RetrogeneDB ID: retro_cfam_2187

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: X:82846630..82847098(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NAGK
• Ensembl ID: ENSCAFG00000030475
• Aliases: None
• Description: N-acetylglucosamine kinase [Source:HGNC Symbol;Acc:17174]

Sequence

>retro_cfam_2187
TTCAACTATTTCCAGGTGCCAGATTGGCTAGGAATCCTCACCCACCTGTATAGGGACTTTGATAAATGCCGCTTTGCTGG
GTTTTGCCAGAAAATTGCAGAAGGTGCTCAGCAGGGAGATCCCCTTTGCCGGTTTATCTTCAGGAAGGCTGGGGAGATGC
TGGGCAGGCACGTGGCAGCAGTGCTGCGAGAGATTGACCCGGTCTTGTTCCAGGGGGAGCTGGGCCTCCCTATCCTGTGT
GTGGGCTCTGTGTGGAAGAGCTGGGAGCTGCTGAGGGAAGGTTTCCTTCTGGCACTGACCCAGGGCCGAGAGATCCAGGC
CTAGAACTCCTTCTCCAGCTTCACCCTGATGAAGCTGCAACACTCATCTGCCCTGGGTGGGGCCAGCCTCGGGGCCAGAC
ACATCGGGCACCTCCTCCCCATGGACTACACTGCCAATGCCGTTGCCTTCTACTCCCACACCTTCTCC

Alignment

ORF - retro_cfam_2187 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.87 %
• Parental protein coverage: 57.99 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  YSVSQVPDRLGILTHLYRDFDKCRFAGFCQKIAEGAQQGDPLCRFIFRKAGEMLGRHVVAVLPEIDPVLF
          ....QVPD.LGILTHLYRDFDKCRFAGFCQKIAEGAQQGDPLCRFIFRKAGEMLGRHV.AVL.EIDPVLF
Retrocopy FNYFQVPDWLGILTHLYRDFDKCRFAGFCQKIAEGAQQGDPLCRFIFRKAGEMLGRHVAAVLREIDPVLF

Parental  QGELGLPILCVGSVWKSWELLREGFLLALTQGREIQAQNSFSSFTLMKLQHSSALGGASLGARHIGHLLP
          QGELGLPILCVGSVWKSWELLREGFLLALTQGREIQA.NSFSSFTLMKLQHSSALGGASLGARHIGHLLP
Retrocopy QGELGLPILCVGSVWKSWELLREGFLLALTQGREIQA*NSFSSFTLMKLQHSSALGGASLGARHIGHLLP

Parental  MDYTANAVAFYSHTFS
          MDYTANAVAFYSHTFS
Retrocopy MDYTANAVAFYSHTFS

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	0.55 RPM	10.21 RPM
SRP017611_brain	0.16 RPM	5.72 RPM
SRP017611_kidney	1.45 RPM	19.08 RPM
SRP017611_liver	0.29 RPM	8.92 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_2187 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_2187 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_2187 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000030475	1 retrocopy	retro_cfam_2187 ,
Tursiops truncatus	ENSTTRG00000012259	1 retrocopy	retro_ttru_1330,