RetrogeneDB ID: retro_cfam_444

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 11:11514850..11515113(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCAFG00000014436
• Aliases: None
• Description: None

Sequence

>retro_cfam_444
AAACTGCCAATACCAATGGAAATCAATGCTGAAATAAAGCATCAGTTAAAAAGGGAAATTTGACAGTGTTGATGAAAATA
TGAAAGAATTTTCAAATTTCTTGAAGGAGTGAGCAGATCTCCAGAAATGTGGGAAAAAATTTCATACATGCCATAAAGGA
AGCAGCAAGATTTAAAAGCCAAGACTTAATAAGGCACCTGGAAAATACACTAGAAAAACTAGAATCTGACCTCTTTCTCA
ACAAAGATAATCACACCTCAAAT

Alignment

ORF - retro_cfam_444 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.81 %
• Parental protein coverage: 59.86 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KLPIPMVINMEIKEQLKKEIREFGGQHEKILKLLEGVQGPPELQRKF-VVYAMKQAVREQRQALIGHLQK
          KLPIPM.IN.EIK.QLK.EI.......E.I.K.LEGV...PE...K.....A.K.A.R...Q.LI.HL..
Retrocopy KLPIPMEINAEIKHQLKREI*QC**KYERIFKFLEGVSRSPEMWEKI<FIHAIKEAARFKSQDLIRHLEN

Parental  VLDKLELDHFLKKDIHTDN
          .L.KLE.D.FL.KD.HT.N
Retrocopy TLEKLESDLFLNKDNHTSN

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	0.04 RPM
SRP017611_brain	0.00 RPM	0.00 RPM
SRP017611_kidney	0.00 RPM	0.00 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_444 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_444 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_444 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000014436	2 retrocopies	retro_cfam_441, retro_cfam_444 ,
Callithrix jacchus	ENSCJAG00000004135	1 retrocopy	retro_cjac_1827,
Dipodomys ordii	ENSDORG00000008443	1 retrocopy	retro_dord_354,
Homo sapiens	ENSG00000242284	1 retrocopy	retro_hsap_3362,
Macaca mulatta	ENSMMUG00000021984	1 retrocopy	retro_mmul_2100,
Nomascus leucogenys	ENSNLEG00000002303	1 retrocopy	retro_nleu_961,
Pongo abelii	ENSPPYG00000020755	1 retrocopy	retro_pabe_2766,
Pan troglodytes	ENSPTRG00000041730	1 retrocopy	retro_ptro_2285,