RetrogeneDB ID: retro_cfam_1419

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 30:19179151..19179679(-)
• Located in intron of: ENSCAFG00000015875

Retrocopy information

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

Parental gene information

• Parental gene symbol: UPRT
• Ensembl ID: ENSCAFG00000017218
• Aliases: None
• Description: uracil phosphoribosyltransferase (FUR1) homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:28334]

Sequence

>retro_cfam_1419
AGGACAGTCAGTAGGGGGGACTTCATGTTTTCTGTGGATCGATTGATCAGACTTGTGGAAAAGGGATTGAATCAGCTGTC
ATATAAAGAATGCATGGTGACCACCCCAACAGGATACAAGTATGAAGGAGTGAAATTTGAGAAGGGAAATTGTGGTGTCA
GCATAATGAGAAGCAGTGAGGCAATGGAACAAGTTTTACAAGACTGCCGTCGATCCATATGCATTGCGAAGATCCTGATT
CAGAGTGATGAAGAGACACAAAGAGCCAACGTATATTATGCTAAGTTCCCCCCAGACATTTACTGGAGAAAAGTCCTTCT
GATGTATCCAATTCTCAGTACTGGAAATACTGTAATTGAAGCTGTAAAGGTTCTTATAAAACATGGAGTTCAACCCAGCG
TTATTATCCTACTCAGTCTGTTCTCTACTCCTCATGGTGCCAAATCAATCATTCAGAAGTTTCCTGAGATCACAATTTAA
ACTACTGTTGCGCCTACACATTTTGGGCAGAAATACTCTGGGACAGAC

Alignment

ORF - retro_cfam_1419 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.85 %
• Parental protein coverage: 58.96 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KTASRGDFMFSADRLIRLVVEEGLNQLPYKECMVTTPTGYKYEGVKFEKGNCGVSIMRSGEAMEQGLRDC
          .T.SRGDFMFS.DRLIRLV.E.GLNQL.YKECMVTTPTGYKYEGVKFEKGNCGVSIMRS.EAMEQ.L.DC
Retrocopy RTVSRGDFMFSVDRLIRLV-EKGLNQLSYKECMVTTPTGYKYEGVKFEKGNCGVSIMRSSEAMEQVLQDC

Parental  CRSIRIGKILIQSDEETQRAKVYYAKFPPDIYRRKVLLMYPILSTGNTVIEAVKVLIEHGVQPSVIILLS
          .RSI.I.KILIQSDEETQRA.VYYAKFPPDIY.RKVLLMYPILSTGNTVIEAVKVLI.HGVQPSVIILLS
Retrocopy RRSICIAKILIQSDEETQRANVYYAKFPPDIYWRKVLLMYPILSTGNTVIEAVKVLIKHGVQPSVIILLS

Parental  LFSTPHGAKSIIQEFPEITILTTEVHPVAPTHFGQKYFGTD
          LFSTPHGAKSIIQ.FPEITI.TT....VAPTHFGQKY.GTD
Retrocopy LFSTPHGAKSIIQKFPEITI*TT----VAPTHFGQKYSGTD

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	0.00 RPM	11.63 RPM
SRP017611_brain	0.00 RPM	11.04 RPM
SRP017611_kidney	0.00 RPM	16.71 RPM
SRP017611_liver	0.00 RPM	5.66 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1419 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1419 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1419 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000017218	1 retrocopy	retro_cfam_1419 ,
Monodelphis domestica	ENSMODG00000027579	1 retrocopy	retro_mdom_191,