RetrogeneDB ID: retro_fcat_361

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: A2:163696232..163697563(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSFCAG00000031275
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: TUBA1C
• Ensembl ID: ENSFCAG00000024852
• Aliases: None
• Description: tubulin, alpha 1c [Source:HGNC Symbol;Acc:20768]

Sequence

>retro_fcat_361
GAGCGCATTGCCATCCACGTTGGCCAGGCTGGTGTCCAGGTCCGCAATGGCCGCTGGGAGCCCTATTGCCTGGAACATAG
CATCCAGCCCAAGGGTCAGGTGCCAAGTGACAAGACCACTGGGGGAGGAGATGGCTCCTTCAACAACTTCTTCAGTGAGA
CGAGTACACGTGCGCAGGCCAGCTTTGGTGACCTGGAACCCGGAGCCGTGGATGAAGTTCACACCGGCAGCCACCATCAG
GTCTACTGCCCTAGAAGCTCCTCACCGGCAAGAAAGATGCCGCTAATAACCATGTCCCAGGGCCCTACACCATTGGCAAG
GAGATCATGGGCCTTGTCTTGGACCGAATTCAGAAACTGGCCCGCCAGCGCACGGGTCTTCAGGGCTTCTTGGTTTCCCA
CAGCTTTGGAGGAGGACCTGTCTCCAGGATCACCTCCCTGCCGGTGCATCGTCTCTCGGTCGATTATGGAGAGAAGCCCG
AGCTGGAGCTCTCCACTTACGCAGTCCCCAAGGTTTCCACGGCTGTAGTTGAGCCCTACAACTCCATCCTCACTACCCAC
ACTGCCCTGGAGCGAGCACTCTGATTGTGCCTTCTTGGTAGACGACGAGGCCATCTATGACATCTGTCGTAGAAACCTCA
GTACCAAACACCCAACCTGGGCTACTGACCTGAACAGGTGGATAAGTCAAACTGCGTCCTCCGTCGCTGCTTCCCTCGGA
TTTGATGGAGCCCTAAGTGTTGATCCGAGAGAATTCCGGACCGATCTGGTGCCCTACCCCCACATCCACGTCCCCGTGGC
CACCTACGCTCCTGTCATCTCCGCTGAGAGGGCCTGCTGTGAACAGCATCCCGTAGCAGAGATCATCGATGCATCCTTTA
AGTCAGCGAACCAGACGGTGAGACGTGACCCTCGCCGTGGCAAATACGTGGCTTGCTGCCCGTTGTACAGTGGTCCTATG
CTTCCCAAAGACGCCAGTGCCGCCATTGCTGCCTTCGAGTCCAAAAGTACCGTCCAGTTTGGGGACTGGTGCCCGGCTGG
CTTCAGAGTTGCCATCAGTAACCTGCCTCCCACCGTGCTACCTGCTGGAGACCCGACCAAGGTGCAGCGAGCTATGTGTA
TGCTGAGAGCACCACGGCCATCCCCGAGACCTGGGCTCACCTAGACCACAAGTTTGACCCGATGTATGCCAGGCACGCCC
TTGTCCACTGGTATGTGGGTAGGGGCACGGAGGAAGAGGCCCATGAGAACACGGCCGCCCTCGAGAAGGATTCTGAGGAG
GTTGGTGTGGATTCTGTGGCAGGAGAGGGTGAGGAAGGAGGAGAGGAGCAC

Alignment

ORF - retro_fcat_361 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.39 %
• Parental protein coverage: 99.55 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  ECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGKHVPRAVFVDLEP
          E.I.IHVGQAGVQ..N..WE.YCLEH.IQP.GQ.PSDKT.GGGD.SFN.FFSET........A.F.DLEP
Retrocopy ERIAIHVGQAGVQVRNGRWEPYCLEHSIQPKGQVPSDKTTGGGDGSFNNFFSETSTRA---QASFGDLEP

Parental  TVIDEVRTGTYRQLFHPE-QLITGKEDAANNYARGHYTIGKEIIDLVLDRIRKLXDLESGIQMTLLLRHV
          ...DEV.TG...Q...P...L.TGK.DAANN...G.YTIGKEI..LVLDRI.KL.....G.Q..L.....
Retrocopy GAVDEVHTGSHHQVYCPR<KLLTGKKDAANNHVPGPYTIGKEIMGLVLDRIQKLARQRTGLQGFLVSHSF

Parental  GSLPGHNWSSLK--RMTLHHSQLHTFPDAYHTLPSKSMDPQEKYSEGLVENST-NRTSEKCLHGRH-EAI
          G..P.....SL...R..................P..S....E.Y...L.......R....CL.GR..EAI
Retrocopy GGGPVSRITSLPVHRLSVDYGEKPELELSTYAVPKVSTAVVEPYNSILTTHTALERAL*LCLLGRR>EAI

Parental  YDICRRNLDIERPTY-TNLNRLISQIVSSITASLRFDGALNVDLTEFQTNLVPYPRIHFPLATYAPVISA
          YDICRRNL....PT..T.LNR.ISQ..SS..ASL.FDGAL.VD..EF.T.LVPYP.IH.P.ATYAPVISA
Retrocopy YDICRRNLSTKHPTWATDLNRWISQTASSVAASLGFDGALSVDPREFRTDLVPYPHIHVPVATYAPVISA

Parental  EKAYHEQLTVAEITNACFEPANQMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRTIQFVDWCP
          E.A..EQ..VAEI..A.F..ANQ.V..DPR.GKY.ACC.LY.G...PKD..AAIA....K.T.QF.DWCP
Retrocopy ERACCEQHPVAEIIDASFKSANQTVRRDPRRGKYVACCPLYSGPMLPKDASAAIAAFESKSTVQFGDWCP

Parental  TGFKVGINYQPPTVVPGGDLAKVQRAVCML-SNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGE
          .GF.V.I...PPTV.P.GD..KVQRA.CML...TTAI.E.WA.LDHKFD.MYA..A.VHWYVG.G.EE..
Retrocopy AGFRVAISNLPPTVLPAGDPTKVQRAMCML<ESTTAIPETWAHLDHKFDPMYARHALVHWYVGRGTEE--

Parental  FSEAREDMAALEKDYEEVGADS--AEGEDEGEEY
          ..EA.E..AALEKD.EEVG.DS...EGE..GEE.
Retrocopy --EAHENTAALEKDSEEVGVDSVAGEGEEGGEEH

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	3.10 RPM
SRP017611_kidney	0.00 RPM	40.71 RPM
SRP017611_liver	0.00 RPM	2.93 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_361 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_361 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 16 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000039992	1 retrocopy	retro_btau_840,
Canis familiaris	ENSCAFG00000008661	2 retrocopies	retro_cfam_960, retro_cfam_978,
Choloepus hoffmanni	ENSCHOG00000008444	2 retrocopies	retro_chof_179, retro_chof_360,
Equus caballus	ENSECAG00000009504	1 retrocopy	retro_ecab_1041,
Erinaceus europaeus	ENSEEUG00000004068	1 retrocopy	retro_eeur_669,
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,
Mus musculus	ENSMUSG00000043091	1 retrocopy	retro_mmus_843,
Oryctolagus cuniculus	ENSOCUG00000028032	1 retrocopy	retro_ocun_111,
Otolemur garnettii	ENSOGAG00000009435	1 retrocopy	retro_ogar_240,
Pteropus vampyrus	ENSPVAG00000004646	1 retrocopy	retro_pvam_929,
Rattus norvegicus	ENSRNOG00000015544	3 retrocopies	retro_rnor_1193, retro_rnor_2260, retro_rnor_960,