RetrogeneDB ID: retro_mmul_1195

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 15:72171319..72172057(-)
• Located in intron of: ENSMMUG00000014558

Retrocopy information

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

Parental gene information

• Parental gene symbol: CSNK1G2
• Ensembl ID: ENSMMUG00000006620
• Aliases: None
• Description: casein kinase 1, gamma 2 [Source:HGNC Symbol;Acc:2455]

Sequence

>retro_mmul_1195
ACCTTCACGCTGAAGACAGTGCTCCCGATTGCCATCCAGCTGATCGCACGCATGGAGTATGTGCACACCAAGAGCCTCAT
TTACCAGGACGTGAAGTCCGAGAACTTCGTGGTGTGGCGCCCGGGGACCAAGCGGCAGCTCGCCATCCACATTATCAACT
TCGGGCCGGCCAAGGGGTACATTGGCCTTGAGACCGAGAAGCACATCCCGTACCGTGAGCACAAGAGCTTGACAGGCAGG
GCGCGCTACATGAACATCAACATGCAGCTGGGCAAGGAGCAGAGCCACTGCAGTGACCTGGAGGTGCTGGGCCACATGTT
CATGTACTTCCTGTGCTGCAGCCTCCCCTGGCAGGGGCTCAAGGCCGACACGATCATGAGCAGTACAGAATATCGGGAAC
ACCAAGCGCACCACGCCCATCGAAGTGCTCTGCTAGAACTTTCCAGAGGAGATGGCCACATACCTGCACTACGTGCGGCG
CCTGGACTTGGAGAAACCCGACTGTGACTACCTGTGGACCTCTCCACCGACCTCTTTGACCGAAGCGGCTTCGTGTTCGA
CTTTGAGTACCACTGGCCCAGGAAGCCCTTGGCGACCCCCATCGGCACCGTCCACACCAACCAACCCTCCCAGCCTCAGC
TTTGGGACAAAGATCAGCCACACAGCAAAAACCAGGTGCTGACCTCCACCAATGGGGAGCTGAATGTGGACGACCCCATG
GCCGGCCAGTCCCGCGCC

Alignment

ORF - retro_mmul_1195 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.09 %
• Parental protein coverage: 60.19 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  TFTLKTVLMIAIQLITRMEYVHTKSLIYRDVKPENFLVGRPGTKRQHAIHIIDFGLAKEYIDPETKKHIP
          TFTLKTVL.IAIQLI.RMEYVHTKSLIY.DVK.ENF.V.RPGTKRQ.AIHII.FG.AK.YI..ET.KHIP
Retrocopy TFTLKTVLPIAIQLIARMEYVHTKSLIYQDVKSENFVVWRPGTKRQLAIHIINFGPAKGYIGLETEKHIP

Parental  YREHKSLTGTARYMSINTHLGKEQSRRDDLEALGHMFMYFLRGSLPWQGLKADTL-KERY-QKIGDTKRA
          YREHKSLTG.ARYM.IN..LGKEQS...DLE.LGHMFMYFL..SLPWQGLKADT...E.Y.Q.IG.TKR.
Retrocopy YREHKSLTGRARYMNINMQLGKEQSHCSDLEVLGHMFMYFLCCSLPWQGLKADTI<HEQY<QNIGNTKRT

Parental  TPIEVLCENFPEEMATYLRYVRRLDFFEKPDYDYL-RKLFTDLFDRSGFVFDYEYDWAGKPLPTPIGTVH
          TPIEVLC.NFPEEMATYL.YVRRLD..EKPD.DYL...L.TDLFDRSGFVFD.EY.W..KPL.TPIGTVH
Retrocopy TPIEVLC*NFPEEMATYLHYVRRLD-LEKPDCDYL<VDLSTDLFDRSGFVFDFEYHWPRKPLATPIGTVH

Parental  TDLPSQPQLRDKGQPHSKNQALNSTNGELNADDPTAGHSNA
          T..PSQPQL.DK.QPHSKNQ.L.STNGELN.DDP.AG.S.A
Retrocopy TNQPSQPQLWDKDQPHSKNQVLTSTNGELNVDDPMAGQSRA

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	12.21 RPM
SRP007412_brain_prefrontal_cortex	0.08 RPM	50.61 RPM
SRP007412_cerebellum	0.00 RPM	14.85 RPM
SRP007412_heart	0.12 RPM	10.13 RPM
SRP007412_kidney	0.00 RPM	15.96 RPM
SRP007412_liver	0.04 RPM	17.38 RPM
SRP007412_testis	0.04 RPM	238.37 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1195 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1195 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1195 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000007923	1 retrocopy	retro_dnov_2552,
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,