RetrogeneDB ID: retro_cfam_154

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 8:26243701..26244022(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000011410
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCAFG00000017688
• Aliases: None
• Description: None

Sequence

>retro_cfam_154
ATGGTCAATGTTCCCAAAACCCGAAGGACTTTCTGTAAGAAGTGTGGAAAGCATCAGCCTCACAAAGTGACCCAGTATAA
GAAGGGCAAGGATTCCCTTTATGCCCAGGGAAAGAGGCGCTATGATCGGAAGCAGAGTGGCTATGGTGGGCAGACAAAGC
CAATTTTCCGGAAGAAGGCTAAAACCACAAAGAAGATTGTGCTGAGGCTTGAATGCGTTGAACCTAACTGCAGGTCCAAG
AGGATGCTGGCCATTAAGAGATGCAAGCATTTCGAACTGGGAGGAGATAAGAAGAGAAAAGGCCAAGTGATCCAGTTCTA
A

Alignment

ORF - retro_cfam_154 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 100.0 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VNVPKTRRTFCKKCGKHQPHKVTQYKKGKDSLYAQGKRRYDRKQSGYGGQTKPIFRKKAKTTKKIVLRLE
          VNVPKTRRTFCKKCGKHQPHKVTQYKKGKDSLYAQGKRRYDRKQSGYGGQTKPIFRKKAKTTKKIVLRLE
Retrocopy VNVPKTRRTFCKKCGKHQPHKVTQYKKGKDSLYAQGKRRYDRKQSGYGGQTKPIFRKKAKTTKKIVLRLE

Parental  CVEPNCRSKRMLAIKRCKHFELGGDKKRKGQVIQF
          CVEPNCRSKRMLAIKRCKHFELGGDKKRKGQVIQF
Retrocopy CVEPNCRSKRMLAIKRCKHFELGGDKKRKGQVIQF

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	48.59 RPM	94.62 RPM
SRP017611_brain	31.60 RPM	25.41 RPM
SRP017611_kidney	155.85 RPM	103.88 RPM
SRP017611_liver	56.63 RPM	55.26 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_154 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_154 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_154 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000008503	1 retrocopy	retro_acar_98,
Canis familiaris	ENSCAFG00000017688	1 retrocopy	retro_cfam_154 ,
Loxodonta africana	ENSLAFG00000017385	1 retrocopy	retro_lafr_114,
Monodelphis domestica	ENSMODG00000025578	2 retrocopies	retro_mdom_1878, retro_mdom_971,
Mustela putorius furo	ENSMPUG00000002168	3 retrocopies	retro_mputfur_269, retro_mputfur_530, retro_mputfur_94,
Sarcophilus harrisii	ENSSHAG00000013479	1 retrocopy	retro_shar_467,
Tupaia belangeri	ENSTBEG00000015808	1 retrocopy	retro_tbel_52,