RetrogeneDB ID: retro_mmul_1131

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 14:131868681..131869214(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMMUG00000001709
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMMUG00000015306
• Aliases: None
• Description: None

Sequence

>retro_mmul_1131
AAGGCCAAGACTAAGGGGCTGCAGAGCGGGGCGGACAGTGGTGACAAGTACTCAGAGAAGCAGGAGTGGGACTTGACGAC
GCCACCATGAAGGCCGGCCAGTGCGTCATCGGGCTGCAAATGGGAACCCTCAAATGCACCAGCCAGTCCGGCATGACCGC
GTACGGCGACAGGAGGCATCTCTACGGACCCCAAGAACCACATCCTTGCCCCCCTACGGACCACTCGACCATCAGCCTCC
AGATGGGTGAAAACACCAGCCAGGTGGGCACGATGGCTCCCGGGACCCGGCGGCACCTCTATGACACCAAGCTGGGAACC
GACAAGTGTGACAACTCTTCCATGTCCCCGCAGACGGGCTACACACAGGACGCCAACCAGAGCTGCCAGGTCTTCGGCCT
GGGCCGGCAGACATACAACCCCAAGTACTGCCCGCAAGGCACAGTGGCCGATGGGGCTCCCTCGGGTGCAGGCGACTGTC
CCGGCCCTGGGGAGGCCCCTGAATATTCCCCTTACTACTAGGAGGACACCGGC

Alignment

ORF - retro_mmul_1131 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.56 %
• Parental protein coverage: 99.44 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  QAKTKGLQSGVDIGVKYSEKQERNF-DDATMKAGQCVIGLQMGTNKCASQSGMTAYGTRRHLYDPKN-HI
          .AKTKGLQSG.D.G.KYSEKQE....DDATMKAGQCVIGLQMGT.KC.SQSGMTAYG.RRHLY.P...H.
Retrocopy KAKTKGLQSGADSGDKYSEKQEWDL<DDATMKAGQCVIGLQMGTLKCTSQSGMTAYGDRRHLYGPQEPHP

Parental  LPPMDHSTISLQMGTNKCASQVGMTAPGTRRHIYDTKLGTDKCDNSSMSLQMGYTQGANQSGQVFGLGRQ
          .PP.DHSTISLQMG.N...SQVG..APGTRRH.YDTKLGTDKCDNSSMS.Q.GYTQ.ANQS.QVFGLGRQ
Retrocopy CPPTDHSTISLQMGEN--TSQVGTMAPGTRRHLYDTKLGTDKCDNSSMSPQTGYTQDANQSCQVFGLGRQ

Parental  IYDPKYCPQGTVADGAPSGAGDCPDPGEVPEYPPYYQEEAG
          .Y.PKYCPQGTVADGAPSGAGDCP.PGE.PEY.PYY.E..G
Retrocopy TYNPKYCPQGTVADGAPSGAGDCPGPGEAPEYSPYY*EDTG

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	1.23 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	5.79 RPM
SRP007412_cerebellum	0.00 RPM	1.03 RPM
SRP007412_heart	0.12 RPM	6.65 RPM
SRP007412_kidney	0.94 RPM	13.15 RPM
SRP007412_liver	0.08 RPM	8.99 RPM
SRP007412_testis	0.11 RPM	8.25 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1131 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1131 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1131 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_943
Pan troglodytes	retro_ptro_653
Gorilla gorilla	retro_ggor_762

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 55 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000020764	1 retrocopy	retro_btau_612,
Dipodomys ordii	ENSDORG00000001141	1 retrocopy	retro_dord_672,
Erinaceus europaeus	ENSEEUG00000015171	1 retrocopy	retro_eeur_581,
Homo sapiens	ENSG00000064666	16 retrocopies	retro_hsap_1168, retro_hsap_1575, retro_hsap_1697, retro_hsap_2127, retro_hsap_2495, retro_hsap_255, retro_hsap_2576, retro_hsap_2764, retro_hsap_3505, retro_hsap_4168, retro_hsap_4170, retro_hsap_4175, retro_hsap_4257, retro_hsap_4269, retro_hsap_4326, retro_hsap_943,
Gorilla gorilla	ENSGGOG00000028153	9 retrocopies	retro_ggor_1199, retro_ggor_1271, retro_ggor_1555, retro_ggor_1612, retro_ggor_1646, retro_ggor_1922, retro_ggor_2370, retro_ggor_305, retro_ggor_762,
Myotis lucifugus	ENSMLUG00000013160	4 retrocopies	retro_mluc_1536, retro_mluc_1965, retro_mluc_2047, retro_mluc_2210,
Macaca mulatta	ENSMMUG00000001690	1 retrocopy	retro_mmul_1747,
Macaca mulatta	ENSMMUG00000004705	1 retrocopy	retro_mmul_2328,
Macaca mulatta	ENSMMUG00000015306	1 retrocopy	retro_mmul_1131 ,
Mus musculus	ENSMUSG00000004665	2 retrocopies	retro_mmus_1824, retro_mmus_2317,
Nomascus leucogenys	ENSNLEG00000001161	2 retrocopies	retro_nleu_1757, retro_nleu_2893,
Otolemur garnettii	ENSOGAG00000010144	2 retrocopies	retro_ogar_1416, retro_ogar_1733,
Pongo abelii	ENSPPYG00000009302	12 retrocopies	retro_pabe_1299, retro_pabe_1397, retro_pabe_1838, retro_pabe_1920, retro_pabe_2171, retro_pabe_2249, retro_pabe_2900, retro_pabe_3512, retro_pabe_3515, retro_pabe_3543, retro_pabe_3823, retro_pabe_407,
Pteropus vampyrus	ENSPVAG00000016570	1 retrocopy	retro_pvam_535,
Ictidomys tridecemlineatus	ENSSTOG00000028367	1 retrocopy	retro_itri_326,