RetrogeneDB ID: retro_cfam_1835

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 7:9749431..9749846(+)
• Located in intron of: ENSCAFG00000012107

Retrocopy information

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

Parental gene information

• Parental gene symbol: GOLT1B
• Ensembl ID: ENSCAFG00000012256
• Aliases: None
• Description: golgi transport 1B [Source:HGNC Symbol;Acc:20175]

Sequence

>retro_cfam_1835
ATGATCTTCTTAATGGACACCCAGAAAATTGGAATGGGATTAACAGAATATGGAGTGTCTTTCCTGTCCTTTGGAGTGAT
TTTCTTATTTGACAAAGCACTGCTGGCTATTGGAAATGTTTGATTTGTAGCTGGCTTGGCTTTTGTAATTGGTTTACAAA
GAACATTCAGATTCTTCTTCCAGAAACCTAAAATGAAAGTTACAGGGTTTTTCTTGGGTGGTGTATTTGTAGTCCTTGTT
GGTTGGCCTTTGATAGGCATAATCTTAGAAATTTATGGATTCTTTATTATGTTTAAGGGCTTCTTTTTATATGGTCATTG
GTGTTATAGGAAGAGTCCCAGTCTTTGGGTTCCTCTTGAATCTATTTGGAATTAGATCATTTGTAGATAAAGTTGGAGAA
AGCAACATTATGGTA

Alignment

ORF - retro_cfam_1835 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.86 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MISLTDTQKIGMGLTGFGVFFLFFGMILFFDKALLAIGNVLFVAGLAFVIGLERTFRFFFQKHKMKATGF
          MI.L.DTQKIGMGLT..GV.FL.FG.I..FDKALLAIGNV.FVAGLAFVIGL.RTFRFFFQK.KMK.TGF
Retrocopy MIFLMDTQKIGMGLTEYGVSFLSFGVIFLFDKALLAIGNV*FVAGLAFVIGLQRTFRFFFQKPKMKVTGF

Parental  FLGGVFVVLIGWPLIGMIFEIYGFFLLFRGF-FPVVIGFIRRVPVLGSLLNLPGIRSFVDKVGESNNMV
          FLGGVFVVL.GWPLIG.I.EIYGFF..F.GF.F..VIG.I.RVPV.G.LLNL.GIRSFVDKVGESN.MV
Retrocopy FLGGVFVVLVGWPLIGIILEIYGFFIMFKGF>FYMVIGVIGRVPVFGFLLNLFGIRSFVDKVGESNIMV

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	16.55 RPM
SRP017611_brain	0.00 RPM	18.02 RPM
SRP017611_kidney	0.00 RPM	26.61 RPM
SRP017611_liver	0.00 RPM	5.15 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1835 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1835 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1835 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016231	1 retrocopy	retro_amel_604,
Canis familiaris	ENSCAFG00000012256	1 retrocopy	retro_cfam_1835 ,
Dasypus novemcinctus	ENSDNOG00000013576	2 retrocopies	retro_dnov_158, retro_dnov_1730,
Felis catus	ENSFCAG00000028655	1 retrocopy	retro_fcat_1782,
Oryctolagus cuniculus	ENSOCUG00000008797	1 retrocopy	retro_ocun_1706,
Otolemur garnettii	ENSOGAG00000004756	1 retrocopy	retro_ogar_3234,
Ictidomys tridecemlineatus	ENSSTOG00000006352	1 retrocopy	retro_itri_1786,