RetrogeneDB ID: retro_fcat_604

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: B1:24843551..24844018(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSFCAG00000026266
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: UFD1L
• Ensembl ID: ENSFCAG00000004294
• Aliases: None
• Description: ubiquitin fusion degradation 1 like (yeast) [Source:HGNC Symbol;Acc:12520]

Sequence

>retro_fcat_604
GCCTGCCTGACCACAGGGGACGTGGTTGCCGTCAACTACAATGAGATTTATGAACTGCGGGTGATGGAGACCAAGCCTGA
CAAAGCCGTGCCCATTATTGGGTGTGACGTGAACCTAGAGCTCGATACCCCACGGGGCTACAAGGAGCCCGAAAGACAGT
TCGGGAGGAGGAGCCCACCGAAAGGCGAAGCTGACCACAGCGACTATGCTGGAGAGCTGGGCTTCGGTGCCTTCTCCGGC
TCTCGAAAGAGACCGGACAGGAAGAAGAAAGGTGTAGGGCCCAGTCCCTCCCCAGTCAAGCCTGGAAACACTAGAACGGG
AATCCCCACTTATGAATTTAAACTTGGTAAGATCACTTTCATCAGAAATTCACATCCACTGTCAGAAAGGTCCAAGCGGA
TGAAGCTGGAGGCAGATTCGTCGCCTTCTCTGGAGAAGGACAGTCGTTGTGTAAAAAGGGAAGAAAG

Alignment

ORF - retro_fcat_604 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.95 %
• Parental protein coverage: 51.14 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ACLTTGDVIAINYNEKIYELRVMETKPDKAVSIIECDMNVDFDAPLGYKEPERQVQHEESAEGEADHSGY
          ACLTTGDV.A.NYNE.IYELRVMETKPDKAV.II.CD.N...D.P.GYKEPERQ........GEADHS.Y
Retrocopy ACLTTGDVVAVNYNE-IYELRVMETKPDKAVPIIGCDVNLELDTPRGYKEPERQFGRRSPPKGEADHSDY

Parental  AGELGFRAFSGSGNRLDGKKKGVEPSPSPIKPGDIKRGIPNYEFKLGKITFIRNSRPL-VKKVEEDEAGG
          AGELGF.AFSGS..R.D.KKKGV.PSPSP.KPG....GIP.YEFKLGKITFIRNS.PL.V.KV..DEAGG
Retrocopy AGELGFGAFSGSRKRPDRKKKGVGPSPSPVKPGNTRTGIPTYEFKLGKITFIRNSHPL<VRKVQADEAGG

Parental  RFVAFSGEGQSLRKKGRK
          RFVAFSGEGQSL.KKGRK
Retrocopy RFVAFSGEGQSLCKKGRK

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	0.00 RPM	13.20 RPM
SRP017611_kidney	0.00 RPM	17.52 RPM
SRP017611_liver	0.00 RPM	43.37 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_604 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_604 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.

---

Parental genes homology:

Parental genes homology involve 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Felis catus	ENSFCAG00000004294	1 retrocopy	retro_fcat_604 ,
Homo sapiens	ENSG00000070010	1 retrocopy	retro_hsap_1929,
Gorilla gorilla	ENSGGOG00000004104	1 retrocopy	retro_ggor_175,
Myotis lucifugus	ENSMLUG00000002466	1 retrocopy	retro_mluc_1244,
Macaca mulatta	ENSMMUG00000031106	1 retrocopy	retro_mmul_1347,
Pongo abelii	ENSPPYG00000011580	1 retrocopy	retro_pabe_1593,
Pteropus vampyrus	ENSPVAG00000006417	1 retrocopy	retro_pvam_1349,