RetrogeneDB ID: retro_cfam_868

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 19:22809819..22810309(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000004335
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: ISOC2
• Ensembl ID: ENSCAFG00000002580
• Aliases: None
• Description: isochorismatase domain containing 2 [Source:HGNC Symbol;Acc:26278]

Sequence

>retro_cfam_868
ATGGCAACTGTGAGGTCCAACCTGGGCTGAGTCCTCCCTGGATCATCCATCCTGTTCCTGTGTGACATGCAGAAGCTCTG
CCAAATCGCATACTTTCCCCATATTGTCTCTGTGGCTGCCATGCTCAAGGTGGCCAGGCTGCTGGAGGTACCTACCAGCT
GTGCTGACAGAGCAGTACCCAGAAGTCCTGGGCCCCACAGGCCCCAAGCTGGGGGCTCAAGGCCTGCAGCCAGTAGCCAA
AACTTGCTTCAGCATGGTGCCTGCAGTGCAACGGGAGCTGGATACATGGCCCCAGCTGTGTTCTGTGCTCCTCTGTGGCA
TTGAGACACAGGCCTGCATCCTGAATACCACCCTGGACCTCTTGGACCGGGGGCTGCAGGTCCATGTGGTGGTGGACGGC
TGCTCTTCTCGAAGCCAGGTGGACAGGCTAGTAGCCCTGGCCAGGATGCGGCAGAGTAGCGCCTTCCTCTCCACCAGCAA
AGGGCTGATT

Alignment

ORF - retro_cfam_868 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.53 %
• Parental protein coverage: 80.39 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MATMRSNLGRVLPGSSILFLCDMQEKFRHIAYFPQIVSVAARMLKVARLLEVPAVLTEQ-YPEGLG-PTV
          MAT.RSNLG.VLPGSSILFLCDMQ.K...IAYFP.IVSVAA.MLKVARLLEVP........P...G.PT.
Retrocopy MATVRSNLG*VLPGSSILFLCDMQ-KLCQIAYFPHIVSVAA-MLKVARLLEVPTSCADRAVPRSPG>PTG

Parental  PELGAQGLRPVAKTCFSMVPAVQKELESRPQLCSVLLCGIETQACILNTTLDLLDRGLQVHVVVDGCSSR
          P.LGAQGL.PVAKTCFSMVPAVQ.EL...PQLCSVLLCGIETQACILNTTLDLLDRGLQVHVVVDGCSSR
Retrocopy PKLGAQGLQPVAKTCFSMVPAVQRELDTWPQLCSVLLCGIETQACILNTTLDLLDRGLQVHVVVDGCSSR

Parental  SQVDRLVALARMRQSGAFLSTSEGLI
          SQVDRLVALARMRQS.AFLSTS.GLI
Retrocopy SQVDRLVALARMRQSSAFLSTSKGLI

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	23.77 RPM
SRP017611_brain	0.00 RPM	17.70 RPM
SRP017611_kidney	0.00 RPM	34.60 RPM
SRP017611_liver	0.00 RPM	11.96 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_868 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_868 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_868 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	ENSCAFG00000002580	1 retrocopy	retro_cfam_868 ,