RetrogeneDB ID: retro_fcat_84

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: B1:65766814..65768692(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSFCAG00000027909
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: TKTL1
• Ensembl ID: ENSFCAG00000011392
• Aliases: None
• Description: transketolase-like 1 [Source:HGNC Symbol;Acc:11835]

Sequence

>retro_fcat_84
ATGGCCAACGACTGCAAGCCTGATGGGAACACCGTGCAGGTGCTGCGGGACGTGGCCAACCGCCTGCGAATCCATTCCAT
CAGGGCCACATGTGCCTCCGGCTCCGGCCACCCCACTTCATGTTGCAGTGCAGCCGAGATCATGTCCGTGCTCTTCTTCC
ACACCATGAGGTATAAACAGACAGACCCGGGACATCCCGACAACGACCGATTCATCCTCTCGAAGGGCCATGCTGCTCCA
ATCCTCTATGCCGCTTGGGCAGAGGTGGGCAACATCCGCGAATCTGACTTGCTGAACTTGAGGAAAATTCACAGTGACTT
GGAGGGACATCCCACCCCAAGAGTGCTGTTTGTTGATGTGGCAACAGGATCACTTGGGCAAGGATTAGGTGCCGCGTGTG
GAATGGCTTATACTGGCAAGTACTTCGACAAGGCCAGCTACCGGGTGTTCTGCCTCATAGGGGATGGCGAATCTTCAGAA
GGCTCTGTCTGGGAGGCTTTGGCCTTTGCTTCTCACTACAATTTAGACAATCTCGTGGCAGTCTTCGACGTGAACCGCTT
AGGACAAAGTGGAGCCACGCCTCTTGAGCACTGCACAGACATCTATCAGAATCGCTGTGAAGTCTTTGGGTGGAATACTT
ACCTAGTGGATGGCCATGATGTGGAGGCATTATGCCAAGCATTTTGGCAAGCGGCTCAAGTGAAGAACAAGCCCACTGCC
ATAGTTGCAAAGACCTTCAAGGGCCGGGGTATTCCAGATATTGAGGATGCAGAAAATTGGCATGGAAAGCCGATGCCAAA
AGAAAGAGTAGATACAATCATCAAATTAATTGAGAGTCAGATACAGACCAACAGGAATCTCATACCAAAACCTCCCATTG
AAGACTCACCTCAAATCAGCATCAGCAATATAAAAATGACCTGTCTGCCTGAATATATAGTTGGTGACACGATAGCTACT
AGGAAAGCATGTGGTTTGGCTTTGGCAAAACTGGGCCATGCAAATGAAAGAGTTATTGTCCTGGATGGTGACACAAAAAA
CGCCACCTTTTCTGAGATATTCAATAAAGAGCACCCTGAGCATTTTATTGAGTGTTTTATTGCTGAGCAAAACATGGTGA
GTGTGGCACTAGGCTGTGCCACACGTGGTCGAACCATTGCTTTTGTTAGTACCTTTGCTGCCTTTTTGGCCAGAGCATTC
GATCAGATAAGGATGGGAGCCATATCTCAAACCAATATCAATCTTATTGGTTCCCACTGTGGGGTATCCATTGGTGACGA
TGGACCCTCCCAGGTGGCCCTGGAGGATCTAGCCATGTTCCGAAGTATTCCCAACTGTACCGTTTTCTATCCAAGTGATG
CCATCTCAACAGAGTATGCTGTTTATCTGGCTGCCAATACCAAAGGAATGTGCTTCATTCGGACCAGCCAACCAGAAACT
GCAGTTATTTATACCCCACAAGAAAATTTTGAGATTGGGCAGGCCAAGGTCATCCGCCAGAGTGTCAATGACAAAGTCAC
AGTTATTGGAGCTGGAGTTACTCTGCATGAAGCCTTAGCAGCTGCTGACAGTCTTTCTCAACAAGGTATTTCTATCCGTG
TTATTGACCCATTTACCATTAAACCCCTGGATGCTGCCAACATCATCTCCAATGCAAGAGCTACAGGTGGCCGGGTTATC
ACAGTGGAGGATCACTACCGGGAAGGTGGCATTGGAGAAGCTGTATGTGCAGCTGTCTCTAGAGAGCCTGACATCCTTGT
TCATCAGCTGGCAGTGTCAGAAGTGCCTCAAAGTGGAAAACCTGGTGAACTGCTGGATAAGTTTGGTATCAGTGCCAGAC
ACATCATAGCAGCTGTGAAAAATACTTTAATGAACTAA

Alignment

ORF - retro_fcat_84 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.6 %
• Parental protein coverage: 96.76 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RPPCAPGPCHPTSSSSAAEVMAVLFFHIMRYKQEDPENPDNDRFILSKGSSLSASSATWVEVGNISGS-M
          R..CA.G..HPTS..SAAE.M.VLFFH.MRYKQ.DP..PDNDRFILSKG.......A.W.EVGNI..S..
Retrocopy RATCASGSGHPTSCCSAAEIMSVLFFHTMRYKQTDPGHPDNDRFILSKGHAAPILYAAWAEVGNIRESDL

Parental  LSSRKIELNLEGYSTRRLSFVDVATGWFGQGLGAACGMAYTGKYFDKASYRVFCLLGDGESSEGSVWEAL
          L..RKI...LEG..T.R..FVDVATG..GQGLGAACGMAYTGKYFDKASYRVFCL.GDGESSEGSVWEAL
Retrocopy LNLRKIHSDLEGHPTPRVLFVDVATGSLGQGLGAACGMAYTGKYFDKASYRVFCLIGDGESSEGSVWEAL

Parental  AFASHYNLDNLVAIFDVNRLGHSGALPIEHCVDVYQKRCEAFGWNTYVVDGRDVEVLCQVFLQASQVKNK
          AFASHYNLDNLVA.FDVNRLG.SGA.P.EHC.D.YQ.RCE.FGWNTY.VDG.DVE.LCQ.F.QA.QVKNK
Retrocopy AFASHYNLDNLVAVFDVNRLGQSGATPLEHCTDIYQNRCEVFGWNTYLVDGHDVEALCQAFWQAAQVKNK

Parental  PTAVVAKTFKGRGTPSIEDAENWHGKPMPRERADAIIKLIESQIQTNENLDPKPPIEDSPQINILDIEMI
          PTA.VAKTFKGRG.P.IEDAENWHGKPMP.ER.D.IIKLIESQIQTN.NL.PKPPIEDSPQI.I..I.M.
Retrocopy PTAIVAKTFKGRGIPDIEDAENWHGKPMPKERVDTIIKLIESQIQTNRNLIPKPPIEDSPQISISNIKMT

Parental  SLPAYTVDEKVATRKACGLALAKLGHANDRVIVLDGDTKNSTFADIFKKEHPERFIECFIAEQNMVSVAL
          .LP.Y.V....ATRKACGLALAKLGHAN.RVIVLDGDTKN.TF..IF.KEHPE.FIECFIAEQNMVSVAL
Retrocopy CLPEYIVGDTIATRKACGLALAKLGHANERVIVLDGDTKNATFSEIFNKEHPEHFIECFIAEQNMVSVAL

Parental  GCATRGRTVAFVSTFAAFLTRAFDQIRMGAVSQTNINLIGSHCGISVGEDGASQMALEDLAMFRAVPNCT
          GCATRGRT.AFVSTFAAFL.RAFDQIRMGA.SQTNINLIGSHCG.S.G.DG.SQ.ALEDLAMFR..PNCT
Retrocopy GCATRGRTIAFVSTFAAFLARAFDQIRMGAISQTNINLIGSHCGVSIGDDGPSQVALEDLAMFRSIPNCT

Parental  IFYPSDAVSTEHAVFLAANSTGMCYIRTSRPETAVIYTQQESFEIGRAKVLRHSVNDKVTVIGAGVTLHE
          .FYPSDA.STE.AV.LAAN..GMC.IRTS.PETAVIYT.QE.FEIG.AKV.R.SVNDKVTVIGAGVTLHE
Retrocopy VFYPSDAISTEYAVYLAANTKGMCFIRTSQPETAVIYTPQENFEIGQAKVIRQSVNDKVTVIGAGVTLHE

Parental  ALAAAEDLSKQDISIRVIDLFTIKPLDTVTIMSSAKATGGRIITVEDHYSEGGIGEAVAAAVSTEPDILV
          ALAAA..LS.Q.ISIRVID.FTIKPLD...I.S.A.ATGGR.ITVEDHY.EGGIGEAV.AAVS.EPDILV
Retrocopy ALAAADSLSQQGISIRVIDPFTIKPLDAANIISNARATGGRVITVEDHYREGGIGEAVCAAVSREPDILV

Parental  RQLAVAGIPRSGKPSELLDMFGISAKHIIVAVKCMLMN
          .QLAV...P.SGKP.ELLD.FGISA.HII.AVK..LMN
Retrocopy HQLAVSEVPQSGKPGELLDKFGISARHIIAAVKNTLMN

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	1.03 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_84 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_84 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 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000018441	1 retrocopy	retro_amel_119,
Equus caballus	ENSECAG00000021992	1 retrocopy	retro_ecab_6,
Felis catus	ENSFCAG00000011392	1 retrocopy	retro_fcat_84 ,
Loxodonta africana	ENSLAFG00000005145	1 retrocopy	retro_lafr_6,
Pongo abelii	ENSPPYG00000020870	1 retrocopy	retro_pabe_205,
Ictidomys tridecemlineatus	ENSSTOG00000005014	1 retrocopy	retro_itri_30,