RetrogeneDB ID: retro_mmul_2012

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 6:70985519..70986437(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ARPC1A
• Ensembl ID: ENSMMUG00000019342
• Aliases: None
• Description: actin related protein 2/3 complex, subunit 1A, 41kDa [Source:HGNC Symbol;Acc:703]

Sequence

>retro_mmul_2012
ATCACAGGTACTGACTGGGGCTCCCAAGAGCGACCGTGTGGTCACTTGTGGGGCAGACCACAAAGCCTATGTCTGGAGTC
AGCAAGATGGTGTCTGGAAGCCAACCCTGATGATCCTAAGAATTAATCACACAGCTACTTTTGTGAAGTGGTCCCCTCCA
GAGAACAAATTTGCTGTGGGAAGTGAAGCACAACTCATTTCTGTTTGTTACTTTGAGTCTGAAAATGACTGGTAGGTGAG
CAAGCACATTAAAAAGCTGATTCGCTCCACAGTCCTCAGCTTGGATTGGCATCCCAACAAAGTTTTGCTGGCAGCAGGAT
CATGTGACTTCAAACACAGTGTGTTTTCTTCCCACATTAAAAAAGTGGATGAAAAGCCAGGCAGCATGACCTGGGACAGC
AAGATGCCTTTTGGGCAGCTGATGTCAGAGTTTGGTGGCAGTGGCACTGGTGGCTGGGTCCACGGGGTCAGCTTCTCTGC
CTGTGGGAGCCACCTGGCCTGGGCCAGCCACGACAGCACCGTGTCTGTTGCTGATGCCTCAAAAAGTGTGCAGGTCTCAA
TCTGAAGACGGAGTTCCAGCTGCTCCTGAGTGTGTCATTCATCTCAGAGAACAGTGTCGTGGCTGCTGGCCATGACTGCT
GACCAATGCTCTGTAACTACGATGACTATGGCTGCCTGACCTTTGTCTCCAAGTTAGAGATTCCAAAACAGAGCATCCAA
CGCAACATGTCTGCCATGGAATGCTTCTGCAATATGGACAAGAGGGCCATGACTGAGGGCTGCAACATGGCTTTGGAGAT
GCTGCACCAGAATAGCATCGCTCAAGTCTCTATTTATGAGGTGGACAAGAAAGATTGTCACAAATATTGCACTACTGGCA
TCGATGGAGCCATGACAATTTGGGATTTCAAGGCCCTC

Alignment

ORF - retro_mmul_2012 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.77 %
• Parental protein coverage: 83.15 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LAGIDW-APKSDRIVTCGADRNAYVWSQKDGVWKPTLVILRINRAATFVKWSPLENKFAVGSGARLISVC
          ..G.DW.APKSDR.VTCGAD..AYVWSQ.DGVWKPTL.ILRIN..ATFVKWSP.ENKFAVGS.A.LISVC
Retrocopy ITGTDW>APKSDRVVTCGADHKAYVWSQQDGVWKPTLMILRINHTATFVKWSPPENKFAVGSEAQLISVC

Parental  YFESENDWWVSKHIKKPIRSTVLSLDWHPNNVLLAAGSCDFKCRVFSAYIKEVDEKPASTPWGSKMPFGQ
          YFESENDW.VSKHIKK.IRSTVLSLDWHPN.VLLAAGSCDFK..VFS..IK.VDEKP.S..W.SKMPFGQ
Retrocopy YFESENDW*VSKHIKKLIRSTVLSLDWHPNKVLLAAGSCDFKHSVFSSHIKKVDEKPGSMTWDSKMPFGQ

Parental  LMSEFGGSGTGGWVHGVSFSASGSRLAWVSHDSTVSVADASKSVQVS-TLKTEFLPLLSVSFVSENSVVA
          LMSEFGGSGTGGWVHGVSFSA.GS.LAW.SHDSTVSVADASKSVQVS..LKTEF..LLSVSF.SENSVVA
Retrocopy LMSEFGGSGTGGWVHGVSFSACGSHLAWASHDSTVSVADASKSVQVS<NLKTEFQLLLSVSFISENSVVA

Parental  AGHDCCPMLFNYDDRGCLTFVSKLDIPKQSIQRNMSAMERFRNMDKRATTEDRNTALETLHQNSITQVSI
          AGHDC.PML.NYDD.GCLTFVSKL.IPKQSIQRNMSAME.F.NMDKRA.TE..N.ALE.LHQNSI.QVSI
Retrocopy AGHDC*PMLCNYDDYGCLTFVSKLEIPKQSIQRNMSAMECFCNMDKRAMTEGCNMALEMLHQNSIAQVSI

Parental  YEVDKQDCRKFCTTGIDGAMTIWDFKTL
          YEVDK.DC.K.CTTGIDGAMTIWDFK.L
Retrocopy YEVDKKDCHKYCTTGIDGAMTIWDFKAL

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	51.88 RPM
SRP007412_brain_prefrontal_cortex	0.16 RPM	67.27 RPM
SRP007412_cerebellum	1.16 RPM	41.26 RPM
SRP007412_heart	0.41 RPM	28.15 RPM
SRP007412_kidney	0.70 RPM	42.84 RPM
SRP007412_liver	0.20 RPM	36.77 RPM
SRP007412_testis	0.26 RPM	32.60 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2012 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2012 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2012 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3191
Pan troglodytes	retro_ptro_2253
Gorilla gorilla	retro_ggor_1337
Pongo abelii	retro_pabe_2647

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Parental genes homology:

Parental genes homology involve 21 parental genes, and 54 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006322	1 retrocopy	retro_amel_1431,
Bos taurus	ENSBTAG00000004242	1 retrocopy	retro_btau_1486,
Callithrix jacchus	ENSCJAG00000015859	3 retrocopies	retro_cjac_2141, retro_cjac_2165, retro_cjac_2263,
Cavia porcellus	ENSCPOG00000001777	2 retrocopies	retro_cpor_452, retro_cpor_981,
Dipodomys ordii	ENSDORG00000016059	1 retrocopy	retro_dord_593,
Equus caballus	ENSECAG00000016467	1 retrocopy	retro_ecab_185,
Homo sapiens	ENSG00000241685	2 retrocopies	retro_hsap_2010, retro_hsap_3191,
Loxodonta africana	ENSLAFG00000014024	1 retrocopy	retro_lafr_1006,
Macropus eugenii	ENSMEUG00000005609	8 retrocopies	retro_meug_1033, retro_meug_1081, retro_meug_1495, retro_meug_1668, retro_meug_1755, retro_meug_1912, retro_meug_2179, retro_meug_492,
Myotis lucifugus	ENSMLUG00000010912	1 retrocopy	retro_mluc_1432,
Macaca mulatta	ENSMMUG00000019342	2 retrocopies	retro_mmul_1383, retro_mmul_2012 ,
Monodelphis domestica	ENSMODG00000001303	9 retrocopies	retro_mdom_1360, retro_mdom_1380, retro_mdom_1438, retro_mdom_1551, retro_mdom_1796, retro_mdom_1917, retro_mdom_686, retro_mdom_699, retro_mdom_808,
Mus musculus	ENSMUSG00000029621	1 retrocopy	retro_mmus_1373,
Nomascus leucogenys	ENSNLEG00000010852	2 retrocopies	retro_nleu_1663, retro_nleu_2069,
Oryctolagus cuniculus	ENSOCUG00000003944	1 retrocopy	retro_ocun_1130,
Otolemur garnettii	ENSOGAG00000010870	6 retrocopies	retro_ogar_1547, retro_ogar_2690, retro_ogar_2697, retro_ogar_381, retro_ogar_610, retro_ogar_656,
Pongo abelii	ENSPPYG00000025816	4 retrocopies	retro_pabe_1647, retro_pabe_1648, retro_pabe_2537, retro_pabe_2647,
Pan troglodytes	ENSPTRG00000033819	2 retrocopies	retro_ptro_1340, retro_ptro_2253,
Sarcophilus harrisii	ENSSHAG00000010673	2 retrocopies	retro_shar_180, retro_shar_727,
Ictidomys tridecemlineatus	ENSSTOG00000001660	1 retrocopy	retro_itri_1834,
Tupaia belangeri	ENSTBEG00000011381	3 retrocopies	retro_tbel_1237, retro_tbel_1241, retro_tbel_82,