RetrogeneDB ID: retro_cfam_228

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: X:2439048..2439447(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000011192
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCAFG00000025410
• Aliases: None
• Description: None

Sequence

>retro_cfam_228
ATGTGTGATGCTTTTGTGGGTACCTGGAAACTTAGCTCCAGTGAAAACTTTGATGATTACATGAAAGAAGTGGGAGTGGG
CTTCGCCACCAGGAAAGTGGCTGGCATGGCCAAACCCAACAGGATCATCAGTGTAAACGGGGATGTGATCACCATTAAAT
CGGAAAGCACCTTTAAAAATACAGAGATTTCCTTCAAACTGGGCCAGGAATTTGATGAAGTTACTGCGGATTACAGAAAC
GTAAAGAGCATCATAACCTTAGATGGAGGTGTCCTGGTACAGGTGCAGAAGTGGGACGGAGAATCAACTACCATAAAGAG
AAAACAAGTGGATGATAAACTGGTGGTGGAATGTATCAGGAAAGGCGTCACTTCTACCAGAATTTATGAGAGAGCATAA

Alignment

ORF - retro_cfam_228 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.45 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MCDAFVGTWKLSSSENFDDYMKEVGVGFATRKVAGMAKPNMIISVNGDVITIKSESTFKNTEISFKLGQE
          MCDAFVGTWKLSSSENFDDYMKEVGVGFATRKVAGMAKPN.IISVNGDVITIKSESTFKNTEISFKLGQE
Retrocopy MCDAFVGTWKLSSSENFDDYMKEVGVGFATRKVAGMAKPNRIISVNGDVITIKSESTFKNTEISFKLGQE

Parental  FDEVTADDRKVKSIITLDGGVLVQVQKWDGKSTTIKRKRVDDKLVVECIMKGVTSTRIYERA
          FDEVTAD.R.VKSIITLDGGVLVQVQKWDG.STTIKRK.VDDKLVVECI.KGVTSTRIYERA
Retrocopy FDEVTADYRNVKSIITLDGGVLVQVQKWDGESTTIKRKQVDDKLVVECIRKGVTSTRIYERA

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	0.00 RPM
SRP017611_brain	0.00 RPM	0.00 RPM
SRP017611_kidney	0.00 RPM	8.25 RPM
SRP017611_liver	0.00 RPM	0.07 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_228 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_228 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_228 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000013564	1 retrocopy	retro_acar_190,
Canis familiaris	ENSCAFG00000019753	1 retrocopy	retro_cfam_1758,
Canis familiaris	ENSCAFG00000025410	3 retrocopies	retro_cfam_132, retro_cfam_137, retro_cfam_228 ,
Latimeria chalumnae	ENSLACG00000008511	3 retrocopies	retro_lcha_37, retro_lcha_45, retro_lcha_57,
Macaca mulatta	ENSMMUG00000010906	1 retrocopy	retro_mmul_1311,
Oryzias latipes	ENSORLG00000008282	1 retrocopy	retro_olat_7,