RetrogeneDB ID: retro_mmul_743

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 1099214780579:0..370(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.17900
• Ensembl ID: ENSMMUG00000007453
• Aliases: None
• Description: ADP-ribosylation factor-like protein 5B [Source:RefSeq peptide;Acc:NP_001180408]

Sequence

>retro_mmul_743
GTACAAGAGAGAGTGATTAATAATACACGTTTCCTAACGTGGGATATTGGTAGCAAGAATCTCTTGGTCTTCCTGGAACA
CCTACTATACTAACACAGAGTTTGTAATAGTGTGGGAAGTACAGAGAGGATTTCTGTAACTAGAGAAGAACTCTAAAATG
TTAGTGCTTGAGGACCTAAGAAAAGCCTGATTGCTGAGTTTAGCTAATAAACAAGATGTTAAAGAATGCATGACTGTAGC
AGAAATCGGCAAGTTTTTGAAGCTACCTTCTGTTAAAGATCACCAGTGGCATATCCAGGCATGATGTGCTCTAACTGGCG
AGGGATTGTGCCGAAGACTTGAATGGATGATGTCTTGACTTAAGATTAGA

Alignment

ORF - retro_mmul_743 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.23 %
• Parental protein coverage: 71.51 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VEEIVVKNTHFLMWDIGG-QESLR-SSWNTYYSNTEFIILVVDSIDRERLAITKEELYRMLAHEDLRKAA
          V.E.V..NT.FL.WDIG..QESL..SSWNTYY.NTEF....V....R..L...K.....ML..EDLRKA.
Retrocopy VQERVINNTRFLTWDIGS<QESLG<SSWNTYYTNTEFV--IVWEVQRGFL*LEKNS--KMLVLEDLRKA*

Parental  VLIFANKQDMKGCMTAAEISKYLTLSSIKDHPWHIQSCCALTGEGLCQGLEWMTSRIGVR
          .L..ANKQD.K.CMT.AEI.K.L.L.S.KDH.WHIQ..CALTGEGLC..LEWM.S....R
Retrocopy LLSLANKQDVKECMTVAEIGKFLKLPSVKDHQWHIQA*CALTGEGLCRRLEWMMS*LKIR

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	10.08 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	7.46 RPM
SRP007412_cerebellum	0.00 RPM	12.27 RPM
SRP007412_heart	0.00 RPM	2.36 RPM
SRP007412_kidney	0.00 RPM	3.64 RPM
SRP007412_liver	0.00 RPM	1.78 RPM
SRP007412_testis	0.00 RPM	6.22 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_743 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_743 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_743 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000005856	2 retrocopies	retro_cpor_558, retro_cpor_747,
Macaca mulatta	ENSMMUG00000007453	3 retrocopies	retro_mmul_614, retro_mmul_726, retro_mmul_743 ,
Macaca mulatta	ENSMMUG00000010521	5 retrocopies	retro_mmul_2519, retro_mmul_2543, retro_mmul_2630, retro_mmul_616, retro_mmul_641,
Oryctolagus cuniculus	ENSOCUG00000014876	1 retrocopy	retro_ocun_79,
Ictidomys tridecemlineatus	ENSSTOG00000027859	1 retrocopy	retro_itri_580,