RetrogeneDB ID: retro_mmul_1561

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 20:46922218..46922985(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: KLF8
• Ensembl ID: ENSMMUG00000014678
• Aliases: None
• Description: None

Sequence

>retro_mmul_1561
GATATGGCTCAACTCATAAACAACTTGGAGGTGCAACTTAATTCAGAAGGTGGCTCAATGCAGGTATTCAGGTCCATCAC
TGGCCCTGTTCAGAGCAGAGATCCCCCTGAGATAGAAGCATAAATAATATGACTTCTCCACCACTTCTGGATGCCAACCC
CATGGAGAACCCAGCACTGTTTAATGACATCAGGTTTGAGACCCCAGAAGAACTTTTGGCGAGTGATTTCAGCCTGTCCC
CAGTGGAACCAGTTGACTTCTCCTCTCCCAAGCCCAAGGCTCCTCTCCAGCCTGTTAGCATGCTGCAAGCTCCAGAACAT
CCTCCCAAGCCACAGTCTGCTCCCCAGACCCTTGTGGTGTTCACTTCAACATCAGCAAACATTCCTACTATTCTGACCAC
AGGCTCTGTCCTGACTCCCTCTCAGGGCACTGGTGGCTAGCAGATCTTACATGTTGTTCACAGCATCCCCTCAGTCTGTC
TTCCAAGTAAGATGGGTGACCTGAATGCCATCCCAGTGGTGGTGCAGTCTCTGCCCATGGTGTATACTACTTTGCCTGCA
AATGAGGGCCCTGCAACCATTACAGTCCCACTCATTGGAGGAGATGGTACAAATGCTGGATCATGATGTGAATGTTGACC
CCACTCCATGTCTCCACTGGAGATTCCAAGTGACAATGAGGAGAGTGTAATTAAAAGTGGATCCTCATTCTCACAGAGTC
TGCAGGGACCACAGCAAGAACCAGCAGCAATGGTCTAAATGCAGGGA

Alignment

ORF - retro_mmul_1561 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.99 %
• Parental protein coverage: 72.42 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  DMDQLINNLEVQLNSEGGSMQVFKQVTSSVRNRDPSEIEY-RSNMTSPTLLDANPMENPALFNDIKIEPP
          DM.QLINNLEVQLNSEGGSMQVF...T..V..RDP.EIE....NMTSP.LLDANPMENPALFNDI..E.P
Retrocopy DMAQLINNLEVQLNSEGGSMQVFRSITGPVQSRDPPEIEA<INNMTSPPLLDANPMENPALFNDIRFETP

Parental  EELLASDFSLPQVEPVDLSFHKPKAPLQPASMLQAPVRPPKPQSAPQTLVVSTSTSDMSTSANIPTVLTP
          EELLASDFSL..VEPVD.S..KPKAPLQP.SM.......P.....PQ.....T.....STSANIPT.LT.
Retrocopy EELLASDFSLSPVEPVDFSSPKPKAPLQPVSM----LQAPEHPPKPQS-APQTLVVFTSTSANIPTILTT

Parental  GSVLTSSQSTGGQQILHVIHTIPSVSLPNKMGGLKTIPVVVQSLPMVYTALPADGGPAAITVPLIGGDGK
          GSVLT.SQ.TGG.QILHV.H.IPSV.LP.KMG.L..IPVVVQSLPMVYT.LPA..GPA.ITVPLIGGDG.
Retrocopy GSVLTPSQGTGG*QILHVVHSIPSVCLPSKMGDLNAIPVVVQSLPMVYTTLPANEGPATITVPLIGGDGT

Parental  NAGS-VKVDPTSMSPLEIPSDSEESTIESGSSALQSLQGLQQEPAAMAQMQG
          NAGS.....P.SMSPLEIPSD.EES.I.SGSS..QSLQG.QQEPAAM..MQG
Retrocopy NAGS*CEC*PHSMSPLEIPSDNEESVIKSGSSFSQSLQGPQQEPAAMV*MQG

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	1.34 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	2.62 RPM
SRP007412_cerebellum	0.00 RPM	2.78 RPM
SRP007412_heart	0.00 RPM	4.65 RPM
SRP007412_kidney	0.00 RPM	10.68 RPM
SRP007412_liver	0.12 RPM	2.30 RPM
SRP007412_testis	0.04 RPM	0.98 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1561 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1561 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1561 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Macaca mulatta	ENSMMUG00000003363	1 retrocopy	retro_mmul_2118,
Macaca mulatta	ENSMMUG00000014678	1 retrocopy	retro_mmul_1561 ,
Pan troglodytes	ENSPTRG00000021957	1 retrocopy	retro_ptro_1104,