RetrogeneDB ID: retro_cfam_1651

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 4:27609016..27609525(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: C1orf194
• Ensembl ID: ENSCAFG00000019853
• Aliases: None
• Description: chromosome 1 open reading frame 194 [Source:HGNC Symbol;Acc:32331]

Sequence

>retro_cfam_1651
ATGCCTTTCACCCGAGACCCTTTCCAGCACCCTACGTTGGAAAACTATGATTCCTACCTGGAGAAACTCCGGGCTTCCAA
GAAACTGCCATATAAGAACCCAACTCACCTTGCTCAGCAACAGGAACCCTGGAGTCAGCTCAGCTCGACTCCCACAATCA
CCTCCATGAGGCAAGATATTTATTTTTTTGATCCTGAGATACCAAAGGATGACCTGGATTTCCGCTTAGCAGCCTTGTAC
AACCACCACACAGGGACATTCAAGAACAAAAGTGAGATACTTTTACACCAGGAGACCACTCAGGATATCCACCGTATCAT
CAAGACCTAATTCCCTGGAGAACTTTTACCCCCTCCTCCGCCACCTTCCATTACTTCCCGAGCTAACATCAGACACTGGA
TCAACCCTAAGGAGTCTATCCACAGCATCCAGGGATCATAGTGTCCCCTCACACTGCAGCCACCAATGGAGGCTACTCCC
GAAAGAATGATGGTGGCTTCTTCTGTACT

Alignment

ORF - retro_cfam_1651 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.28 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MPFPRDPLQRPTLENDDSYLGKLRASKKLPYKNPTHLAQQQEPWSRLSSTPTITSTRRDIYFLDPEIPKD
          MPF.RDP.Q.PTLEN.DSYL.KLRASKKLPYKNPTHLAQQQEPWS.LSSTPTITS.R.DIYF.DPEIPKD
Retrocopy MPFTRDPFQHPTLENYDSYLEKLRASKKLPYKNPTHLAQQQEPWSQLSSTPTITSMRQDIYFFDPEIPKD

Parental  DLDFRLAALYNHHTGTFKNKSEILLHQETTQDIHGIIKTQFPGELLPPPPPPSVTSRANIRHWINPKKES
          DLDFRLAALYNHHTGTFKNKSEILLHQETTQDIH.IIKT.FPGELLPPPPPPS.TSRANIRHWINP.KES
Retrocopy DLDFRLAALYNHHTGTFKNKSEILLHQETTQDIHRIIKT*FPGELLPPPPPPSITSRANIRHWINP-KES

Parental  IHSIQGS-IVSPHTAATNGGYSRKNDGGFFST
          IHSIQGS.IVSPHTAATNGGYSRKNDGGFF.T
Retrocopy IHSIQGS<IVSPHTAATNGGYSRKNDGGFFCT

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	4.41 RPM
SRP017611_brain	0.00 RPM	14.53 RPM
SRP017611_kidney	0.00 RPM	1.12 RPM
SRP017611_liver	0.00 RPM	0.00 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1651 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1651 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1651 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000019853	3 retrocopies	retro_cfam_1217, retro_cfam_1651 , retro_cfam_1827,
Monodelphis domestica	ENSMODG00000002197	1 retrocopy	retro_mdom_1332,
Mustela putorius furo	ENSMPUG00000002787	3 retrocopies	retro_mputfur_561, retro_mputfur_568, retro_mputfur_672,