RetrogeneDB ID: retro_cfam_1952

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 8:35874024..35874819(-)
• Located in intron of: ENSCAFG00000015639

Retrocopy information

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

Parental gene information

• Parental gene symbol: UBFD1
• Ensembl ID: ENSCAFG00000017670
• Aliases: None
• Description: ubiquitin family domain containing 1 [Source:HGNC Symbol;Acc:30565]

Sequence

>retro_cfam_1952
GAGGACTCCTGCGCAGCGCCAGGCAACCTGCAGCCAGCCCCGGCCCAGCCCCCTGGGGACCCTGCAGCCCAGGCCTCAGT
CAGCAACAGCAAAGACGCCGGCGGCGGCGCAGGCAGGAAGCTAGTGGACCTGAAGATCATCTGGAACAAGACTAAACACG
ATGTGAAGCTCCCCTTGGATAGCACAGGTTCCGAGCTGAAACAGAAGATTCACTCGATTACAGGTCTCCTTCCTGCCATG
CAGAAAGTCATGTATAAGGGACTCGTCCCTGAGGATAAGACGTTGAGAGAAATAAAAGTGACCAGCGGAGCAGAGATCAT
GGTGGTTGGCTCCACGATAAATGATGTTTTGGCTGTAAACACACCCAAAGATGCTGCCCAGCAGGATGCAAAGGCCGAAG
AGAACAAGAAGGAGCCACTCTGCAGGCAGAAACAACACAGGAAAGTGTTGGATAAAGGAAAACCCGAAGATGTGATGCCA
TCTGCTAAGGGTGCCCAGGAGCGCCTGCAGACGGTACCCTTATCTGGCATGTACAAGAAGTCTGAAGGCAAAGTGAGGCT
CACCTTCAAGCTAGAACAAGACCAGCTGTGGATCAGCACTAAACAGCAGACTGCGAAATTGCCGGTGGGCTCCATTAAAA
ATGTGCTCAGTGAACCTATCGAAGGACACGAAGACTACCACATGATGGCGTTTCAGTTGGGCCCCACGGAAGCCTCTTAC
TACTGGGTGTACTGGGTCCCAACTCAATATGTGGATACAATCAAAGACACCGTACTGGGGAAGTGGCAGTATTTT

Alignment

ORF - retro_cfam_1952 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.21 %
• Parental protein coverage: 73.82 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EDSCAARGNLQPAPAQPPGDPAAQASVSNGEDAGGGAGRELVDLKIIWNKTKHDVKFPLDSTGSELKQKI
          EDSCAA.GNLQPAPAQPPGDPAAQASVSN..DAGGGAGR.LVDLKIIWNKTKHDVK.PLDSTGSELKQKI
Retrocopy EDSCAAPGNLQPAPAQPPGDPAAQASVSNSKDAGGGAGRKLVDLKIIWNKTKHDVKLPLDSTGSELKQKI

Parental  HSITGLPPAMQKVMYKGLVPEDKTLREIKVTSGAKIMVVGSTINDVLAVNTPKDAAQQDAKAEENKKEPL
          HSITGL.PAMQKVMYKGLVPEDKTLREIKVTSGA.IMVVGSTINDVLAVNTPKDAAQQDAKAEENKKEPL
Retrocopy HSITGLLPAMQKVMYKGLVPEDKTLREIKVTSGAEIMVVGSTINDVLAVNTPKDAAQQDAKAEENKKEPL

Parental  CRQKQHRKVLDKGKPEDVMPSVKGAQERLPTVPLSGMYNKSGGKVRLTFKLEQDQLWIGTKERTEKLPMG
          CRQKQHRKVLDKGKPEDVMPS.KGAQERL.TVPLSGMY.KS.GKVRLTFKLEQDQLWI.TK..T.KLP.G
Retrocopy CRQKQHRKVLDKGKPEDVMPSAKGAQERLQTVPLSGMYKKSEGKVRLTFKLEQDQLWISTKQQTAKLPVG

Parental  SIKNVVSEPIEGHEDYHMMAFQLGPTEASYYWVYWVPTQYVDAIKDTVLGKWQYF
          SIKNV.SEPIEGHEDYHMMAFQLGPTEASYYWVYWVPTQYVD.IKDTVLGKWQYF
Retrocopy SIKNVLSEPIEGHEDYHMMAFQLGPTEASYYWVYWVPTQYVDTIKDTVLGKWQYF

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	31.33 RPM
SRP017611_brain	0.00 RPM	18.82 RPM
SRP017611_kidney	0.00 RPM	21.20 RPM
SRP017611_liver	0.00 RPM	10.08 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1952 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1952 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1952 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000029331	2 retrocopies	retro_acar_106, retro_acar_204,
Canis familiaris	ENSCAFG00000017670	1 retrocopy	retro_cfam_1952 ,
Callithrix jacchus	ENSCJAG00000020614	1 retrocopy	retro_cjac_372,
Monodelphis domestica	ENSMODG00000006727	2 retrocopies	retro_mdom_1162, retro_mdom_1298,
Pongo abelii	ENSPPYG00000007191	1 retrocopy	retro_pabe_2528,