RetrogeneDB ID: retro_cfam_50

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 23:20270177..20271011(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000005780
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCAFG00000002306
• Aliases: None
• Description: None

Sequence

>retro_cfam_50
GGAAAGTCTTTTTCTCAGTTGCCTTTGCATTCAAATAAAGAAAATGCTTATGATGGAGTCACATCAACTGAAAGTATGAG
GAATGGACTGGTTAATAATGAAGTCCATAATGAAGATGGGAGAGGTGGAGATGTCTCTCAGTTTCCGTATGTGGAATTTA
CAGGAAGAGATAGTGTCACTTGCCCCACTTGTCAAGGAACGGGAAGAATTCCTAGAGGGCAAGAAAACCAGCTGGTGGCA
TTGATTCCATATAGTGATCAGAGATTAAGGCCAAGAAGGACAAAGCTGTATGTGATGGCTTCTGTGTTTGTTTGTCTGCT
CCTTTCTGGATTGGCTGTATTTTTCCTTTTCCCTCGCTCTATTGACGCGAAATACATTGGCGTAAAATCAGCATACGTCA
TATGTTCAAAAGCGTACAGTATAAAAAAAAAGCATATGGTATATTTAAATATCACGAACACACTAAATATAACAAACAAT
AACTACTATTCTGTTGAAGTTGAAAACATCACTGCACAAGTTCAATTATCAAAAACAGTTATTGGAAAGGCACGCTTAAA
CAACATAACCAATATTGGCCCACTGGATATGAAACAAATTGATTATACAGTACCTACTATCATAGCAGAGGAAATGAGTT
ATATGTATGATTTCTGTACACTGATATCCATCAAAGTGCATAACATAGTACTCATGATGCAAGTTACTGTGACAACAACA
TACTTCGGACACTCTGAACAGATATCGCAGGAGAGGTACCAGTATGTTGACTGTGGAAGGAACACAACTTATCAGTTGGG
GCAATCTGAGTATCTAAATGTACTTCAGCCACAA

Alignment

ORF - retro_cfam_50 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.6 %
• Parental protein coverage: 85.85 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GKSFSQLPLHSNKEDAYDGVTSTESMRNGLVNNEVHNEDGRGGDVSQFPYVEFTGRDSVTCPTCQGTGRI
          GKSFSQLPLHSNKE.AYDGVTSTESMRNGLVNNEVHNEDGRGGDVSQFPYVEFTGRDSVTCPTCQGTGRI
Retrocopy GKSFSQLPLHSNKENAYDGVTSTESMRNGLVNNEVHNEDGRGGDVSQFPYVEFTGRDSVTCPTCQGTGRI

Parental  PRGQENQLVALIPYSDQRLRPRRTKLYVMASVFVCLLLSGLAVFFLFPRSIDVKYIGVKSAYV----SYD
          PRGQENQLVALIPYSDQRLRPRRTKLYVMASVFVCLLLSGLAVFFLFPRSID.KYIGVKSAYV.....Y.
Retrocopy PRGQENQLVALIPYSDQRLRPRRTKLYVMASVFVCLLLSGLAVFFLFPRSIDAKYIGVKSAYVICSKAYS

Parental  VQKR-TVYLNITNTLNITNNNYYSVEVENITAQVQFSKTVIGKARLNNITNIGPLDMKQIDYTVPTIIAE
          ..K...VYLNITNTLNITNNNYYSVEVENITAQVQ.SKTVIGKARLNNITNIGPLDMKQIDYTVPTIIAE
Retrocopy IKKKHMVYLNITNTLNITNNNYYSVEVENITAQVQLSKTVIGKARLNNITNIGPLDMKQIDYTVPTIIAE

Parental  EMSYMYDFCTLMSIKVHNIVLMMQVTVTTTYFGHSEQISQERYQYVDCGRNTTYQLGQSEYLNVLQPQ
          EMSYMYDFCTL.SIKVHNIVLMMQVTVTTTYFGHSEQISQERYQYVDCGRNTTYQLGQSEYLNVLQPQ
Retrocopy EMSYMYDFCTLISIKVHNIVLMMQVTVTTTYFGHSEQISQERYQYVDCGRNTTYQLGQSEYLNVLQPQ

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	24.82 RPM
SRP017611_brain	0.08 RPM	21.44 RPM
SRP017611_kidney	0.07 RPM	31.37 RPM
SRP017611_liver	0.00 RPM	8.99 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_50 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_50 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_50 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000002306	1 retrocopy	retro_cfam_50 ,
Mustela putorius furo	ENSMPUG00000014079	1 retrocopy	retro_mputfur_72,
Otolemur garnettii	ENSOGAG00000009729	1 retrocopy	retro_ogar_2133,