RetrogeneDB ID: retro_ptro_2424

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 6:29576739..29577733(-)
• 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_2424
AATAATAGCACTCAACCACAAGCGCAGAGTATGACCACCACTATTAAGCCTGGTGATAACTGGAAAAAGACTTTAAAACT
CCTTCCAAAGGATCTAAGAATCAAAATGTTGGATGTGACCTCCACAAGAGGAAATTAACTTGAAGATTACTGTTTGAAAC
GGCAGTTACTGATGAGAATTTTTGAAATGGGATGGAAAAAGCCATCTCCTTTCCAAGAAGAGAGCATTCCCATTGCTTTA
TCTGGTAGGGATATCTTAGCTAGAGCAAAAAATGGAACAGGCAAGAGCAGTGCCCATGACATTCCCCTACTTAAAAGGCT
AGACCTGAAGAAGGACACTATACAAACAATGGTGATTGTTCCCACAGGAGGACCTGCTCTACAGGTCAGTCAAATTTGCA
TCCAGGTCAGCAAACACATGGGAGGAGTCAAAGTGGTGATGACCACAGGAGGAACCAATTCAGGAGATGACGTACTGAGG
CTGGATGATACAGTGCACATGGTGATTGCTGCCCCTGGGAGAATCCTGAATCTTATTAAGAAAGGAGTAGCAAAGGTCAG
TCATGTCCAGGTGATAGTATTGGATGAGGCAGATAAGTTGCTGTCCCAGGATTTTCTGCAGTTAATGGAAGATATTATTC
TCATGCTACCTGAAGACAGGCAGATTTTACTATATTCTGCTACTTTCCCTCTTAGTATACAGAAGTTCATGAATTCCCAT
TTGCAGAAACCCTGAGACTAACCTGATGGAAAAACTAACTCTGAAGGACATAACCCAGTACTATGCATATGTAACTGAGC
ACCAAAAAGTACACGGCCTCACCACACTTTTCTCCAGGCTTCAGCTAAACCAGATGATCATTTTCTTTAACTGCTCTCAG
CGAGTTGAATGGCCAGCCAAAATTTCTCAACTGGGTTATTTTTGTTTCTACGTTCATGCTAAAATGAGGCAGGAACATCA
AAATTGTGTATTTTATTACTTCTGAAATGGCTTA

Alignment

ORF - retro_ptro_2424 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.54 %
• Parental protein coverage: 68.94 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  NNGTQQQAQSMTTTIKPGDDWKKTLKLPPKDLRIKTSDVTSTKGNEFEDYCLKRELLMGIFEMGWEKPSP
          NN.TQ.QAQSMTTTIKPGD.WKKTLKL.PKDLRIK..DVTST.GN..EDYCLKR.LLM.IFEMGW.KPSP
Retrocopy NNSTQPQAQSMTTTIKPGDNWKKTLKLLPKDLRIKMLDVTSTRGN*LEDYCLKRQLLMRIFEMGWKKPSP

Parental  IQEESIPIALSGRDILARAKNGTGKSGAYLIPLLERLDLKKDNIQAMVIVPTRELALQVSQICIQVSKHM
          .QEESIPIALSGRDILARAKNGTGKS.A..IPLL.RLDLKKD.IQ.MVIVPT...ALQVSQICIQVSKHM
Retrocopy FQEESIPIALSGRDILARAKNGTGKSSAHDIPLLKRLDLKKDTIQTMVIVPTGGPALQVSQICIQVSKHM

Parental  GGAKVMATTGGTNLRDDIMRLDDTVHVVIATPGRILDLIKKGVAKVDHVQMIVLDEADKLLSQDFVQIME
          GG.KV..TTGGTN..DD..RLDDTVH.VIA.PGRIL.LIKKGVAKV.HVQ.IVLDEADKLLSQDF.Q.ME
Retrocopy GGVKVVMTTGGTNSGDDVLRLDDTVHMVIAAPGRILNLIKKGVAKVSHVQVIVLDEADKLLSQDFLQLME

Parental  DIILTLPKNRQILLYSATFPLSVQKFMNSHL-QKPYEINLMEELTLKGVTQYYAYVTERQKVHCLNTLFS
          DIIL.LP..RQILLYSATFPLS.QKFMNSHL...P.E.NLME.LTLK..TQYYAYVTE.QKVH.L.TLFS
Retrocopy DIILMLPEDRQILLYSATFPLSIQKFMNSHL>RNP-ETNLMEKLTLKDITQYYAYVTEHQKVHGLTTLFS

Parental  RLQINQSIIFCNSSQRVELLAKKISQLGYSCFYIHAKMRQEHRNRVFHDFRNGL
          RLQ.NQ.IIF.N.SQRVE..A.KISQLGY.CFY.HAKMRQEH.N.VF..F.NGL
Retrocopy RLQLNQMIIFFNCSQRVEWPA-KISQLGYFCFYVHAKMRQEHQNCVFYYF*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	49.21 RPM
SRP007412_cerebellum	0.04 RPM	100.23 RPM
SRP007412_heart	0.00 RPM	67.47 RPM
SRP007412_kidney	0.00 RPM	53.06 RPM
SRP007412_liver	0.00 RPM	19.54 RPM
SRP007412_testis	0.32 RPM	84.73 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2424 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2424 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2424 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3569
Pongo abelii	retro_pabe_2941
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,