RetrogeneDB ID: retro_mmul_1656

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 3:187692763..187693105(+)
• Located in intron of: ENSMMUG00000030049

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.2621
• Ensembl ID: ENSMMUG00000000007
• Aliases: None
• Description: BET1 homolog [Source:RefSeq peptide;Acc:NP_001247657]

Sequence

>retro_mmul_1656
ATGAAGCATGCAGGCCTGGGTGAAGGAGTACCTCCTGGCAACTCTGGGAACGATGGCTATGCTAATAGTGGGTATAGTGC
CTGTGAAGAAAAAAACAAGAGACTCACTGAAAGTCTGAGAAGCAAAGTAACTGTTATAAAATATTTTTCCATTGAAATAG
GCCATGAAGTTAAAACCCAAAATAAATTATTAGCTGAAATGGATTCACAATTTGATTCTACAACTGGATTTCTAGGTAAA
ACTATGGGCAAAGTGGAGATTTTATCCATAGGGAGCCAAAACAAAAAAGCTGCTGGGCTCTACAATGCTGTTTTATTTAT
TTGTCTTTTTTTGTCATTTATT

Alignment

ORF - retro_mmul_1656 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.81 %
• Parental protein coverage: 96.61 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MRRAGLGEGVPPGSYGNYGYANSGYSACEEENERLTESLRSKVTAIKSLSIEIGHEVKTQNKLLSEMDSQ
          M..AGLGEGVPPG..GN.GYANSGYSACEE.N.RLTESLRSKVT.IK..SIEIGHEVKTQNKLL.EMDSQ
Retrocopy MKHAGLGEGVPPGNSGNDGYANSGYSACEEKNKRLTESLRSKVTVIKYFSIEIGHEVKTQNKLLAEMDSQ

Parental  FDSTTGFLGKTMGKLKILSRGSQTKLLCYMMLFSLFVFFIIYWI
          FDSTTGFLGKTMGK..ILS.GSQ.K.........LF.......I
Retrocopy FDSTTGFLGKTMGKVEILSIGSQNKKAAGLYNAVLFICLFLSFI

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	1.57 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	1.27 RPM
SRP007412_cerebellum	0.00 RPM	2.26 RPM
SRP007412_heart	0.18 RPM	1.35 RPM
SRP007412_kidney	0.12 RPM	2.35 RPM
SRP007412_liver	0.04 RPM	2.81 RPM
SRP007412_testis	0.00 RPM	2.90 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1656 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1656 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1656 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 28 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000003424	1 retrocopy	retro_btau_1054,
Choloepus hoffmanni	ENSCHOG00000001276	1 retrocopy	retro_chof_2211,
Callithrix jacchus	ENSCJAG00000013720	3 retrocopies	retro_cjac_1411, retro_cjac_2019, retro_cjac_3155,
Dasypus novemcinctus	ENSDNOG00000001012	3 retrocopies	retro_dnov_1683, retro_dnov_393, retro_dnov_60,
Homo sapiens	ENSG00000105829	1 retrocopy	retro_hsap_3809,
Gorilla gorilla	ENSGGOG00000002176	1 retrocopy	retro_ggor_2560,
Loxodonta africana	ENSLAFG00000000587	1 retrocopy	retro_lafr_1023,
Macaca mulatta	ENSMMUG00000000007	1 retrocopy	retro_mmul_1656 ,
Nomascus leucogenys	ENSNLEG00000015441	1 retrocopy	retro_nleu_2151,
Oryctolagus cuniculus	ENSOCUG00000017029	2 retrocopies	retro_ocun_1116, retro_ocun_355,
Ochotona princeps	ENSOPRG00000004536	4 retrocopies	retro_opri_201, retro_opri_249, retro_opri_388, retro_opri_880,
Pan troglodytes	ENSPTRG00000019408	1 retrocopy	retro_ptro_2584,
Rattus norvegicus	ENSRNOG00000011008	2 retrocopies	retro_rnor_2195, retro_rnor_2196,
Sus scrofa	ENSSSCG00000015325	2 retrocopies	retro_sscr_455, retro_sscr_516,
Tupaia belangeri	ENSTBEG00000000765	2 retrocopies	retro_tbel_3115, retro_tbel_4272,
Tarsius syrichta	ENSTSYG00000009729	2 retrocopies	retro_tsyr_136, retro_tsyr_1843,