RetrogeneDB ID: retro_rnor_901

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 13:5346916..5347996(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Ddx6
• Ensembl ID: ENSRNOG00000012453
• Aliases: Ddx6, RGD1564560
• Description: probable ATP-dependent RNA helicase DDX6 [Source:RefSeq peptide;Acc:NP_001102762]

Sequence

>retro_rnor_901
GAGGAGAGCATTCCCATTGCTTTATCTGGTAGGGATATCTTAGCTAGAGCAAAAAATGGAACAGGCAAAAGCGGTGCCTA
CCTCATCCCCTTACTTGAACGGCTGGACCTGAAGAAGGACAATATTCAAGCAATGGTGATTGTTCCCACTAGAGAACTTG
CTCTACAGGTCAGTCAAATTTGCATCCAGGTCAGCAAACACATGGGAGGGGCCAAAGTGATGGCGACCACTGGAGGAACC
AATTTACGGGATGACATAATGAGGCTTGACGATACAGTGCATGTGGTGATTGCTACCCCTGGCAGAATCCTGGATCTTAT
CAAGAAAGGAGTAGCAAAGGTTGATCATGTCCAGATGATAGTATTGGATGAGGCAGATAAGTTGTTGTCACAGGACTTTG
TGCAGATAATGGAGGATATTATTCTCACACTACCTAAAAATAGGCAGATTTTACTATATTCCGCTACTTTCCCTCTTAGT
GTACAAAAGTTTATGAATTCCCATCTGCAAAAACCCTACGAGATAAACCTGATGGAGGAGCTAACTCTGAAAGGGGTGAC
CCAGTACTACGCATATGTAACGGAGCGCCAAAAAGTGCACTGCCTCAATACACTCTTCTCCAGGCTTCAGATAAACCAGT
CGATCATTTTCTGCAACTCTTCTCAGTGAGTTGAGTTACTGGCCAAGAAGATTTCTCAGCTGGGTTACTCTTGCTTCTAT
ATCCATGCTAAAATGAGGCAGGAACATAGAAATCGTGTCTTTCATGATTTCCGAAATGGCTTATGCCGCAATCTTGTTTG
CACTGATCTGTTTACCCGAGGTATTGATATACAAGCTGTGAATGTGGTAATAAACTTTGACTTCCCAAAGCTGGCAGAGA
CCTATCTTCATCGGATTGGAAGGTCAGGTCGCTTTGGTCATCTTGGCTTAGCCATCAACTTGATCACATATGATGATCGC
TTCAACCTGAAGAGTATTGAGGAGCAGCTGGGGACAGAGATCAAACCCATCCCAAGCAACATTGACAAGAGCCTGTATGT
GGCAGAATACCACAGTGAGCCTGCAGAAGATGAGAAACCT

Alignment

ORF - retro_rnor_901 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.72 %
• Parental protein coverage: 74.53 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EESIPIALSGRDILARAKNGTGKSGAYLIPLLERLDLKKDNIQAMVIVPTRELALQVSQICIQVSKHMGG
          EESIPIALSGRDILARAKNGTGKSGAYLIPLLERLDLKKDNIQAMVIVPTRELALQVSQICIQVSKHMGG
Retrocopy EESIPIALSGRDILARAKNGTGKSGAYLIPLLERLDLKKDNIQAMVIVPTRELALQVSQICIQVSKHMGG

Parental  AKVMATTGGTNLRDDIMRLDDTVHVVIATPGRILDLIKKGVAKVDHVQMIVLDEADKLLSQDFVQIMEDI
          AKVMATTGGTNLRDDIMRLDDTVHVVIATPGRILDLIKKGVAKVDHVQMIVLDEADKLLSQDFVQIMEDI
Retrocopy AKVMATTGGTNLRDDIMRLDDTVHVVIATPGRILDLIKKGVAKVDHVQMIVLDEADKLLSQDFVQIMEDI

Parental  ILTLPKNRQILLYSATFPLSVQKFMNSHLQKPYEINLMEELTLKGVTQYYAYVTERQKVHCLNTLFSRLQ
          ILTLPKNRQILLYSATFPLSVQKFMNSHLQKPYEINLMEELTLKGVTQYYAYVTERQKVHCLNTLFSRLQ
Retrocopy ILTLPKNRQILLYSATFPLSVQKFMNSHLQKPYEINLMEELTLKGVTQYYAYVTERQKVHCLNTLFSRLQ

Parental  INQSIIFCNSSQRVELLAKKISQLGYSCFYIHAKMRQEHRNRVFHDFRNGLCRNLVCTDLFTRGIDIQAV
          INQSIIFCNSSQ.VELLAKKISQLGYSCFYIHAKMRQEHRNRVFHDFRNGLCRNLVCTDLFTRGIDIQAV
Retrocopy INQSIIFCNSSQ*VELLAKKISQLGYSCFYIHAKMRQEHRNRVFHDFRNGLCRNLVCTDLFTRGIDIQAV

Parental  NVVINFDFPKLAETYLHRIGRSGRFGHLGLAINLITYDDRFNLKSIEEQLGTEIKPIPSNIDKSLYVAEY
          NVVINFDFPKLAETYLHRIGRSGRFGHLGLAINLITYDDRFNLKSIEEQLGTEIKPIPSNIDKSLYVAEY
Retrocopy NVVINFDFPKLAETYLHRIGRSGRFGHLGLAINLITYDDRFNLKSIEEQLGTEIKPIPSNIDKSLYVAEY

Parental  HSEPAEDEKP
          HSEPAEDEKP
Retrocopy HSEPAEDEKP

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
SRP017611_brain	0.00 RPM	21.71 RPM
SRP017611_kidney	0.07 RPM	25.89 RPM
SRP017611_liver	0.07 RPM	17.95 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

1 EST(s) were mapped to retro_rnor_901 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
CB773053	5346944	5347338	99	374	4	369

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_901 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_901 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 ,