RetrogeneDB ID: retro_mmul_472

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 1:24880976..24881477(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.10170
• Ensembl ID: ENSMMUG00000008541
• Aliases: None
• Description: BRCA2 and CDKN1A interacting protein [Source:RefSeq peptide;Acc:NP_001252600]

Sequence

>retro_mmul_472
GCTTACTCCCTATCAGATAATGATTATGATGGAATTAAGAAATTACTGCAGCAGCTTTTTCTAAAGGATCCTGTGAACAC
TGCAGAACTAACAGATCTCTTAATTCAACAGAACCATATTGTGAGTGTGATTAAGCAAATGGATGTTTCAGAAGACAGCG
AATACGATGTGGATGAAGATGAGGTTTTTGGTTTCATAAGCCTTTTAAATTTAACTGAAAGAAAGGGTACCCAGTGTGCT
GAACAAATTCAAGAGTTGATTCTAAGCTTCTGTGAGAAGAACCGTGAAAAGAGCATGGTTGAACAGCTGGACAAGTTTTT
AAATGACACCACCAAGCCTGTGGGCCTTCTCCTAAGTGAAAGATTTATTAATATCCCTCCACAGATCGCTCTGCCCATGT
ACCAGCAGCTTCAGAAAGAACTGGCAGAGGCACACAGAACCAATAAACCATGTGGGAAGTGCTACTTTTACCTTCTGATT
AGTAAGACATTTGTGGAAGCA

Alignment

ORF - retro_mmul_472 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.41 %
• Parental protein coverage: 51.86 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AYSLSDNDYDGIKKLLQQLFLKAPVNTAELTDLLIQQNHIGSVIKQTDVSEDSDDDVDEDEVFGFISLLN
          AYSLSDNDYDGIKKLLQQLFLK.PVNTAELTDLLIQQNHI.SVIKQ.DVSEDS..DVDEDEVFGFISLLN
Retrocopy AYSLSDNDYDGIKKLLQQLFLKDPVNTAELTDLLIQQNHIVSVIKQMDVSEDSEYDVDEDEVFGFISLLN

Parental  LTERKGTQCAEQIQELILSFCEKNCEKSMVEQLDKFLNDTTKPVGLLLSERFINIPPQIALPMYQQLQKE
          LTERKGTQCAEQIQELILSFCEKN.EKSMVEQLDKFLNDTTKPVGLLLSERFINIPPQIALPMYQQLQKE
Retrocopy LTERKGTQCAEQIQELILSFCEKNREKSMVEQLDKFLNDTTKPVGLLLSERFINIPPQIALPMYQQLQKE

Parental  LAEAHRTNKPCGKCYFYLLISKTFVEA
          LAEAHRTNKPCGKCYFYLLISKTFVEA
Retrocopy LAEAHRTNKPCGKCYFYLLISKTFVEA

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	33.28 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	28.72 RPM
SRP007412_cerebellum	0.00 RPM	40.94 RPM
SRP007412_heart	0.00 RPM	50.17 RPM
SRP007412_kidney	0.12 RPM	70.30 RPM
SRP007412_liver	0.00 RPM	26.84 RPM
SRP007412_testis	0.00 RPM	19.00 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_472 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_472 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_472 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000012873	1 retrocopy	retro_cfam_1356,
Callithrix jacchus	ENSCJAG00000012411	1 retrocopy	retro_cjac_2838,
Dasypus novemcinctus	ENSDNOG00000002939	1 retrocopy	retro_dnov_530,
Macaca mulatta	ENSMMUG00000008541	1 retrocopy	retro_mmul_472 ,
Oryctolagus cuniculus	ENSOCUG00000008761	1 retrocopy	retro_ocun_843,
Otolemur garnettii	ENSOGAG00000010901	1 retrocopy	retro_ogar_1184,
Ictidomys tridecemlineatus	ENSSTOG00000011828	4 retrocopies	retro_itri_1004, retro_itri_1130, retro_itri_1513, retro_itri_559,
Tupaia belangeri	ENSTBEG00000002570	4 retrocopies	retro_tbel_1259, retro_tbel_1260, retro_tbel_2963, retro_tbel_3044,