RetrogeneDB ID: retro_cfam_1951

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 8:34769686..34770004(-)
• Located in intron of: ENSCAFG00000015570

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: WDR83OS
• Ensembl ID: ENSCAFG00000028908
• Aliases: None
• Description: WD repeat domain 83 opposite strand [Source:HGNC Symbol;Acc:30203]

Sequence

>retro_cfam_1951
ATGTCCACTAACAATATGTTGGACCAGCGAAGGCCGAACAAAGTGCTCAGGTACAAGCCCCCACCGAGCGAGTGTATCCC
AGCCTTGGACGACCCAACGCCGGACTACATGAACCTGCTCGGCATGATCTTCAGCATGTGTGGCCTCATGCTCAAGCTGA
AGTGGTGTGCGTGGGTGGCCATCTACTGCTCCTTCATAAGCTTTGCCAACTCCCTGAGTTCTGAGGACACTTAACCAATG
ATGAGTACCTTCATGCTGTCCATCTCTGCTGTGGTCATGTCATATCTGCAGAACCCTCAGCCCATGACATCCCCCTGG

Alignment

ORF - retro_cfam_1951 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.51 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSTNNMSDPRRPNKVLRYKPPPSECNPALDDPTPDYMNLLGMIFSMCGLMLKLKWCAWVAVYCSFISFAN
          MSTNNM.D.RRPNKVLRYKPPPSEC.PALDDPTPDYMNLLGMIFSMCGLMLKLKWCAWVA.YCSFISFAN
Retrocopy MSTNNMLDQRRPNKVLRYKPPPSECIPALDDPTPDYMNLLGMIFSMCGLMLKLKWCAWVAIYCSFISFAN

Parental  SRSSEDTKQMMSSFMLSISAVVMSYLQNPQPMTPPW
          S.SSEDT..MMS.FMLSISAVVMSYLQNPQPMT.PW
Retrocopy SLSSEDT*PMMSTFMLSISAVVMSYLQNPQPMTSPW

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	0.04 RPM	56.91 RPM
SRP017611_brain	0.00 RPM	30.80 RPM
SRP017611_kidney	0.00 RPM	55.54 RPM
SRP017611_liver	0.00 RPM	21.97 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1951 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1951 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1951 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000028908	2 retrocopies	retro_cfam_1489, retro_cfam_1951 ,
Callithrix jacchus	ENSCJAG00000005285	1 retrocopy	retro_cjac_133,
Echinops telfairi	ENSETEG00000019481	1 retrocopy	retro_etel_1133,
Felis catus	ENSFCAG00000000463	1 retrocopy	retro_fcat_1902,
Macropus eugenii	ENSMEUG00000014450	3 retrocopies	retro_meug_1695, retro_meug_1733, retro_meug_2081,
Mus musculus	ENSMUSG00000059355	2 retrocopies	retro_mmus_1327, retro_mmus_2061,
Pteropus vampyrus	ENSPVAG00000013403	1 retrocopy	retro_pvam_1464,
Sus scrofa	ENSSSCG00000013721	1 retrocopy	retro_sscr_488,
Tupaia belangeri	ENSTBEG00000001250	1 retrocopy	retro_tbel_2034,