RetrogeneDB ID: retro_cfam_809

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 18:51083969..51084265(+)
• Located in intron of: ENSCAFG00000012965

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCAFG00000020317
• Aliases: LOC479974, SAMD1, SAMD13
• Description: None

Sequence

>retro_cfam_809
CTGAGCTCTGCACAGCAGGGAAAGCCTCCTGGTACCCGCCACTCAGGGAGTTCCATGAAGAATGGGAGGCCACTAGATCC
TGCAGACAAGACTGTGATGGATGTCAACTATTTCCAAACAGCAGGATTTGAGGAGCAAGGTAGTGCTTTTCAGGAATAGG
AAATTGATGGAAAATCCCTGCTATTGATGACAAGAAATGACATGTTGACAGGACTTCAGTTAAATGGGGTCCTGCTCTGA
ATATCTGTAAGTATCATGTAAAACCTCTACAGGCAAAACATTGAAACAACTCTTCA

Alignment

ORF - retro_cfam_809 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.31 %
• Parental protein coverage: 98.04 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LSVDMENKENGSVGVKNSMENGRPPDPADWAVMDVVNYFRTAGFEEQASAFQEQEIDGKSLLLMTRNDVL
          LS.....K..G......SM.NGRP.DPAD..VMDV.NYF.TAGFEEQ.SAFQE.EIDGKSLLLMTRND.L
Retrocopy LSSAQQGKPPGTRHSGSSMKNGRPLDPADKTVMDV-NYFQTAGFEEQGSAFQE*EIDGKSLLLMTRNDML

Parental  TGLQL-KLGPALKIYEYHVKPLQTKHLKNNS
          TGLQL.K.GPAL.I..YHVKPLQ.KH..N.S
Retrocopy TGLQL<KWGPALNICKYHVKPLQAKH*NNSS

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	2.35 RPM
SRP017611_brain	0.00 RPM	1.27 RPM
SRP017611_kidney	0.00 RPM	0.33 RPM
SRP017611_liver	0.00 RPM	0.29 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_809 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_809 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_809 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000005174	6 retrocopies	retro_cfam_155, retro_cfam_201, retro_cfam_2085, retro_cfam_2131, retro_cfam_527, retro_cfam_8,
Canis familiaris	ENSCAFG00000020317	1 retrocopy	retro_cfam_809 ,