RetrogeneDB ID: retro_mmul_1470

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 2:145052356..145052866(+)
• Located in intron of: ENSMMUG00000012406

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.4150
• Ensembl ID: ENSMMUG00000013379
• Aliases: None
• Description: 60S ribosomal protein L8 [Source:RefSeq peptide;Acc:NP_001253030]

Sequence

>retro_mmul_1470
TTGTATTGCGGCAAGAAGGCCCAACTCAACATTGGCAGTATGCTCCCTGTGGGCACCATGCCTGAGGGTATGATCGTGTG
CTGCCTGGAGGAGAAGCCTGGAGGCCGTAGCAAGCTGTCCTGGGCATCTGGGAACTATGCCACCATTATCTCCCACAACT
CTGAGACCAAGAAGACCCGTGTGAAGCTGCCCTCTGGCTCCAAGAAGGTTATCTTCTCAGCCAACAGAGCTGTGGTTGGT
GTGGTGGCTGGAGGTTGCCGAATTGACAAACCCATCTTGAAGGCTGGCTGAGCCTACCACAAATATAAGGCAAAGGGGAA
CTGCTGGCCACGAGTATAGGATGTGGCCATGAACCCTATGGAGCATCCTTTTGGAGGCGGCAACCACCAGCACATCGGCA
AGCCCTCCACCGTCTGCAGAGATGACCCTGCTGGCTGCAAAGTGGATCTCACTGCTGCCCGCCAGACTGGACGTCTCTGG
GGAACCAAGACCGTGCAGGAGAAAGAGAAC

Alignment

ORF - retro_mmul_1470 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.29 %
• Parental protein coverage: 66.15 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VYCGKKAQLNIGNVLPVGTMPEGTIVCCLEEKPGDRGKLARASGNYATVISHNPETKKTRVKLPSGSKKV
          .YCGKKAQLNIG..LPVGTMPEG.IVCCLEEKPG.R.KL..ASGNYAT.ISHN.ETKKTRVKLPSGSKKV
Retrocopy LYCGKKAQLNIGSMLPVGTMPEGMIVCCLEEKPGGRSKLSWASGNYATIISHNSETKKTRVKLPSGSKKV

Parental  ISSANRAVVGVVAGGGRIDKPILKAGRAYHKYKAKRNCWPRVRGVAMNPVEHPFGGGNHQHIGKPSTIRR
          I.SANRAVVGVVAGG.RIDKPILKAG.AYHKYKAK.NCWPRV..VAMNP.EHPFGGGNHQHIGKPST..R
Retrocopy IFSANRAVVGVVAGGCRIDKPILKAG*AYHKYKAKGNCWPRV*DVAMNPMEHPFGGGNHQHIGKPSTVCR

Parental  DAPAGRKVGLIAARRTGRLRGTKTVQEKEN
          D.PAG.KV.L.AAR.TGRL.GTKTVQEKEN
Retrocopy DDPAGCKVDLTAARQTGRLWGTKTVQEKEN

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	45.94 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	185.71 RPM
SRP007412_cerebellum	0.00 RPM	48.50 RPM
SRP007412_heart	0.06 RPM	220.53 RPM
SRP007412_kidney	0.00 RPM	119.83 RPM
SRP007412_liver	0.00 RPM	344.14 RPM
SRP007412_testis	0.00 RPM	118.58 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1470 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1470 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1470 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2851
Pan troglodytes	retro_ptro_1931
Gorilla gorilla	retro_ggor_1974

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Parental genes homology:

Parental genes homology involve 23 parental genes, and 47 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000017933	1 retrocopy	retro_acar_31,
Ailuropoda melanoleuca	ENSAMEG00000005395	1 retrocopy	retro_amel_241,
Bos taurus	ENSBTAG00000026327	1 retrocopy	retro_btau_96,
Canis familiaris	ENSCAFG00000001677	1 retrocopy	retro_cfam_1132,
Callithrix jacchus	ENSCJAG00000021388	4 retrocopies	retro_cjac_1109, retro_cjac_1169, retro_cjac_1579, retro_cjac_2047,
Cavia porcellus	ENSCPOG00000003854	2 retrocopies	retro_cpor_1006, retro_cpor_1415,
Dasypus novemcinctus	ENSDNOG00000009300	2 retrocopies	retro_dnov_2505, retro_dnov_503,
Echinops telfairi	ENSETEG00000007104	4 retrocopies	retro_etel_1100, retro_etel_264, retro_etel_296, retro_etel_916,
Homo sapiens	ENSG00000161016	1 retrocopy	retro_hsap_2851,
Gorilla gorilla	ENSGGOG00000008164	1 retrocopy	retro_ggor_1974,
Macropus eugenii	ENSMEUG00000013824	9 retrocopies	retro_meug_1116, retro_meug_1354, retro_meug_1757, retro_meug_1817, retro_meug_1881, retro_meug_670, retro_meug_941, retro_meug_960, retro_meug_974,
Macaca mulatta	ENSMMUG00000013379	2 retrocopies	retro_mmul_1470 , retro_mmul_1531,
Monodelphis domestica	ENSMODG00000004283	3 retrocopies	retro_mdom_1055, retro_mdom_1696, retro_mdom_253,
Mustela putorius furo	ENSMPUG00000006022	1 retrocopy	retro_mputfur_1517,
Mus musculus	ENSMUSG00000003970	2 retrocopies	retro_mmus_2004, retro_mmus_2112,
Nomascus leucogenys	ENSNLEG00000010952	2 retrocopies	retro_nleu_1603, retro_nleu_594,
Ornithorhynchus anatinus	ENSOANG00000002646	1 retrocopy	retro_oana_93,
Oryctolagus cuniculus	ENSOCUG00000024716	1 retrocopy	retro_ocun_146,
Pan troglodytes	ENSPTRG00000020716	1 retrocopy	retro_ptro_1931,
Rattus norvegicus	ENSRNOG00000048523	2 retrocopies	retro_rnor_122, retro_rnor_239,
Sarcophilus harrisii	ENSSHAG00000013568	2 retrocopies	retro_shar_482, retro_shar_558,
Tupaia belangeri	ENSTBEG00000010363	2 retrocopies	retro_tbel_2826, retro_tbel_3453,
Tursiops truncatus	ENSTTRG00000013858	1 retrocopy	retro_ttru_1147,