RetrogeneDB ID: retro_ptro_838

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 13:86327311..86328061(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DDX6
• Ensembl ID: ENSPTRG00000004353
• Aliases: None
• Description: None

Sequence

>retro_ptro_838
GTAGCAAAGGTTGATCATGTCCAGATGATAGTATTGCATGAGCAGACAGATAAGTTGCTGTCACAGGATTTTGTGCAGAT
AATGGAGGATATTATTATCATGCTACCTAAAAACAGTAAGATTTTACTACATTCTGCTACTTTCCCTCTTAGTGTACAGA
AGTTCATGAATTCCCACTTGCAGAAACCCTGTGAGATTAACCTGATGGAGGAACTAACTCTAAAGGGAGTAACCCAGTAC
TATGCATGTGTAACTGAGCTTCAAAAAGTACACTGCCTCAACGCACTTTTCTCCAGGCTTCAGATAAACCAGTCGATCAT
TTTCTGTAACTCCTCTCAGCAAGTTGAATTGCTAGCCAAGACTTCTCAACTAGGTTATTCTTGCTTCTATATTCATGCTA
AAAAGAGGCAGGAACATCAAAATCGTGTATTTCATGATTTCTGAAATGGCTTATGATGCAATCTTGTTTACACTGATCTG
TTTACCCGAGGTATTGATATACAAGGTGTGAATGTGTTAATAAACTTTGATTTCCCAAAGCTGGCAGAGACCTATCTCCA
TCGTATTGGAAGATCAGGTCGCTTTGGTCATCCTGGCTTAGCCATCAACTTGATCACATATGATGATCGCTTCAACCTGA
AAAGTATTGAGGAGCAGCTGGGAACAGAAATTAAACCTATTCCAAGCAACATTGACAAGAGCCTGTGTGTGGCAGAATAC
CACAGCGAGCCTGTAGAAGATGAGAAGCCT

Alignment

ORF - retro_ptro_838 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.04 %
• Parental protein coverage: 51.76 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VAKVDHVQMIVLDE-ADKLLSQDFVQIMEDIILTLPKNRQILLYSATFPLSVQKFMNSHLQKPYEINLME
          VAKVDHVQMIVL.E..DKLLSQDFVQIMEDII..LPKN..ILL.SATFPLSVQKFMNSHLQKP.EINLME
Retrocopy VAKVDHVQMIVLHEQTDKLLSQDFVQIMEDIIIMLPKNSKILLHSATFPLSVQKFMNSHLQKPCEINLME

Parental  ELTLKGVTQYYAYVTERQKVHCLNTLFSRLQINQSIIFCNSSQRVELLAKKISQLGYSCFYIHAKMRQEH
          ELTLKGVTQYYA.VTE.QKVHCLN.LFSRLQINQSIIFCNSSQ.VELLAK..SQLGYSCFYIHAK.RQEH
Retrocopy ELTLKGVTQYYACVTELQKVHCLNALFSRLQINQSIIFCNSSQQVELLAKT-SQLGYSCFYIHAKKRQEH

Parental  RNRVFHDFRNGLCRNLVCTDLFTRGIDIQAVNVVINFDFPKLAETYLHRIGRSGRFGHLGLAINLITYDD
          .NRVFHDF.NGL..NLV.TDLFTRGIDIQ.VNV.INFDFPKLAETYLHRIGRSGRFGH.GLAINLITYDD
Retrocopy QNRVFHDF*NGL*CNLVYTDLFTRGIDIQGVNVLINFDFPKLAETYLHRIGRSGRFGHPGLAINLITYDD

Parental  RFNLKSIEEQLGTEIKPIPSNIDKSLYVAEYHSEPVEDEKP
          RFNLKSIEEQLGTEIKPIPSNIDKSL.VAEYHSEPVEDEKP
Retrocopy RFNLKSIEEQLGTEIKPIPSNIDKSLCVAEYHSEPVEDEKP

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	0.07 RPM	49.21 RPM
SRP007412_cerebellum	0.00 RPM	100.23 RPM
SRP007412_heart	0.06 RPM	67.47 RPM
SRP007412_kidney	0.00 RPM	53.06 RPM
SRP007412_liver	0.00 RPM	19.54 RPM
SRP007412_testis	0.00 RPM	84.73 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_838 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_838 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_838 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1224
Pongo abelii	retro_pabe_1018
Macaca mulatta	retro_mmul_1300
Callithrix jacchus	retro_cjac_379

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000012442	1 retrocopy	retro_cfam_1347,
Callithrix jacchus	ENSCJAG00000013591	3 retrocopies	retro_cjac_1427, retro_cjac_1924, retro_cjac_379,
	ENSG00000110367	0 retrocopies
Gorilla gorilla	ENSGGOG00000016751	1 retrocopy	retro_ggor_955,
Macaca mulatta	ENSMMUG00000018651	2 retrocopies	retro_mmul_1300, retro_mmul_1826,
Mus musculus	ENSMUSG00000032097	1 retrocopy	retro_mmus_1896,
Nomascus leucogenys	ENSNLEG00000007372	1 retrocopy	retro_nleu_695,
Otolemur garnettii	ENSOGAG00000007978	1 retrocopy	retro_ogar_2861,
Pongo abelii	ENSPPYG00000003942	2 retrocopies	retro_pabe_1018, retro_pabe_2941,
Pan troglodytes	ENSPTRG00000004353	2 retrocopies	retro_ptro_2424, retro_ptro_838 ,
Rattus norvegicus	ENSRNOG00000012453	4 retrocopies	retro_rnor_2546, retro_rnor_2613, retro_rnor_900, retro_rnor_901,