RetrogeneDB ID: retro_mmul_1498

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 2:20853102..20853448(-)
• Located in intron of: ENSMMUG00000002862

Retrocopy information

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

Parental gene information

• Parental gene symbol: GMFB
• Ensembl ID: ENSMMUG00000012326
• Aliases: None
• Description: None

Sequence

>retro_mmul_1498
AGTGAGTCTCTGGTGGTTTGTAATGTTGCTGAAGATTTAGTGGAAAAGCTGAGAAAGTTTCATTTTCACAAAGAAATGAA
CAATATGAAAACTGACAAGGATAAACGCCGGGTAGTACTGGATAAGGAGCTGGAGGGTATTTCACCAGATGAACTTAAAG
ATGAACTGCCTGAACGACAACCTCACTTCATTGTGCATAGTTATAAATATCAACATAATGGATGGGAGAGTTCCATATCC
TTTGTGCTTTATTTTCTCCAGTTCTGTTGGACGTAAGCCTGAACAACAGATGATGTATGCTGGGAGTAAGAATAAGCTAG
TCTAGAGAGCTGAACTAACCAAGGTA

Alignment

ORF - retro_mmul_1498 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.34 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SESLVVCDVAEDLVEKLRKFRFRKETNNAAIIMKIDKDKRLVVLDEELEGISPDELKDELPERQPRYPFL
          SESLVVC.VAEDLVEKLRKF.F.KE.NN....MK.DKDKR.VVLD.ELEGISPDELKDELPERQP.....
Retrocopy SESLVVCNVAEDLVEKLRKFHFHKEMNN----MKTDKDKRRVVLDKELEGISPDELKDELPERQPHF-IV

Parental  NLYKYQHD-DGRVSYPLCFIFSSPVGCKPEQQMMYAGSKNKLVQTAELTKV
          ..YKYQH..DGRV.YPLCFIFSS.VG.KPEQQMMYAGSKNKLV..AELTKV
Retrocopy HSYKYQHN>DGRVPYPLCFIFSSSVGRKPEQQMMYAGSKNKLV*RAELTKV

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	15.69 RPM
SRP007412_brain_prefrontal_cortex	0.24 RPM	13.72 RPM
SRP007412_cerebellum	0.06 RPM	13.75 RPM
SRP007412_heart	0.00 RPM	2.41 RPM
SRP007412_kidney	0.00 RPM	7.04 RPM
SRP007412_liver	0.04 RPM	1.50 RPM
SRP007412_testis	0.04 RPM	5.54 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1498 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1498 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1498 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2818
Gorilla gorilla	retro_ggor_1960
Pongo abelii	retro_pabe_2209

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000007312	1 retrocopy	retro_cjac_736,
Homo sapiens	ENSG00000197045	1 retrocopy	retro_hsap_2818,
Loxodonta africana	ENSLAFG00000004659	1 retrocopy	retro_lafr_493,
Macaca mulatta	ENSMMUG00000012326	1 retrocopy	retro_mmul_1498 ,
Nomascus leucogenys	ENSNLEG00000012717	1 retrocopy	retro_nleu_1197,
Oryctolagus cuniculus	ENSOCUG00000004488	2 retrocopies	retro_ocun_1849, retro_ocun_1881,
Pongo abelii	ENSPPYG00000005830	1 retrocopy	retro_pabe_2209,