RetrogeneDB ID: retro_mmul_530

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 1:127371006..127371866(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: IGF2BP2
• Ensembl ID: ENSMMUG00000023416
• Aliases: None
• Description: None

Sequence

>retro_mmul_530
CAACAAGAGAAGAAAATAGACATGGAGAAGCTAAGTGGGCATCAGTTTGAGAACTACTTCTTCAAGATTTCCTACATCCC
AGACGAAGAGGTGAGCTCCCCTTCGTCCCCTCAGTGAGCCCAGTGTGGGGACCTCTCTTCCCGGGGAGCAAGGCCAGCCC
CTGGGGGCACTTCTCAGGCTAGACAGATTGATTTCCTGTTGAGGATCCTGGTCCCCACCCAGTTTGTTGGTGCCATCATC
AGGAAGGAGGGCTTGACCATAAAGGACATCACTAAGCAGACCCAGTCCCAGGTAGACATCCATAGAAAAGAGAACTCTGG
AGCTGCAGAGAAGCCTGTCACCATCCATGTCACCCCCGGGGGGACTTCTGAAGCATGCCGCATGATCCCGAAATCATGCA
GAAAGAGGCAGATGAGACCAAACTAGCCGAAGAGATTCCTCTGAAAATCTTTGCCCACAATGGCTTGGTTGGAAGACTGA
CTGGAAAAGAAGGCAGGAATTTGAAGAAAATTGAACATGAAACAGGGATCAAGATAGCAATCTCATCTTTGTAGGATTTG
AGCATATACAACCCGGAAAGAACCATCACTGTGAAGGGCACAATTGAGGCCTGTGCCAGTGCTGAGATAGAGATTATGAA
GAAGCTGCATGAGGCCTTTGAAAATGATATGTTGGCTGTTAATACCCACTCTGGATACTTCTCCAGCCTGTATCCCTATC
ACCAGTTTGGCCCGTTCTCGCATCATCACTGTTATCCAGAGGAGGAGATTGTGAATCTCTTCATCCCAACCCAGGCTGTG
GGCGCCATCATCGGGAAGAAGGGGGCACATATCAAACAGCTGGCGAGATTCGCCCCTGCA

Alignment

ORF - retro_mmul_530 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.19 %
• Parental protein coverage: 51.62 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  REEAKIAMEKLSGHQFENYSFKISYIPDEEVSSPSPPQRAQRGDHSSREQGHAPGGTSQARQIDFPLRIL
          ..E.KI.MEKLSGHQFENY.FKISYIPDEEVSSPS.PQ.AQ.GD.SSR....APGGTSQARQIDF.LRIL
Retrocopy QQEKKIDMEKLSGHQFENYFFKISYIPDEEVSSPSSPQ*AQCGDLSSRGARPAPGGTSQARQIDFLLRIL

Parental  VPTQFVGAIIGKEGLTIKNITKQTQSRVDIHRKENSGAAEKPVTIHATPEGTSEACRMIL-EIMQKEADE
          VPTQFVGAII.KEGLTIK.ITKQTQS.VDIHRKENSGAAEKPVTIH.TP.GTSEACRMI..EIMQKEADE
Retrocopy VPTQFVGAIIRKEGLTIKDITKQTQSQVDIHRKENSGAAEKPVTIHVTPGGTSEACRMIP<EIMQKEADE

Parental  TKLAEEIPLKILAHNGLVGRLIGKEGRNLKKIEHETGTKITISSLQDLSIYNPERTITVKGTVEACASAE
          TKLAEEIPLKI.AHNGLVGRL.GKEGRNLKKIEHETG.KI.ISSL.DLSIYNPERTITVKGT.EACASAE
Retrocopy TKLAEEIPLKIFAHNGLVGRLTGKEGRNLKKIEHETGIKIAISSL*DLSIYNPERTITVKGTIEACASAE

Parental  IEIMKKLREAFENDMLAVNTHSGYFSSLYPHHQFGPFPHHHSYPEQEVVNLFIPTQAVGAIIGKKGAHIK
          IEIMKKL.EAFENDMLAVNTHSGYFSSLYP.HQFGPF.HHH.YPE.E.VNLFIPTQAVGAIIGKKGAHIK
Retrocopy IEIMKKLHEAFENDMLAVNTHSGYFSSLYPYHQFGPFSHHHCYPEEEIVNLFIPTQAVGAIIGKKGAHIK

Parental  QLARFAGA
          QLARFA.A
Retrocopy QLARFAPA

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	0.11 RPM	0.34 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	0.32 RPM
SRP007412_cerebellum	0.26 RPM	4.97 RPM
SRP007412_heart	0.06 RPM	5.18 RPM
SRP007412_kidney	0.00 RPM	6.81 RPM
SRP007412_liver	0.00 RPM	0.28 RPM
SRP007412_testis	0.08 RPM	2.22 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_530 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_530 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_530 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000073792	2 retrocopies	retro_hsap_216, retro_hsap_4096,
Gorilla gorilla	ENSGGOG00000015035	2 retrocopies	retro_ggor_2679, retro_ggor_2748,
Myotis lucifugus	ENSMLUG00000002631	1 retrocopy	retro_mluc_599,
Macaca mulatta	ENSMMUG00000023416	3 retrocopies	retro_mmul_2361, retro_mmul_409, retro_mmul_530 ,
Pongo abelii	ENSPPYG00000014373	3 retrocopies	retro_pabe_1723, retro_pabe_281, retro_pabe_837,