RetrogeneDB ID: retro_ptro_2378

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 6:112001458..112001998(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PDAP1
• Ensembl ID: ENSPTRG00000041711
• Aliases: None
• Description: PDGFA associated protein 1 [Source:HGNC Symbol;Acc:14634]

Sequence

>retro_ptro_2378
ATACCTAAAGGAGGGAGAAAGGGAGGCCACAAAGGCTGGGCGAGGCAATATACAAGCCCTGAGGAGATAGACACGCAGCT
GCAGTCTGAGAAGCAGAAGGCCAGGGAAGAAGAGGAGCAAAAAGAAGGTGGAGACGGGGCTGCAGGTGACCCCAAAAAGG
AGAAGAAATCTCTAGACTCAGATGAGAGTGAGGATGAAGATGACTACCAGCAAAGGCGCAAAGGTGTTGAAGGGCTCATT
GACATTGAGAATCCCAACTGGGTGGCACAGACAACCAAAAAGATCACACAACTGGATCTGGACGGGCCAAAGGAGATTTT
GAGGAGAGAACGAGAGGAGATTGAGAAGCAGAAGGCAAAAGAGCGTTACATGAAAATGCACTTGGCTGGGAAGAGATAGC
AAACCAAGGCCAACCTGGCCTGGCTGGTCATCATCTGGAAACAGCAGGAGGACACTGCCCAGAAGAAGGAAGAGGAAAGG
AAAGCAAAAGACGATGCCACATTGTCAGGAAAACGAATGCAGTCACTCTCCCTGAATAAG

Alignment

ORF - retro_ptro_2378 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.4 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MPKGGRKGGHKGRARQYTSPEEIDAQLQAEKQKAREEEEQKEGGDGAAGDPKKEKKSLDSDESEDEEDDY
          .PKGGRKGGHKG.ARQYTSPEEID.QLQ.EKQKAREEEEQKEGGDGAAGDPKKEKKSLDSDESEDE.DDY
Retrocopy IPKGGRKGGHKGWARQYTSPEEIDTQLQSEKQKAREEEEQKEGGDGAAGDPKKEKKSLDSDESEDE-DDY

Parental  QQKRKGVEGLIDIENPNRVAQTTKKVTQLDLDGPKELSRREREEIEKQKAKERYMKMHLAGKTEQAKADL
          QQ.RKGVEGLIDIENPN.VAQTTKK.TQLDLDGPKE..RREREEIEKQKAKERYMKMHLAGK..Q.KA.L
Retrocopy QQRRKGVEGLIDIENPNWVAQTTKKITQLDLDGPKEILRREREEIEKQKAKERYMKMHLAGKR*QTKANL

Parental  ARLAIIRKQREEAARKKEEERKAKDDATLSGKRMQSLSLNK
          A.L.II.KQ.E..A.KKEEERKAKDDATLSGKRMQSLSLNK
Retrocopy AWLVIIWKQQEDTAQKKEEERKAKDDATLSGKRMQSLSLNK

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_prefrontal_cortex	0.09 RPM	86.71 RPM
SRP007412_cerebellum	0.11 RPM	84.14 RPM
SRP007412_heart	0.06 RPM	51.82 RPM
SRP007412_kidney	0.05 RPM	61.64 RPM
SRP007412_liver	0.10 RPM	67.11 RPM
SRP007412_testis	0.53 RPM	54.38 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2378 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2378 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2378 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3506
Gorilla gorilla	retro_ggor_2371
Pongo abelii	retro_pabe_2901

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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,