RetrogeneDB ID: retro_fcat_709

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: B2:72729468..72730140(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSFCAG00000007862
• Aliases: None
• Description: None

Sequence

>retro_fcat_709
TCTTTCATGATGTCTACTGTTCACAAAATTCTCTGTGAGCTCAGTCTGGAGGGTGATCACTCCATGCCCCAAGTGCATAC
GAGTCGGTCAAAGCATACACCAATTTTGATGCTGAGCATGATGCTCTGAACATTGAAATGGCCATCAAGACCAAAAGTGT
GGGTGAGGCCACCATTGTCAAGATTTTGACAAACCTCGGTGATGAATGGAGGGAGGATATTGCCTTTGCCCACAAGAGAA
GGACCAAAAAGGAATTTGCATCAGCACTGAAGTCAGCCTTGTTCAGCCACCTGGAGACTGTGATTTTTTGGGTCTATTTA
AAACACCTGCTCAGTATGATGCTTCTTAGCTGAATGCCTCCATGAAGGGGCTAGGGACTGATGAAGGCTCCCTCATTGAG
ATCATCTGCTTGAGGACCAACCAGGAGCTTCAGGAAATTAAAAGTCTACAAGGAAATGTACAAGACTCATCTAGAGACCC
CATAATTTCTGACACATCTGGCAACGTCCACAATTGGATGGTTGCCCTCACAAAAGGTAGAAAAGCAGAGGATGGCTCTG
TCATTGATTATGAACTGTTTGGCCAAGATGCTCAGATCTCTGTGATGCTGGAGTGAAGAGGAAAGGAACTCACGTGCCCG
AGTGCATCAGCATCATGACCAACAGGAACGTC

Alignment

ORF - retro_fcat_709 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.05 %
• Parental protein coverage: 65.79 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  SFKMSTVHEILCKLSLEGDHSTP-PSAYGSVKAYTNFDAERDALNIETAIKTKGVDEVTIVNILTNRSNE
          SF.MSTVH.ILC.LSLEGDHS.P.PSAY.SVKAYTNFDAE.DALNIE.AIKTK.V.E.TIV.ILTN...E
Retrocopy SFMMSTVHKILCELSLEGDHSMP<PSAYESVKAYTNFDAEHDALNIEMAIKTKSVGEATIVKILTNLGDE

Parental  QRQDIAFAYQRRTKKELTSALKSALSGHLETVILGL-LK-TPAQYDASELKASMKGLGTDEDSLIEIICS
          .R.DIAFA..RRTKKE..SALKSAL..HLETVI....LK.TPAQYDAS.L.ASMKGLGTDE.SLIEIIC.
Retrocopy WREDIAFAHKRRTKKEFASALKSALFSHLETVIFWVYLK<TPAQYDAS*LNASMKGLGTDEGSLIEIICL

Parental  RTNQELQEINRVYKEMYKTDLEKDIISDTSGDFRKLMVALAKGRRAEDGSVIDYELIDQDAR-DLYDAGV
          RTNQELQEI...............IISDTSG.....MVAL.KGR.AEDGSVIDYEL..QDA..DL.DAGV
Retrocopy RTNQELQEIKSLQGNVQDSSRD-PIISDTSGNVHNWMVALTKGRKAEDGSVIDYELFGQDAQ<DLCDAGV

Parental  KRKGTDVPKWISIMTERSV
          KRKGT.VP..ISIMT.R.V
Retrocopy KRKGTHVPECISIMTNRNV

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	15.49 RPM
SRP017611_kidney	0.00 RPM	124.08 RPM
SRP017611_liver	0.00 RPM	84.92 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_709 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_709 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 29 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000008055	2 retrocopies	retro_amel_1531, retro_amel_1836,
Bos taurus	ENSBTAG00000009615	2 retrocopies	retro_btau_634, retro_btau_985,
Canis familiaris	ENSCAFG00000016686	3 retrocopies	retro_cfam_1631, retro_cfam_367, retro_cfam_707,
Choloepus hoffmanni	ENSCHOG00000012143	3 retrocopies	retro_chof_1028, retro_chof_1965, retro_chof_815,
Equus caballus	ENSECAG00000012670	1 retrocopy	retro_ecab_759,
Felis catus	ENSFCAG00000007862	2 retrocopies	retro_fcat_594, retro_fcat_709 ,
Macropus eugenii	ENSMEUG00000008980	3 retrocopies	retro_meug_1000, retro_meug_312, retro_meug_389,
Myotis lucifugus	ENSMLUG00000002464	3 retrocopies	retro_mluc_1569, retro_mluc_2223, retro_mluc_2431,
Monodelphis domestica	ENSMODG00000011604	1 retrocopy	retro_mdom_1471,
Mustela putorius furo	ENSMPUG00000000762	2 retrocopies	retro_mputfur_73, retro_mputfur_79,
Otolemur garnettii	ENSOGAG00000009952	1 retrocopy	retro_ogar_3510,
Pteropus vampyrus	ENSPVAG00000011401	1 retrocopy	retro_pvam_389,
Tupaia belangeri	ENSTBEG00000001276	1 retrocopy	retro_tbel_3335,
Tarsius syrichta	ENSTSYG00000003719	1 retrocopy	retro_tsyr_2086,
Tursiops truncatus	ENSTTRG00000007705	1 retrocopy	retro_ttru_1725,
Vicugna pacos	ENSVPAG00000007888	2 retrocopies	retro_vpac_241, retro_vpac_27,