RetrogeneDB ID: retro_mmul_1622

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 3:98732588..98733511(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCDC86
• Ensembl ID: ENSMMUG00000000019
• Aliases: None
• Description: coiled-coil domain-containing protein 86 [Source:RefSeq peptide;Acc:NP_001252857]

Sequence

>retro_mmul_1622
ATGGATACACCGCTAAGGCACAGCCAAGGGCTGGAAGGCCTAGGGCCTGAATCCCCCGAGAGCCTCACCTCAGTTTTGCG
GGTGAGACGAGTCCTTGTGGAGTTCGAGTCAAACCCAGAAGAAACGAGGGAGCCCGGGTCTCCTCCGAGTGTGCAACAAG
CTGACCTGGGGCGCCCCGCTGAAAGGTCACTGGAGACAATCCAGGATCACCCAGTCTTTGCAGCAGGGTGCAGACTTGGA
GCCCCCCCAGGGGCGGCCAGAATCAGGCCCAGGGTCCCCACAGCGTCAGCAAGACCTACACCTGGAGTCACCTCAAAGAC
AGCTGGAGTCAGTCCTGAATCCCCACGATGTCAGCCGAAGCCAAGTGAGGAGGCACCCAACTGTTCTCAGGGCGAGGGAG
TACTGGCCTCGGTGTTGGCCCAAAGTAAGGAGGAGCTGACCCCAGGGGCCTCCCAGCATCAGCTGCTGCCAGGCCCAGGA
TCACCAGAGCCTTAACCCCATTCAGCAAGCTCCGGGTCCGGAGCCCTCTCAGCTACTACTGGAGCTGACACTCGAGGTAC
CTGGCTTCCCCCGGGGTCAGGGTCAGCACGAGCAGAGCAAACCACCTCCAGCTGGGGAGGTGGTGACACACGGCTTCGGC
AAAGAAGCGAAAGGGTTCTTCATCCCAGGCCCCAGCGTCCAAGAAGCTGAAGAAAGAGCAGCTTTCTGTAATCCCGAAGG
GGAAGCCCAAATCGGGCTGAGTGTGGAAGAACCACTCCAAGAAAAGATTCTCTCTGATGCTTCAGGACAAGCCCCTGCGC
CCATCGTGGCAGGGGAAGCTGAAGCAGGAGAGGAAGCTGGCCTAGGACTTTGCCCCTCACCTGGAGGAGGAGTAGGAGAG
GCGCCGCCAGGAGAAGAAACAGCACCGGGCCGAGAACCTGAAA

Alignment

ORF - retro_mmul_1622 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.11 %
• Parental protein coverage: 85.28 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MDTPLRRSRRLGGLRPESPESLTSVSRVRRALVELQSNPEETREPGSPPSVQQAGLGSP-ERPPETSPGS
          MDTPLR.S..L.GL.PESPESLTSV.RVRR.LVE..SNPEETREPGSPPSVQQA.LG.P.ER..ET....
Retrocopy MDTPLRHSQGLEGLGPESPESLTSVLRVRRVLVEFESNPEETREPGSPPSVQQADLGRPAERSLETIQDH

Parental  P-RLQQGAGLESPQVQPEPGPGSPQRQQDLHLESPQRQPES-RPESPRCQPKSSEEASKCSQDQGVLASE
          P..LQQGA.LE.PQ..PE.GPGSPQRQQDLHLESPQRQ.ES..PESPRCQPK.SEEA..CSQ..GVLAS.
Retrocopy P>SLQQGADLEPPQGRPESGPGSPQRQQDLHLESPQRQLES<SPESPRCQPKPSEEAPNCSQGEGVLASV

Parental  LAQSKEELTPGAPQHQLPPGPGSPEPYPG-QQAPGPEPSQPLLELTPKAPGSPRGQ--HEPSKPPPAGET
          LAQSKEELTPGA.QHQL.PGPGSPEP.P..QQAPGPEPSQ.LLELT...PG.PRGQ..HE.SK.PP....
Retrocopy LAQSKEELTPGASQHQLLPGPGSPEP*PH>QQAPGPEPSQLLLELTLEVPGFPRGQGQHEQSK-PPPAGE

Parental  VTGG-LGAKKRKGSSSQAPASKKLNKEELPVIPKGKPKSGRVWKDRSKKRFSQMLQDKPLRTSWQRKMKE
          V......AKKRKGSSSQAPASKKL.KE.L.VIPKGKPKSG.VWK..SKKRFS.MLQDKPLR.SWQ.K.K.
Retrocopy VVTH>ASAKKRKGSSSQAPASKKLKKEQLSVIPKGKPKSG*VWKNHSKKRFSLMLQDKPLRPSWQGKLK-

Parental  RQERKLAKDFARHLEEEKERRRQEKKQRKAENLK
          .QERKLA.DFA.HLEEE.ERRRQEKKQ..AENLK
Retrocopy -QERKLA*DFAPHLEEE*ERRRQEKKQHRAENLK

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	1.57 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	4.05 RPM
SRP007412_cerebellum	0.00 RPM	1.81 RPM
SRP007412_heart	0.00 RPM	2.30 RPM
SRP007412_kidney	0.00 RPM	4.58 RPM
SRP007412_liver	0.00 RPM	4.79 RPM
SRP007412_testis	0.00 RPM	4.22 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1622 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1622 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1622 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3834
Pan troglodytes	retro_ptro_2610
Gorilla gorilla	retro_ggor_2582

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000110104	2 retrocopies	retro_hsap_3276, retro_hsap_3834,
Gorilla gorilla	ENSGGOG00000013670	1 retrocopy	retro_ggor_2582,
Macaca mulatta	ENSMMUG00000000019	1 retrocopy	retro_mmul_1622 ,
Nomascus leucogenys	ENSNLEG00000013582	1 retrocopy	retro_nleu_2131,
Pongo abelii	ENSPPYG00000003205	1 retrocopy	retro_pabe_2818,
Pan troglodytes	ENSPTRG00000003721	2 retrocopies	retro_ptro_2216, retro_ptro_2610,