RetrogeneDB ID: retro_mmul_626

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 10:33021623..33022166(-)
• Located in intron of: ENSMMUG00000005119

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.17996
• Ensembl ID: ENSMMUG00000009043
• Aliases: None
• Description: None

Sequence

>retro_mmul_626
ATGTTCAAGAAGTTTGATGAAAAGGAAAGTGTGTCCAACTGCATCCAGTTGAAAACGTCAGTTATTAAGGGCATTAAGAG
CCAACTGGTAGAGCAGTTTCCAGGTATTGAACCATGGCTTAATCAAATCATGCCTAAGAAAGATCCTGTCAAAATAGTAC
GATGCCACGAACATACAGAAATCCTTACCGTAAGTGGAGAATTACTGTTTTTTAGACAAAGAAAGGGGCCTTTTTGTCCA
ACTCTAAGATTGCTTCACAAATACCCTTTTATCCTGCCACACCAGCAGGTTGATAAAGGAGCTATCAAATTTGTACTCAG
CGGCGCAAATATTATGTGTCCAGGTTTAACTTCTCCTGGAGCTAAGCTGTACCCTGCTGCGGTAGATACCATTGTAGCAG
TCACAGCAGAAGGAAAACAGCATGCTCTGTGTGTTGGGGTCATGAAGATGTCTGCAGAAGACATTGAGAAAGTCAACAAA
GGAATTGGCATTGAAAACATCCATTATTTAAATGATGGGCTGTGGCACATGAAGACATATAAA

Alignment

ORF - retro_mmul_626 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.92 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MFXXFDEKENVSNCIQLKTSVIKGIKNQLIEQFPGIEPWLNQIMPKKDPVKIVRCHEHIEILTVNGELLF
          MF..FDEKE.VSNCIQLKTSVIKGIK.QL.EQFPGIEPWLNQIMPKKDPVKIVRCHEH.EILTV.GELLF
Retrocopy MFKKFDEKESVSNCIQLKTSVIKGIKSQLVEQFPGIEPWLNQIMPKKDPVKIVRCHEHTEILTVSGELLF

Parental  FRQREGPFYPTLRLLHKYPFILPHQQVDKGAIKFVLSGANIMCPGLTSPGAKLYPAAVDTIVAIMAEGKQ
          FRQR.GPF.PTLRLLHKYPFILPHQQVDKGAIKFVLSGANIMCPGLTSPGAKLYPAAVDTIVA..AEGKQ
Retrocopy FRQRKGPFCPTLRLLHKYPFILPHQQVDKGAIKFVLSGANIMCPGLTSPGAKLYPAAVDTIVAVTAEGKQ

Parental  HALCVGVMKMSAEDIEKVNKGIGIENIHYLNDGLWHMKTYK
          HALCVGVMKMSAEDIEKVNKGIGIENIHYLNDGLWHMKTYK
Retrocopy HALCVGVMKMSAEDIEKVNKGIGIENIHYLNDGLWHMKTYK

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	1.90 RPM	10.53 RPM
SRP007412_brain_prefrontal_cortex	0.87 RPM	6.03 RPM
SRP007412_cerebellum	1.61 RPM	8.39 RPM
SRP007412_heart	0.53 RPM	6.48 RPM
SRP007412_kidney	0.70 RPM	9.39 RPM
SRP007412_liver	0.44 RPM	7.01 RPM
SRP007412_testis	2.90 RPM	1.28 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_626 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_626 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_626 has 6 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2422
Pan troglodytes	retro_ptro_1396
Gorilla gorilla	retro_ggor_1507
Pongo abelii	retro_pabe_1786
Mus musculus	retro_mmus_69
Rattus norvegicus	retro_rnor_1841

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000034992	1 retrocopy	retro_btau_116,
Canis familiaris	ENSCAFG00000018545	1 retrocopy	retro_cfam_94,
Cavia porcellus	ENSCPOG00000005502	1 retrocopy	retro_cpor_1411,
Echinops telfairi	ENSETEG00000015462	1 retrocopy	retro_etel_19,
Macaca mulatta	ENSMMUG00000009043	1 retrocopy	retro_mmul_626 ,
Monodelphis domestica	ENSMODG00000010354	1 retrocopy	retro_mdom_203,
Mustela putorius furo	ENSMPUG00000001407	1 retrocopy	retro_mputfur_98,
Mus musculus	ENSMUSG00000000355	3 retrocopies	retro_mmus_2504, retro_mmus_2505, retro_mmus_69,
Nomascus leucogenys	ENSNLEG00000015021	1 retrocopy	retro_nleu_2442,
Oryctolagus cuniculus	ENSOCUG00000014315	1 retrocopy	retro_ocun_212,
Ictidomys tridecemlineatus	ENSSTOG00000011496	2 retrocopies	retro_itri_1136, retro_itri_1468,
Vicugna pacos	ENSVPAG00000001801	1 retrocopy	retro_vpac_138,