RetrogeneDB ID: retro_fcat_1894

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: X:14068878..14069303(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FKBP3
• Ensembl ID: ENSFCAG00000027304
• Aliases: None
• Description: FK506 binding protein 3, 25kDa [Source:HGNC Symbol;Acc:3719]

Sequence

>retro_fcat_1894
GTATCTGAGCAGGTGAAAAATGTGAAGTTTAATGAAGACAGACCCAAAGAAACCAAGCCTGAAGAGACTCTAAATGAGGG
TCCACCAAAATAAATTCTGTTCTTAAAAATGGAGATAAAACCAACTTTCCCCAAAAGAGACAGGTTGTTCACTGTTAGTA
TACAGGAACACTATAGGATAGGACTGTTTATGATATTAATATTCAAACAAGTTCAAAGAAGAAGAAAAATGCCAAGGCTT
TAAGTTTTAAGGTTGGAACAGGCAAAGTTACCAGAGGATGGGATGAAGTTCTCTTGACCATGAGTAAAGGAGAAAAGGCT
CGACTAGAGATTGAGCCAGAATGGGCTTATGGAAAGAAAGGACAGCCTGATGCCAAAATTCCACCAAATGCAAAACTCAT
TCTTAAAGTGGAATTACTGGATATT

Alignment

ORF - retro_fcat_1894 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.94 %
• Parental protein coverage: 64.13 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VSEQVKNVKLNEDKPKETKSEETLDE-GPPKYVKSVLKKGDKTNFPKKGDVVHCWYTGTLQDGTVFDTNI
          VSEQVKNVK.NED.PKETK.EETL.E.G..K...SVLK.GDKTNFP.K..VVHC.YTGTL.D.TV.D.NI
Retrocopy VSEQVKNVKFNEDRPKETKPEETLNE<GSTK-INSVLKNGDKTNFPQKRQVVHC*YTGTL*DRTVYDINI

Parental  QTSSKKKKNAKPLSFKVGIGKVIRGWDEALLTMSKGEKARLEIEPEWAYGKKGQPDAKIPPNAKLIFEVE
          QTSSKKKKNAK.LSFKVG.GKV.RGWDE.LLTMSKGEKARLEIEPEWAYGKKGQPDAKIPPNAKLI..VE
Retrocopy QTSSKKKKNAKALSFKVGTGKVTRGWDEVLLTMSKGEKARLEIEPEWAYGKKGQPDAKIPPNAKLILKVE

Parental  LVDI
          L.DI
Retrocopy LLDI

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	50.96 RPM
SRP017611_kidney	0.00 RPM	44.21 RPM
SRP017611_liver	0.00 RPM	24.77 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_1894 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_1894 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 15 parental genes, and 36 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000014018	4 retrocopies	retro_cfam_1788, retro_cfam_440, retro_cfam_616, retro_cfam_798,
Dipodomys ordii	ENSDORG00000009462	1 retrocopy	retro_dord_106,
Felis catus	ENSFCAG00000026097	2 retrocopies	retro_fcat_168, retro_fcat_751,
Felis catus	ENSFCAG00000027304	1 retrocopy	retro_fcat_1894 ,
Loxodonta africana	ENSLAFG00000003572	2 retrocopies	retro_lafr_357, retro_lafr_76,
Macropus eugenii	ENSMEUG00000004962	1 retrocopy	retro_meug_679,
Microcebus murinus	ENSMICG00000005808	2 retrocopies	retro_mmur_1582, retro_mmur_351,
Macaca mulatta	ENSMMUG00000016512	2 retrocopies	retro_mmul_2094, retro_mmul_735,
Monodelphis domestica	ENSMODG00000007352	1 retrocopy	retro_mdom_1554,
Mus musculus	ENSMUSG00000020949	1 retrocopy	retro_mmus_1322,
Otolemur garnettii	ENSOGAG00000003012	2 retrocopies	retro_ogar_2247, retro_ogar_3472,
Ochotona princeps	ENSOPRG00000011126	2 retrocopies	retro_opri_204, retro_opri_600,
Rattus norvegicus	ENSRNOG00000004629	1 retrocopy	retro_rnor_1165,
Ictidomys tridecemlineatus	ENSSTOG00000002249	1 retrocopy	retro_itri_650,
Tupaia belangeri	ENSTBEG00000006017	13 retrocopies	retro_tbel_1032, retro_tbel_1125, retro_tbel_1696, retro_tbel_1783, retro_tbel_2151, retro_tbel_2569, retro_tbel_3297, retro_tbel_3567, retro_tbel_3807, retro_tbel_4222, retro_tbel_4482, retro_tbel_730, retro_tbel_800,