RetrogeneDB ID: retro_fcat_1321

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: C2:13342010..13342368(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: UCHL1
• Ensembl ID: ENSFCAG00000025457
• Aliases: None
• Description: ubiquitin carboxyl-terminal esterase L1 (ubiquitin thiolesterase) [Source:HGNC Symbol;Acc:12513]

Sequence

>retro_fcat_1321
AAGATGCAGCTCAAACTGCTGGAGATTAACCTTGAGATGCTGAACAAAGTGCTGGCCTGGCTGGGGGTCGCCGGCCAGGG
GCGCTTCGAGGACGTGCTGGGGCTGGAGGCGGCTCTGGGCTTGGGACCAGTGCCTGACTGAGCACTGCTGCTTCTGCTGC
TGCTGTTTCCCCTCACGGCCCAGCAGGAGACCTTGAGGAAGAAAACAGACTGGAGACCAGAAGGGAAGAGAAGTCAGTCC
TAAGGAGCACTTCATGAAGCGGACCATCGGGAACTTGCGAGGTACCACTGGACTTACACAGGCGGTGGCCAGTAACCAAG
ACAAACTGGAGTGTGAGGACAGATTCTTTCTGAAACAG

Alignment

ORF - retro_fcat_1321 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.64 %
• Parental protein coverage: 50.88 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KMQLKPMEINPEV--SVRSRLGVAGQWRFADVLGLEEEALGSVPAPACA---LLLLFPLTAQHENFRKK-
          KMQLK..EIN.E....V...LGVAGQ.RF.DVLGLE..ALG..P.P..A...LLLLFPLTAQ.E..RKK.
Retrocopy KMQLKLLEINLEMLNKVLAWLGVAGQGRFEDVLGLEA-ALGLGPVPD*ALLLLLLLFPLTAQQETLRKK>

Parental  QIEELKGQEVSPKVYFMKQTIGNSCGTIGLIHAVANNQDKLEFEDGSVLKQ
          Q....KG.EVSPK..FMK.TIGN..GT.GL..AVA.NQDKLE.ED...LKQ
Retrocopy QTGDQKGREVSPKEHFMKRTIGNLRGTTGLTQAVASNQDKLECEDRFFLKQ

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	301.97 RPM
SRP017611_kidney	0.00 RPM	10.82 RPM
SRP017611_liver	0.10 RPM	0.10 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_1321 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_1321 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 9 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000003295	1 retrocopy	retro_chof_1737,
Callithrix jacchus	ENSCJAG00000019346	1 retrocopy	retro_cjac_365,
Echinops telfairi	ENSETEG00000012347	1 retrocopy	retro_etel_44,
Felis catus	ENSFCAG00000025457	1 retrocopy	retro_fcat_1321 ,
Macropus eugenii	ENSMEUG00000013774	1 retrocopy	retro_meug_8,
Oryctolagus cuniculus	ENSOCUG00000001353	1 retrocopy	retro_ocun_309,
Ictidomys tridecemlineatus	ENSSTOG00000015507	1 retrocopy	retro_itri_288,
Tupaia belangeri	ENSTBEG00000011438	1 retrocopy	retro_tbel_306,
Tursiops truncatus	ENSTTRG00000012095	1 retrocopy	retro_ttru_1370,