RetrogeneDB ID: retro_mmul_1262

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 16:46032093..46032354(-)
• Located in intron of: ENSMMUG00000016566

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.942
• Ensembl ID: ENSMMUG00000001282
• Aliases: None
• Description: pre-mRNA branch site protein p14 [Source:RefSeq peptide;Acc:NP_001247813]

Sequence

>retro_mmul_1262
ATATTTGGGAAATATGGACCTATTCATCAAATCAGAGTAGGGAACACACCTGAAACTAGAGGAACAGCTTATGTGGTCTA
TGAATACATCTTTGTTGCCGAGAATGCTTGTGATCACCTACCAAGATTCAATTTTTGTGACAGATAACTTGCGGTTTTGT
ACTACAATGCCAACAGGGCAGTTCAGAAGATGGACACGAAGGAGGAGGAACAGCTGAAGCTTCTCATGGAGAAATATGGT
ATCAAGATAGATGCACCAAAA

Alignment

ORF - retro_mmul_1262 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.68 %
• Parental protein coverage: 70.4 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  IFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNACDHLSGFNVCNRYLVVLYYNANRAFQKMDTKKKE
          IFGKYGPI.QIRVGNTPETRGTAYVVYE.IF.A.NACDHL..FN.C.R.L.VLYYNANRA.QKMDT.K.E
Retrocopy IFGKYGPIHQIRVGNTPETRGTAYVVYEYIFVAENACDHLPRFNFCDR*LAVLYYNANRAVQKMDT-KEE

Parental  EQLKLLKEKYGINTDPPK
          EQLKLL.EKYGI..D.PK
Retrocopy EQLKLLMEKYGIKIDAPK

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	16.70 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	14.04 RPM
SRP007412_cerebellum	0.00 RPM	15.63 RPM
SRP007412_heart	0.00 RPM	13.54 RPM
SRP007412_kidney	0.00 RPM	22.77 RPM
SRP007412_liver	0.08 RPM	14.69 RPM
SRP007412_testis	0.08 RPM	14.63 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1262 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1262 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1262 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000002786	1 retrocopy	retro_amel_1594,
Bos taurus	ENSBTAG00000003407	1 retrocopy	retro_btau_606,
Choloepus hoffmanni	ENSCHOG00000000689	3 retrocopies	retro_chof_1217, retro_chof_2457, retro_chof_351,
Callithrix jacchus	ENSCJAG00000007716	2 retrocopies	retro_cjac_2632, retro_cjac_487,
Dasypus novemcinctus	ENSDNOG00000007148	1 retrocopy	retro_dnov_1313,
Equus caballus	ENSECAG00000015618	1 retrocopy	retro_ecab_733,
Felis catus	ENSFCAG00000031365	1 retrocopy	retro_fcat_247,
Homo sapiens	ENSG00000115128	1 retrocopy	retro_hsap_1773,
Macaca mulatta	ENSMMUG00000001282	1 retrocopy	retro_mmul_1262 ,
Mustela putorius furo	ENSMPUG00000013957	1 retrocopy	retro_mputfur_882,
Nomascus leucogenys	ENSNLEG00000000815	1 retrocopy	retro_nleu_2806,
Otolemur garnettii	ENSOGAG00000004468	1 retrocopy	retro_ogar_2877,
Pongo abelii	ENSPPYG00000012603	2 retrocopies	retro_pabe_1098, retro_pabe_1461,
Pan troglodytes	ENSPTRG00000011709	1 retrocopy	retro_ptro_1187,
Sorex araneus	ENSSARG00000011902	1 retrocopy	retro_sara_638,