RetrogeneDB ID: retro_mmul_2300

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 8:87514920..87515235(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMMUG00000007118
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: MMU.3127
• Ensembl ID: ENSMMUG00000022096
• Aliases: None
• Description: immunoglobulin J polypeptide, linker protein for immunoglobulin alpha and mu polypeptides precursor [Source:RefSeq peptide;Acc:NP_001247815]

Sequence

>retro_mmul_2300
ATGAAGAACTATTTTCTCTTCTGGACAGTCTAGGCCATTTTTGTTAAGGCTGTTCTTGTGACACCTCAAGATGAAGATGA
GAGGATCATTCCTGTTGATGACAAATGTAAGTGGGCCCAGGTTATTTTCACCATCATCTCTTCTACCAAAGATCCTAATG
AGGACACTGTGGAGAGAAACATCCAAATTGCTGTTCTCCTGGACAATAAGAAGAATATCTCTGATCTCGTCTCAAGGTTG
AGAACCAAATTTGTGTACCATTTGTCGTACCTCTGTAAAAAATGTGATCCTACAGAAGTGGAACTGGATAATCAG

Alignment

ORF - retro_mmul_2300 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.52 %
• Parental protein coverage: 65.41 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MKNHLLFWGVLAIFVKAVHVKAQ-EGERIVLVDNKCKCARITSRIIRSSEDPNEDIVERNIRIIVPLNNR
          MKN..LFW.V.AIFVKAV.V..Q.E.ERI..VD.KCK.A.....II.S..DPNED.VERNI.I.V.L.N.
Retrocopy MKNYFLFWTV*AIFVKAVLVTPQDEDERIIPVDDKCKWAQVIFTIISSTKDPNEDTVERNIQIAVLLDNK

Parental  ENISDPTSPLRTKFVYHLSDLCKKCDPTEVELDNQ
          .NISD..S.LRTKFVYHLS.LCKKCDPTEVELDNQ
Retrocopy KNISDLVSRLRTKFVYHLSYLCKKCDPTEVELDNQ

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	0.34 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	0.32 RPM
SRP007412_cerebellum	0.00 RPM	0.19 RPM
SRP007412_heart	0.00 RPM	2.24 RPM
SRP007412_kidney	0.00 RPM	26.17 RPM
SRP007412_liver	0.00 RPM	2.65 RPM
SRP007412_testis	0.00 RPM	1.24 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2300 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2300 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2300 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pongo abelii	retro_pabe_3272

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000014618	1 retrocopy	retro_cjac_1466,
Homo sapiens	ENSG00000132465	1 retrocopy	retro_hsap_4086,
Macaca mulatta	ENSMMUG00000022096	1 retrocopy	retro_mmul_2300 ,
Nomascus leucogenys	ENSNLEG00000007714	1 retrocopy	retro_nleu_3069,
Pongo abelii	ENSPPYG00000014809	1 retrocopy	retro_pabe_3272,
Pan troglodytes	ENSPTRG00000016134	1 retrocopy	retro_ptro_2771,