RetrogeneDB ID: retro_cfam_781

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 17:51282378..51282756(-)
• Located in intron of: ENSCAFG00000009067

Retrocopy information

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

Parental gene information

• Parental gene symbol: EFCAB2
• Ensembl ID: ENSCAFG00000029154
• Aliases: None
• Description: EF-hand calcium binding domain 2 [Source:HGNC Symbol;Acc:28166]

Sequence

>retro_cfam_781
AGAGAGATCAGAACAATTATCAGGTCACTAGGGTGCTGCCCAAGCGAAGGAGAGCTGCATGACCTGATCGTAGAGATAGA
GGAGGAAGAACCCACTGGATACATTCGATTTGAAAAATTTCTTCCAGTGATGACCAAAGTACTACTAGAAAAAAGGTACA
GACCAATTCCAGAAGATATCCTTCTTCGATCATTTGAGGTGTTAGATCCATCCAAACGTGGATTTCTAACTAAGGAAGAA
TTGATCAAGTATATGACCGAAGAAGGTGAGCCTTTTTCTCAGGAAGAAATGGAAGAAATGTTGTCCGCTGCAATTGACCC
AGAATCGAATTCCATTCGTTACAAGGACTACATAGCCATGATGGTGGTAGATGACGGC

Alignment

ORF - retro_cfam_781 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.62 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  REIGTIIRSLGCCPSEGELHDLIVEVEEEEPTGYIRFEKFLPVMTKVLLEKRYRPIPEDILLRAFEVLDP
          REI.TIIRSLGCCPSEGELHDLIVE.EEEEPTGYIRFEKFLPVMTKVLLEKRYRPIPEDILLR.FEVLDP
Retrocopy REIRTIIRSLGCCPSEGELHDLIVEIEEEEPTGYIRFEKFLPVMTKVLLEKRYRPIPEDILLRSFEVLDP

Parental  SKRGFLTKEELIKYMTEEGEPFSQEEMEEMLSAAIDPESNSIRYKDYIAMMVVDDG
          SKRGFLTKEELIKYMTEEGEPFSQEEMEEMLSAAIDPESNSIRYKDYIAMMVVDDG
Retrocopy SKRGFLTKEELIKYMTEEGEPFSQEEMEEMLSAAIDPESNSIRYKDYIAMMVVDDG

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	1.85 RPM	10.37 RPM
SRP017611_brain	1.19 RPM	3.65 RPM
SRP017611_kidney	0.99 RPM	3.96 RPM
SRP017611_liver	0.22 RPM	0.44 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_781 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_781 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_781 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000019170	1 retrocopy	retro_cfam_199,
Canis familiaris	ENSCAFG00000029154	1 retrocopy	retro_cfam_781 ,
Callithrix jacchus	ENSCJAG00000016907	1 retrocopy	retro_cjac_3944,
Equus caballus	ENSECAG00000022403	1 retrocopy	retro_ecab_874,
Oryctolagus cuniculus	ENSOCUG00000029593	1 retrocopy	retro_ocun_612,
Tarsius syrichta	ENSTSYG00000006254	2 retrocopies	retro_tsyr_1584, retro_tsyr_317,