RetrogeneDB ID: retro_cfam_2181

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: X:72438452..72439064(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000024749
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PDCD7
• Ensembl ID: ENSCAFG00000032076
• Aliases: None
• Description: programmed cell death 7 [Source:HGNC Symbol;Acc:8767]

Sequence

>retro_cfam_2181
CTAGAGGCGGTGTTCGGAACCCCTCGCGGGCAAGCTACCCTGTGCCTCCGCGCGTGCCCGCCGGGCCCAGGCTGGGCGAA
GTGCGCCGGTGGCTGCGAGAGGCTCTGCTCCTGGCGTGGCAGGGGCGTGGCCTGAGCCAGGCCCTGCGTGAGGCCGAGGT
GGATGGTGCGGCCTGGGTACTGCTACATGCCCAGCCAGCACCGCTGCGCACTGAATTGGTCGAGAGACTGCAGCTGCTGA
CCCAGGCCGCCTATGTGGATGAGGCGCGGGGGAGGCTGGAGAGGGTCCAGCGCCGCCGACTGCAGCTTAGCGAGAGGGTG
CTAGAACACGAGGCCGAGGCCGAGGCCAAGTGGAAAGCTGAGTGCGAGCAGGAGATTGACCTCTGGAGGGTCAAGTGCGT
TGCAGGAGGTGGAGAAGAAGCAGGAGCAGGAACTTAAAGCTGCTGCTGAAGGTGTCTTACCTGAAGTGAGGAAAAAGCAA
GGAAATACCAAAAGGATGGTGGACATTCTTCAGACCTTGGAGAAATTGAGGAAACTCAGGAAAGAGGCAGCAGCAAGGAA
AGGCGTCTGTCCTTCAGCTTCAGGGACTAAGAAAACTCATTTAAAAACTCTC

Alignment

ORF - retro_cfam_2181 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.41 %
• Parental protein coverage: 57.42 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LEAVVVTPR-RAGCPVPPRAPAGPSLGEVRARLRGALRLVRRLRDLGQALREAEADGAAWVLLHAQAAPL
          LEAV..TPR.RA..PVPPR.PAGP.LGEVR..LR.AL.L....R.L.QALREAE.DGAAWVLLHAQ.APL
Retrocopy LEAVFGTPR<RASYPVPPRVPAGPRLGEVRRWLREALLLAWQGRGLSQALREAEVDGAAWVLLHAQPAPL

Parental  RAELAERLQLLTQAAYVGEARRRLERVRRRRLRLRERARERDAEREAEAARAAEREQEIDLWRVKCV-QE
          R.EL.ERLQLLTQAAYV.EAR.RLERV.RRRL.L.ER..E..A..EAEA...AE.EQEIDLWRVKCV.QE
Retrocopy RTELVERLQLLTQAAYVDEARGRLERVQRRRLQLSERVLEHEA--EAEAKWKAECEQEIDLWRVKCV>QE

Parental  VEEKKREQELKAAADGVLSEVRKKQADTKRMVDILRALEKLRKLRKEAAARKGVCPPASADETFEHHLQR
          V.EKK.EQELKAAA.GVL.EVRKKQ..TKRMVDIL..LEKLRKLRKEAAARKGVCP.AS...T...HL..
Retrocopy V-EKKQEQELKAAAEGVLPEVRKKQGNTKRMVDILQTLEKLRKLRKEAAARKGVCPSASG--TKKTHLKT

Parental  L
          L
Retrocopy L

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	13.69 RPM
SRP017611_brain	0.00 RPM	12.94 RPM
SRP017611_kidney	0.00 RPM	5.68 RPM
SRP017611_liver	0.00 RPM	4.28 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_2181 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_2181 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_2181 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	ENSCAFG00000032076	1 retrocopy	retro_cfam_2181 ,
Choloepus hoffmanni	ENSCHOG00000007218	1 retrocopy	retro_chof_1625,
Rattus norvegicus	ENSRNOG00000014340	1 retrocopy	retro_rnor_443,