RetrogeneDB ID: retro_cfam_842

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 19:18833983..18834600(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SCCPDH
• Ensembl ID: ENSCAFG00000015884
• Aliases: None
• Description: saccharopine dehydrogenase (putative) [Source:HGNC Symbol;Acc:24275]

Sequence

>retro_cfam_842
ATTGTTGGTCCAAAATTGAAAAGAAGGTGGCCAATTTTTTACCGCAGAGAACTGAATAGCTATTCTATTCCTTTCTTGGG
AGCAGATGTCTCTGTTGTGAGGCGGACTCAGCGTTACTTGCATGAGAATTTGGAGCAATCGCCTGTTCAGTGAGCCGCTT
ACTGACTGTGGGAGGCATCACCTCCGTTATTAAGCTGATGTTTGCAGGACTTTTCTTTTTATTCTTTGTGAAGTGTGGCA
TTGGCAGGCAGCTTCTCATAAAATTTCCATGGCTCTTCTCCTTTGGTTATTTTTCAAAACAAGGTCCAACACAAAAACAG
ATGGATGCCGCCTCGTTTACAATGACATTCTTTGGTCAAGGATACAGTCAAGGCTTTGGTCTGGAGAAGAACAAACCAAA
TATGAGAATTTGTACTCAGGTGAAAGGACCAGAGGCTGGCTACGTGGCTACCCCCATAGCCATGGTCCAGGCAGCCATGA
CCCTTCTAAACGATACCTCTGATCTTCCTAACAGGGGCGGGGTCTTCACACCTGGAGCAGCCTTCTGCAGAACAAAGTTG
ATTGACAGACTCAATCAACCTGGCATTGAATTTAGTGTCATTAGCAGCTCTGAAGTC

Alignment

ORF - retro_cfam_842 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.14 %
• Parental protein coverage: 53.51 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  IVGPKLKRRWPISYCRELNSYSIPFLGADVSVVRRTQRYLHENLEQSPVQYAAY-VTVGGITSVIKLMFA
          IVGPKLKRRWPI.Y.RELNSYSIPFLGADVSVVRRTQRYLHENLEQSPVQ.AAY..TVGGITSVIKLMFA
Retrocopy IVGPKLKRRWPIFYRRELNSYSIPFLGADVSVVRRTQRYLHENLEQSPVQ*AAY<LTVGGITSVIKLMFA

Parental  GLFFLFFVKCGIGRQLLIKFPWLFSFGYFSKQGPTQKQMDAASFTMTFFGQGYSQGFGPEKNKPNMRICT
          GLFFLFFVKCGIGRQLLIKFPWLFSFGYFSKQGPTQKQMDAASFTMTFFGQGYSQGFG.EKNKPNMRICT
Retrocopy GLFFLFFVKCGIGRQLLIKFPWLFSFGYFSKQGPTQKQMDAASFTMTFFGQGYSQGFGLEKNKPNMRICT

Parental  QVKGPEAGYVATPIAMVQAAMTLLNDTSDLPNTGGVFTPGAAFCRTKLIDRLNQRGIEFSVISSSEV
          QVKGPEAGYVATPIAMVQAAMTLLNDTSDLPN.GGVFTPGAAFCRTKLIDRLNQ.GIEFSVISSSEV
Retrocopy QVKGPEAGYVATPIAMVQAAMTLLNDTSDLPNRGGVFTPGAAFCRTKLIDRLNQPGIEFSVISSSEV

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	0.13 RPM	55.86 RPM
SRP017611_brain	0.08 RPM	59.94 RPM
SRP017611_kidney	70.79 RPM	164.96 RPM
SRP017611_liver	0.15 RPM	58.45 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_842 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_842 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_842 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	ENSCAFG00000015884	1 retrocopy	retro_cfam_842 ,
Dasypus novemcinctus	ENSDNOG00000016354	1 retrocopy	retro_dnov_1482,
Monodelphis domestica	ENSMODG00000006356	1 retrocopy	retro_mdom_553,