RetrogeneDB ID: retro_cfam_2207

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: X:107357185..107357782(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000018971
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SLC37A3
• Ensembl ID: ENSCAFG00000003973
• Aliases: None
• Description: solute carrier family 37, member 3 [Source:HGNC Symbol;Acc:20651]

Sequence

>retro_cfam_2207
TACTCACTGGCCTATGCCTGCTTGAAGTTAGTAAATTACTCCTTCTTCTTCTGGTTAACCTTTTATCTGAGTAACAACTT
CGGATGGAAGGAGGCTGAAGCTGACAAGCTGTCCATTTGGTACGATGTTGGAGGAATTATAGGTGGGACTTTGCAAGGTT
TCATCTCTGACATATTACAGAAGAGAGCACCCGTTTTAGCTCTCAGTCTACTTCTGGCCATTGGGTCCCCAGTTGGATAT
AGCCGTTCTCCAAACGATAAATCCATTAATGCACTTCTGATGGCAGTTACAGGATTTTTTACCGGTGGGCCTTCTAAAAT
GATTAGTTCTGCTATTTCTGTGGACCTGGGTCGCCAAGAGCTGATCCAAGGGAGCATTGAGGCTTTGGCGACTGTCACAG
GAATTGTTGATGGAACTGGAAGCATTGGAGCTGCAGTGGGCCAGTACCTAGTGTCTTTGATCCAGGACAATCTGGGATTA
TGGGTATTCTACTTTTTCATTCTCATGACAAGTTGTACAATTTTGTTTATATCGCCATTAATAGTGAGGGAAATCTGCTA
TCTTATGCAAAGATGACAAGCTCACGTATTGAGTGAG

Alignment

ORF - retro_cfam_2207 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.5 %
• Parental protein coverage: 76.92 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  YSLAYACLKLVNYSFFFWLPFYLSNNFGWKEAEADKLSIWYDVGGIIGGTLQGFISDVLQKRAPVLALSL
          YSLAYACLKLVNYSFFFWL.FYLSNNFGWKEAEADKLSIWYDVGGIIGGTLQGFISD.LQKRAPVLALSL
Retrocopy YSLAYACLKLVNYSFFFWLTFYLSNNFGWKEAEADKLSIWYDVGGIIGGTLQGFISDILQKRAPVLALSL

Parental  LLAIGSLVGYSRSPNDKSINALLMAVTGFFIGGPSNMISSAISADLGRQELIQGSSEALATVTGIVDGTG
          LLAIGS.VGYSRSPNDKSINALLMAVTGFF.GGPS.MISSAIS.DLGRQELIQGS.EALATVTGIVDGTG
Retrocopy LLAIGSPVGYSRSPNDKSINALLMAVTGFFTGGPSKMISSAISVDLGRQELIQGSIEALATVTGIVDGTG

Parental  SIGAAVGQYLVSLIQDNLGWIWVFYFFILMTSCTILFISPLIVRETCYLMQRRQAHVLSE
          SIGAAVGQYLVSLIQDNLG..WVFYFFILMTSCTILFISPLIVRE.CYLMQR.QAHVLSE
Retrocopy SIGAAVGQYLVSLIQDNLG-LWVFYFFILMTSCTILFISPLIVREICYLMQR*QAHVLSE

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	27.51 RPM
SRP017611_brain	0.00 RPM	23.82 RPM
SRP017611_kidney	0.00 RPM	11.75 RPM
SRP017611_liver	0.00 RPM	8.34 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_2207 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_2207 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_2207 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000012239	1 retrocopy	retro_btau_1471,
Canis familiaris	ENSCAFG00000003973	1 retrocopy	retro_cfam_2207 ,
Mus musculus	ENSMUSG00000029924	1 retrocopy	retro_mmus_3670,
Ictidomys tridecemlineatus	ENSSTOG00000010929	1 retrocopy	retro_itri_1795,
Tursiops truncatus	ENSTTRG00000009525	1 retrocopy	retro_ttru_921,