RetrogeneDB ID: retro_fcat_565

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: B1:124520946..124521359(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: JOSD1
• Ensembl ID: ENSFCAG00000002821
• Aliases: None
• Description: Josephin domain containing 1 [Source:HGNC Symbol;Acc:28953]

Sequence

>retro_fcat_565
GAATCCGAATCTGAATCTTTGGAGCTGCCCCAAGCAGCATCCCCCCAAATCTACCGTGAAAAAACAGCACAGGGACCTTC
GTGCCTTGCATGCCTTCCGTAACAACTTCAAGGACAGCAGTGCCTTTGCCCAGGAAATGCTGCAAGAGATTCTCCAGAGG
TTGTCTCTGAACACCACAGTGATCCCCCCGCCGCGAGCAGAACATGCTGGGAAATGGGAACTAGGACGTGAACGTCATTA
TGGTGGCAGTTCAAGCCAAAGCCTATGATGCTGTCCGGTGGGACGAGCGCAGTGACGTCAGTGCCATTGCTCTCGCTAAA
ATCATGGGATTCATTGTGCATCTGCCCTCCAGCAGGTGCTTCTCACTGAAGTTGCCTCTCAACAGGCAGCACTGGATCTG
TGTTTGAGAGGTG

Alignment

ORF - retro_fcat_565 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.71 %
• Parental protein coverage: 67.82 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KAKSESVELPQAAPPQIYHEK-QRRELCALHALNNVFQDSNAFTRETLQEIFQRLSPNTMV-TPHKK-SM
          ...SES.ELPQAA.PQIY.EK.Q.R.L.ALHA..N.F.DS.AF..E.LQEI.QRLS.NT.V..P.....M
Retrocopy ESESESLELPQAASPQIYREK>QHRDLRALHAFRNNFKDSSAFAQEMLQEILQRLSLNTTV>SPRREQNM

Parental  LGNGNYDVNVIMAALQTKGYEAVWWDKRRDVSAIALTNVMGFIMNLPSSLCWGPLKLPLKRQHWICVREV
          LGNGN.DVNVIM.A.Q.K.Y.AV.WD.R.DVSAIAL...MGFI..LPSS.C...LKLPL.RQHWICV.EV
Retrocopy LGNGN*DVNVIMVAVQAKAYDAVRWDERSDVSAIALAKIMGFIVHLPSSRCFS-LKLPLNRQHWICV*EV

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	17.79 RPM
SRP017611_kidney	0.00 RPM	7.63 RPM
SRP017611_liver	0.00 RPM	6.17 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_565 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_565 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.

---

Parental genes homology:

Parental genes homology involve 15 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000010171	1 retrocopy	retro_btau_1508,
Canis familiaris	ENSCAFG00000001379	1 retrocopy	retro_cfam_1500,
Choloepus hoffmanni	ENSCHOG00000001723	2 retrocopies	retro_chof_1576, retro_chof_233,
Equus caballus	ENSECAG00000015546	1 retrocopy	retro_ecab_251,
Felis catus	ENSFCAG00000002821	1 retrocopy	retro_fcat_565 ,
Macropus eugenii	ENSMEUG00000002899	2 retrocopies	retro_meug_1507, retro_meug_531,
Microcebus murinus	ENSMICG00000011798	1 retrocopy	retro_mmur_1202,
Myotis lucifugus	ENSMLUG00000003764	1 retrocopy	retro_mluc_1868,
Mus musculus	ENSMUSG00000022426	1 retrocopy	retro_mmus_3014,
Otolemur garnettii	ENSOGAG00000007520	3 retrocopies	retro_ogar_1462, retro_ogar_2911, retro_ogar_3487,
Pteropus vampyrus	ENSPVAG00000010148	1 retrocopy	retro_pvam_181,
Rattus norvegicus	ENSRNOG00000014440	2 retrocopies	retro_rnor_2954, retro_rnor_906,
Sarcophilus harrisii	ENSSHAG00000015931	1 retrocopy	retro_shar_643,
Ictidomys tridecemlineatus	ENSSTOG00000024999	1 retrocopy	retro_itri_193,
Tarsius syrichta	ENSTSYG00000008846	1 retrocopy	retro_tsyr_1076,