RetrogeneDB ID: retro_mmul_1041

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 13:89589956..89590915(-)
• Located in intron of: ENSMMUG00000030769

Retrocopy information

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

Parental gene information

• Parental gene symbol: IMPACT
• Ensembl ID: ENSMMUG00000004664
• Aliases: None
• Description: protein IMPACT [Source:RefSeq peptide;Acc:NP_001252980]

Sequence

>retro_mmul_1041
ATGGCTGAGGGAGACGCAGGCAGCGACCAGAGGCAGAATGAGGAAATTGAAGCAATGGCAGCCATTTATGGCGAGGAATG
GTGTGTCATTGACGACTGTGCCAAAATATTTTGTATTAGAATTAGCGACGATATAGATGACCCCAAATGGACGCTTTGCT
TGCAGATGATGCTGCCGAATGAATACTCAGGTACAGCTCCACTTATCTACCAGTTGAGTGCTCCTTGGCTTAAAGGGCTA
GAATGCGCGGATTTATCAAATAGCCTCGAGGAAATATATATACAGAATATTGGTGAAAGTATTCTTTACCTGTGGGTGGA
GAAAATAAGAGATGTTCTAATACAAACATCTCAGACGACAGAACCAGGCCCAGATGTAAAGAAGAAAACTGAAGAGGAAG
AGGTTGAATGTGAAGATGATCTCATTTTAGCACGTCAGCCAGAAGGTTCGGTTAAAGCACTGGATTTTGATATCAGTGAA
ACTCGGACAGAAGTAGAAATAGAAGAATTACCTCCGATTGATCATGGCATTCCTATTACAGACCAAAGAAGTACTTTTCA
GGCACACTTGGCTCCAGTAGTTTGTCCCAAACAGGTGAAAATGGTTCCTTCCAAATTGTATGAGAATAAGAAAATAGCTA
GTGCCACCCACAACATCTCTGCCTACAGAATATATTGTGAGGATAAACAGACTTTCTTACAGGATTGTGAGGATTATGGG
GAAACAGCAGCTGGTGGGCGTCTTCTTCATCTCATGGAGATTTTGAATGTGAAGAATGTCATGATGGTAGTATCACGCTG
GTATGGAGGGATTCTGCTAGGACCAGATCGCTTTAAACATATCAACAACTGTGCCAGAAACATACTAGTGGAAAAGAACT
ACACAAATTCACCTGAGGAGTCATCTAAGGTTTTGGGAAAGAACAAAAAGTAAGAAAAGACAAGTAGAAGAATGAATAT

Alignment

ORF - retro_mmul_1041 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.46 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAEGDAGSDQRQNEEIEAMAAIYGEEWCVIDDCAKIFCIRISDDIDDPKWTLCLQVMLPNEYPGTAPPIY
          MAEGDAGSDQRQNEEIEAMAAIYGEEWCVIDDCAKIFCIRISDDIDDPKWTLCLQ.MLPNEY.GTAP.IY
Retrocopy MAEGDAGSDQRQNEEIEAMAAIYGEEWCVIDDCAKIFCIRISDDIDDPKWTLCLQMMLPNEYSGTAPLIY

Parental  QLNAPWLKGQERADLSNSLEEIYIQNIGESILYLWVEKIRDVLIQKSQMTEPGPDVKKKTEEEDVECEDD
          QL.APWLKG.E.ADLSNSLEEIYIQNIGESILYLWVEKIRDVLIQ.SQ.TEPGPDVKKKTEEE.VECEDD
Retrocopy QLSAPWLKGLECADLSNSLEEIYIQNIGESILYLWVEKIRDVLIQTSQTTEPGPDVKKKTEEEEVECEDD

Parental  LILACQPESSVKALDFDISETRTEVEVEELPPIDHGIPITDRRSTFQAHLAPVVCPKQVKMVLSKLYENK
          LILA.QPE.SVKALDFDISETRTEVE.EELPPIDHGIPITD.RSTFQAHLAPVVCPKQVKMV.SKLYENK
Retrocopy LILARQPEGSVKALDFDISETRTEVEIEELPPIDHGIPITDQRSTFQAHLAPVVCPKQVKMVPSKLYENK

Parental  KIASATHNIYAYRIYCEDKQTFLQDCEDDGETAAGGRLLHLMEILNVKNVMVVVSRWYGGILLGPDRFKH
          KIASATHNI.AYRIYCEDKQTFLQDCED.GETAAGGRLLHLMEILNVKNVM.VVSRWYGGILLGPDRFKH
Retrocopy KIASATHNISAYRIYCEDKQTFLQDCEDYGETAAGGRLLHLMEILNVKNVMMVVSRWYGGILLGPDRFKH

Parental  INNCARNILVEKNYTNSPEESSKSLGKNK-KVRKDKKKNEH
          INNCARNILVEKNYTNSPEESSK.LGKNK.KVRKDK.KNE.
Retrocopy INNCARNILVEKNYTNSPEESSKVLGKNK<KVRKDK*KNEY

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	6.95 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	6.98 RPM
SRP007412_cerebellum	0.19 RPM	7.68 RPM
SRP007412_heart	0.00 RPM	4.48 RPM
SRP007412_kidney	0.00 RPM	5.40 RPM
SRP007412_liver	0.00 RPM	2.26 RPM
SRP007412_testis	0.11 RPM	11.80 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1041 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1041 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1041 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000013068	1 retrocopy	retro_chof_2523,
Erinaceus europaeus	ENSEEUG00000003962	1 retrocopy	retro_eeur_409,
Homo sapiens	ENSG00000154059	1 retrocopy	retro_hsap_3341,
Macaca mulatta	ENSMMUG00000004664	1 retrocopy	retro_mmul_1041 ,
Nomascus leucogenys	ENSNLEG00000006582	1 retrocopy	retro_nleu_1166,
Pongo abelii	ENSPPYG00000009071	1 retrocopy	retro_pabe_2753,
Pan troglodytes	ENSPTRG00000009927	1 retrocopy	retro_ptro_2141,
Sorex araneus	ENSSARG00000002836	1 retrocopy	retro_sara_719,