RetrogeneDB ID: retro_mmul_2283

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 8:28386420..28386845(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PDLIM7
• Ensembl ID: ENSMMUG00000003146
• Aliases: None
• Description: None

Sequence

>retro_mmul_2283
CTGAGTCTCAGCAGGTCTCAGCCAGTTCACAGCAAACCACAGGAGGTTCTGGCTCCTGCCACAAACCCCCTGCAGTTCAC
GCTTGCACCCAGCACCTTCCTCAACAAGACAGCCTGGCCCTTCAGGTCACCCCCACCTGCTGGCAGTGCACCACAGCAGA
ATGGACAGCTGCTCCAACTGCTGGTCCCAGATGCCACCAAGCAGTGGCTGATGGAGAACACCAAGGACTGGCCACCACAG
CTTGGGACAGGCCAGTCACGTTCCTTCAGCATCCTTGTCCACCTCATAGACACCGAGTTCATACAAGACCTGGATGAGGA
GCACCTGAAGAAATCAAGGGAAAAGTATGTCCTAGGGCTATAGAGTCCACGCTAACCTGCCTCCAGGATTGGCACCACCA
GAACTCTGCCCACATGCACAATGTA

Alignment

ORF - retro_mmul_2283 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.33 %
• Parental protein coverage: 64.13 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LGLSRAQPVQSKPQKAVAPCRAPPWGGLSPRHSVPPCPRLFTPPHLSSSPPHPPHRQPLRPLVPDASKQR
          L.LSR.QPV.SKPQ...AP...P....L.P..........F..P....S.P.....Q.L..LVPDA.KQ.
Retrocopy LSLSRSQPVHSKPQEVLAPATNPLQFTLAPSTFLNKTAWPFRSPPPAGSAPQQ-NGQLLQLLVPDATKQW

Parental  LMENTEDWRPRPGTGQSRSFRILAHLTGTEFMQDPDEEHLKKSREKYVLELQSPR-YTRLRDWHHQRSAH
          LMENT.DW.P..GTGQSRSF.IL.HL..TEF.QD.DEEHLKKSREKYVL.L.SPR..T.L.DWHHQ.SAH
Retrocopy LMENTKDWPPQLGTGQSRSFSILVHLIDTEFIQDLDEEHLKKSREKYVLGL*SPR<LTCLQDWHHQNSAH

Parental  VLNV
          ..NV
Retrocopy MHNV

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	1.46 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	2.14 RPM
SRP007412_cerebellum	0.00 RPM	0.32 RPM
SRP007412_heart	0.06 RPM	20.37 RPM
SRP007412_kidney	0.00 RPM	2.70 RPM
SRP007412_liver	0.04 RPM	1.07 RPM
SRP007412_testis	0.00 RPM	5.65 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2283 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2283 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2283 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000006678	1 retrocopy	retro_cjac_1124,
Homo sapiens	ENSG00000196923	1 retrocopy	retro_hsap_3940,
Macaca mulatta	ENSMMUG00000003146	1 retrocopy	retro_mmul_2283 ,
Macaca mulatta	ENSMMUG00000004179	1 retrocopy	retro_mmul_1939,
Macaca mulatta	ENSMMUG00000007922	1 retrocopy	retro_mmul_1458,