RetrogeneDB ID: retro_cfam_475

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 12:1002310..1002553(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DDA1
• Ensembl ID: ENSCAFG00000031251
• Aliases: None
• Description: DET1 and DDB1 associated 1 [Source:HGNC Symbol;Acc:28360]

Sequence

>retro_cfam_475
TTTTTGAAAGGACTGCCTGTCTACAACAAAAGCAATTTTAGTCAATTTCGTGCTGACTCTGTGTGCAAAGCTTCGAACCG
GCGTCCTTCAGTCTACCTGCCCACCTGGGAGTACCCATCTGAACAGATCATTGTGACAGAAAAGACAAACATCCTTTTGC
GCTACCTACATCAGCAATAGGACAAAAAGAACACCGCCAAGAAGAGAGACCAGAAGCAAGTGGACCTTGAGGGTGAGAAC
TCT

Alignment

ORF - retro_cfam_475 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.36 %
• Parental protein coverage: 80.2 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  FLKGLPVYNKSNFSRFHADSVCKASNRRPSVYLPTREYPSEQIIVTEKTNILLRYLHQQWDKKNAAKKRD
          FLKGLPVYNKSNFS.F.ADSVCKASNRRPSVYLPT.EYPSEQIIVTEKTNILLRYLHQQ.DKKN.AKKRD
Retrocopy FLKGLPVYNKSNFSQFRADSVCKASNRRPSVYLPTWEYPSEQIIVTEKTNILLRYLHQQ*DKKNTAKKRD

Parental  QEQVDLEGESS
          Q.QVDLEGE.S
Retrocopy QKQVDLEGENS

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	0.04 RPM	17.22 RPM
SRP017611_brain	0.08 RPM	15.01 RPM
SRP017611_kidney	0.07 RPM	8.39 RPM
SRP017611_liver	0.00 RPM	5.95 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_475 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_475 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_475 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000017068	3 retrocopies	retro_btau_1152, retro_btau_536, retro_btau_74,
Canis familiaris	ENSCAFG00000031251	3 retrocopies	retro_cfam_1089, retro_cfam_2033, retro_cfam_475 ,
Cavia porcellus	ENSCPOG00000006944	1 retrocopy	retro_cpor_435,
Felis catus	ENSFCAG00000001001	1 retrocopy	retro_fcat_487,
Homo sapiens	ENSG00000130311	1 retrocopy	retro_hsap_1409,
Gorilla gorilla	ENSGGOG00000005802	1 retrocopy	retro_ggor_1093,
Microcebus murinus	ENSMICG00000001763	1 retrocopy	retro_mmur_1162,
Myotis lucifugus	ENSMLUG00000003990	1 retrocopy	retro_mluc_1014,
Macaca mulatta	ENSMMUG00000016231	1 retrocopy	retro_mmul_2248,
Nomascus leucogenys	ENSNLEG00000005738	2 retrocopies	retro_nleu_1427, retro_nleu_1428,
Otolemur garnettii	ENSOGAG00000003701	1 retrocopy	retro_ogar_2375,
Pongo abelii	ENSPPYG00000009710	2 retrocopies	retro_pabe_1167, retro_pabe_1214,
Pan troglodytes	ENSPTRG00000010668	1 retrocopy	retro_ptro_966,
Rattus norvegicus	ENSRNOG00000039417	1 retrocopy	retro_rnor_1511,