RetrogeneDB ID: retro_mmul_1865

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 4:153011414..153011952(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PDAP1
• Ensembl ID: ENSMMUG00000001460
• Aliases: None
• Description: 28 kDa heat- and acid-stable phosphoprotein [Source:RefSeq peptide;Acc:NP_001253212]

Sequence

>retro_mmul_1865
ATACCTAAAGGAGGGAGAAAGGGAGGCCACAAAGGCCGGGCAAGGCAGTGTATGAGCCCTGAGGAGATCGACGTGCAGCT
GCAGGCTGAGAAGCAGAAGGCCAGGGAAGAAGAGGAGCAAAAAGAAAGTGGAGATGGAGCTGCAGGTGACCCCAAAAGGA
GAAGAAATCTCTAGACTCAGATGACAATGAGGATGAAGATGACTACCAGCAAAGGCGCAAACGTGTGGAAGGGCTCATCA
ACAATAAGAACCCCAACCCGGTGGCACAGACAACCAAAAAGCTCACACAACTGGATCTGGATGGGCCAAAGGAGCTTTCA
AGGAGAGAATGACAGGAGATTGAGAAGCAGAAGGCAAAAGAGCGTTACATGAAAATGCACTTGGCCGGGAAGACAGAGCA
ACCAAGGCCGACCTGGCCCGGGTGGCCATCATCTGGAAACAGCAGGACGACGCTGCCCGGAAGAAGGAAGAGGAAAGGAA
AGCAAAAGACAATGCCACATTGTCAGGAAAACCAATGCAGTCGCTCTCCCTGAATAAG

Alignment

ORF - retro_mmul_1865 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.79 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MPKGGRKGGHKGRARQYTSPEEIDAQLQAEKQKAREEEEQKESGDGAAGDPK-KEKKSLDSDESEDEEDD
          .PKGGRKGGHKGRARQ..SPEEID.QLQAEKQKAREEEEQKESGDGAAGDPK.KEKKSLDSD..EDE.DD
Retrocopy IPKGGRKGGHKGRARQCMSPEEIDVQLQAEKQKAREEEEQKESGDGAAGDPK<KEKKSLDSDDNEDE-DD

Parental  YQQKRKGVEGLIDIENPNRVAQTTKKVTQLDLDGPKELSRREREEIEKQKAKERYMKMHLAGKTEQ-AKA
          YQQ.RK.VEGLI...NPN.VAQTTKK.TQLDLDGPKELSRRE..EIEKQKAKERYMKMHLAGKTEQ..KA
Retrocopy YQQRRKRVEGLINNKNPNPVAQTTKKLTQLDLDGPKELSRRE*QEIEKQKAKERYMKMHLAGKTEQ<TKA

Parental  DLARLAIIRKQREEAARKKEEERKAKDDATLSGKRMQSLSLNK
          DLAR.AII.KQ...AARKKEEERKAKD.ATLSGK.MQSLSLNK
Retrocopy DLARVAIIWKQQDDAARKKEEERKAKDNATLSGKPMQSLSLNK

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	50.98 RPM
SRP007412_brain_prefrontal_cortex	0.08 RPM	85.28 RPM
SRP007412_cerebellum	0.00 RPM	38.87 RPM
SRP007412_heart	0.00 RPM	61.77 RPM
SRP007412_kidney	0.00 RPM	41.78 RPM
SRP007412_liver	0.00 RPM	37.45 RPM
SRP007412_testis	0.04 RPM	83.83 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1865 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1865 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1865 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 36 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000015838	2 retrocopies	retro_cjac_2676, retro_cjac_2725,
Equus caballus	ENSECAG00000024426	1 retrocopy	retro_ecab_449,
Echinops telfairi	ENSETEG00000009926	1 retrocopy	retro_etel_900,
Felis catus	ENSFCAG00000015067	1 retrocopy	retro_fcat_1227,
Homo sapiens	ENSG00000106244	3 retrocopies	retro_hsap_1061, retro_hsap_3210, retro_hsap_3506,
Gorilla gorilla	ENSGGOG00000025196	5 retrocopies	retro_ggor_1776, retro_ggor_1778, retro_ggor_2179, retro_ggor_2371, retro_ggor_837,
Macaca mulatta	ENSMMUG00000001460	2 retrocopies	retro_mmul_1865 , retro_mmul_943,
Mus musculus	ENSMUSG00000029623	1 retrocopy	retro_mmus_2581,
Nomascus leucogenys	ENSNLEG00000011017	1 retrocopy	retro_nleu_1158,
Otolemur garnettii	ENSOGAG00000010874	2 retrocopies	retro_ogar_2199, retro_ogar_789,
Ochotona princeps	ENSOPRG00000013615	2 retrocopies	retro_opri_262, retro_opri_512,
Pongo abelii	ENSPPYG00000017375	4 retrocopies	retro_pabe_2659, retro_pabe_2806, retro_pabe_2901, retro_pabe_884,
Pan troglodytes	ENSPTRG00000041711	4 retrocopies	retro_ptro_1711, retro_ptro_2240, retro_ptro_2378, retro_ptro_722,
Ictidomys tridecemlineatus	ENSSTOG00000001679	1 retrocopy	retro_itri_765,
Tupaia belangeri	ENSTBEG00000010152	5 retrocopies	retro_tbel_1365, retro_tbel_3543, retro_tbel_4066, retro_tbel_766, retro_tbel_975,
Tursiops truncatus	ENSTTRG00000003004	1 retrocopy	retro_ttru_1343,