDRIIDE..EVEA.RNVNHL.SL.LSDTMKTGLK.EFDE........ESMS.PSME
Retrocopy ENQCEVA*SKLQEIEDRIIDE--EVEAHRNVNHLRSLLLSDTMKTGLKKEFDELYXXXXXXESMSHPSME

Parental  LVLWKPLPELLSDKPKPSSNTKNYTGESQAKHAAAGTAFPQRTELFLEPRQPGMSLYNSLETATSTEEEM
          LVL.KPL.ELL...PKPSSN.KNYTGESQAKHAAAG.AF.QRTELF.E.R..GMS.YN.LE.ATSTE.EM
Retrocopy LVL*KPLTELLPNEPKPSSNAKNYTGESQAKHAAAGIAFSQRTELFWELRHTGMSPYNGLEIATSTEAEM

Parental  EL
          EL
Retrocopy EL

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	17.14 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	11.74 RPM
SRP007412_cerebellum	0.00 RPM	25.57 RPM
SRP007412_heart	0.00 RPM	9.36 RPM
SRP007412_kidney	0.00 RPM	8.69 RPM
SRP007412_liver	0.00 RPM	8.31 RPM
SRP007412_testis	0.00 RPM	27.33 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2580 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2580 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2580 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000020088	1 retrocopy	retro_cjac_2465,
Microcebus murinus	ENSMICG00000004228	2 retrocopies	retro_mmur_431, retro_mmur_914,
Macaca mulatta	ENSMMUG00000007214	1 retrocopy	retro_mmul_2580 ,
Tursiops truncatus	ENSTTRG00000011845	1 retrocopy	retro_ttru_1174,