RetrogeneDB ID: retro_fcat_963

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: B4:57173540..57174024(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSFCAG00000029095
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: MRPS23
• Ensembl ID: ENSFCAG00000005711
• Aliases: None
• Description: mitochondrial ribosomal protein S23 [Source:HGNC Symbol;Acc:14509]

Sequence

>retro_fcat_963
ATGGTAGGGATCTGGCTAAAGACCATGGGGAGAGTTTTCTCACAGATTTGGGACCTGATTGGGGCTGGGGTGTTGAGGAG
ATGCCCCTCTGGTTTGACATATATAACGCCTTTCCCCCACTGAGAGAGTTGGTCTTCCAAAGGCCCTGCTTGCAATATGA
CAAAGCCAAAGCTGCAATCCAGAACACGTTGTACCCCAAAGATTGGATTAGAGTGAAATTTTATTCAGCCATTAATCTGG
TCAGAAAGCTTTTGATCTGTTCAATCCAAACTTCAAGTCTACCTGTCAACAGTTTGTAGAGAAGTACATTGAACTACAGA
AACTCGGAGAAACAGATAAAGAGAAGATATTTGTGGAAACAGAGAAAGTTTTATCAACAGAAGGTTTCATTTTAAGACAA
GTAGGAGAAGCAAGGACTCAAAAGGAAGATAGTCATGTTTCCTGCGAATCTGAACCCACAGGTGCCAAACCTCAAACAGT
ATTG

Alignment

ORF - retro_fcat_963 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75. %
• Parental protein coverage: 85.26 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAGSRLQTVGSVFSRTRDLIRAGVLK-EKPLWFDIYNAFPPLREPVFRRPRLRYGKAKAAIQDILYPEDR
          M.G..L.T.G.VFS...DLI.AGVL..E.PLWFDIYNAFPPLRE.VF.RP.L.Y.KAKAAIQ..LYP.D.
Retrocopy MVGIWLKTMGRVFSQIWDLIGAGVLR<EMPLWFDIYNAFPPLRELVFQRPCLQYDKAKAAIQNTLYPKDW

Parental  IRAKFYSAYG-SGQKAFDLFNPNFKSTCQQFVEKYIELQKLGETDEEKLFVETGKALLAEGVILRRVGEA
          IR.KFYSA...SGQKAFDLFNPNFKSTCQQFVEKYIELQKLGETD.EK.FVET.K.L..EG.ILR.VGEA
Retrocopy IRVKFYSAIN<SGQKAFDLFNPNFKSTCQQFVEKYIELQKLGETDKEKIFVETEKVLSTEGFILRQVGEA

Parental  RTQKAGSHVSWESEPPDVKSQTVL
          RTQK..SHVS.ESEP...K.QTVL
Retrocopy RTQKEDSHVSCESEPTGAKPQTVL

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	15.15 RPM
SRP017611_kidney	0.00 RPM	21.44 RPM
SRP017611_liver	0.00 RPM	10.41 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_963 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_963 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 10 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000014008	1 retrocopy	retro_cjac_3047,
Cavia porcellus	ENSCPOG00000008761	1 retrocopy	retro_cpor_1175,
Felis catus	ENSFCAG00000005711	1 retrocopy	retro_fcat_963 ,
Homo sapiens	ENSG00000181610	1 retrocopy	retro_hsap_3727,
Macaca mulatta	ENSMMUG00000001913	1 retrocopy	retro_mmul_1691,
Mustela putorius furo	ENSMPUG00000015372	1 retrocopy	retro_mputfur_1274,
Nomascus leucogenys	ENSNLEG00000008072	1 retrocopy	retro_nleu_1972,
Pongo abelii	ENSPPYG00000025941	1 retrocopy	retro_pabe_3131,
Pan troglodytes	ENSPTRG00000009440	1 retrocopy	retro_ptro_2523,
Tarsius syrichta	ENSTSYG00000009862	1 retrocopy	retro_tsyr_2077,