RetrogeneDB ID: retro_fcat_1193

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: C1:74788242..74788960(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ZDHHC6
• Ensembl ID: ENSFCAG00000030784
• Aliases: None
• Description: zinc finger, DHHC-type containing 6 [Source:HGNC Symbol;Acc:19160]

Sequence

>retro_fcat_1193
CTCAAGATAGTAAAGTGTTGCCACGCATATAAGTCACCACAGTTGCATCGCCACAGAAGGTGCAACAGATGTGTGATGAA
ATTGGACCATCACTGTCCTTGGGTCAACAACTGTTTGGTTACCAAAGTCATGCCTTGTTCACCCCGCATCTCCTTTTAGC
ACCGCTGGGTTGCATTCATGCTGCCTTCATTTTTGTTATGACTATGTTTACATGGCTTTACAATTGGCTCTCCTTTGGAT
GGAACACGGTAAAGACTGAGGAAGGCAGCCCGGAGAGATCCTCTTCCAATTATTCCCTTTGAATTAGTGGCACTTGTAGG
CAGCTTGTTTGCCTTGGGATTAGCTTTGGGAACAACCATAGCTGTTGGGATGTCGTTTTGTAGCCAGACGAAAATAATTC
TCAGAAACAAAACTTCTATTGAATCACGGACTGAAGAAAAGGCTAAACATCGAATTCAATATTACTGACTAGATGAGGTC
TCTGTTTTACCATATGAAACAGGAAGTAGATGGAAGAACTTTAAACAGGTATTTACATGGTCAGGTTTCCCTGAAGGAGA
TGAGCTAGAGTGGCCAATAAGAGGAGGCTGTCACCAGTACAATAGAACAATTAAAACAAAAAGCAAATAGAGGAATCAGA
AGGGTTCAGTGTAAAGCAATAGAAGATTATAGTGGTACCTGCTGTCCTCTAAATAAAGGAATTGAAATCTTCATGAGC

Alignment

ORF - retro_fcat_1193 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.7 %
• Parental protein coverage: 58.84 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  LQYCKVCQAYKAPRSHHCRKCNRCVLKMDHHCPWINNCC-GFQNHASFTLFLLLAPLGCIHAAFIFVMTM
          L...K.C.AYK.P..H..R.CNRCV.K.DHHCPW.NNC..G.Q.HA.FT..LLLAPLGCIHAAFIFVMTM
Retrocopy LKIVKCCHAYKSPQLHRHRRCNRCVMKLDHHCPWVNNCL<GYQSHALFTPHLLLAPLGCIHAAFIFVMTM

Parental  YTQLYNRLSFGWNTVKID-MSAARRDPLPLIPFGLAAFAATLFALGLALGTTIAVGMLFFIQMKIILRNK
          .T.LYN.LSFGWNTVK.....A.R.DPLP.IPF.L.A....LFALGLALGTTIAVGM.F..Q.KIILRNK
Retrocopy FTWLYNWLSFGWNTVKTE>KAARR-DPLPIIPFELVALVGSLFALGLALGTTIAVGMSFCSQTKIILRNK

Parental  TSIESWIEEKAKDRIQYYQLDEVFVFPYDMGSRWKNFKQVFTWSGVPEGDGLAWPIREGCHQYDLTI-EQ
          TSIES..EEKAK.RIQYY.LDEV.V.PY..GSRWKNFKQVFTWSG.PEGD.L.WPIR.GCHQY..TI..Q
Retrocopy TSIESRTEEKAKHRIQYY*LDEVSVLPYETGSRWKNFKQVFTWSGFPEGDELEWPIRGGCHQYNRTI>KQ

Parental  LKQKADKRVRSVRYRVIEDYSGACCPLNKGIKTFFT
          .......RV.......IEDYSG.CCPLNKGI..F..
Retrocopy KANRGIRRVQC---KAIEDYSGTCCPLNKGIEIFMS

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	1.49 RPM	24.10 RPM
SRP017611_kidney	0.10 RPM	42.67 RPM
SRP017611_liver	0.20 RPM	23.15 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_1193 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_1193 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
Ailuropoda melanoleuca	ENSAMEG00000015401	1 retrocopy	retro_amel_1120,
Canis familiaris	ENSCAFG00000010960	1 retrocopy	retro_cfam_2178,
Choloepus hoffmanni	ENSCHOG00000012828	1 retrocopy	retro_chof_1480,
Felis catus	ENSFCAG00000030784	1 retrocopy	retro_fcat_1193 ,
Loxodonta africana	ENSLAFG00000008129	1 retrocopy	retro_lafr_304,
Mustela putorius furo	ENSMPUG00000002043	1 retrocopy	retro_mputfur_668,
Mus musculus	ENSMUSG00000024982	1 retrocopy	retro_mmus_1740,
Otolemur garnettii	ENSOGAG00000030535	1 retrocopy	retro_ogar_1652,
Ictidomys tridecemlineatus	ENSSTOG00000013840	1 retrocopy	retro_itri_308,
Tarsius syrichta	ENSTSYG00000009673	2 retrocopies	retro_tsyr_1653, retro_tsyr_1771,