RetrogeneDB ID: retro_mmul_1627

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 3:102651575..102652148(+)
• Located in intron of: ENSMMUG00000030291

Retrocopy information

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

Parental gene information

• Parental gene symbol: CLK2
• Ensembl ID: ENSMMUG00000023141
• Aliases: None
• Description: None

Sequence

>retro_mmul_1627
CGGAAAGCCAAGCGTGCAGAGGACCACGCTGAGGGCCGCCTCATCTACCACGTCGGGGACTGGCTACAAGAGCGATATGA
AATCGTTAGCACTTTAGGAAGGGGGACCTTCGGCCGAGTTGTACAATGTGTTGACCATTGCAGGGGTGGGACTCGAGTTG
CCCTGAAGATCGTTAAAAATGTGGAGAAGTGTAAGGAAGCAGCTTGACTTGAGATCAACGTGCTGGAGAAGATCAACGAG
AAAGACCCTGACAACAAGAACCTCTGTGTCCAGATGTTTGACTGGTTTGACTACCATGGCCACGTGTGCATCTCCTTTGA
GCTTCTGGGCCTTAGCACCTTCGATTTCCTCAAAGACAACAACTACCTGCCCTACCCCATCTACCAAGTGTGCCACATGG
CCTTCCAGCTGTGCCAGGCTGTCAAGTTCCTCCATGATAACAAGCCGATGCATACAGACCTCAAACCTGAAAATATTCTG
TTTGTGAATTCAGACTATGAGCTCACCTACAACCTAGAGAAGAAGCGAGATGAGCGCAGTGTGAAGAGCACAGCTGTGCA
GGTGGGAGACTGG

Alignment

ORF - retro_mmul_1627 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.05 %
• Parental protein coverage: 52.33 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RRAKSVEDDAEGHLIYHVGDWLQERYEIVSTLGEGTFGRVVQCVDHRRGGARVALKIIKNVEKYKEAARL
          R.AK..ED.AEG.LIYHVGDWLQERYEIVSTLG.GTFGRVVQCVDH.RGG.RVALKI.KNVEK.KEAA.L
Retrocopy RKAKRAEDHAEGRLIYHVGDWLQERYEIVSTLGRGTFGRVVQCVDHCRGGTRVALKIVKNVEKCKEAA*L

Parental  EINVLEKINEKDPDNKNLCVQMFDWFDYHGHMCISFELLGLSTFDFLKDNNYLPYPIHQVRHMAFQLCQA
          EINVLEKINEKDPDNKNLCVQMFDWFDYHGH.CISFELLGLSTFDFLKDNNYLPYPI.QV.HMAFQLCQA
Retrocopy EINVLEKINEKDPDNKNLCVQMFDWFDYHGHVCISFELLGLSTFDFLKDNNYLPYPIYQVCHMAFQLCQA

Parental  VKFLHDNKLTHTDLKPENILFVNSDYELTYNLEKKRDERSVKSTAVRVVDF
          VKFLHDNK..HTDLKPENILFVNSDYELTYNLEKKRDERSVKSTAV.V.D.
Retrocopy VKFLHDNKPMHTDLKPENILFVNSDYELTYNLEKKRDERSVKSTAVQVGDW

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	21.29 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	13.72 RPM
SRP007412_cerebellum	0.00 RPM	36.94 RPM
SRP007412_heart	0.00 RPM	13.90 RPM
SRP007412_kidney	0.12 RPM	31.45 RPM
SRP007412_liver	0.00 RPM	21.69 RPM
SRP007412_testis	5.58 RPM	10.59 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1627 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1627 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1627 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Macaca mulatta	ENSMMUG00000011069	1 retrocopy	retro_mmul_457,
Macaca mulatta	ENSMMUG00000023141	1 retrocopy	retro_mmul_1627 ,
Tupaia belangeri	ENSTBEG00000000216	2 retrocopies	retro_tbel_4081, retro_tbel_4274,