RetrogeneDB ID: retro_mmul_505

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 1:80882886..80883373(-)
• Located in intron of: None

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_505
GCAACTTTCGACTTGGCCCTCATCCAGCTTCAAGTTTCTTCATCAAATCAGATAACAACACGCGAGCTTGTAGCCTTGTC
CAGGAGACAGCAACAAAAGGAGCCAAAATAGTTTCTTTGCTGGGATGCTTTAATTCTCCATATGGCACAAAATATTTTCC
TGAATATGCAGCGAAAATTCCTGGTAAATCCACACAGAAGCTTTCTGAAGTAGCAAAGGAATACAGCCTCACTAGAGGTT
CCATCCTTGAAGAGGATGCTGGGAAATCATATAACACCTGTGCTCTGTTTGCACCTCATGGAACTTTACTAGTAAAGCAC
AGAAAGGTCCATCTGCTTGACACTGGTGTTCCTGGAAAAATGACATTTCAAGAATCCAGAATGTTGAGTCCGGGCAATAG
TTTCTCCCCATTTGATACTCCAAACTGCAGAATGGGTTGGGGCATCTGTTATGACATTGGTTTGCAGAGCTTGCACAAGC
ACAGGCT

Alignment

ORF - retro_mmul_505 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.85 %
• Parental protein coverage: 59.78 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  ATFRLALIQLQISS-IKSDNVTRACSFIREAATQGAKIVSLPECFNSPYGTKYFPEYAEKIPGESTQKLS
          ATF.LALIQLQ.SS.IKSDN.TRACS...E.AT.GAKIVSL..CFNSPYGTKYFPEYA.KIPG.STQKLS
Retrocopy ATFDLALIQLQVSS<IKSDNNTRACSLVQETATKGAKIVSLLGCFNSPYGTKYFPEYAAKIPGKSTQKLS

Parental  EVAKECSIYLIGGSIPEEDAGKLYNTCAVFGPDGTLLAKYRKIHLFDIDVPGKITFQESETLSPGDSFST
          EVAKE.S..L..GSI.EEDAGK.YNTCA.F.P.GTLL.K.RK.HL.D..VPGK.TFQES..LSPG.SFS.
Retrocopy EVAKEYS--LTRGSILEEDAGKSYNTCALFAPHGTLLVKHRKVHLLDTGVPGKMTFQESRMLSPGNSFSP

Parental  FDTPYCRVGLGICYDMR-FAELAQIYA
          FDTP.CR.G.GICYD...FAELAQ..A
Retrocopy FDTPNCRMGWGICYDIG<FAELAQAQA

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	12.89 RPM
SRP007412_brain_prefrontal_cortex	0.08 RPM	14.20 RPM
SRP007412_cerebellum	0.00 RPM	5.62 RPM
SRP007412_heart	0.00 RPM	17.55 RPM
SRP007412_kidney	0.00 RPM	83.92 RPM
SRP007412_liver	0.04 RPM	46.27 RPM
SRP007412_testis	0.04 RPM	4.26 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_505 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_505 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_505 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_411
Pan troglodytes	retro_ptro_315
Gorilla gorilla	retro_ggor_406
Callithrix jacchus	retro_cjac_3014

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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,