RetrogeneDB ID: retro_mmul_1778

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 4:85695122..85695551(+)
• Located in intron of: ENSMMUG00000029536

Retrocopy information

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

Parental gene information

• Parental gene symbol: FAM64A
• Ensembl ID: ENSMMUG00000017760
• Aliases: None
• Description: family with sequence similarity 64, member A [Source:HGNC Symbol;Acc:25483]

Sequence

>retro_mmul_1778
GCCATGTCACAGAGAATCCACAAGTCCTGCCAAAGTAGCACCAAGTGGCTGGTGGAGACCCAGGTGAAGGCCAGGAGGAG
GAAAAAAAGGTTTAAAAAGGGAGGGCAGTGGCTCCCCAACTTGCAGCCTGAGCCAGAAGAGTATTCGGCTGTCCAGAGCT
GCCCCTGACCACTCAGCCACAGACCCCCCGTGCATCACCACCTCTCTACCTGGACAGGCTCACGTGCCCACCCTCTACGG
CAGTGGAAGCAGGAGGCTGCCTTCCAGAGCCCCTGCTCCTCGACAGAGCTCCTCTGCTCTCCTAGCGAGTATGATAGTGA
CCTAGAGGCTATGGGGGGCAGGAATTCGGCATCTCCAGAAGCTGTCCCAAGAGCTGGATGAAGCCATTATGGCGGAAGAG
AGTGGTGAAATGACACTCTCATTCATGAT

Alignment

ORF - retro_mmul_1778 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.41 %
• Parental protein coverage: 60.5 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  AMSQRIQESCQSGTKWLVETHVKARRRKRGAQTGSG-SPAHSLSQKSTRLSGAAPAHSATEPWEKE-RHH
          AMSQRI..SCQS.TKWLVET.VKA.RR........G...A..L.....R..G.......T.P......HH
Retrocopy AMSQRIHKSCQSSTKWLVETQVKA-RRRKKRFKKGG<AVAPQLAA*ARRVFGCPELPLTTQPQTPR>HHH

Parental  LSARMGSRAHPSRRSRREAAFRSPYSSTEPLCSPRQSDSDPEPV-GAGIQHLQKLSQELEEAIMAXXSGD
          LS...GSRAHP.R....EAAF.SP.SSTE.LCSP...DSD.E...GAGI.HLQKLSQEL.EAIMA..SG.
Retrocopy LSTWTGSRAHPLRQWKQEAAFQSPCSSTELLCSPSEYDSDLEAM>GAGIRHLQKLSQELDEAIMAEESGE

Parental  II-SLIHD
          ....LIHD
Retrocopy MT<TLIHD

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	0.22 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	0.00 RPM
SRP007412_cerebellum	0.06 RPM	0.06 RPM
SRP007412_heart	0.06 RPM	0.06 RPM
SRP007412_kidney	0.00 RPM	0.00 RPM
SRP007412_liver	0.00 RPM	0.00 RPM
SRP007412_testis	0.11 RPM	0.11 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1778 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1778 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1778 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006997	1 retrocopy	retro_amel_1136,
Homo sapiens	ENSG00000129195	3 retrocopies	retro_hsap_2371, retro_hsap_3030, retro_hsap_3071,
Gorilla gorilla	ENSGGOG00000012309	3 retrocopies	retro_ggor_1801, retro_ggor_2091, retro_ggor_2109,
Macaca mulatta	ENSMMUG00000017760	3 retrocopies	retro_mmul_1778 , retro_mmul_1935, retro_mmul_959,
Mus musculus	ENSMUSG00000020808	1 retrocopy	retro_mmus_3385,
Nomascus leucogenys	ENSNLEG00000009164	3 retrocopies	retro_nleu_361, retro_nleu_725, retro_nleu_843,
Otolemur garnettii	ENSOGAG00000027433	1 retrocopy	retro_ogar_1490,
Pongo abelii	ENSPPYG00000007877	3 retrocopies	retro_pabe_2141, retro_pabe_2509, retro_pabe_2545,
Pan troglodytes	ENSPTRG00000008641	3 retrocopies	retro_ptro_1734, retro_ptro_2044, retro_ptro_2070,
Rattus norvegicus	ENSRNOG00000008040	1 retrocopy	retro_rnor_1325,