RetrogeneDB ID: retro_fcat_596

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: B1:190579169..190579990(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TUBA4A
• Ensembl ID: ENSFCAG00000027277
• Aliases: None
• Description: tubulin, alpha 4a [Source:HGNC Symbol;Acc:12407]

Sequence

>retro_fcat_596
GAGTATATCTCCATACATGTTGGCCAGGCTGGTGTTCAGATTGGCAGTGCCTGCTGGGAGCTCTATGGCCTGGAACACAG
CATCCAGCCCAATGGCCAGATGTCAAGTGACAAGACCACTGGGGGAGGAGATGACTCCTTCAACACCTTCTTCAATGAGA
TGGGTGCTGGAAAGCAAATGCCCAGGGCAGTTTTTGCAGACCTGAAACCCAAAGTCATTGATGAAGTTCACACTGGCACC
TACTTCCAGTTCTTCCATCATGAGCAGCTCGTCACAAGCAAGGAAGATGCTGCCAATAACGATACCCGAGGACACTACAC
CATTGGCAAGGAGATCACTGACCTTGTCTTAGAATTCGTAAGCTGGCTGACCAGTGCACAGGTCTTCAGGGTTTCTTGGT
TTTCCACAGCTTTGGAGGGGAAACTAGTTCCATGTTCACCTGCCTGATGGAATGTTTCTCTCTCGATTATAGCAAGAAGT
TCAACCTGGAGTTCTCCTTTTATCCAACCCCCTATGTTTCCACAGCTGTAGTGGAACCCTACAACTACCTCCTGACTACC
CACACCACCCTGGAGCACTTTGATTGCACCTTCATGGTAGACAATGAGACCATCTATGACATCTGTTGTAGAAACCTTGA
TATTGAACACCCAAACTGTACTAATCTTAACCGCCTAATTAGTCAGACTGTGTCTTCCATTACTGCTTCCCTCAGATACG
ATGGAGCCCTGAATGTTGATCTGACAGAATTCCAGACCAGCCTGATGCCCATGGTAAAAGCCTATCATGAACAGCTTACT
GCAGCAGAGATCACCAATGCA

Alignment

ORF - retro_fcat_596 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.29 %
• Parental protein coverage: 57.26 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ECISVHVGQAGVQMGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFTTFFCETGAGKHVPRAVFVDLEP
          E.IS.HVGQAGVQ.G.ACWELY.LEH.IQP.GQM.SDKT.GGGDDSF.TFF.E.GAGK..PRAVF.DL.P
Retrocopy EYISIHVGQAGVQIGSACWELYGLEHSIQPNGQMSSDKTTGGGDDSFNTFFNEMGAGKQMPRAVFADLKP

Parental  TVIDEIRNGPYRQLFHPEQLITGKEDAANNYARGHYTIGKEIID-PVLDRIRKLSDQCTGLQGFLVFHSF
          .VIDE...G.Y.Q.FH.EQL.T.KEDAANN..RGHYTIGKEI.D.P.L.RIRKL.DQCTGLQGFLVFHSF
Retrocopy KVIDEVHTGTYFQFFHHEQLVTSKEDAANNDTRGHYTIGKEITD<PCL-RIRKLADQCTGLQGFLVFHSF

Parental  GGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTAVVEPYNSILTTHTTLEHSDCAFMVDNEAIYD
          GG.T.S.FT.L.ME..S.DY.KK..LEFS.YP.P.VSTAVVEPYN..LTTHTTLEH.DC.FMVDNE.IYD
Retrocopy GGETSSMFTCL-MECFSLDYSKKFNLEFSFYPTPYVSTAVVEPYNYLLTTHTTLEHFDCTFMVDNETIYD

Parental  ICRRNLDIERPTYTNLNRLISQIVSSITASLRFDGALNVDLTEFQTNLVPYPRIHFPLATYAPVISA
          IC.RNLDIE.P..TNLNRLISQ.VSSITASLR.DGALNVDLTEFQT.L.P.........T.A....A
Retrocopy ICCRNLDIEHPNCTNLNRLISQTVSSITASLRYDGALNVDLTEFQTSLMPMVKAYHEQLTAAEITNA

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	131.19 RPM
SRP017611_kidney	0.00 RPM	151.91 RPM
SRP017611_liver	0.00 RPM	13.55 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_596 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_596 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 15 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000008444	2 retrocopies	retro_chof_179, retro_chof_360,
Dipodomys ordii	ENSDORG00000000154	3 retrocopies	retro_dord_460, retro_dord_564, retro_dord_786,
Echinops telfairi	ENSETEG00000010296	2 retrocopies	retro_etel_1816, retro_etel_1993,
Felis catus	ENSFCAG00000022091	2 retrocopies	retro_fcat_1375, retro_fcat_647,
Felis catus	ENSFCAG00000024852	1 retrocopy	retro_fcat_361,
Felis catus	ENSFCAG00000027011	1 retrocopy	retro_fcat_588,
Felis catus	ENSFCAG00000027277	1 retrocopy	retro_fcat_596 ,
Felis catus	ENSFCAG00000028689	3 retrocopies	retro_fcat_1802, retro_fcat_254, retro_fcat_798,
Macropus eugenii	ENSMEUG00000010779	2 retrocopies	retro_meug_1648, retro_meug_2174,
Microcebus murinus	ENSMICG00000000804	1 retrocopy	retro_mmur_103,
Otolemur garnettii	ENSOGAG00000009435	1 retrocopy	retro_ogar_240,
Pteropus vampyrus	ENSPVAG00000010798	1 retrocopy	retro_pvam_1019,
Rattus norvegicus	ENSRNOG00000003597	1 retrocopy	retro_rnor_2819,
Ictidomys tridecemlineatus	ENSSTOG00000019497	1 retrocopy	retro_itri_203,
Tursiops truncatus	ENSTTRG00000010042	1 retrocopy	retro_ttru_531,