RetrogeneDB ID: retro_mmul_1419

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 2:18977423..18977953(+)
• Located in intron of: ENSMMUG00000017436

Retrocopy information

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

Parental gene information

• Parental gene symbol: PDLIM1
• Ensembl ID: ENSMMUG00000000454
• Aliases: None
• Description: None

Sequence

>retro_mmul_1419
ATGTTACTTTCTTATTTAGAAACAGAGAGCCCAGGACCATGAGGCTTCCGCCTGCTGGACAGCAAGGACCTCCAGCAGCC
TCTCAGCTGTTTCCCAGTCACTTTCAGAAGCAAGGCTGCTATAGCTAATTGATGTATGAAAGATGTAATTGCAGCCATTG
ATAGGGAAAATATCAGCAATATGATGCACTTGGAAGCTCAGAAAAAAATCAAAGGCTACACAGACAACATGACTGTCACA
GTAGCCAGATCTGAATATAAAATCTAGTCTCTTCTGGTGACGGAGGAAAGGAAGTGTCATCCATACAAGATGAATTTACA
CTCTGAACCCCAGGAGGTCCTGCACATAGGAAGTGCCTGCAATCCAAATACTGTGCTCTTTACTGCCTCTCCTGCTTCCA
GCACTTTCCCTGGGGTCATCCAAACCAGTACAGCAACCCGGCTGGCCTCTCTTCTTCTGAAAACATCTCCAACTTTAACA
ACACCTTGAGATAACATACTGCTGGTATTTCAAAAACTGCTGCCAGCAGG

Alignment

ORF - retro_mmul_1419 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.25 %
• Parental protein coverage: 66.17 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MTTQQIVLQGPGPWGFRLVGGKDFEQPLAISRVTPGSKAALANLCIGDVITAIDGENTSNMTHLEAQNRI
          M.........PGP.GFRL...KD..QPL....VT..SKAA.AN.C..DVI.AID.EN.SNM.HLEAQ..I
Retrocopy MLLSYLETESPGP*GFRLLDSKDLQQPLSCFPVTFRSKAAIAN*CMKDVIAAIDRENISNMMHLEAQKKI

Parental  KGCTDNMTLTVARSEHKVWSPLVTEEGGKRHPYKMNLASEPQEVLHIGSAHNRSAMPFTASPASSTTARV
          KG.TDNMT.TVARSE.K..S.LVTEE..K.HPYKMNL.SEPQEVLHIGSA.N.....FTASPASST...V
Retrocopy KGYTDNMTVTVARSEYKI*SLLVTEE-RKCHPYKMNLHSEPQEVLHIGSACNPNTVLFTASPASSTFPGV

Parental  I-TNQYNNPAGLYSSENISNFNNALESKTAASGVEANSR
          I..NQY.NPAGL.SSENISNFNN.L...TA.....A.SR
Retrocopy I<PNQYSNPAGLSSSENISNFNNTLR*HTAGISKTAASR

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	6.39 RPM
SRP007412_brain_prefrontal_cortex	0.48 RPM	3.57 RPM
SRP007412_cerebellum	0.19 RPM	1.10 RPM
SRP007412_heart	0.18 RPM	84.97 RPM
SRP007412_kidney	0.35 RPM	15.26 RPM
SRP007412_liver	0.20 RPM	32.50 RPM
SRP007412_testis	0.00 RPM	3.13 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1419 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1419 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1419 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000011182	1 retrocopy	retro_btau_690,
Canis familiaris	ENSCAFG00000028553	1 retrocopy	retro_cfam_2080,
Dasypus novemcinctus	ENSDNOG00000012381	1 retrocopy	retro_dnov_1119,
Homo sapiens	ENSG00000107438	2 retrocopies	retro_hsap_1815, retro_hsap_2681,
Macaca mulatta	ENSMMUG00000000454	2 retrocopies	retro_mmul_1250, retro_mmul_1419 ,
Mus musculus	ENSMUSG00000055044	2 retrocopies	retro_mmus_2558, retro_mmus_779,
Nomascus leucogenys	ENSNLEG00000013055	3 retrocopies	retro_nleu_1819, retro_nleu_2767, retro_nleu_2970,
Oryctolagus cuniculus	ENSOCUG00000013643	1 retrocopy	retro_ocun_417,
Pongo abelii	ENSPPYG00000002507	2 retrocopies	retro_pabe_1109, retro_pabe_1485,
Pan troglodytes	ENSPTRG00000002783	1 retrocopy	retro_ptro_912,
Tarsius syrichta	ENSTSYG00000000834	2 retrocopies	retro_tsyr_1056, retro_tsyr_1224,
Tursiops truncatus	ENSTTRG00000012118	2 retrocopies	retro_ttru_1777, retro_ttru_976,