RetrogeneDB ID: retro_fcat_452

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: A3:115092426..115092733(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSFCAG00000031083
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SNCA
• Ensembl ID: ENSFCAG00000011488
• Aliases: None
• Description: synuclein, alpha (non A4 component of amyloid precursor) [Source:HGNC Symbol;Acc:11138]

Sequence

>retro_fcat_452
ATGGATGTATTCATGAAAGGACTTTCAAAGGCCAAGGAGGAAGTCGTGGCTGCTGCTGAAAAAACCAAACAGGGTGTGGC
AGAAGCTGCAGGAAAGACAAAAGAGGGTGTTTTCTACGTAGGCTCCAAAACCAAGGAAGGAGCGGTTCATGATGTGACAA
CAGTGGCTGAGAAGACCAAAGAGCAAGTGACAAATGTTGGTGAGGTGGTGATGACCGGTGATGACAGCAGTCACACAAAA
GACAGTGGAGGGAGCAGGGAGCATCGCAGCTGCCACTGGCTTTGGCAAAAAGGATCAGTTGGGCAAG

Alignment

ORF - retro_fcat_452 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.26 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MDVFMKGLSKAKEGVVAAAEKTKQGVAEAAGKTKEGVLYVGSKTKEGVVHGVTTVAEKTKEQVTNVGEAV
          MDVFMKGLSKAKE.VVAAAEKTKQGVAEAAGKTKEGV.YVGSKTKEG.VH.VTTVAEKTKEQVTNVGE.V
Retrocopy MDVFMKGLSKAKEEVVAAAEKTKQGVAEAAGKTKEGVFYVGSKTKEGAVHDVTTVAEKTKEQVTNVGEVV

Parental  VTG-VTAVAQKTVEGAGSIAAATGFGKKDQLGK
          .TG..TAV.QKTVEGAGSIAAATGFGKKDQLGK
Retrocopy MTG>MTAVTQKTVEGAGSIAAATGFGKKDQLGK

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
SRP017611_brain	9.53 RPM	70.36 RPM
SRP017611_kidney	0.00 RPM	0.00 RPM
SRP017611_liver	0.00 RPM	0.20 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_452 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_452 was not experimentally validated.

Homology

Retrocopy orthology:

Felis catus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000007186	1 retrocopy	retro_chof_92,
Felis catus	ENSFCAG00000011488	1 retrocopy	retro_fcat_452 ,
Microcebus murinus	ENSMICG00000005634	1 retrocopy	retro_mmur_272,
Oryctolagus cuniculus	ENSOCUG00000023825	1 retrocopy	retro_ocun_422,