RetrogeneDB ID: retro_rnor_2546

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 8:4259838..4261285(+)
• 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_2546
ATGAGCACGGCCAGGACAGAGAACCCTGTTATCATGGGTCTGTCCAGTCAGAACGGCCAGCTGAGGGGCCCCGTGAAGGC
CAGTGCCGGCCCTGGAGGAGGGGGCCCACAGACACAGACACAGATGAACCAGTTGAAGAACACCAGCACAATCAATAATG
GCACTCAGCAGCAAGCACAGAGCATGGCCACCACCATTAAACCTGGTGATGACTGGAAAAAGACTTTAAAACTCCCTCCA
AAGGATCTAAGCATTAAAACTTCGGATGTGACCTCCACAAAAGGAAATGAGTTTGAAGATTACTGTTTGAAATGAGAGTT
GCTAATGGGAATTTTTGAAATGGGCTGGGAAAAACCATCTCCTATTCAGGAGGAGAGCATCCCATTGCTTTATCTGGTAT
GGATATCTTAGCTAGAGCAAAAAATGGAACAGGCAAAAGCGGTGCCTACATCATCCCCTTACTTGAACGGCTTGACCTGA
AGAAGGACAATATTCAAGCAATGGTGATTGTTCCCACTAGAGAACTTGCTCTACAGGTCAGTCAAATTTGCATCCAGGTC
AGCAAACACATGGGAGGGGCCAAAGTGATGGCGACCACTGGAGGAACCAATTTACGGGATGACATAATGAGGCTTGACGA
TACAGTGCATGTGGTGATTGCTACCCCTGGCAGAATCCTGGATCTTATCAAGAAAGGAGTAGCAAAGGTTGATCATGTCC
AGATGATAGTATTGGATGAGGCAGATAAGTTGTTGTCACAGGACTTTGTGGAGATAATGGAGGATATTATTCTCACACTA
CCTAAAAATAGGCAGATTTTACTATATTCCGCTACTTCCCTTTTAGTGTACAAAAGTTTATGAATTCTCATTTGCAAAAA
CTCTACGAGATAAACCTGATGGAGGAGCTGACTCTGAAAGGGGTGACCCAGTACTACGCATATGTAACGGAGCGCCAAAA
AGTGCACTGCCTCAATACACTCTTCTCCAGGCTTCAGATAAACCAGTCGATCATTTTCTGCAACTCTTCTCAAAGAGTTG
AGTTACTGGCCAAGAAGATTTCTCAGCTGGGTTACTCTTGCTTCTATATCCATGCTAAAATGAGGCAGGAACATAGAAAT
CGTGTCTTTCATGATTTCCGAAATGGCTTATGCCGCCATCTTGTTTGCACTGATCTGTTTACCCGAGGTATTGATATACA
AGCTGTGAATGTGGTAATAAACTTTGACTTCCCAAAGCTGGCAGAGACCTATCTTCATCGGATTGGAAGGTCAGGTCGCT
TTGGTCGTCTTGGCTTAGCCATCAACTTGATCACATATGATGATCGCTTCAACCTGAAGAGTATTGAGGAGCAGCTGGGG
ACAGAGATCAAACCCATCCCAAGCAACATTGACAAGAGCCTGTATGTGGCAGAATACCACAGTGAGCCTGCAGAAGATGA
GAAACCT

Alignment

ORF - retro_rnor_2546 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.53 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MSTARTENPVIMGLSSQNGQLRGPVKASAGPGGGGPQTQTQMNQLKNTSTINNGTQQQAQSMAATIKPGD
          MSTARTENPVIMGLSSQNGQLRGPVKASAGPGGGGPQTQTQMNQLKNTSTINNGTQQQAQSMA.TIKPGD
Retrocopy MSTARTENPVIMGLSSQNGQLRGPVKASAGPGGGGPQTQTQMNQLKNTSTINNGTQQQAQSMATTIKPGD

Parental  DWKKTLKLPPKDLRIKTSDVTSTKGNEFEDYCLKRELLMGIFEMGWEKPSPIQEESIP-IALSGRDILAR
          DWKKTLKLPPKDL.IKTSDVTSTKGNEFEDYCLK.ELLMGIFEMGWEKPSPIQEESIP.IALSG.DILAR
Retrocopy DWKKTLKLPPKDLSIKTSDVTSTKGNEFEDYCLK*ELLMGIFEMGWEKPSPIQEESIP<IALSGMDILAR

Parental  AKNGTGKSGAYLIPLLERLDLKKDNIQAMVIVPTRELALQVSQICIQVSKHMGGAKVMATTGGTNLRDDI
          AKNGTGKSGAY.IPLLERLDLKKDNIQAMVIVPTRELALQVSQICIQVSKHMGGAKVMATTGGTNLRDDI
Retrocopy AKNGTGKSGAYIIPLLERLDLKKDNIQAMVIVPTRELALQVSQICIQVSKHMGGAKVMATTGGTNLRDDI

Parental  MRLDDTVHVVIATPGRILDLIKKGVAKVDHVQMIVLDEADKLLSQDFVQIMEDIILTLPKNRQILLYSAT
          MRLDDTVHVVIATPGRILDLIKKGVAKVDHVQMIVLDEADKLLSQDFV.IMEDIILTLPKNRQILLYSAT
Retrocopy MRLDDTVHVVIATPGRILDLIKKGVAKVDHVQMIVLDEADKLLSQDFVEIMEDIILTLPKNRQILLYSAT

Parental  -FPLSVQKFMNSHLQKPYEINLMEELTLKGVTQYYAYVTERQKVHCLNTLFSRLQINQSIIFCNSSQRVE
          .FP.SVQKFMNSHLQK.YEINLMEELTLKGVTQYYAYVTERQKVHCLNTLFSRLQINQSIIFCNSSQRVE
Retrocopy <FPFSVQKFMNSHLQKLYEINLMEELTLKGVTQYYAYVTERQKVHCLNTLFSRLQINQSIIFCNSSQRVE

Parental  LLAKKISQLGYSCFYIHAKMRQEHRNRVFHDFRNGLCRNLVCTDLFTRGIDIQAVNVVINFDFPKLAETY
          LLAKKISQLGYSCFYIHAKMRQEHRNRVFHDFRNGLCR.LVCTDLFTRGIDIQAVNVVINFDFPKLAETY
Retrocopy LLAKKISQLGYSCFYIHAKMRQEHRNRVFHDFRNGLCRHLVCTDLFTRGIDIQAVNVVINFDFPKLAETY

Parental  LHRIGRSGRFGHLGLAINLITYDDRFNLKSIEEQLGTEIKPIPSNIDKSLYVAEYHSEPAEDEKP
          LHRIGRSGRFG.LGLAINLITYDDRFNLKSIEEQLGTEIKPIPSNIDKSLYVAEYHSEPAEDEKP
Retrocopy LHRIGRSGRFGRLGLAINLITYDDRFNLKSIEEQLGTEIKPIPSNIDKSLYVAEYHSEPAEDEKP

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	0.13 RPM	17.95 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2546 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2546 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2546 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,