RetrogeneDB ID: retro_pabe_1018

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 13:87929702..87930448(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DDX6
• Ensembl ID: ENSPPYG00000003942
• Aliases: None
• Description: probable ATP-dependent RNA helicase DDX6 [Source:RefSeq peptide;Acc:NP_001128971]

Sequence

>retro_pabe_1018
GTAGCAAAGGTTGATCATGTCCAGATGATAGTACTAGATGAGCAGGCAGATAAGTTGCTGTCACAGGATTTTGTGCAGAT
AATGGAGGATATTATTCTCATGCTACCTAAAAACAGGAAGACTTTACTACATTCTGCTACTTTCCCTCTTAGTGTACAGA
AGTTCATGAATTCCCACTTGCAGAAACCCTATGAGATTAACCTGATGGAGGAACTAACTCTAAAGGGAGTAACCCAGTAC
TATGCATGTGTAACTGAGCTCCAAAAAGTACACTGCCTCAACACACTTTTCTCCAGGCTTCAGATAAACCAGTCGATCAT
TTTCTGTAACTCCTCTCAGGAAGTTGAATTGCTAGCCAAGACTTCTCAACTAGGTTATTCTTGCTTCTATATTCATGCTA
AAATGAGGCAGGAACATCAAAATCGTGTATTTCATGATTTCTGAAATGGCTTATGATGCAATCTTGTTTACACTGATCTG
TTTACCCGAGGTATTGATATACAAGGTGTGAATGTGATAATAAACTTTGATTTCCCAAAGCTGGAAGAGACCTGTCTCCA
TCATATTGGAAGATCAGGTCGCTTTGGTCATCCTGGCTTAGCCATCAACTTGATCACATATGATGATTGCTTCGACCTGA
AAAGTATTGAGGAGCAGCTGGGAACAGAAATTAAACCTATTCAAACAACATTGACAAGAGCCTGTATGTGGCAGAACACC
ACAGCCAGTGTGTAGATGAGAAGCCT

Alignment

ORF - retro_pabe_1018 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.1 %
• Parental protein coverage: 51.87 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VAKVDHVQMIVLDE-ADKLLSQDFVQIMEDIILTLPKNRQILLYSATFPLSVQKFMNSHLQKPYEINLME
          VAKVDHVQMIVLDE.ADKLLSQDFVQIMEDIIL.LPKNR..LL.SATFPLSVQKFMNSHLQKPYEINLME
Retrocopy VAKVDHVQMIVLDEQADKLLSQDFVQIMEDIILMLPKNRKTLLHSATFPLSVQKFMNSHLQKPYEINLME

Parental  ELTLKGVTQYYAYVTERQKVHCLNTLFSRLQINQSIIFCNSSQRVELLAKKISQLGYSCFYIHAKMRQEH
          ELTLKGVTQYYA.VTE.QKVHCLNTLFSRLQINQSIIFCNSSQ.VELLA.K.SQLGYSCFYIHAKMRQEH
Retrocopy ELTLKGVTQYYACVTELQKVHCLNTLFSRLQINQSIIFCNSSQEVELLA-KTSQLGYSCFYIHAKMRQEH

Parental  RNRVFHDFRNGLCRNLVCTDLFTRGIDIQAVNVVINFDFPKLAETYLHRIGRSGRFGHLGLAINLITYDD
          .NRVFHDF.NGL..NLV.TDLFTRGIDIQ.VNV.INFDFPKL.ET.LH.IGRSGRFGH.GLAINLITYDD
Retrocopy QNRVFHDF*NGL*CNLVYTDLFTRGIDIQGVNVIINFDFPKLEETCLHHIGRSGRFGHPGLAINLITYDD

Parental  RFNLKSIEEQLGTEIKPI-PSNIDKSLYVAEYHSEPVEDEKP
          .F.LKSIEEQLGTEIKPI...NIDKSLYVAE.HS..V.DEKP
Retrocopy CFDLKSIEEQLGTEIKPI<SNNIDKSLYVAEHHSQCV-DEKP

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	133.80 RPM
SRP007412_cerebellum	0.00 RPM	215.11 RPM
SRP007412_heart	0.00 RPM	63.76 RPM
SRP007412_kidney	0.00 RPM	98.71 RPM
SRP007412_liver	0.00 RPM	45.57 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1018 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1018 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1018 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1224
Pan troglodytes	retro_ptro_838
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,
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,