RetrogeneDB ID: retro_cfam_80

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: X:89171984..89172845(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000018270
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCAFG00000013855
• Aliases: None
• Description: None

Sequence

>retro_cfam_80
ATGAATGCCGTCTTCTCCCTGCCACGCTGGCGGCGGCGGCTGTGGCTCTGGCTGTGGCGGCGGCGGAGGAACCCGCCACG
CACCAGCCTTGCTCCCGCCCCACTCGGAGCCGAAGCTGCAGCCGGGCGGGGGCCTTGGGGCCTGAGGACGGAGGTGGAGG
CAGCGGGGCCACCGCTGGAGCCGGGAGACTTTGTGCAGCTGCCCGTGCCCATCATCCAGCAGCTCTCCCACTGGGACTGC
GGCCTGGCCTGCTCCAAGATGGTGCTGCGGTACCTGGGCCAGGTGGACGACAATGAGTTTGAGAGTGCCCTGCGGGAGCT
GCAGCTAACCAGGAACATCTGGACCATTGATCTGGCCTACCTGATGCGCCACTTTGGTGTGAGGCACCGCTTCTGCACAC
AGACCCTGGGTGTTGACAAGGGCTACAAGAACCAGTCCTTCTACAGGAAGCACTTTGACACAGAGGAGACCCGGGTGAAC
CAGTTGTTTGCACAAGCCAAGGCTTGCAAGGTGCTCGTGGAGAAATGCACAGTGAGCGTGCAGGACATCCAGGAGCACCT
GGCACAGGGCCACGTGGCCATCGTGCTGGTGAACTCTGGGGTACTGCACTGCGACCTTTGCTCCAGTCCTGTCAAGTACT
CCTGCTTTGCCCCCAGTGGCCACCGCTGCTTCTGTGGCACCCCTGACTACCAGGGCCACTTCATCGTGCTGTGCGGCTAC
AGCCGGGCCACGGGCTGCATCTTCTACAACAATCCAGCCTACGCCGACCGAATGTGCAGCACCAGCATCAGTAACTTCGA
GGGAGCCAGAACCAGTTACGGCACAGATGAGGACATCCTCTTAGTCTACCTGGATAGCTGA

Alignment

ORF - retro_cfam_80 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.54 %
• Parental protein coverage: 94.82 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MRTEAEAAGPPLEPEDFVQLPVPIIQQLYHWDCGLACSKMVLRYLGQVDDNEFESALQELRLTRSIWTID
          .RTE.EAAGPPLEP.DFVQLPVPIIQQL.HWDCGLACSKMVLRYLGQVDDNEFESAL.EL.LTR.IWTID
Retrocopy LRTEVEAAGPPLEPGDFVQLPVPIIQQLSHWDCGLACSKMVLRYLGQVDDNEFESALRELQLTRNIWTID

Parental  LAYLMRHFGVRHRFCTQTLGVDKGYKNQSFYRKHFDTEETRVNQLFAQAKACKVLVEKCTVSVQDIQEHL
          LAYLMRHFGVRHRFCTQTLGVDKGYKNQSFYRKHFDTEETRVNQLFAQAKACKVLVEKCTVSVQDIQEHL
Retrocopy LAYLMRHFGVRHRFCTQTLGVDKGYKNQSFYRKHFDTEETRVNQLFAQAKACKVLVEKCTVSVQDIQEHL

Parental  AQGHVAIVLVNSGVLHCDLCSSPVKYCCFAPSGHRCFCRTPDYQGHFIVLRGYNRATGCIFYNNPAYADR
          AQGHVAIVLVNSGVLHCDLCSSPVKY.CFAPSGHRCFC.TPDYQGHFIVL.GY.RATGCIFYNNPAYADR
Retrocopy AQGHVAIVLVNSGVLHCDLCSSPVKYSCFAPSGHRCFCGTPDYQGHFIVLCGYSRATGCIFYNNPAYADR

Parental  MCSTSISNFEEARTSYGTDEDILFVYLD
          MCSTSISNFE.ARTSYGTDEDIL.VYLD
Retrocopy MCSTSISNFEGARTSYGTDEDILLVYLD

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	16.25 RPM
SRP017611_brain	0.00 RPM	7.07 RPM
SRP017611_kidney	0.07 RPM	92.72 RPM
SRP017611_liver	0.00 RPM	74.11 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_80 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_80 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_80 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	ENSCAFG00000013855	1 retrocopy	retro_cfam_80 ,
Felis catus	ENSFCAG00000001511	1 retrocopy	retro_fcat_1846,