RetrogeneDB ID: retro_mmul_1973

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 5:118060612..118061231(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.14891
• Ensembl ID: ENSMMUG00000015843
• Aliases: TMEM248, C3H7orf42, C7orf42
• Description: UPF0458 protein C7orf42 [Source:RefSeq peptide;Acc:NP_001180706]

Sequence

>retro_mmul_1973
ATTTTTAACATCAACCCCCTGGAGAATCTGAAGGTATACATCATCGGTCCGCCTCCTTGGTGGTCTTTATGATCGTTGTG
GGCACCATGGCATAGCTTTCCGAACCCTGGACTGTTTCTTCAAAATCATGGAGATTAAGTCACCAGAAATGGCAGAAGAT
CGGAATACTTTTCTGCTGTGGTTTAATGATTTGGACTTGCATGCATCAGAAAACGAAACATTAAGGCATCTCAAAAATGA
CACCAAAACTTCGGGAAGCATAATGACCATGCAGACCAGAGCATCCACTGGGTCTTCCCAGGCCCTGGAGGATTCAGGCC
CAGTTAACATCTCAGTCAAAATCATCCTAACCCTGAACCCACTCAAATTATTTGGAGGGTACTCTCATGGCATCACTCAT
CTGTATTCAATCATTTTAGGTCATCAGATTGGACTTTGAGACAGAGAAGCCCACGAAGGGATAAATATTACCTTTACTCT
GCCTGCAACTTGAACATCAGATAGTTGTGCTCTTGATGGTCCCCATGAGCAGATGGTGTTCACAGCATGCATGACCCTCA
GGGACACCCTGGGTGTGTTCCCCTTCACTGTGCAGCCACCGCACTGTGTTTCTGACACA

Alignment

ORF - retro_mmul_1973 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.81 %
• Parental protein coverage: 66.24 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MFSINPLENLKVYISSRPP-LVVFMISVSAMA-IAFLTLGYFFKIKEIKSPEMAEDWNTFLLRFNDLDLC
          .F.INPLENLKVYI...PP.LVVFMI.V..MA.IAF.TL..FFKI.EIKSPEMAED.NTFLL.FNDLDL.
Retrocopy IFNINPLENLKVYIIGPPP<LVVFMIVVGTMA<IAFRTLDCFFKIMEIKSPEMAEDRNTFLLWFNDLDLH

Parental  VSENETLKHLTNDTTTPESTMTSGQARASTQSPQALEDSGPVNISVAITLTLDPLKPFGGYSRNVTHLYS
          .SENETL.HL.NDT.T..S.MT..Q.RAST.S.QALEDSGPVNISV.I.LTL.PLK.FGGYS...THLYS
Retrocopy ASENETLRHLKNDTKTSGSIMTM-QTRASTGSSQALEDSGPVNISVKIILTLNPLKLFGGYSHGITHLYS

Parental  TILGHQIGLSGREAHEEINITFTLPTAWSSDDCALHGHCEQVVFTACMTLTASPGVFPVTVQPPHCVPDT
          .ILGHQIGL..REAHE.INITFTLP....SD.CAL.G..EQ.VFTACMTL....GVFP.TVQPPHCV.DT
Retrocopy IILGHQIGL*DREAHEGINITFTLPAT*TSDSCALDGPHEQMVFTACMTLRDTLGVFPFTVQPPHCVSDT

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	40.79 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	44.58 RPM
SRP007412_cerebellum	0.00 RPM	37.20 RPM
SRP007412_heart	0.00 RPM	25.44 RPM
SRP007412_kidney	0.00 RPM	46.01 RPM
SRP007412_liver	0.00 RPM	49.52 RPM
SRP007412_testis	0.00 RPM	26.84 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1973 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1973 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1973 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3093
Pan troglodytes	retro_ptro_2089
Gorilla gorilla	retro_ggor_2124

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000004278	1 retrocopy	retro_cjac_2145,
Cavia porcellus	ENSCPOG00000000830	1 retrocopy	retro_cpor_330,
Echinops telfairi	ENSETEG00000015971	1 retrocopy	retro_etel_2097,
Homo sapiens	ENSG00000106609	1 retrocopy	retro_hsap_3093,
Gorilla gorilla	ENSGGOG00000022776	1 retrocopy	retro_ggor_2124,
Myotis lucifugus	ENSMLUG00000000616	1 retrocopy	retro_mluc_1974,
Macaca mulatta	ENSMMUG00000015843	1 retrocopy	retro_mmul_1973 ,
Nomascus leucogenys	ENSNLEG00000013326	1 retrocopy	retro_nleu_2235,
Pan troglodytes	ENSPTRG00000019253	1 retrocopy	retro_ptro_2089,
Pteropus vampyrus	ENSPVAG00000002978	2 retrocopies	retro_pvam_988, retro_pvam_997,
Sorex araneus	ENSSARG00000001884	1 retrocopy	retro_sara_563,