RetrogeneDB ID: retro_ptro_424

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 10:44973519..44974131(+)
• 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_424
ATGGCCAAAGACACCTCTTCACACAAGATGGTAGCCACAAATCGCAGGAGCAATCACACCAAATTCACAGAAGATCAATT
GAAAATCCTTATCAACACCTTCAATCAAAAACCTTACCCAGATTATGCTACCAAACAAAAACTTGCTTTAGAAATCAATA
CAGAAAAGTACAGAATCCAGATTTGGTTTCAGAATCAAAGAGCTAGGCACAGATTCCAGAAAAGACCAGAACCTGAGACT
TTAGATTCAAGCCAGAGCCATGGGCAAGATCAACCTGGGGTGGAATTTCAAAGTAGAGAAGCCAGACGGTGTCATACCAC
CTACAGCGCCTCTCAATTACACACTCTCATCAAGGCATTTATGAAAAATCCATACCCTGGGATTGATTCCAGAGAACAAC
TTGCTGAAGAAATTGGTGCTCCAGAGTCAAGAGTCCAAATTTGGTTCCAAAAATTGAAGATCTAGATTTCATCTCCAGAG
AAAAGGGAACCTGTTATGTCCTTAGAACAAGAAGACCAGGGGCAAGATTTCTGAGGGACTTCAAGGTACAGAAGATACAC
AAAATGGCACCAACCTCACTAGCACTCTCATTTCTCTAGAGCCAGAACATGG

Alignment

ORF - retro_ptro_424 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.17 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MAEDTYSHKMVKTNHRRCRTKFTEEQLKILINTFNQKPYPGYATKQKLALEINTEESRIQIWFQNRRARH
          MA.DT.SHKMV.TN.R...TKFTE.QLKILINTFNQKPYP.YATKQKLALEINTE..RIQIWFQN.RARH
Retrocopy MAKDTSSHKMVATNRRSNHTKFTEDQLKILINTFNQKPYPDYATKQKLALEINTEKYRIQIWFQNQRARH

Parental  GFQKRPEAETLESSQSQGQDQPGVEFPSREARRCRTTYSASQLHTLIKAFMKNPYPGIDSREELAKEIGV
          .FQKRPE.ETL.SSQS.GQDQPGVEF.SREARRC.TTYSASQLHTLIKAFMKNPYPGIDSRE.LA.EIG.
Retrocopy RFQKRPEPETLDSSQSHGQDQPGVEFQSREARRCHTTYSASQLHTLIKAFMKNPYPGIDSREQLAEEIGA

Parental  PESRVQIWFQ-NRRSRLLLQR-KREPVASLEQEEQ-GKIPEGLQGAEDTQNGTNFTS-DSHFSEARTW
          PESRVQIWFQ.N.RSR..LQR.KREPV.SLEQE.Q.GKI.EGLQG.EDTQNGTN.TS..SHFS.ARTW
Retrocopy PESRVQIWFQ>N*RSRFHLQR<KREPVMSLEQEDQ>GKISEGLQGTEDTQNGTNLTS<HSHFSRARTW

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	0.11 RPM	0.00 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_424 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_424 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_424 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_566
Gorilla gorilla	retro_ggor_510
Pongo abelii	retro_pabe_518
Macaca mulatta	retro_mmul_2396

---

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,