RetrogeneDB ID: retro_mmul_1038

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 13:85658069..85658346(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.12924
• Ensembl ID: ENSMMUG00000023126
• Aliases: None
• Description: U6 snRNA-associated Sm-like protein LSm3 [Source:RefSeq peptide;Acc:NP_001248293]

Sequence

>retro_mmul_1038
ACCAACACTGTAGAGGAGCCCCTGGATTTTATCAGGCTCAGCCTAGATGAACTAATTTATGTGAAAATGAGAAATGACCA
AGAGTTTTGAGGCAGATTACCATGCTTATGATCAACATTTAAACATGACCTTGGGAGATGTGGAAGAAACTGTGACTACT
GTAGACATTGATGAAGAAACATATGAAGAGATATATAAATCAATGAAATAGAATATTCCAGTGCTCTTTGTCCAGGGAGA
TGTCATTGTCCTGGTTGCCCCTCCACTGAGAGTTGGC

Alignment

ORF - retro_mmul_1038 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.87 %
• Parental protein coverage: 90.2 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  TNTVEEPLDLIRLSLDERIYVKMRNDRELRGRL-HAYDQHLNMILGDVEETVTTIEIDEETYEEIYKSTK
          TNTVEEPLD.IRLSLDE.IYVKMRND.E..GRL.HAYDQHLNM.LGDVEETVTT..IDEETYEEIYKS.K
Retrocopy TNTVEEPLDFIRLSLDELIYVKMRNDQEF*GRL>HAYDQHLNMTLGDVEETVTTVDIDEETYEEIYKSMK

Parental  RNIPMLFVRGDGVVLVAPPLRVG
          .NIP.LFV.GD..VLVAPPLRVG
Retrocopy *NIPVLFVQGDVIVLVAPPLRVG

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	10.31 RPM
SRP007412_brain_prefrontal_cortex	0.08 RPM	7.93 RPM
SRP007412_cerebellum	0.00 RPM	9.88 RPM
SRP007412_heart	0.00 RPM	13.13 RPM
SRP007412_kidney	0.00 RPM	30.05 RPM
SRP007412_liver	0.00 RPM	10.25 RPM
SRP007412_testis	0.00 RPM	56.99 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1038 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1038 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1038 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2286
Pan troglodytes	retro_ptro_1619
Gorilla gorilla	retro_ggor_1699
Pongo abelii	retro_pabe_1936

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 48 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000007363	1 retrocopy	retro_btau_1732,
Callithrix jacchus	ENSCJAG00000016977	1 retrocopy	retro_cjac_54,
Cavia porcellus	ENSCPOG00000006671	1 retrocopy	retro_cpor_1445,
Dasypus novemcinctus	ENSDNOG00000018032	7 retrocopies	retro_dnov_1046, retro_dnov_135, retro_dnov_1728, retro_dnov_1818, retro_dnov_229, retro_dnov_230, retro_dnov_2408,
Echinops telfairi	ENSETEG00000016207	8 retrocopies	retro_etel_117, retro_etel_1678, retro_etel_1852, retro_etel_2131, retro_etel_472, retro_etel_521, retro_etel_598, retro_etel_833,
Homo sapiens	ENSG00000170860	5 retrocopies	retro_hsap_1045, retro_hsap_1654, retro_hsap_1839, retro_hsap_2286, retro_hsap_2986,
Loxodonta africana	ENSLAFG00000023308	1 retrocopy	retro_lafr_1013,
Macaca mulatta	ENSMMUG00000023126	5 retrocopies	retro_mmul_1038 , retro_mmul_1657, retro_mmul_1908, retro_mmul_554, retro_mmul_828,
Oryctolagus cuniculus	ENSOCUG00000011088	1 retrocopy	retro_ocun_126,
Oreochromis niloticus	ENSONIG00000000370	1 retrocopy	retro_onil_12,
Pongo abelii	ENSPPYG00000013402	4 retrocopies	retro_pabe_1366, retro_pabe_1936, retro_pabe_2475, retro_pabe_874,
Pan troglodytes	ENSPTRG00000014650	5 retrocopies	retro_ptro_1125, retro_ptro_1161, retro_ptro_1619, retro_ptro_2020, retro_ptro_712,
Rattus norvegicus	ENSRNOG00000008733	1 retrocopy	retro_rnor_1187,
Sus scrofa	ENSSSCG00000011601	6 retrocopies	retro_sscr_1134, retro_sscr_1140, retro_sscr_395, retro_sscr_396, retro_sscr_457, retro_sscr_64,
Tursiops truncatus	ENSTTRG00000011197	1 retrocopy	retro_ttru_601,