RetrogeneDB ID: retro_ptro_1034

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 15:89661487..89662091(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DUXA
• Ensembl ID: ENSPTRG00000028871
• Aliases: None
• Description: double homeobox A [Source:HGNC Symbol;Acc:32179]

Sequence

>retro_ptro_1034
ATGGCTGAAGACACCTCTTCACATAAGATGGTGACAACAAATCACAGGCGCAGTCTCACCAAATTCACAGATCAGTTGAA
AATCCTCATCAATACCTTCAATCAAAAACCTTACCCAGGTTATGCTACCAAACAAAAACTTGCTTTAGAAATCAATACAG
AAGAGTCCAGAACCCAGATTTGGTTTCAGAATCGAAGAGCTGGATTCCAGAAAAGACCAGAACCTGGGACTTTAGAATCA
AGTCAGAGCCATGGGCAAGATCGACCTGACGCAGAGTTTCAAAGTAGAGAAGCCAGATGGTGTTGTACCACCTACAGCGC
CTCTCAATTAAGCACTCTCATCAAGGCATCTATGAAAAACCCATACCCTGCGATTGATTCCAGAGAACAAGTTGCTGAAG
AAATTGGTGTTCCAGAGTTAAGAGTCCAAATCTGGTTCCAAAACTGAAGATCTAGATTTCATCTCCAGAGAAACAGGGAA
CCTGTTGTGTCCTTAGAACAAGAAGACCAGGGGCAAGATTTCTGAGGGACATCAAGGTACAGAAGATACACAAAATGGCA
CCAACCTCACTAGCAATTCTCATTTCTCTAGAGCCAGAAGATGG

Alignment

ORF - retro_ptro_1034 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.98 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAEDTYSHKMVKTNHRRCRTKFTEEQLKILINTFNQKPYPGYATKQKLALEINTEESRIQIWFQNRRARH
          MAEDT.SHKMV.TNHRR..TKFT..QLKILINTFNQKPYPGYATKQKLALEINTEESR.QIWFQNRRA..
Retrocopy MAEDTSSHKMVTTNHRRSLTKFTD-QLKILINTFNQKPYPGYATKQKLALEINTEESRTQIWFQNRRA--

Parental  GFQKRPEAETLESSQSQGQDQPGVEFPSREARRCRTTYSASQLHTLIKAFMKNPYPGIDSREELAKEIGV
          GFQKRPE..TLESSQS.GQD.P..EF.SREAR.C.TTYSASQL.TLIKA.MKNPYP.IDSRE..A.EIGV
Retrocopy GFQKRPEPGTLESSQSHGQDRPDAEFQSREARWCCTTYSASQLSTLIKASMKNPYPAIDSREQVAEEIGV

Parental  PESRVQIWFQNRRSRLLLQRKREPVASLEQEEQ-GKIPEGLQGAEDTQNGTNFTSDSHFSEARTW
          PE.RVQIWFQN.RSR..LQR.REPV.SLEQE.Q.GKI.EG.QG.EDTQNGTN.TS.SHFS.AR.W
Retrocopy PELRVQIWFQN*RSRFHLQRNREPVVSLEQEDQ>GKISEGHQGTEDTQNGTNLTSNSHFSRARRW

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	0.00 RPM	0.00 RPM
SRP007412_cerebellum	0.00 RPM	0.00 RPM
SRP007412_heart	0.00 RPM	0.00 RPM
SRP007412_kidney	0.00 RPM	0.00 RPM
SRP007412_liver	0.00 RPM	0.00 RPM
SRP007412_testis	0.00 RPM	0.00 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1034 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1034 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1034 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1525
Gorilla gorilla	retro_ggor_1167
Macaca mulatta	retro_mmul_2157

---

Parental genes homology:

Parental genes homology involve 14 parental genes, and 42 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000025505	1 retrocopy	retro_dnov_701,
Felis catus	ENSFCAG00000007545	1 retrocopy	retro_fcat_1027,
Homo sapiens	ENSG00000258873	5 retrocopies	retro_hsap_1525, retro_hsap_2454, retro_hsap_4100, retro_hsap_566, retro_hsap_663,
Gorilla gorilla	ENSGGOG00000005650	7 retrocopies	retro_ggor_1017, retro_ggor_1076, retro_ggor_1167, retro_ggor_1528, retro_ggor_2133, retro_ggor_2752, retro_ggor_510,
Loxodonta africana	ENSLAFG00000030167	1 retrocopy	retro_lafr_996,
Macaca mulatta	ENSMMUG00000007788	5 retrocopies	retro_mmul_2157, retro_mmul_2363, retro_mmul_2396, retro_mmul_2441, retro_mmul_636,
Nomascus leucogenys	ENSNLEG00000010886	3 retrocopies	retro_nleu_1935, retro_nleu_2214, retro_nleu_568,
Oryctolagus cuniculus	ENSOCUG00000011331	1 retrocopy	retro_ocun_981,
Pongo abelii	ENSPPYG00000010457	8 retrocopies	retro_pabe_1192, retro_pabe_1328, retro_pabe_1805, retro_pabe_3357, retro_pabe_3376, retro_pabe_518, retro_pabe_660, retro_pabe_802,
Pan troglodytes	ENSPTRG00000028871	5 retrocopies	retro_ptro_1034 , retro_ptro_1418, retro_ptro_2781, retro_ptro_424, retro_ptro_482,
Pteropus vampyrus	ENSPVAG00000003020	1 retrocopy	retro_pvam_870,
Tupaia belangeri	ENSTBEG00000005321	1 retrocopy	retro_tbel_3384,
Tarsius syrichta	ENSTSYG00000014223	1 retrocopy	retro_tsyr_1577,
Tursiops truncatus	ENSTTRG00000014200	2 retrocopies	retro_ttru_1277, retro_ttru_1768,