RetrogeneDB ID: retro_fcat_1225

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: C1:158715952..158716881(-)
• Located in intron of: ENSFCAG00000031648

Retrocopy information

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

Parental gene information

• Parental gene symbol: HADH
• Ensembl ID: ENSFCAG00000022260
• Aliases: None
• Description: hydroxyacyl-CoA dehydrogenase [Source:HGNC Symbol;Acc:4799]

Sequence

>retro_fcat_1225
ATGGTTTTCATAACCTGGCAATTTGTGTACTCTGTGTGCTCCTCATCTGCTACCTCAGCCTCCGTGAAGAAAATCATCAT
CAACTACATGTTGGTTACTGGCAGCAAGATGATGGGCACTGACATCACCCAGGTTGCTGCAGCAACTGGCCACAACGGTG
TTGGTGGACCAGACAGAGGACATGCTGGCAAAATCTAGAAATGAGATTGAGGAAAGCCTTAGGAAAGTGGCAGAGAAGAA
GTCTGCATAAAACCCCAAGGCGGGTGATGAATTTGTGGAGAAGACCCTGAGCAACATATCAACCAGCATGGATGCAGCAT
CCATAATCCACAGCATGGACTTGGTGGTAGAGGCCATTCTGGAGAATTTAAAGATGAAGAATGACTTCTTCAAGAGGTTG
AACAAGTTTGCCTCTGAACGTACAATCTTTGCCAGCAACATTTCCTCTCTGCAGTCTACAAACATAGCCAATGCCACCAT
AAGACAGGACTGATTCGCTGGACTCCATTTCTTCAACCCAGTGCCCTTGATAAAGCTTGTGGAGGTCATTAAAACACCAC
TGACCGACCAGAATACACCTGAATCTCTGACAGACTTCAGCAAAGCCCTGGAAAACCATCCGGTTTCTTGTAAGAACACG
TCTGAGTTTACTGTGAACTGTCTCCTAGTGCCATACCTCATGGAAGCAGTCAGGCTGCATGAATGAGTAACACATCCAAA
GGAAGATATCAACACTGCTATGAAGCTAGGAGCTGGTTACTCCATGGGCCCATTTGAGCTTGATTACATAGGGCTGGATA
CTACAAAGTTCATCATGGACAGGTGGCATGAAATGGAACCCTTTGCTTCAACCCAGCCTGTCCTTGAAGAAGTTGGTAGC
AGAGAATAAGCTTGGCAAGAAGACTGAAGAAGGACATTGCAAATACAAG

Alignment

ORF - retro_fcat_1225 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.15 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAFVTRQFVRSVSSSSTASASAKKIIIKHVTVIGGGLMGAGIAQVAAATGH-TVMLVDQTEDILAKSRKG
          M.F.T.QFV.SV.SSS..SAS.KKIII....V.G...MG..I.QVAAATGH.TV.LVDQTED.LAKSR..
Retrocopy MVFITWQFVYSVCSSSATSASVKKIIINYMLVTGSKMMGTDITQVAAATGH>TV-LVDQTEDMLAKSRNE

Parental  IEESLRKVAKKKFAENPKAGDEFVEKTLNSISTSTDAASVVHSTDLVVEAIVENLKMKNELFKRLDKFAS
          IEESLRKVA.KK.A.NPKAGDEFVEKTL..ISTS.DAAS..HS.DLVVEAI.ENLKMKN..FKRL.KFAS
Retrocopy IEESLRKVAEKKSA*NPKAGDEFVEKTLSNISTSMDAASIIHSMDLVVEAILENLKMKNDFFKRLNKFAS

Parental  EHTIFASNTSSLHITDIANATTRQDRFAGLHFFNPVPMMKLVEVIKTPMTSQKTTESLIDFSKALGKHPV
          E.TIFASN.SSL..T.IANAT.RQD.FAGLHFFNPVP..KLVEVIKTP.T.Q.T.ESL.DFSKAL..HPV
Retrocopy ERTIFASNISSLQSTNIANATIRQD*FAGLHFFNPVPLIKLVEVIKTPLTDQNTPESLTDFSKALENHPV

Parental  SCKDTPGFIVNRLLVPYLMEAIRLHERGDASKEDIDTAMKLGAGYPMGPFELLDYVGLDTVKFIIDGWHE
          SCK.T..F.VN.LLVPYLMEA.RLHE.....KEDI.TAMKLGAGY.MGPFE.LDY.GLDT.KFI.D.WHE
Retrocopy SCKNTSEFTVNCLLVPYLMEAVRLHE*VTHPKEDINTAMKLGAGYSMGPFE-LDYIGLDTTKFIMDRWHE

Parental  VDAKNPLFQPSPSL-NKLVAENKVGKKTGEGYYKYK
          .....P.....P.L..KLVAENK.GKKT.EG..KYK
Retrocopy ME---PFASTQPVL>KKLVAENKLGKKTEEGHCKYK

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	23.18 RPM
SRP017611_kidney	0.00 RPM	1478.36 RPM
SRP017611_liver	0.00 RPM	237.86 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_1225 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_1225 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 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000002049	2 retrocopies	retro_btau_1111, retro_btau_1685,
Callithrix jacchus	ENSCJAG00000015938	1 retrocopy	retro_cjac_772,
Echinops telfairi	ENSETEG00000013807	1 retrocopy	retro_etel_1694,
Felis catus	ENSFCAG00000022260	1 retrocopy	retro_fcat_1225 ,
Homo sapiens	ENSG00000138796	1 retrocopy	retro_hsap_1571,
Gorilla gorilla	ENSGGOG00000004423	1 retrocopy	retro_ggor_1196,
Macaca mulatta	ENSMMUG00000023254	1 retrocopy	retro_mmul_2217,
Nomascus leucogenys	ENSNLEG00000012951	1 retrocopy	retro_nleu_1738,
Pongo abelii	ENSPPYG00000014986	1 retrocopy	retro_pabe_1296,
Pan troglodytes	ENSPTRG00000016351	1 retrocopy	retro_ptro_1058,