RetrogeneDB ID: retro_cfam_1449

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 31:18652912..18653321(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RCHY1
• Ensembl ID: ENSCAFG00000032536
• Aliases: None
• Description: ring finger and CHY zinc finger domain containing 1, E3 ubiquitin protein ligase [Source:HGNC Symbol;Acc:17479]

Sequence

>retro_cfam_1449
ATGACAGCTTCGGTGCAGGAAGATGGCGCCCTGGCCAAAAGCAAGGGTGGCGGGGCTGCGAGCACTATGACAGAGGATGT
CTCCTGAAGGCACCTTGCTGTGACAAACTGTATACTTGCCGGTTGTGTCATGATAACAATGAAGATCATCAGCTAGATGG
CTTTAAAGTAAAGGAAGTGCAGTGCATAAACTGTGAAAAAATTCAACATGCCCAACAGACCTGTGAAGAATGTAGCACAT
TGTTTGGGGAATATTATTGCAGTATATGCCATCTCTTTGACCAAGACAAGAAGCAGTATCATTGTGAAACTGTGGAATTT
GTAGGATTGGTCCAAAGGAAGATTTTTTCCATTGTTTGAAATGTAATTTATGCCTAGGTATGAATCTCCAAGGAAAGCAC
AAGGACATT

Alignment

ORF - retro_cfam_1449 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.21 %
• Parental protein coverage: 52.9 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAAAAREDGAR-GREQGLRGCEHYDRGCLLKAPCCDKLYTCRLCHDNNEDHQLDRFKVKEVQCINCEKIQ
          M.A...EDGA..G..QG.RGCEHYDRGCLLKAPCCDKLYTCRLCHDNNEDHQLD.FKVKEVQCINCEKIQ
Retrocopy MTASVQEDGAL<GQKQGWRGCEHYDRGCLLKAPCCDKLYTCRLCHDNNEDHQLDGFKVKEVQCINCEKIQ

Parental  HAQQSCEECSTLFGEYYCSICHLFDKDKKQYHCE-NCGICRIGPKEDFFHCLKCNLCLAMNLQGKHKCI
          HAQQ.CEECSTLFGEYYCSICHLFD.DKKQYHCE.NCGICRIGPKEDFFHCLKCNLCL.MNLQGKHK.I
Retrocopy HAQQTCEECSTLFGEYYCSICHLFDQDKKQYHCE<NCGICRIGPKEDFFHCLKCNLCLGMNLQGKHKDI

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	0.17 RPM	20.71 RPM
SRP017611_brain	0.08 RPM	11.99 RPM
SRP017611_kidney	0.53 RPM	92.58 RPM
SRP017611_liver	0.07 RPM	14.14 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1449 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1449 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1449 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000032536	1 retrocopy	retro_cfam_1449 ,
Choloepus hoffmanni	ENSCHOG00000011650	1 retrocopy	retro_chof_1142,
Macropus eugenii	ENSMEUG00000003266	1 retrocopy	retro_meug_1564,
Monodelphis domestica	ENSMODG00000019197	2 retrocopies	retro_mdom_314, retro_mdom_991,
Rattus norvegicus	ENSRNOG00000002546	2 retrocopies	retro_rnor_1127, retro_rnor_607,
Tursiops truncatus	ENSTTRG00000013786	1 retrocopy	retro_ttru_1333,