RetrogeneDB ID: retro_mmul_1736

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 3:169137779..169138156(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.807
• Ensembl ID: ENSMMUG00000015493
• Aliases: None
• Description: None

Sequence

>retro_mmul_1736
AAGCGGGCGCTGCACCACCTCGAGTTGTGGTGCATCCAAAGCGACAAATACCAATACTTTGCTTATCTGATGAGAGCTGG
TTTGAAGAACATAAGAATGAAAAGGATATGATGAAGGCCACCCAGCTGCTGAAGAAGGCTGAGGAAGAATTCTGTTATTT
TCAGCATCCACAGCCATACACCTTCCCTGACTCTCCTAGGGGTGCCTCCTATGTGACATATGAGTGCTACAAGGTACCAG
AATGGTGCTTAGGAGACTGGCATCCTTCTGAGAAGGCAGTGTATCCTGATTACTTTGCCAAGAGAAAACAGTGGAAGAAA
CTGCAGAGGGAAAGCTGGAAACGAGAGGTTAAGCAGCTAGAGAAGCAAATGCCACCT

Alignment

ORF - retro_mmul_1736 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.95 %
• Parental protein coverage: 70.39 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KRALRHLESWCVHRDKYRYFACLMRAR-FEEHKNEKDMMKATQLLKEAEEEFWFCQHPQPYIFPDSPGGT
          KRAL.HLE.WC...DKY.YFA.LMRA..FEEHKNEKDMMKATQLLK.AEEEF...QHPQPY.FPDSP.G.
Retrocopy KRALHHLELWCIQSDKYQYFAYLMRAG<FEEHKNEKDMMKATQLLKKAEEEFCYFQHPQPYTFPDSPRGA

Parental  SYERYDCYKVPEWCLDDWHPSEKAMYPDYFAKREQWKKLRRESWEREVKQLQEETPP
          SY..Y.CYKVPEWCL.DWHPSEKA.YPDYFAKR.QWKKL.RESW.REVKQL....PP
Retrocopy SYVTYECYKVPEWCLGDWHPSEKAVYPDYFAKRKQWKKLQRESWKREVKQLEKQMPP

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	66.67 RPM
SRP007412_brain_prefrontal_cortex	0.08 RPM	109.87 RPM
SRP007412_cerebellum	0.00 RPM	46.36 RPM
SRP007412_heart	0.00 RPM	82.44 RPM
SRP007412_kidney	0.00 RPM	49.65 RPM
SRP007412_liver	0.00 RPM	30.28 RPM
SRP007412_testis	0.04 RPM	27.78 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1736 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1736 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1736 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 30 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000010022	1 retrocopy	retro_acar_132,
Ailuropoda melanoleuca	ENSAMEG00000015852	2 retrocopies	retro_amel_1680, retro_amel_553,
Callithrix jacchus	ENSCJAG00000012818	1 retrocopy	retro_cjac_2125,
Equus caballus	ENSECAG00000018238	1 retrocopy	retro_ecab_541,
Felis catus	ENSFCAG00000004678	1 retrocopy	retro_fcat_689,
Homo sapiens	ENSG00000147684	2 retrocopies	retro_hsap_3905, retro_hsap_4112,
Gorilla gorilla	ENSGGOG00000015883	2 retrocopies	retro_ggor_2632, retro_ggor_2759,
Microcebus murinus	ENSMICG00000017481	1 retrocopy	retro_mmur_1494,
Myotis lucifugus	ENSMLUG00000003765	1 retrocopy	retro_mluc_1339,
Macaca mulatta	ENSMMUG00000015493	1 retrocopy	retro_mmul_1736 ,
Monodelphis domestica	ENSMODG00000001831	3 retrocopies	retro_mdom_1176, retro_mdom_1193, retro_mdom_1582,
Nomascus leucogenys	ENSNLEG00000005484	2 retrocopies	retro_nleu_1141, retro_nleu_578,
Otolemur garnettii	ENSOGAG00000030772	2 retrocopies	retro_ogar_1654, retro_ogar_925,
Pongo abelii	ENSPPYG00000018869	3 retrocopies	retro_pabe_2643, retro_pabe_3182, retro_pabe_3366,
Pan troglodytes	ENSPTRG00000020569	2 retrocopies	retro_ptro_2656, retro_ptro_2791,
Pteropus vampyrus	ENSPVAG00000009153	1 retrocopy	retro_pvam_243,
Ictidomys tridecemlineatus	ENSSTOG00000021955	1 retrocopy	retro_itri_611,
Tupaia belangeri	ENSTBEG00000006895	3 retrocopies	retro_tbel_1901, retro_tbel_2663, retro_tbel_610,