RetrogeneDB ID: retro_mmul_333

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 11:44263293..44264592(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMMUG00000002203
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: MMU.18817
• Ensembl ID: ENSMMUG00000005200
• Aliases: None
• Description: protein FAM113A [Source:RefSeq peptide;Acc:NP_001181592]

Sequence

>retro_mmul_333
ATGATCCTCCTGAGGGCCTCCGAAGTGCGGCAGCTGCTCCACAATAAGTTCGTGGTCATCCTGGGGGACTCTGTGCATAG
GGCGGTATACAAGGACCTGGTACTTCTGCTGCAGAAGGACTGCCTGCTCACTCCCCAGCAGCTCAAAGCAAAGGGGGAGC
TGAACTTCGAACAAGATGAGCTGGTGGACGGAGGCCAGCGGGGCCACATGCACAACGGCTGTAACTACCGTGAGGTCCGC
GAGTTCCGCTCCGACCACCATCTGGTGCGTTTTTACTTCCTCACCCGCGTGTACTCCGACTACCTCCAGACCATCTTGAA
AGAGCTGCAGTCGGGCGAGCATGCCCCCGACCTGGTCATCATGAATTCCTGCCTCTGGGACATCTCCAGGTATGGTTCGA
ACTCCTGGTGGAGCTACCTGGAGAACCTGGAGAACCTGTTCCGGTGCCTGGGCCAGGTGCTGCCCGAGTCTTGCCTCCTG
GTGTGGAACACGGCCATGCCTGTGGGCGAGGAAGTCAACGCGAGTTTTCTTCCGCCCGAGCTCCGGCAGCAGAAGGCCAC
CTTCCTGAAAAACAGAGTGGTCGAAGCCAACTTCTATAGCGCCACCGAGGCACGTAAATATAACTTCGATGTACTGGACT
TGCATTTTTACTTCCGCCACGCGAGGGAGAACCTGCACTTCGACGGGGTGCACTGGAATGGACGCGTGCACCGCTGCCTC
TCCCAGCTGCTGCTGGCCCATGTGGCTGACGCCTGGGGTGTGGAGTTGCCCCAGCGCCATCCTGTGGGAAAGTGGATCAA
GAAGAAAAAACCTGGCCCGAGAGTTGAAGGGCCGCCCCAGGCCAACAGAAATCACCCGGCCTTACCTCTGTCCCCACCCT
TACCTTCCCCCACATACTGCCCCCTGCTTGGGTTCCCACCCCAGCAATTGCCGCTGCTTCCGCTCCTGCCCCCACAGCCT
CCTCCTCCCATTCCCCTTCACCAGGGAATGCCCCGGTTCCCACAGGGTCCCCCAGATGCCTGTTTTTCATCAGACCATAC
TTTCCAGTCAGATCAATTCTATTGCCATTCAGATGTCCCCTCATCAGCCCATACAGGTTTCTTCTTCCAAGACAACTTTG
CGATTGGTCCCCAGCTGCCTATGCCCTTCTTCCCCACACCCCGTTATCAGCGGCCTGCCCCTGTGGTCCATAGGGGTTTT
GGCAGGTATCGTCCCCGTGGCCCCTATGTGCCCTGGGGACAGCAGCCTCGACCTTCAAAGAGAAGGGCCCTAGCCAACCC
CCAGCCAAGGCCTCAATAG

Alignment

ORF - retro_mmul_333 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.04 %
• Parental protein coverage: 59.03 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MVHFQASEVQQLLHNKFVVILGDSIQRAVYKDLVLLLQKDSLLTAAQLKAKGELSFEQDQLVAGGQLGEL
          M....ASEV.QLLHNKFVVILGDS..RAVYKDLVLLLQKD.LLT..QLKAKGEL.FEQD.LV.GGQ.G..
Retrocopy MILLRASEVRQLLHNKFVVILGDSVHRAVYKDLVLLLQKDCLLTPQQLKAKGELNFEQDELVDGGQRGHM

Parental  HNGTQYREVRQFCSGSGHHLVRFYFLTRVYSEYLEDVLEELTYGP-APDLVIINSCLWDLSRYGRCSMES
          HNG..YREVR.F...S.HHLVRFYFLTRVYS.YL...L.EL..G..APDLVI.NSCLWD.SRYG..S..S
Retrocopy HNGCNYREVREF--RSDHHLVRFYFLTRVYSDYLQTILKELQSGEHAPDLVIMNSCLWDISRYGSNSWWS

Parental  YRKNLERVFVRMDQVLPDSCLLVWNMAMPLGERITGGFLLPEL-QPLAGSLRRDVVEGNFYSATLAGDHC
          Y..NLE..F....QVLP.SCLLVWN.AMP.GE.....FL.PEL.Q..A..L...VVE.NFYSAT.A....
Retrocopy YLENLENLFRCLGQVLPESCLLVWNTAMPVGEEVNASFLPPELRQQKATFLKNRVVEANFYSATEARKYN

Parental  FDVLDLHFHFRHAVQHRHRDGVHWDQHAHRHLSHLLLTHVADAWGVELPKRDYPPDPWIE
          FDVLDLHF.FRHA....H.DGVHW....HR.LS.LLL.HVADAWGVELP.R..P...WI.
Retrocopy FDVLDLHFYFRHARENLHFDGVHWNGRVHRCLSQLLLAHVADAWGVELPQR-HPVGKWIK

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	1.46 RPM	12.77 RPM
SRP007412_brain_prefrontal_cortex	3.57 RPM	31.26 RPM
SRP007412_cerebellum	0.45 RPM	19.05 RPM
SRP007412_heart	1.00 RPM	8.48 RPM
SRP007412_kidney	1.53 RPM	19.13 RPM
SRP007412_liver	3.33 RPM	25.97 RPM
SRP007412_testis	1.73 RPM	10.03 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

1 EST(s) were mapped to retro_mmul_333 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
DR767828	44263234	44263830	96.4	545	9	525

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_333 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_333 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000003863	1 retrocopy	retro_btau_182,
Cavia porcellus	ENSCPOG00000025475	2 retrocopies	retro_cpor_343, retro_cpor_79,
Equus caballus	ENSECAG00000016497	1 retrocopy	retro_ecab_87,
Felis catus	ENSFCAG00000002886	1 retrocopy	retro_fcat_18,
Homo sapiens	ENSG00000132635	2 retrocopies	retro_hsap_2207, retro_hsap_82,
Microcebus murinus	ENSMICG00000016578	2 retrocopies	retro_mmur_163, retro_mmur_278,
Myotis lucifugus	ENSMLUG00000028662	2 retrocopies	retro_mluc_222, retro_mluc_647,
Macaca mulatta	ENSMMUG00000005200	2 retrocopies	retro_mmul_333 , retro_mmul_341,
Mus musculus	ENSMUSG00000037773	2 retrocopies	retro_mmus_1001, retro_mmus_332,
Otolemur garnettii	ENSOGAG00000004701	1 retrocopy	retro_ogar_81,
Pongo abelii	ENSPPYG00000010833	2 retrocopies	retro_pabe_192, retro_pabe_2080,
Pan troglodytes	ENSPTRG00000013185	1 retrocopy	retro_ptro_105,
Pteropus vampyrus	ENSPVAG00000006834	1 retrocopy	retro_pvam_9,
Sus scrofa	ENSSSCG00000007168	1 retrocopy	retro_sscr_23,
Ictidomys tridecemlineatus	ENSSTOG00000016356	2 retrocopies	retro_itri_1190, retro_itri_783,
Tursiops truncatus	ENSTTRG00000003464	1 retrocopy	retro_ttru_16,