RetrogeneDB ID: retro_cfam_1347

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 3:60193882..60195329(+)
• Located in intron of: ENSCAFG00000014566

Retrocopy information

• Ensembl ID: ENSCAFG00000014560
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: DDX6
• Ensembl ID: ENSCAFG00000012442
• Aliases: None
• Description: DEAD (Asp-Glu-Ala-Asp) box helicase 6 [Source:HGNC Symbol;Acc:2747]

Sequence

>retro_cfam_1347
ATGAGCACGGCCAGAACAGAGAACCCTGTTATAATGGGTCTTTCCAGTCAAAATGGTCAGCTGAGGGGCCCTGTGAAGCC
CAGTGGTGGCCCCGGAGGACGGGGGCACACAGACACAGCAACAGATGAACCAGCTGAAAAATACCAACACAATCAATAAT
GGCACTCAGCAGCAAGCACAGAGTATGACCACCACTATTAAACCTGGTGATGACTGGAAAAAGACTTTAAAACTCCCTCC
AAAGGATCTAAGAATCAAAACTTCGGATGTGACCTCCACAAAAGGAAATGAGTTTGAAGATTACTGTTTGAAATGGGAGT
TACTGATGGGAATTTTTGAAATGGGCTGGGAAAAGCCATCTCCTATTCAGGAGGAGAGCATTCCCATTGCTTTATCTGGT
AGGGATATCTTAGCTAGAGCAAAAAATGGAACAGGCAAGAGCGGTGCCTACTTCATTCCCTTACTTGAACGGCTAGACCT
GAAGAAGGACAATATACAAGCAATGGTGATTGTTCCCACTAGAGAAGTTGCTCTACAGGTCAGTCAAATTTGCATCCAGG
TCAGCAAGCACATGGGAGGGGCCAAAGTGATGGCAACCACAGGAGGAACCAATTTACGGGATGACATAATGAGGCTTGAT
GACACAGTGCACGTGGTGATAGCTACCCCTGGAAGAATCCTGGATGTTATCAAGAAAGGAGCAGCAAAAGTTGATCATGT
CCAGATGATAGTATTGGATGAGGCAGATAAGTTGCTGTCACAGGATTTTGTGCAGATAATGGAGGATATTATTCTCACGC
TACCTAAAAACAGACAGATTTTATTATATTCTGCTACTTTCCCTCTTAGTGTACAGAAGTTCATGAATTCCCATTTGCGG
AAACCCTGTGAGATTAACCTGATGGAGGAACTAACTTTGAAGGGAGTAACCCAGTACTACGCCTATGTAACTGAGCGCCA
AAAAGTACTCTGCCTCAACACACTTTTTTCCAGGCTTCAGATAAACCAGTCGATCATTTTCTGTAACTCCTCTCAGCGAG
TTGAATTGCTAGCCAAGATTTCTCTACTGGGTTATTCTTGCTTCTATATCCATGCTAAAATGAGGCAGGAACATCGAAAT
CGTGTATTTCATGATTTCCGAAATGGCTTATGCCGCAATCTTGTTTGCACTGATTTGTTTCCCCGAGGTATTGATATACA
AGCTGTGAATGTGGTAATAAACTTTGACTTCCCAAAGCTGGCAGAGACCTATCTCCATCGTATTGGAAGATCAGGTCGCT
TTGGTCATCTTGGCTTAGCCATCAACTTGATCACATATGATGATCGCTTCAACCTGAAAAATATTGAGGAGCAGCTGGGA
ACAGAAATTAAACCGATCCCAAGCAACATCGACAAGAGCCTGTATGAGGCAGAATACCACAGCGAGCCCGTGGAGGACGA
GAAGCCC

Alignment

ORF - retro_cfam_1347 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.11 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSTARTENPVIMGLSSQNGQLRGPVKPSGGPGG-GGTQTQQQMNQLKNTNTINNGTQQQAQSMTTTIKPG
          MSTARTENPVIMGLSSQNGQLRGPVKPSGGPGG.GGTQTQQQMNQLKNTNTINNGTQQQAQSMTTTIKPG
Retrocopy MSTARTENPVIMGLSSQNGQLRGPVKPSGGPGG>GGTQTQQQMNQLKNTNTINNGTQQQAQSMTTTIKPG

Parental  DDWKKTLKLPPKDLRIKTSDVTSTKGNEFEDYCLKRELLMGIFEMGWEKPSPIQEESIPIALSGRDILAR
          DDWKKTLKLPPKDLRIKTSDVTSTKGNEFEDYCLK.ELLMGIFEMGWEKPSPIQEESIPIALSGRDILAR
Retrocopy DDWKKTLKLPPKDLRIKTSDVTSTKGNEFEDYCLKWELLMGIFEMGWEKPSPIQEESIPIALSGRDILAR

Parental  AKNGTGKSGAYLIPLLERLDLKKDNIQAMVIVPTRELALQVSQICIQVSKHMGGAKVMATTGGTNLRDDI
          AKNGTGKSGAY.IPLLERLDLKKDNIQAMVIVPTRE.ALQVSQICIQVSKHMGGAKVMATTGGTNLRDDI
Retrocopy AKNGTGKSGAYFIPLLERLDLKKDNIQAMVIVPTREVALQVSQICIQVSKHMGGAKVMATTGGTNLRDDI

Parental  MRLDDTVHVVIATPGRILDLIKKGVAKVDHVQMIVLDEADKLLSQDFVQIMEDIILTLPKNRQILLYSAT
          MRLDDTVHVVIATPGRILD.IKKG.AKVDHVQMIVLDEADKLLSQDFVQIMEDIILTLPKNRQILLYSAT
Retrocopy MRLDDTVHVVIATPGRILDVIKKGAAKVDHVQMIVLDEADKLLSQDFVQIMEDIILTLPKNRQILLYSAT

Parental  FPLSVQKFMNSHLQKPYEINLMEELTLKGVTQYYAYVTERQKVHCLNTLFSRLQINQSIIFCNSSQRVEL
          FPLSVQKFMNSHL.KP.EINLMEELTLKGVTQYYAYVTERQKV.CLNTLFSRLQINQSIIFCNSSQRVEL
Retrocopy FPLSVQKFMNSHLRKPCEINLMEELTLKGVTQYYAYVTERQKVLCLNTLFSRLQINQSIIFCNSSQRVEL

Parental  LAKKISQLGYSCFYIHAKMRQEHRNRVFHDFRNGLCRNLVCTDLFTRGIDIQAVNVVINFDFPKLAETYL
          LA.KIS.LGYSCFYIHAKMRQEHRNRVFHDFRNGLCRNLVCTDLF.RGIDIQAVNVVINFDFPKLAETYL
Retrocopy LA-KISLLGYSCFYIHAKMRQEHRNRVFHDFRNGLCRNLVCTDLFPRGIDIQAVNVVINFDFPKLAETYL

Parental  HRIGRSGRFGHLGLAINLITYDDRFNLKSIEEQLGTEIKPIPSNIDKSLYVAEYHSEPVEDEKP
          HRIGRSGRFGHLGLAINLITYDDRFNLK.IEEQLGTEIKPIPSNIDKSLY.AEYHSEPVEDEKP
Retrocopy HRIGRSGRFGHLGLAINLITYDDRFNLKNIEEQLGTEIKPIPSNIDKSLYEAEYHSEPVEDEKP

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
SRP012049_cerebellum	1.01 RPM	40.70 RPM
SRP017611_brain	2.06 RPM	33.74 RPM
SRP017611_kidney	1.52 RPM	18.69 RPM
SRP017611_liver	0.22 RPM	11.17 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1347 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1347 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1347 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,