RetrogeneDB ID: retro_fcat_588

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: B1:165060705..165062033(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSFCAG00000027011
• Aliases: None
• Description: None

Sequence

>retro_fcat_588
ATTTCCATCGACATTGGTCAGGCTGGTGTCCAGATTGGTAATGCTTGCTGGTAACTCTATTGCCTGGAACACAGCATCCA
ACTCAATGGCCAGATGCTAAGTGACAAGACCATTGTGGGGAGGAGGAGATGACTTGTTTAACATTTGTTCAGTGAGACAG
GTGCTGGAAAGCACGTGCCCAGGGCAGTGTTTGTAGACCTGGAACCCACAGTCATTGATGAAGTTTGCACTGGCACCTCC
CACCAGGTTTTCCACCCAAAGTAGCTCATCACAGGTAAGGATAATGCTGCCTATAGCTACGCCCAAGGGAACTACACCAC
TGACAAGGAGAACATTGACCTTGTCTTGGACCGAATTGGGAAATTAGCTGGCCAGTGCCCAGGTCTTCAAGGCTTCTTGG
TTTTCCACAGCTTTGGAGGGGGAACTGGCTCTGGGTTCATCTCCCTGATAATGGAACATCTGTTTGTCAATTATGGAAAG
AAATTCAAGCTGGATTTCTCCATTTACCCAGCCCCTGAATTTTCCATAGCTGTAGTTGAGCCCTATAACTCCATTCTCAC
TACTCATACCACCCTGGAGTACTCTGATTGTGCCTTCATGGTAGACAATGAGGCCGTGTATGACATCTGCCATAGAAAGT
GCAATATTGAACACCCAACCTACACTAACTTCATTGCCTTATTAGCCAGAGTGTGTTTCCATCACTGCTTCCCTCAGATT
AGATGGAGCCCTGAATGTTGATCTGACAACATTCCAGACCAACCTGGTGCCCTATCCTCGCATCCACTTCCCCTACCCAC
AAATACTCCTGTCATCTCTACTGAGAAAGCCTACAATGAACAGTTTTCTGTAGCAGAGATCAACAATGCATGCTTCAAAC
CAGCCAACCAGGTGAAATGTGCCCTCTGGTATGGCAACTACATGGCTTTCTGCCTGTTGTACCATGGCAATGTGTTCCCA
AAGGTGTCAATGCTGCCATTGCCACCATCAAGACCAAGCATTCCATCCAGTTTGTGGGCTGGTGCAGCACTGGCTTCCAG
GTTGGCATTAATTACCAGCCTGTGGTACCTGGTGGAGACCTGGCCAAAGTACAGAGAACTGTGTGCACGCTGAGCAACAC
CAGAGCCATTGCTGAGGTCTGATCTTGTCCGGACCACAAGTTTGACCTGATGTATGCCAAGCGAGCTTTTGTTTAGTGGT
ATACGGGTGAGAGTATGAAGGAAGGAGAGTTTTCTGAGACCTGTGAGGACACGGCTGCCCCTGAGAAGGATTATGAAGTG
GGTGTGGATTTTGTTGAAGGAGAGAGTGAAGAAGAAGGGGAGGAACAT

Alignment

ORF - retro_fcat_588 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.09 %
• Parental protein coverage: 99.11 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  ISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTI-GGGDDS-FNT-FFSETGAGKHVPRAVFVDLE
          ISI..GQAGVQIGNACW.LYCLEH.IQ..GQM.SDKTI..GG.D..FN...FSETGAGKHVPRAVFVDLE
Retrocopy ISIDIGQAGVQIGNACW*LYCLEHSIQLNGQMLSDKTI>WGGGDDLFNI<LFSETGAGKHVPRAVFVDLE

Parental  PTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLDRIRKLADQCTGLQGFLVFHSF
          PTVIDEV.TGT..Q.FHP..LITGK..AA..YA.G.YT..KE.IDLVLDRI.KLA.QC.GLQGFLVFHSF
Retrocopy PTVIDEVCTGTSHQVFHPK*LITGKDNAAYSYAQGNYTTDKENIDLVLDRIGKLAGQCPGLQGFLVFHSF

Parental  GGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTAVVEPYNSILTTHTTLEHSDCAFMVDNEAIYD
          GGGTGSGF.SL.ME.L.V.YGKK.KL.FSIYPAP..S.AVVEPYNSILTTHTTLE.SDCAFMVDNEA.YD
Retrocopy GGGTGSGFISLIMEHLFVNYGKKFKLDFSIYPAPEFSIAVVEPYNSILTTHTTLEYSDCAFMVDNEAVYD

Parental  ICRRNLDIERPTYTN-LNRLISQIV-SSITASLRFDGALNVDLTEFQTNLVPYPRIHF-PLATYAPVISA
          IC.R...IE.PTYTN.L..LISQ.V..SITASLR.DGALNVDLT.FQTNLVPYPRIHF.PL.T..PVIS.
Retrocopy ICHRKCNIEHPTYTN<LHCLISQSV<VSITASLRLDGALNVDLTTFQTNLVPYPRIHF<PLPTNTPVIST

Parental  EKAYHEQLSVAEITNACFEPANQMVKCDPRHGKYMACCLLYRGDV-VPKDVNAAIATIKTKRSIQFVDWC
          EKAY.EQ.SVAEI.NACF.PANQ.VKC....G.YMA.CLLY.G.V.VPK.VNAAIATIKTK.SIQFV.WC
Retrocopy EKAYNEQFSVAEINNACFKPANQ-VKCALWYGNYMAFCLLYHGNV<VPKGVNAAIATIKTKHSIQFVGWC

Parental  PTGFKVGINYQPPTVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGE
          .TGF.VGINYQP..VVPGGDLAKVQR.VC.LSNT.AIAE.....DHKFDLMYAKRAFV.WY.GE.M.EGE
Retrocopy STGFQVGINYQP--VVPGGDLAKVQRTVCTLSNTRAIAEV*SCPDHKFDLMYAKRAFV*WYTGESMKEGE

Parental  FSEAREDMAALEKDYEEVGVDSVEGEGEEEGEEY
          FSE..ED.AA.EKDY.EVGVD.VEGE.EEEGEE.
Retrocopy FSETCEDTAAPEKDY-EVGVDFVEGESEEEGEEH

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	265.93 RPM
SRP017611_kidney	0.00 RPM	74.30 RPM
SRP017611_liver	0.00 RPM	26.49 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_588 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_588 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 41 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006872	4 retrocopies	retro_amel_1162, retro_amel_1367, retro_amel_1387, retro_amel_1895,
Canis familiaris	ENSCAFG00000008640	8 retrocopies	retro_cfam_1481, retro_cfam_1751, retro_cfam_1895, retro_cfam_1917, retro_cfam_1979, retro_cfam_2000, retro_cfam_463, retro_cfam_926,
Choloepus hoffmanni	ENSCHOG00000008444	2 retrocopies	retro_chof_179, retro_chof_360,
Cavia porcellus	ENSCPOG00000013016	1 retrocopy	retro_cpor_96,
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,
Loxodonta africana	ENSLAFG00000010021	1 retrocopy	retro_lafr_326,
Microcebus murinus	ENSMICG00000017551	3 retrocopies	retro_mmur_144, retro_mmur_705, retro_mmur_885,
Myotis lucifugus	ENSMLUG00000002622	4 retrocopies	retro_mluc_154, retro_mluc_186, retro_mluc_234, retro_mluc_270,
Otolemur garnettii	ENSOGAG00000009435	1 retrocopy	retro_ogar_240,
Tupaia belangeri	ENSTBEG00000001671	1 retrocopy	retro_tbel_3700,
Tarsius syrichta	ENSTSYG00000013266	7 retrocopies	retro_tsyr_1014, retro_tsyr_1278, retro_tsyr_1281, retro_tsyr_1679, retro_tsyr_1834, retro_tsyr_243, retro_tsyr_6,
Tursiops truncatus	ENSTTRG00000004794	1 retrocopy	retro_ttru_407,