RetrogeneDB ID: retro_fcat_1784

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: F1:36634548..36634826(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSFCAG00000027354
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PFDN6
• Ensembl ID: ENSFCAG00000028199
• Aliases: None
• Description: prefoldin subunit 6 [Source:HGNC Symbol;Acc:4926]

Sequence

>retro_fcat_1784
GAGCTAATCCAGAAGAAGCTACAGGGAGACGTGGAGAAAGAGCTTGAGCTACAGCAGGATTTGAGTAAATCCATGTTAGG
GAGGCAGAAGCTTGAGGCGCAACTAACAGAAAATGATATCGTGGCCCTGCTGGATGGGCCCAACGTGGTCTTTACACTTC
TGGTTTCCTGCTGGTCAGGCAGGAGCGGGGAGAGGCTCCAGCCACAGGGGGGAAGAGGCTGGACTACATCACTGCGGATA
TTGAGCGCTGCGACCGCAGAAGGCAGTCGAGCAACAGA

Alignment

ORF - retro_fcat_1784 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.37 %
• Parental protein coverage: 75.19 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ELIQKKLQGEVEKYQQLQKDLSKSMSGRQKLEAQLTENNIVKEELALLDGSNVVFKLL-GPVLVKQELGE
          ELIQKKLQG.VEK...LQ.DLSKSM.GRQKLEAQLTEN.IV....ALLDG.NVVF.LL.G..LV.QE.GE
Retrocopy ELIQKKLQGDVEKELELQQDLSKSMLGRQKLEAQLTENDIV----ALLDGPNVVFTLL<GFLLVRQERGE

Parental  ARATVGKRLDYITAEIKRYESQLRDLER
          A.AT.GKRLDYITA.I.R.........R
Retrocopy APATGGKRLDYITADIERCDRRRQSSNR

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	7.00 RPM
SRP017611_kidney	0.00 RPM	13.71 RPM
SRP017611_liver	0.00 RPM	6.57 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_1784 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_1784 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 12 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001576	2 retrocopies	retro_amel_221, retro_amel_824,
Bos taurus	ENSBTAG00000010723	1 retrocopy	retro_btau_619,
Canis familiaris	ENSCAFG00000000956	2 retrocopies	retro_cfam_1749, retro_cfam_1981,
Dipodomys ordii	ENSDORG00000013828	1 retrocopy	retro_dord_453,
Felis catus	ENSFCAG00000028199	1 retrocopy	retro_fcat_1784 ,
Macropus eugenii	ENSMEUG00000016778	1 retrocopy	retro_meug_1930,
Microcebus murinus	ENSMICG00000000922	1 retrocopy	retro_mmur_1520,
Mustela putorius furo	ENSMPUG00000002364	1 retrocopy	retro_mputfur_608,
Oryctolagus cuniculus	ENSOCUG00000010559	1 retrocopy	retro_ocun_711,
Otolemur garnettii	ENSOGAG00000028341	4 retrocopies	retro_ogar_1185, retro_ogar_2023, retro_ogar_3508, retro_ogar_85,
Ochotona princeps	ENSOPRG00000000983	1 retrocopy	retro_opri_12,
Pteropus vampyrus	ENSPVAG00000001910	1 retrocopy	retro_pvam_391,