RetrogeneDB ID: retro_mmul_942

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 12:23008828..23009647(-)
• Located in intron of: ENSMMUG00000006182

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.3877
• Ensembl ID: ENSMMUG00000015668
• Aliases: None
• Description: F-actin-capping protein subunit alpha-1 [Source:RefSeq peptide;Acc:NP_001248143]

Sequence

>retro_mmul_942
GTACGCATAGCTGCTGAATTCATCACTCATGCACCCCCAGGGGAATTTAATGAAGTATTCAGTGATGTTTGGCTACTACG
TAATAATGACAACCTCCTCAGGGAAAGGGCAGAACATGCATTTGCTCATTACAACGTGAATCAGTTCACACCTGTGAAGA
TAGAAGGATATGAAGATCAGGTCTTAATTACAGAGCATGGTGACCTGGGCAATAGCAGAGTTTTAGATCCAAGAAACAAC
TTTTCCTTTAAATTTGATCACTTACAGAAAGAAGCAAGTGACCCCCAGCCAGAACAAGTAGATGGAGGTCTGAAGTCTTG
GAGATAATCCTGTGACAGTGCTTTAAGAGCCTGTGTGAAAGACCGTTATTCCAACTGCTTCTGTATTGTTTATGCTAAAA
CTATCGATGGGCAACAGACTATTATTGCGTGTATTGAAAGCCACCAGAGTCAGCCTAAAAACTTATGGAATGGTCGTTGG
AGATCAGAGTGGAAGTTGACCATCACACCACCTACAGGCCAGGTGGTTGGAGTGCTTAAGATTCAGGTTCACTATTATGA
AGATGGCAATGTTCAGTTGGTTAGTCATAAAGATGTACATGATTCACTAACTGTTTCGAATGACACACAAACTGCCAAGG
AGTTTATTAAAATCATAGAGAATGCAGAAAATGAGCGTCAGACAGCAATTAGTGAAAACTATCAAACAATGTCAGATACC
ACATTCAAGGTCTTGCGCTGGCAGCTTCCAGGTACCCACACCAAAATCGACTAGAACAAGATACTCAGCTACAACATTGC
CAAAGAAATGCAGAATGCC

Alignment

ORF - retro_mmul_942 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.55 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VRIAAKFITHAPPGEFNEVFNDVRLLLNNDNLLREGAAHAFAQYNMDQFTPVKIEGYEDQVLITEHGDLG
          VRIAA.FITHAPPGEFNEVF.DV.LL.NNDNLLRE.A.HAFA.YN..QFTPVKIEGYEDQVLITEHGDLG
Retrocopy VRIAAEFITHAPPGEFNEVFSDVWLLRNNDNLLRERAEHAFAHYNVNQFTPVKIEGYEDQVLITEHGDLG

Parental  NSRFLDPRNKISFKFDHLRKEASDPQPEEVDGGLKSWRESCDSALRAYVKDHYSNGFCTVYAKTIDGQQT
          NSR.LDPRN..SFKFDHL.KEASDPQPE.VDGGLKSWR.SCDSALRA.VKD.YSN.FC.VYAKTIDGQQT
Retrocopy NSRVLDPRNNFSFKFDHLQKEASDPQPEQVDGGLKSWR*SCDSALRACVKDRYSNCFCIVYAKTIDGQQT

Parental  IIACIESHQFQPKNFWNGRWRSEWKFTITPPTAQVVGVLKIQVHYYEDGNVQLVSHKDVQDSLTVSNEAQ
          IIACIESHQ.QPKN.WNGRWRSEWK.TITPPT.QVVGVLKIQVHYYEDGNVQLVSHKDV.DSLTVSN..Q
Retrocopy IIACIESHQSQPKNLWNGRWRSEWKLTITPPTGQVVGVLKIQVHYYEDGNVQLVSHKDVHDSLTVSNDTQ

Parental  TAKEFIKIIENAENEYQTAISENYQTMSDTTFKALRRQLPVTRTKIDWNKILSYKIGKEMQNA
          TAKEFIKIIENAENE.QTAISENYQTMSDTTFK.LR.QLP.T.TKID.NKILSY.I.KEMQNA
Retrocopy TAKEFIKIIENAENERQTAISENYQTMSDTTFKVLRWQLPGTHTKID*NKILSYNIAKEMQNA

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	0.11 RPM	46.39 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	31.18 RPM
SRP007412_cerebellum	0.06 RPM	49.21 RPM
SRP007412_heart	0.29 RPM	34.51 RPM
SRP007412_kidney	0.47 RPM	50.12 RPM
SRP007412_liver	0.12 RPM	33.77 RPM
SRP007412_testis	0.45 RPM	98.87 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_942 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_942 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_942 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2338
Pan troglodytes	retro_ptro_1710
Gorilla gorilla	retro_ggor_1774
Pongo abelii	retro_pabe_2116

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 41 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000003570	1 retrocopy	retro_amel_219,
Callithrix jacchus	ENSCJAG00000013548	3 retrocopies	retro_cjac_2259, retro_cjac_2850, retro_cjac_4125,
Cavia porcellus	ENSCPOG00000014532	1 retrocopy	retro_cpor_1155,
Dipodomys ordii	ENSDORG00000000671	3 retrocopies	retro_dord_224, retro_dord_265, retro_dord_44,
Felis catus	ENSFCAG00000013303	2 retrocopies	retro_fcat_700, retro_fcat_746,
Homo sapiens	ENSG00000116489	2 retrocopies	retro_hsap_2338, retro_hsap_4871,
Gorilla gorilla	ENSGGOG00000023677	1 retrocopy	retro_ggor_1216,
Latimeria chalumnae	ENSLACG00000017963	1 retrocopy	retro_lcha_20,
Macaca mulatta	ENSMMUG00000015668	2 retrocopies	retro_mmul_2612, retro_mmul_942 ,
Mus musculus	ENSMUSG00000070372	4 retrocopies	retro_mmus_179, retro_mmus_1828, retro_mmus_3370, retro_mmus_349,
Nomascus leucogenys	ENSNLEG00000004191	1 retrocopy	retro_nleu_1689,
Oryctolagus cuniculus	ENSOCUG00000000270	6 retrocopies	retro_ocun_1315, retro_ocun_1417, retro_ocun_1787, retro_ocun_301, retro_ocun_527, retro_ocun_555,
Otolemur garnettii	ENSOGAG00000014074	4 retrocopies	retro_ogar_1640, retro_ogar_2159, retro_ogar_3217, retro_ogar_845,
Pongo abelii	ENSPPYG00000001021	2 retrocopies	retro_pabe_2116, retro_pabe_3789,
Pan troglodytes	ENSPTRG00000001110	2 retrocopies	retro_ptro_1710, retro_ptro_3245,
Rattus norvegicus	ENSRNOG00000013538	1 retrocopy	retro_rnor_77,
Tupaia belangeri	ENSTBEG00000001727	5 retrocopies	retro_tbel_1870, retro_tbel_3525, retro_tbel_4327, retro_tbel_638, retro_tbel_868,