RetrogeneDB ID: retro_fcat_2014

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: X:102288941..102289449(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPS25
• Ensembl ID: ENSFCAG00000027687
• Aliases: None
• Description: mitochondrial ribosomal protein S25 [Source:HGNC Symbol;Acc:14511]

Sequence

>retro_fcat_2014
ATGCCCAGGAAGGGCTGCTTCCTGATCCACTGTACCCTGCAGTACCTGAGCCGGGTAGCATAGTGTTCAAAGTCAGTGAA
GGTCATGACTGTGAACTACAAGACGCATGGGGAGCTGGGCGAGGAGGCCAGGAAATTTGTGTTTTTCAACATATCTCAAA
TCCAGTACAAAAACCCTTGAGTGCAGATCATGGTGTTTAAGAACATGAGACTGTCCCCCTTCCTGCAGTTCTATCTGGAT
TCCGGGTAGCAGGTCCTCGCGGATGTGAAGACCAAGGGTAATAAGGATATCATGGAGCATATCAAAAAATATTGGGGAAG
AACCAAGAAACCCTTGATAAAGAGGAACAGAAAAGCAGCTTTCTCACCCGACTCACTTTGGCCCCTGAAAGTACTGCCTG
GGGGCCTACATCTGTGAGGTGGAAGGGCAGGTCCCCTTCCTGGACCTGGTGCCCCTACATAAGGAGATGACAGAGAAATA
CAAAACAACACTGAAAGCCAGAGCCCAG

Alignment

ORF - retro_fcat_2014 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.84 %
• Parental protein coverage: 99.42 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MPMKGRFPIRRTLQYLGQGDVVFKDSVKVMTVNYNTHGELGEGARKFVFFNIPQIQYKNPWVQIIMFKNM
          MP.KG.F.I..TLQYL.......K.SVKVMTVNY.THGELGE.ARKFVFFNI.QIQYKNP.VQI..FKNM
Retrocopy MPRKGCFLIHCTLQYLSRVA*CSK-SVKVMTVNYKTHGELGEEARKFVFFNISQIQYKNP*VQIMVFKNM

Parental  TPSPFLRFYLDSGEQVLVDVETKSNKEIMEHVK-KILGKSKETLEREEQ-EKKQLSHPAHFGPRKYCLRE
          ..SPFL.FYLDSG.QVL.DV.TK.NK.IMEH.K.KILGK..ETL..EEQ.EK.QLSHP.HFGP.KYCL..
Retrocopy RLSPFLQFYLDSG*QVLADVKTKGNKDIMEHIK<KILGKNQETLDKEEQ<EK-QLSHPTHFGP*KYCLGA

Parental  CICEVEGQVPCPGLVPLPKEMTGKYRAMLKASAQ
          .ICEVEGQVP...LVPL.KEMT.KY...LKA.AQ
Retrocopy YICEVEGQVPFLDLVPLHKEMTEKYKTTLKARAQ

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	11.36 RPM
SRP017611_kidney	0.00 RPM	25.66 RPM
SRP017611_liver	0.00 RPM	6.87 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_2014 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_2014 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 11 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000004349	1 retrocopy	retro_amel_1861,
Canis familiaris	ENSCAFG00000028683	1 retrocopy	retro_cfam_2200,
Echinops telfairi	ENSETEG00000008261	2 retrocopies	retro_etel_1144, retro_etel_1227,
Felis catus	ENSFCAG00000027687	1 retrocopy	retro_fcat_2014 ,
Latimeria chalumnae	ENSLACG00000009006	1 retrocopy	retro_lcha_49,
Loxodonta africana	ENSLAFG00000022178	1 retrocopy	retro_lafr_1068,
Mustela putorius furo	ENSMPUG00000017248	1 retrocopy	retro_mputfur_1608,
Oryctolagus cuniculus	ENSOCUG00000006984	1 retrocopy	retro_ocun_1040,
Ochotona princeps	ENSOPRG00000009370	3 retrocopies	retro_opri_288, retro_opri_690, retro_opri_951,
Pelodiscus sinensis	ENSPSIG00000008882	1 retrocopy	retro_psin_36,
Tursiops truncatus	ENSTTRG00000009881	1 retrocopy	retro_ttru_140,