RetrogeneDB ID: retro_ptro_1559

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 2A:100783584..100783920(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ARPP19
• Ensembl ID: ENSPTRG00000042183
• Aliases: None
• Description: None

Sequence

>retro_ptro_1559
ATGTCTGTGGAAGTCTCCGAGGCAGCCTCTGTGGAGGAGCAGAAGGAAATGGAAGATACGGTGACTAGTCCAGAGAAAGT
TGAAGCAGCAAAATTGAAAGCGAGATATCCTCATCTGGGACAAATGCCTGGAGGTTCAGATTTCTTAAGGAAACCATTGC
AGAAAGGGCAAAAATATTTTGATTCTGGGGATTACAACATGGCTAAAGCAAAAATGAAGAACGAGCAACTTCCTACTGCA
GCTCTGGATAAGATGGAGGTCACGGGTGACCACATTCCCACTCCAGAGGACCTTCCTCAACAGAAACCATCCATTGTTGC
TAGCAAGCTGGCTGGT

Alignment

ORF - retro_ptro_1559 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.5 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSAEVPEAASAEEQKEMEDKVTSPEKAEEAKLKARYPHLGQKPGGSDFLRKRLQKGQKYFDSGDYNMAKA
          MS.EV.EAAS.EEQKEMED.VTSPEK.E.AKLKARYPHLGQ.PGGSDFLRK.LQKGQKYFDSGDYNMAKA
Retrocopy MSVEVSEAASVEEQKEMEDTVTSPEKVEAAKLKARYPHLGQMPGGSDFLRKPLQKGQKYFDSGDYNMAKA

Parental  KMKNKQLPTAAPDKTEVTGDHIPTPQDLPQRKPSLVASKLAG
          KMKN.QLPTAA.DK.EVTGDHIPTP.DLPQ.KPS.VASKLAG
Retrocopy KMKNEQLPTAALDKMEVTGDHIPTPEDLPQQKPSIVASKLAG

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	0.02 RPM	142.14 RPM
SRP007412_cerebellum	0.00 RPM	25.99 RPM
SRP007412_heart	0.00 RPM	27.86 RPM
SRP007412_kidney	0.00 RPM	24.11 RPM
SRP007412_liver	0.00 RPM	10.51 RPM
SRP007412_testis	0.00 RPM	67.66 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1559 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1559 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1559 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2130

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 35 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000011022	5 retrocopies	retro_btau_1259, retro_btau_1821, retro_btau_1845, retro_btau_952, retro_btau_981,
Canis familiaris	ENSCAFG00000032515	2 retrocopies	retro_cfam_1375, retro_cfam_1402,
Dasypus novemcinctus	ENSDNOG00000004474	9 retrocopies	retro_dnov_1086, retro_dnov_1576, retro_dnov_1960, retro_dnov_2150, retro_dnov_2427, retro_dnov_557, retro_dnov_616, retro_dnov_644, retro_dnov_662,
Dipodomys ordii	ENSDORG00000011321	2 retrocopies	retro_dord_194, retro_dord_33,
Echinops telfairi	ENSETEG00000015550	1 retrocopy	retro_etel_585,
Homo sapiens	ENSG00000128989	2 retrocopies	retro_hsap_2130, retro_hsap_3280,
Gorilla gorilla	ENSGGOG00000025250	1 retrocopy	retro_ggor_198,
Otolemur garnettii	ENSOGAG00000013865	1 retrocopy	retro_ogar_591,
Pongo abelii	ENSPPYG00000006487	2 retrocopies	retro_pabe_120, retro_pabe_1923,
Pan troglodytes	ENSPTRG00000042183	1 retrocopy	retro_ptro_1559 ,
Sus scrofa	ENSSSCG00000004618	1 retrocopy	retro_sscr_603,
Ictidomys tridecemlineatus	ENSSTOG00000003677	7 retrocopies	retro_itri_1075, retro_itri_1290, retro_itri_1339, retro_itri_1643, retro_itri_1657, retro_itri_1865, retro_itri_594,
Tursiops truncatus	ENSTTRG00000004804	1 retrocopy	retro_ttru_172,