RetrogeneDB ID: retro_mmul_1758

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 4:34812192..34812901(+)
• Located in intron of: ENSMMUG00000029762

Retrocopy information

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

Parental gene information

• Parental gene symbol: NIT2
• Ensembl ID: ENSMMUG00000020024
• Aliases: None
• Description: None

Sequence

>retro_mmul_1758
GCTTTGCCGGAATGCTTTAATTCTCCATATGGAACGAAATATTTTCCTGAATATGCAGAGAAAATTCCTGGTGAATCCAC
ACAGAAGCTTTCTGAAGTAGCAAAGGAATGCAGCATATTTCTCATTGGAGGCTCTATCCCTGCAGAGGATGCTGGGAAAT
TATATAACACCTGTGCTGTGTTTGGGCCTGATGGAACTTTACTAGCAAAGTACAGAAAGATCCATCTGTTGACATTGATG
TTCCTGGAAAAATTACATTTCAAGAATCTAAAACGTTGAGTCCGGGTGATAGTTTCTCCACATTTGATACTCCTTACTGC
AGAGTGGGTCTGGGCATCTGCTACGACACGCGGTTTGCAGAGCTTGCACAAATCTAGCACAGAGAGGCTGCCAGCTGTTG
GTATATCCAGGAGCTTTTAATCTGACCACTGGACCAGCCCACTGGGAGTTGCTTCAGCGAAGCCGGGCTGTTGATAATCA
GGTGTATGTGGCCACAGCCTCTCCTGCCCGGGATGACAAAGCCTCCTACGTTGCCTGGGGACACAGCACCATGGTGAACC
CTTAGGGGGAGGTCCTAGCCAAAGCTGGCACAGAAGAAGCAATCGTGTATTCAGACATAGACCTGAAGAAGCTGGTTGAA
ATACGCCAGCAAATCCCCGTTTTTAGACAGAAGCGATCAGACCTCTATGCTGTGGAGATGAAAAAGCCC

Alignment

ORF - retro_mmul_1758 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.56 %
• Parental protein coverage: 85.87 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SLPECFNSPYGTKYFPEYAEKIPGESTQKLSEVAKECSIYLIGGSIPEEDAGKLYNTCAVFGPDGTLLAK
          .LPECFNSPYGTKYFPEYAEKIPGESTQKLSEVAKECSI.LIGGSIP.EDAGKLYNTCAVFGPDGTLLAK
Retrocopy ALPECFNSPYGTKYFPEYAEKIPGESTQKLSEVAKECSIFLIGGSIPAEDAGKLYNTCAVFGPDGTLLAK

Parental  YRKIHLF-DIDVPGKITFQESETLSPGDSFSTFDTPYCRVGLGICYDMRFAELAQI-YAQRGCQLLVYPG
          YRKIHL..DIDVPGKITFQES.TLSPGDSFSTFDTPYCRVGLGICYD.RFAELAQI..AQRGCQLLVYPG
Retrocopy YRKIHLL<DIDVPGKITFQESKTLSPGDSFSTFDTPYCRVGLGICYDTRFAELAQI<LAQRGCQLLVYPG

Parental  AFNLTTGPAHWELLQRSRAVDNQVYVATASPARDDKASYVAWGHSTVVNPWGEVLAKAGTEEAIVYSDID
          AFNLTTGPAHWELLQRSRAVDNQVYVATASPARDDKASYVAWGHST.VNP.GEVLAKAGTEEAIVYSDID
Retrocopy AFNLTTGPAHWELLQRSRAVDNQVYVATASPARDDKASYVAWGHSTMVNP*GEVLAKAGTEEAIVYSDID

Parental  LKKLAEIRQQMPVFRQKRSDLYAVEMKKP
          LKKL.EIRQQ.PVFRQKRSDLYAVEMKKP
Retrocopy LKKLVEIRQQIPVFRQKRSDLYAVEMKKP

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	0.34 RPM	12.89 RPM
SRP007412_brain_prefrontal_cortex	1.03 RPM	14.20 RPM
SRP007412_cerebellum	0.06 RPM	5.62 RPM
SRP007412_heart	0.12 RPM	17.55 RPM
SRP007412_kidney	0.23 RPM	83.92 RPM
SRP007412_liver	0.04 RPM	46.27 RPM
SRP007412_testis	1.02 RPM	4.26 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1758 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1758 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1758 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000003980	1 retrocopy	retro_amel_1002,
Callithrix jacchus	ENSCJAG00000000590	1 retrocopy	retro_cjac_3014,
Homo sapiens	ENSG00000114021	1 retrocopy	retro_hsap_411,
Gorilla gorilla	ENSGGOG00000003724	1 retrocopy	retro_ggor_406,
Macaca mulatta	ENSMMUG00000020024	2 retrocopies	retro_mmul_1758 , retro_mmul_505,
Mustela putorius furo	ENSMPUG00000011450	1 retrocopy	retro_mputfur_805,
Nomascus leucogenys	ENSNLEG00000002631	1 retrocopy	retro_nleu_1009,
Pan troglodytes	ENSPTRG00000015161	1 retrocopy	retro_ptro_315,