RetrogeneDB ID: retro_cfam_2050

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: X:29183320..29183782(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000013780
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: NPC2
• Ensembl ID: ENSCAFG00000016932
• Aliases: NPC2, CE1
• Description: Canis lupus familiaris Niemann-Pick disease, type C2 (NPC2), mRNA. [Source:RefSeq mRNA;Acc:NM_001003242]

Sequence

>retro_cfam_2050
ACCTGCCTAGCCGCGATGCGTCTCTTGGTCGCCGCGTTCCTGCTCCTGGCGCTCGGCGCCTCGGCCCTGGCGGAGCCCGT
GCATTTCAAGGACGGTGGTTCTGCAGTTGGAGTTATAAAAGAACTGAATGTGAACCCATGCCCTACCCAGCCTTGCAAAC
TGCACAAAGGCCAATCTTACAGTGTCAATGTCACCTTCACCAGTAATATTCCATCTCAAAGTAGCAAAGCCGTGGTGCAT
GGCATCGTGTTGGGCGTCGCAGTTCCCTTTCCCATTCCTGAGGCTGATGGTTGTAAGAGTGGAATCAACTGCCCCATCCA
GAAAGATAAGACCTACAGCTACCTGAACAAACTGCCAGTGAAGAACGAATACCCCTCTATAAAACTGGTGGTGCAGTGGA
TGCTTCTGGGCGACAACAATCAACATCTCTTCTGCTGGGAAATCCCAGTTCAGATTGAAGGC

Alignment

ORF - retro_cfam_2050 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.7 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TCLAAMRLLVAAFLLLALGASALAEPVHFKDCGSAVGVIKELNVNPCPAQPCKLHKGQSYSVNVTFTSNI
          TCLAAMRLLVAAFLLLALGASALAEPVHFKD.GSAVGVIKELNVNPCP.QPCKLHKGQSYSVNVTFTSNI
Retrocopy TCLAAMRLLVAAFLLLALGASALAEPVHFKDGGSAVGVIKELNVNPCPTQPCKLHKGQSYSVNVTFTSNI

Parental  PSQSSKAVVHGIVLGVAVPFPIPEADGCKSGINCPIQKDKTYSYLNKLPVKNEYPSIKLVVQWMLLGDNN
          PSQSSKAVVHGIVLGVAVPFPIPEADGCKSGINCPIQKDKTYSYLNKLPVKNEYPSIKLVVQWMLLGDNN
Retrocopy PSQSSKAVVHGIVLGVAVPFPIPEADGCKSGINCPIQKDKTYSYLNKLPVKNEYPSIKLVVQWMLLGDNN

Parental  QHLFCWEIPVQIEG
          QHLFCWEIPVQIEG
Retrocopy QHLFCWEIPVQIEG

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	0.13 RPM	54.51 RPM
SRP017611_brain	0.08 RPM	18.82 RPM
SRP017611_kidney	0.99 RPM	594.33 RPM
SRP017611_liver	0.00 RPM	27.34 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_2050 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_2050 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_2050 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000016932	1 retrocopy	retro_cfam_2050 ,
Choloepus hoffmanni	ENSCHOG00000009488	1 retrocopy	retro_chof_2335,
Echinops telfairi	ENSETEG00000003719	2 retrocopies	retro_etel_1610, retro_etel_1866,
Loxodonta africana	ENSLAFG00000002876	1 retrocopy	retro_lafr_289,
Tursiops truncatus	ENSTTRG00000013025	1 retrocopy	retro_ttru_85,