RetrogeneDB ID: retro_mmul_1040

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 13:89353725..89354428(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CSNK1G3
• Ensembl ID: ENSMMUG00000006646
• Aliases: None
• Description: casein kinase I isoform gamma-3 [Source:RefSeq peptide;Acc:NP_001244979]

Sequence

>retro_mmul_1040
GGGAAAAAATTATACGCAAATAAATATGTGGCAATGAAGCTGGAGCCCGTGAAATCAAAACACCACAGCTACATTTGGAA
AACAGATTCTATAAGCGGTTAGGACCTGGAGATTGTATACCTCAAGTTTACTATTTCTGGCCTTGTGGTAAATACAATGC
TATGGTGCTGGAACTGCTGGGACCTAGTTTGGAATATTTGTTTGACTTGTGTGACAGAACATTTTCTTTTAAAACACTTC
TCGTGATAGCTCTACAACTGATTTCTCTCATGGAATATGTCCATTCAAAGAACTTGATATACAGAGATTAAAACCTGAGA
ACTTCTTAATAGGACGACCAGGAAACAAAGCCCAGCAAGTTATTCATATTATAGATTTTGGTTTGGCAAAGAAACATATT
GATCCAGAGACAAAGAAACACATACCATACAGAGAACATAAGGGCCCTATGAGAACAGCTAGATATACGAGCGTAAACAC
ACATTTAGGAAAAGGACAAAGTAGAAGAGATGATTTAGAAGCTTTAGGTCACATGTTCATGTATTTTCTGAGAGGCAGTC
TTCCTTGGCAAGGCTTAAAAGCCGACACATTAAAAGAGAGGTATCAGAAAATTGGAGATACAAAACGGGCTACACCAATA
GAAGTGTTAGGTGAAAATTTTCCAGAAATGGCAACGTATCTTTGTTATGTAAGAAGGTTAGAT

Alignment

ORF - retro_mmul_1040 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.08 %
• Parental protein coverage: 55.56 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  GKNLYTNEYVAIKLEPMKSR-APQLHLEYRFYKQLGSGDGIPQVYYFGPCGKYNAMVLELLGPSLEDLFD
          GK.LY.N.YVA.KLEP.KS...PQLHLE.RFYK.LG.GD.IPQVYYF.PCGKYNAMVLELLGPSLE.LFD
Retrocopy GKKLYANKYVAMKLEPVKSK<TPQLHLENRFYKRLGPGDCIPQVYYFWPCGKYNAMVLELLGPSLEYLFD

Parental  LCDRTFSLKTVLMIAIQLISRMEYVHSKNLIYRD-VKPENFLIGRPGNKTQQVIHIIDFGLAKEYIDPET
          LCDRTFS.KT.L.IA.QLIS.MEYVHSKNLIYRD..KPENFLIGRPGNK.QQVIHIIDFGLAK..IDPET
Retrocopy LCDRTFSFKTLLVIALQLISLMEYVHSKNLIYRD<LKPENFLIGRPGNKAQQVIHIIDFGLAKKHIDPET

Parental  KKHIPYREHKSLTGTARYMSINTHLGKEQSRRDDLEALGHMFMYFLRGSLPWQGLKADTLKERYQKIGDT
          KKHIPYREHK....TARY.S.NTHLGK.QSRRDDLEALGHMFMYFLRGSLPWQGLKADTLKERYQKIGDT
Retrocopy KKHIPYREHKGPMRTARYTSVNTHLGKGQSRRDDLEALGHMFMYFLRGSLPWQGLKADTLKERYQKIGDT

Parental  KRATPIEVLCENFPEMATYLRYVRRLD
          KRATPIEVL.ENFPEMATYL.YVRRLD
Retrocopy KRATPIEVLGENFPEMATYLCYVRRLD

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	0.11 RPM	24.88 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	13.57 RPM
SRP007412_cerebellum	0.00 RPM	30.41 RPM
SRP007412_heart	0.06 RPM	5.71 RPM
SRP007412_kidney	0.12 RPM	12.56 RPM
SRP007412_liver	0.00 RPM	4.95 RPM
SRP007412_testis	0.04 RPM	14.85 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1040 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1040 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1040 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000017550	1 retrocopy	retro_btau_1659,
Callithrix jacchus	ENSCJAG00000017348	2 retrocopies	retro_cjac_2695, retro_cjac_3279,
Macaca mulatta	ENSMMUG00000001758	2 retrocopies	retro_mmul_2207, retro_mmul_295,
Macaca mulatta	ENSMMUG00000006620	1 retrocopy	retro_mmul_1195,
Macaca mulatta	ENSMMUG00000006646	1 retrocopy	retro_mmul_1040 ,
Mus musculus	ENSMUSG00000073563	1 retrocopy	retro_mmus_3454,
Otolemur garnettii	ENSOGAG00000011587	1 retrocopy	retro_ogar_246,
Rattus norvegicus	ENSRNOG00000016677	1 retrocopy	retro_rnor_2189,