RetrogeneDB ID: retro_cfam_85

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: X:92910864..92911530(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000018548
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: CIDEB
• Ensembl ID: ENSCAFG00000012240
• Aliases: None
• Description: None

Sequence

>retro_cfam_85
ATGGAGTATCTCTCAGCCCTGAACCCCAGTGGCCTGCTCAGGTCAGTATCCAATATGAGCTCTGAGTTTGGCCGGAAAGT
CTGGACTTCACCTCCACCACCCCAGCGACCCTTCCGAGTCTGTGATCACAAGCGGACTACCCGGAAAGGTCTGACAGCTG
CCACCCGCCAGGAACTGCTGGACAAGGCAACAGAGGCCCTCCTGCTGAGTGGGATGTTAACATTGGTGCTGGAGGAGGAT
GGGACCGCTGTGGAGAGTGAGGACTTCTTCCAGCTTTTGGAGGATGACACGTGCCTGATGGTGCTGGAGTGTGGGCAGAG
CTGGAGCCCCAGCAGGAGTGGGATGCTGTCATATGGCCTGGGCCGGGAGAAGCCCAAGCACAGCAAAGACATCGCCCGCA
TCACCTTCGAAGTATACAAGCAAAACCCTCGAGACCTCTTTGGCAGCCTCAATGTCAAAGCCACATTCTACGGGCTCTAC
TCCATGAGTTGTGATTTTCAAGGACTTGGCCCAAAGAAAGTACTCAGGGAGCTCCTCCGCTGGACATCTGCACTGCTGCA
AGGCCTAGGCCACATGCTGCTGGGAATTTCCTCCAGCCTTCGCCACCTAGTAGAAGGGGCCGAGCAGTGGCATTGGCAGC
GGCAGGGTCGCCTCCATCCCTACTGA

Alignment

ORF - retro_cfam_85 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.55 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MEYLSALNPSGLLRSVSNMSSEFGRKVWTSPPPPQRPFRVCDHKRTTRKGLTAATRQELLDKATEALLLS
          MEYLSALNPSGLLRSVSNMSSEFGRKVWTSPPPPQRPFRVCDHKRTTRKGLTAATRQELLDKATEALLLS
Retrocopy MEYLSALNPSGLLRSVSNMSSEFGRKVWTSPPPPQRPFRVCDHKRTTRKGLTAATRQELLDKATEALLLS

Parental  GMLTLVLEEDGTAVESEDFFQLLEDDTCLMVLECGQSWSPSRSGMLSYGLGREKPKHSKDIARITFDVYK
          GMLTLVLEEDGTAVESEDFFQLLEDDTCLMVLECGQSWSPSRSGMLSYGLGREKPKHSKDIARITF.VYK
Retrocopy GMLTLVLEEDGTAVESEDFFQLLEDDTCLMVLECGQSWSPSRSGMLSYGLGREKPKHSKDIARITFEVYK

Parental  QNPRDLFGSLNVKATFYGLYSMSCDFQGLGPKKVLRELLRWTSALLQGLGHMLLGISSSLRHLVEGAEQW
          QNPRDLFGSLNVKATFYGLYSMSCDFQGLGPKKVLRELLRWTSALLQGLGHMLLGISSSLRHLVEGAEQW
Retrocopy QNPRDLFGSLNVKATFYGLYSMSCDFQGLGPKKVLRELLRWTSALLQGLGHMLLGISSSLRHLVEGAEQW

Parental  HWQRQGRLHPY
          HWQRQGRLHPY
Retrocopy HWQRQGRLHPY

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	0.04 RPM
SRP017611_brain	0.00 RPM	0.08 RPM
SRP017611_kidney	0.26 RPM	6.93 RPM
SRP017611_liver	0.07 RPM	9.06 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_85 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_85 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_85 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016089	1 retrocopy	retro_amel_633,
Canis familiaris	ENSCAFG00000005266	1 retrocopy	retro_cfam_293,
Canis familiaris	ENSCAFG00000012240	1 retrocopy	retro_cfam_85 ,
Equus caballus	ENSECAG00000010495	1 retrocopy	retro_ecab_943,
Felis catus	ENSFCAG00000026821	1 retrocopy	retro_fcat_1418,
Pteropus vampyrus	ENSPVAG00000007036	1 retrocopy	retro_pvam_523,