RetrogeneDB ID: retro_ggor_955

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 13:69130087..69130837(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DDX6
• Ensembl ID: ENSGGOG00000016751
• Aliases: None
• Description: None

Sequence

>retro_ggor_955
GTAGCAAAGGTTGATCATGTCCAGATGATAGTATTGCATGAGCAGGCAGATAAGTTGCCGTCACAGGATTTAGTGCAGAT
AATGGAGGATATTATTATCATGCTACCTAAAAACAGGAAGATTTTACTACATTCTGCTACTTTCCCTCTTAGTGTACAGA
AGTTCATGAATTCCCACTTGCAGAAACCCTATGAGATTAACCTGATGGAGGAACTAACTCTAAAGGGAGTAATCCAGTAC
TATGCATGTGTAACTGAGCTTCAGAAAGTACACTGCCTCAACGCACTTTTCTCCAGGCTTCAGATAAACCAGTTGATCAT
TTTCTGTAACTCCTCTCAGCAAGTTGAATTGCTAGCCAAGACTTCTCAACTAGGTTATTCTTGCTTCTATATTCATGCTA
AAATGAGGCAGGAATATCAAAATCGTGTATTTCATGATTTCTGAAATGGCTTATGATGCAATCTTGTTTACACTGATCTG
TTTACCCGAGGTATTGATATACAAGGTGTGAATGTGTTAATAAACTTTGATTTCCCAAAGCTGGCAGAGACCTATCTCCA
TCGTACTGGAAGATCAGGTCGCTTTGGTCATCCTGGCTTAGCCATCAACTTGATCACATATGATGATCGCTTCAACCTGA
AAAGTATTGAGGAGCAGCTGGGAACAGAAATTAAACCTATTCCAAGCAACATTGACAAGAGCCTGTGTGTGGCAGAATAC
CACAGCGAGCCTGTAGAAGATGAGAAGCCT

Alignment

ORF - retro_ggor_955 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.59 %
• Parental protein coverage: 52.07 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VAKVDHVQMIVLDE-ADKLLSQDFVQIMEDIILTLPKNRQILLYSATFPLSVQKFMANYF-KPLALSSVD
          VAKVDHVQMIVL.E.ADKL.SQD.VQIMEDII..LPKNR.ILL.SATFPLSVQKFM.....KP.......
Retrocopy VAKVDHVQMIVLHEQADKLPSQDLVQIMEDIIIMLPKNRKILLHSATFPLSVQKFMNSHLQKPYEINLME

Parental  QLKIINCITLVDSYVALKKYTPIQLIFFCAQLQINQSIIFCNSSQRVELLAKKISQLGYSCFYIHAKMRQ
          .L.....I........L.K.......F....LQINQ.IIFCNSSQ.VELLAK..SQLGYSCFYIHAKMRQ
Retrocopy ELTLKGVIQYYACVTELQKVHCLNALF--SRLQINQLIIFCNSSQQVELLAKT-SQLGYSCFYIHAKMRQ

Parental  EHRNRVFHDFRNGLCRNLVCTEDLFTRGIDIQAVNVVINFDFPKLAETYLHRIGRSGRFGHLGLAINLIT
          E..NRVFHDF.NGL..NLV.T.DLFTRGIDIQ.VNV.INFDFPKLAETYLHR.GRSGRFGH.GLAINLIT
Retrocopy EYQNRVFHDF*NGL*CNLVYT-DLFTRGIDIQGVNVLINFDFPKLAETYLHRTGRSGRFGHPGLAINLIT

Parental  YDDRFNLKSIEEQLGTEIKPIPSNIDKSLYVAEYHSEPVEDEKP
          YDDRFNLKSIEEQLGTEIKPIPSNIDKSL.VAEYHSEPVEDEKP
Retrocopy YDDRFNLKSIEEQLGTEIKPIPSNIDKSLCVAEYHSEPVEDEKP

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	1.53 RPM	25.61 RPM
SRP007412_cerebellum	1.85 RPM	25.29 RPM
SRP007412_heart	0.22 RPM	4.25 RPM
SRP007412_kidney	1.43 RPM	17.99 RPM
SRP007412_liver	0.63 RPM	5.96 RPM
SRP007412_testis	2.38 RPM	40.51 RPM

ChIP-Seq

Gorilla gorilla was not studied using ChIP-Seq data.

EST

Gorilla gorilla was not studied using EST data.

TSS

Gorilla gorilla was not studied using FANTOM5 data.

Lab

retro_ggor_955 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_955 has 0 orthologous retrocopies within eutheria group .

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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,