RetrogeneDB ID: retro_cfam_744

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 16:59368793..59369487(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ADA
• Ensembl ID: ENSCAFG00000009498
• Aliases: ADA, ADA-like
• Description: adenosine deaminase [Source:HGNC Symbol;Acc:186]

Sequence

>retro_cfam_744
GAGGTGGTGGCCCTGGTGAGCCAGAGCCTGCAGGAGGGAGAACGGGACTTCAAGGTGAAAGTGAGGTCCATCCTGTGCCA
CCTGCGCCACCAGCCCAGTTGGCCCCTGGAGGTGGTGGAGCTGTGTCCGAAGTACCAGCAGACTGTGGTGGCCATCGACC
TGGCAGGAGACGAGACCATTAAAGGGAGCAGTGTCTTCCTGGGACACGTGAAGGGCTACCAGGAGGCTGTGAGGAGAGGC
ATCCACCGCACTGTGCATGCAGGGGAGTGGGCTCAGCGGAGGTGGTCAAAGAGGCTGTGGACATGCTCAAGACGGAGAGG
CTGGGCCATGGCTACCACACGCTGCAGGACGAGGCCCTTTATGACAGGCTGCAGCAGGAAAACATGCACTTCGAGATCTG
CCCCTGGTCCCGTTACCTCACAGGCCCCTGGAACTCGGACACGGAGCATGCAGTGGTTCGGCTCAAACATGACCAGGCTA
CCTACTCCCTCAACACGGATGACCCACTCATCTTCAAGTACACCCTGGAACGGATTACCAGATGCCCAAAGAGGGCATGG
ACTTTGCCGAGGAGGAGTTTAAGAGACTGAACATCAATGCGGCAAAGTTTAGTTTCCTCCCAGAAGATGAAAAGAAGCAG
CTTCTTGATCTGCTCTCTAAAGCCTATGGGATGTCATCTTTGGATGCTTCAGGG

Alignment

ORF - retro_cfam_744 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.03 %
• Parental protein coverage: 64.09 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  EVVALVSQSLQEGERDFKVKVRSILCCLRHQPSEYTEVVELCQKYQQTVVAIDLAGDETIKGSSLFPGHV
          EVVALVSQSLQEGERDFKVKVRSILC.LRHQPS...EVVELC.KYQQTVVAIDLAGDETIKGSS.F.GHV
Retrocopy EVVALVSQSLQEGERDFKVKVRSILCHLRHQPSWPLEVVELCPKYQQTVVAIDLAGDETIKGSSVFLGHV

Parental  KAYEEAVRRGIHRTVHAGE-VGSAEVVKEAVDTLKTERLGHGYHTLEDEALYARLRQENMHFEICPWSSY
          K.Y.EAVRRGIHRTVHAGE.VGSAEVVKEAVD.LKTERLGHGYHTL.DEALY.RL.QENMHFEICPWS.Y
Retrocopy KGYQEAVRRGIHRTVHAGE<VGSAEVVKEAVDMLKTERLGHGYHTLQDEALYDRLQQENMHFEICPWSRY

Parental  LTGAWKSDTEHAVVRLKNDQANYSLNTDDPLIFKSTLE-TDYQMTKQGMDFTEEEFKRLNINAAKSSFLP
          LTG.W.SDTEHAVVRLK.DQA.YSLNTDDPLIFK.TLE.TDYQM.K.GMDF.EEEFKRLNINAAK.SFLP
Retrocopy LTGPWNSDTEHAVVRLKHDQATYSLNTDDPLIFKYTLE<TDYQMPKEGMDFAEEEFKRLNINAAKFSFLP

Parental  EDEKKQLLDLLYKAYGMPSLDAAG
          EDEKKQLLDLL.KAYGM.SLDA.G
Retrocopy EDEKKQLLDLLSKAYGMSSLDASG

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	1.64 RPM
SRP017611_brain	0.00 RPM	4.76 RPM
SRP017611_kidney	0.00 RPM	8.92 RPM
SRP017611_liver	0.00 RPM	14.94 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_744 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_744 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_744 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000009498	1 retrocopy	retro_cfam_744 ,
Macaca mulatta	ENSMMUG00000010603	1 retrocopy	retro_mmul_382,
Monodelphis domestica	ENSMODG00000016207	1 retrocopy	retro_mdom_1365,