RetrogeneDB ID: retro_cfam_1372

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 3:32485194..32485452(-)
• Located in intron of: ENSCAFG00000009908

Retrocopy information

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

Parental gene information

• Parental gene symbol: ATP5D
• Ensembl ID: ENSCAFG00000019536
• Aliases: None
• Description: ATP synthase, H+ transporting, mitochondrial F1 complex, delta subunit [Source:HGNC Symbol;Acc:837]

Sequence

>retro_cfam_1372
GGGCTGGTGGTTGTCCACGCCGAGGACGGCACCATCTCCAAATACTTCGTGAGCAGTGGCTCAGTCATGGTGAACGCTGA
TTCCTCAGTGCAGTTGCTGGCTGAAGAGGCTGTGACACTAGACATGCTGGACGTGGGGGCAGCCAAGATGAATCTGGAGA
AGGCGCATTCGGAGCTGTCAGGGGCAGCGAAAGAGGCTTCCAGGGCTGAGATCCAAATCCGCATCGAGGCCAATGAGTCC
CTGGTGAAAGCTCTCGAG

Alignment

ORF - retro_cfam_1372 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.35 %
• Parental protein coverage: 51.19 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GLVVVHAEDGTISKYFVSSGSVTVNADSSVQLLAEEAVTLDMLDVGAAKMNLEKAQSELSGAADEASRAE
          GLVVVHAEDGTISKYFVSSGSV.VNADSSVQLLAEEAVTLDMLDVGAAKMNLEKA.SELSGAA.EASRAE
Retrocopy GLVVVHAEDGTISKYFVSSGSVMVNADSSVQLLAEEAVTLDMLDVGAAKMNLEKAHSELSGAAKEASRAE

Parental  IQIRIEANEALVKALE
          IQIRIEANE.LVKALE
Retrocopy IQIRIEANESLVKALE

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	169.21 RPM
SRP017611_brain	0.16 RPM	94.00 RPM
SRP017611_kidney	0.13 RPM	254.38 RPM
SRP017611_liver	0.00 RPM	89.99 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1372 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1372 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1372 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000002168	1 retrocopy	retro_acar_96,
Canis familiaris	ENSCAFG00000019536	1 retrocopy	retro_cfam_1372 ,
Myotis lucifugus	ENSMLUG00000015004	1 retrocopy	retro_mluc_2544,
Monodelphis domestica	ENSMODG00000005314	1 retrocopy	retro_mdom_1079,