RetrogeneDB ID: retro_fcat_1323

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: C2:16749110..16749348(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PFDN1
• Ensembl ID: ENSFCAG00000001272
• Aliases: None
• Description: prefoldin subunit 1 [Source:HGNC Symbol;Acc:8866]

Sequence

>retro_fcat_1323
AAACGCATGCACATCTTACAGATAAGGAGATTATGCCTGCTGAATAACAGTAATGTATATGAAGGTGTAGGAGAAATGTT
TATGCTTCAGACCAAGGAGGCAATTCACAATCAACTGTTAGAGAAACAAAAATAGAAGAACAATTAAAGAATTGGAACAG
AAAGAAATCCTACCTGGAGCGGTGTTTGTTTCTGCCGAGGACAACATCTGGGATGTGGTGATGGCACCAAAGGCACAG

Alignment

ORF - retro_fcat_1323 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 53.01 %
• Parental protein coverage: 66.39 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KHAHLTDTEIMTLIDETNMYEGVGRMFILQSKEVIHNQLLEKQK-IAEEKIKELEQKKSYLERSV-KEAE
          K..H........L....N.YEGVG.MF.LQ.KE.IHNQLLEKQK.I.E...K....KKSYLER.....AE
Retrocopy KRMHILQIRRLCLLNNSNVYEGVGEMFMLQTKEAIHNQLLEKQK<IEEQ-LKNWNRKKSYLERCL<VSAE

Parental  DNIREMLMARRAQ
          DNI....MA..AQ
Retrocopy DNIWDVVMAPKAQ

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	19.86 RPM
SRP017611_kidney	0.00 RPM	21.85 RPM
SRP017611_liver	0.00 RPM	11.52 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_1323 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_1323 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 9 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000005742	8 retrocopies	retro_cfam_1742, retro_cfam_1893, retro_cfam_1943, retro_cfam_251, retro_cfam_276, retro_cfam_417, retro_cfam_788, retro_cfam_997,
Equus caballus	ENSECAG00000011843	1 retrocopy	retro_ecab_53,
Echinops telfairi	ENSETEG00000019281	1 retrocopy	retro_etel_1629,
Felis catus	ENSFCAG00000001272	1 retrocopy	retro_fcat_1323 ,
Macropus eugenii	ENSMEUG00000002726	3 retrocopies	retro_meug_380, retro_meug_686, retro_meug_801,
Microcebus murinus	ENSMICG00000000349	1 retrocopy	retro_mmur_1121,
Oryctolagus cuniculus	ENSOCUG00000009432	4 retrocopies	retro_ocun_1049, retro_ocun_1885, retro_ocun_804, retro_ocun_999,
Otolemur garnettii	ENSOGAG00000003376	6 retrocopies	retro_ogar_1025, retro_ogar_1216, retro_ogar_1412, retro_ogar_2217, retro_ogar_3129, retro_ogar_89,
Rattus norvegicus	ENSRNOG00000018653	1 retrocopy	retro_rnor_985,