RetrogeneDB ID: retro_pabe_2941

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 6:30271073..30272066(-)
• 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_2941
AATAATAGCACTCAGCCGCAAGCGCAGAGTATGACCACCACTATTAAGCCTGGTGATAACTGGAAGAAGACTTTAAAACT
CCTTCCAAAGGATCTAAGAATCAAAACGTTGGATGTGACCTCCACAAGAGGAAATTAATTTGAAGATTACTGTTTGAAGC
GGGAGTTACTGATGAGAATTTTTGAAATGGGATGGAAAAAGCCATCTCCTTTTCAAGAAGAGAGCATTCCCATTGCTTTA
TCTGGTAGGGATATCTTAGCTAGAGCAAAAAATGGAACAGGCAAGAGCAGTGCCCATGACTTCCCCCACTTAAAAGGCTA
GACCTGAAGAAGGACACTATACAAACAATGGTGATTGTTCCCACAGGAGGACCTGCTCTACAGGTCAGTCAAATTTGCAT
CCAGGTCAGCAAACACATGGGAGGAGTCAAAGTGATTACGACCACAGGAGGAACCAATTCAGGAGATGACGTACTGAGGC
TTGATGATACAGTGCACATGGTGATTGCTGCCCCTGGGAGAATCCTGAATCTTATTAAGAAAGGAGTAGCAAAGTTCAGT
CATGTCCAGGTGACAGTATTGGATGAGGCAGATAAGTTGCTGTCACAGGATTTTGTGCAGTTAATGGAAGATATTATTCT
CATGCTACCTGAAGACAGGCAGATTTTACTGTATTCTGCTACTTTCCCTCTTAGTATACAGAAGTTCATGAATTCCCATT
TGCAGAAACCCTGAGACTAACCTGATGGAAAAACTAACTCTGAAGGACATAACCTAGTATTACGCATATGTAACTGAGCA
CGAAAAAGTACACGGCCTCACCACGCTTTTCTCCAGGCTTCAGCTAAACCAGACGATCATTTTCTTTAACTGCTCTCAGC
AAGTTGAATGGCCAGCCAAAATTTCTCAACTGGGTTATTTGTGTTTCTATATTCATGCTAAAATGAGGCAAGAATGTCAA
AATTGTGTATTTTATTATTTCTGAAATGGCTTA

Alignment

ORF - retro_pabe_2941 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.52 %
• Parental protein coverage: 68.88 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  NNGTQQQAQSMTTTINAMINFLKHVNL-PKDTKFTNSDVTSTKGNEFEDYCLKRELLMGIFEMGWEKPSP
          NN.TQ.QAQSMTTTI....N..K...L.PKD......DVTST.GN.FEDYCLKRELLM.IFEMGW.KPSP
Retrocopy NNSTQPQAQSMTTTIKPGDNWKKTLKLLPKDLRIKTLDVTSTRGN*FEDYCLKRELLMRIFEMGWKKPSP

Parental  IQEESIPIALSGRDILARAKNGTGKSGAYL-IPLLERLDLKKDNIQAMVIVPTRELALQVSQICIQVSKH
          .QEESIPIALSGRDILARAKNGTGKS.A....P.L.RLDLKKD.IQ.MVIVPT...ALQVSQICIQVSKH
Retrocopy FQEESIPIALSGRDILARAKNGTGKSSAHD<LPPLKRLDLKKDTIQTMVIVPTGGPALQVSQICIQVSKH

Parental  MGGAKVMATTGGTNLRDDIMRLDDTVHVVIATPGRILDLIKKGVAKVDHVQMIVLDEADKLLSQDFVQIM
          MGG.KV..TTGGTN..DD..RLDDTVH.VIA.PGRIL.LIKKGVAK..HVQ..VLDEADKLLSQDFVQ.M
Retrocopy MGGVKVITTTGGTNSGDDVLRLDDTVHMVIAAPGRILNLIKKGVAKFSHVQVTVLDEADKLLSQDFVQLM

Parental  EDIILTLPKNRQILLYSATFPLSVQKFMNSHL-QKPYEINLMEELTLKGVTQYYAYVTERQKVHCLNTLF
          EDIIL.LP..RQILLYSATFPLS.QKFMNSHL...P.E.NLME.LTLK..T.YYAYVTE..KVH.L.TLF
Retrocopy EDIILMLPEDRQILLYSATFPLSIQKFMNSHL>RNP-ETNLMEKLTLKDIT*YYAYVTEHEKVHGLTTLF

Parental  SRLQINQSIIFCNSSQRVELLAKKISQLGYSCFYIHAKMRQEHRNRVFHDFRNGL
          SRLQ.NQ.IIF.N.SQ.VE..A.KISQLGY.CFYIHAKMRQE..N.VF..F.NGL
Retrocopy SRLQLNQTIIFFNCSQQVEWPA-KISQLGYLCFYIHAKMRQECQNCVFYYF*NGL

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	0.12 RPM	215.11 RPM
SRP007412_heart	0.00 RPM	63.76 RPM
SRP007412_kidney	0.03 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_2941 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2941 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2941 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3569
Pan troglodytes	retro_ptro_2424
Macaca mulatta	retro_mmul_1826

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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,