RetrogeneDB ID: retro_cfam_1516

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 33:1481777..1482573(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ACD
• Ensembl ID: ENSCAFG00000020352
• Aliases: None
• Description: adrenocortical dysplasia homolog (mouse) [Source:HGNC Symbol;Acc:25070]

Sequence

>retro_cfam_1516
TCCATTCTGATGTTGACAGGCCCTTGCACAGCGCCCCCCACTCACCCGCTGGGCCTCCACCCGCTATAGGGCTGCGGGAG
AAGCTGTGTACACTGTCCCCAGCTCCTGGCTGCACATCTCGGAGAATGACCAGCGAGTTCTGAGCTCTCTGGGCCCAGGC
CCCAGGGCCCAGGCTCCAGAGCTGCCCCCACCAGACCCAGCTTTGCAGGACCTATCGCTGACTATCATCTCTCCTTCCTC
ACCTACTTCCTCAGGAACCCCAGCTTTACCCAGCCACGTGTCCTCAGAGGAAAGTGGTGCCAGCATCAGCCTTCTGCCTG
CCCTGTCCTTGGCAGCTTCAGACCTAGTGCAGAAGAGCAGCTCCCAGGCTGTACCAGCCATCTGTTCAGCCCATGGCCCC
CTGCCCCCTGGCTCCCCACACTCTAACCCTGTACCCAGTTCCCCACTCCTGAGCTGCACCCCAAGTCTGTCATCCCTTGG
CCATGTATCCAGCCCACATCAGGCCACTGTGACCAAGGCCCAGAAACCCAGCCTGGAGTTCAAGGAGCTAGGGTTGCCCC
TCAAGAACTGGCATCACTCTCCAAGGACAAAAAACGCCACAGGAGCCCTGGAATCCAGTCCCGTTTGGGACCCTCCAAAG
AGGCATCGTGATGGTTCCGCCTTCCAGTATGAGTACGAGCCACCCTGCACCTCCCTGTGTGCCCAAGTCCAAGCTGTCAG
GCTTCCTCCCCAGCTCGTGGCCTGGGCCTTGCACTTTCTGATGGAGCCACAGCCGGAGTCTGAGCTAACCCAGGTG

Alignment

ORF - retro_cfam_1516 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.35 %
• Parental protein coverage: 50.96 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SCLMLTGPCTAPP-LTRWASTRCRATGEAVYTVPSSWLHISENDQRVLSSLGPGSRTQAPELPPPDPALQ
          S.LMLTGPCTAPP.LTRWASTR.RA.GEAVYTVPSSWLHISENDQRVLSS...........LPPPDPALQ
Retrocopy SILMLTGPCTAPP>LTRWASTRYRAAGEAVYTVPSSWLHISENDQRVLSSXXXXXXXXXXXLPPPDPALQ

Parental  DLSLTIVSPSSPTSSGTPALPSHVSSEENGASISLLPALSLAASDLVQKGSSQAVPAICSAHGPLPPGSP
          DLSLTI.SPSSPTSSGTPALPSHVSSEE.GASISLLPALSLAASDLVQK.SSQAVPAICSAHGPLPPGSP
Retrocopy DLSLTIISPSSPTSSGTPALPSHVSSEESGASISLLPALSLAASDLVQKSSSQAVPAICSAHGPLPPGSP

Parental  HSNPVPSSPLLSCTPSLSPLGHVPSPHQAIVTKAQKPSLEFKELGLPLKNWHQSPRTKNATGALESSPVW
          HSNPVPSSPLLSCTPSLS.LGHV.SPHQA.VTKAQKPSLEFKELGLPLKNWH.SPRTKNATGALESSPVW
Retrocopy HSNPVPSSPLLSCTPSLSSLGHVSSPHQATVTKAQKPSLEFKELGLPLKNWHHSPRTKNATGALESSPVW

Parental  DPPKRHRDGSAFQYEYEPPCTSLCAQVQAVKLPPQLVAWALHFLMEPQPESELTQV
          DPPKRHRDGSAFQYEYEPPCTSLCAQVQAV.LPPQLVAWALHFLMEPQPESELTQV
Retrocopy DPPKRHRDGSAFQYEYEPPCTSLCAQVQAVRLPPQLVAWALHFLMEPQPESELTQV

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	1.34 RPM	27.47 RPM
SRP017611_brain	0.16 RPM	11.27 RPM
SRP017611_kidney	0.13 RPM	7.86 RPM
SRP017611_liver	0.07 RPM	5.22 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1516 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1516 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1516 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000020352	1 retrocopy	retro_cfam_1516 ,