RetrogeneDB ID: retro_mmul_1782

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 4:96460485..96461260(+)
• Located in intron of: ENSMMUG00000022287

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.13215
• Ensembl ID: ENSMMUG00000010552
• Aliases: None
• Description: DCN1-like protein 1 [Source:RefSeq peptide;Acc:NP_001244383]

Sequence

>retro_mmul_1782
AACAAGTTGAAATCATCACAGAAAGATAAAGTTCATCAGTTTATGATCTTCACACAATTTAGTGAAAAGAACCTCAGTAA
GTTGTCTATCTCAAAATGACTGGAAGTTTGATGTTGTAACAGATAATTTTTTCCAAAATCCTGAACTTTATATACAAGAG
AGTGTAAAAGGATCGCTGGACAGGAAGAAGTTAGAACAAATGTACAATAGATACAAAGATCCTCAACATGAGAATAAAAT
TGGAATAGATGGTATATAGCAGTTCTGTGATGGCCTGGCACTCAATCCAGCCAGCATTAGTGTGTTGATTATTGCATGGA
AGTTCAGAGCAACAACACAGTGTGAGTTCTCCAAACAGGAGTTTATGGATGGCATGGCAGAAGTAGGATGTGACAGCATA
GAAAAACTAAAGGCCCAGATACCCAAGACGGAACAAGAATTGAAAGAACCAGGACGATTTAAGGACTTTTACCAGGTTAC
TTTTAATTTTGCAAAGAATCCAGGACAAAAAGGAGTAGATCTAGAAATGGCCATTGTCTACTGGAACTCAGTGCTTAATA
GAAGATTTAAATTCTTAGACTTATGGAATAAATTTTTGTTGGAACATCATAAACGATCAATACCAAAAGACACTTGGAAT
CTTCTTTTAGACTTCACTACAGTGATTGCAGATCACGTGTCTAATTGTGATAAAGAAGGAGCATGGCCTGTTCTTATTGA
TGACTTTGTGGAATTTGCATGCCCTCAAATTGCTGGGACAAAAAGTACAAGAGTG

Alignment

ORF - retro_mmul_1782 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.8 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  NKLKSSQKDKVRQFMIFTQSSEK-TAVSCLSQNDWKLDVATDNFFQNPELYIRESVKGSLDRKKLEQLYN
          NKLKSSQKDKV.QFMIFTQ.SEK.T.VSCLSQNDWK.DV.TDNFFQNPELYI.ESVKGSLDRKKLEQ.YN
Retrocopy NKLKSSQKDKVHQFMIFTQFSEK>TSVSCLSQNDWKFDVVTDNFFQNPELYIQESVKGSLDRKKLEQMYN

Parental  RYKDPQDENKIGIDGIQQFCDDLALDPASISVLIIAWKFRAATQCEFSKQEFMDGMTELGCDSIEKLKAQ
          RYKDPQ.ENKIGIDGI.QFCD.LAL.PASISVLIIAWKFRA.TQCEFSKQEFMDGM.E.GCDSIEKLKAQ
Retrocopy RYKDPQHENKIGIDGI*QFCDGLALNPASISVLIIAWKFRATTQCEFSKQEFMDGMAEVGCDSIEKLKAQ

Parental  IPKMEQELKEPGRFKDFYQFTFNFAKNPGQKGLDLEMAIAYWNLVLNGRFKFLDLWNKFLLEHHKRSIPK
          IPK.EQELKEPGRFKDFYQ.TFNFAKNPGQKG.DLEMAI.YWN.VLN.RFKFLDLWNKFLLEHHKRSIPK
Retrocopy IPKTEQELKEPGRFKDFYQVTFNFAKNPGQKGVDLEMAIVYWNSVLNRRFKFLDLWNKFLLEHHKRSIPK

Parental  DTWNLLLDFSTMIADDMSNYDEEGAWPVLIDDFVEFARPQIAGTKSTTV
          DTWNLLLDF.T.IAD..SN.D.EGAWPVLIDDFVEFA.PQIAGTKST.V
Retrocopy DTWNLLLDFTTVIADHVSNCDKEGAWPVLIDDFVEFACPQIAGTKSTRV

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	21.40 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	12.69 RPM
SRP007412_cerebellum	0.06 RPM	25.51 RPM
SRP007412_heart	0.00 RPM	9.77 RPM
SRP007412_kidney	0.00 RPM	15.61 RPM
SRP007412_liver	0.04 RPM	7.92 RPM
SRP007412_testis	0.57 RPM	247.80 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1782 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1782 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1782 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3502
Pan troglodytes	retro_ptro_2374
Gorilla gorilla	retro_ggor_2368
Pongo abelii	retro_pabe_2894

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 32 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000013358	14 retrocopies	retro_chof_1054, retro_chof_1129, retro_chof_1198, retro_chof_1373, retro_chof_1546, retro_chof_1728, retro_chof_2049, retro_chof_232, retro_chof_2329, retro_chof_2369, retro_chof_2373, retro_chof_479, retro_chof_767, retro_chof_812,
Callithrix jacchus	ENSCJAG00000005148	2 retrocopies	retro_cjac_1423, retro_cjac_2358,
Cavia porcellus	ENSCPOG00000022086	4 retrocopies	retro_cpor_1289, retro_cpor_756, retro_cpor_758, retro_cpor_870,
Dasypus novemcinctus	ENSDNOG00000019073	2 retrocopies	retro_dnov_1494, retro_dnov_840,
Echinops telfairi	ENSETEG00000000166	1 retrocopy	retro_etel_1460,
Homo sapiens	ENSG00000043093	1 retrocopy	retro_hsap_3502,
Gorilla gorilla	ENSGGOG00000010767	1 retrocopy	retro_ggor_2368,
Macaca mulatta	ENSMMUG00000010552	1 retrocopy	retro_mmul_1782 ,
Mustela putorius furo	ENSMPUG00000002369	1 retrocopy	retro_mputfur_919,
Mus musculus	ENSMUSG00000027708	1 retrocopy	retro_mmus_1009,
Nomascus leucogenys	ENSNLEG00000005983	1 retrocopy	retro_nleu_793,
Otolemur garnettii	ENSOGAG00000000658	1 retrocopy	retro_ogar_3499,
Pan troglodytes	ENSPTRG00000015661	1 retrocopy	retro_ptro_2374,
Tarsius syrichta	ENSTSYG00000012276	1 retrocopy	retro_tsyr_669,