RetrogeneDB ID: retro_fcat_1978

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: X:41119457..41119720(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: POLR3K
• Ensembl ID: ENSFCAG00000009110
• Aliases: None
• Description: polymerase (RNA) III (DNA directed) polypeptide K, 12.3 kDa [Source:HGNC Symbol;Acc:14121]

Sequence

>retro_fcat_1978
CTCTTCCACCCGGACTAGAGGAATGGGCTGATCGTGGAGGAGGGACAGTGCTCCCGCCGCTTCGCCTGCAACACCTGCCC
CTACCTGCACAACATCACCTGCAAGGTAACAAAACAAAGTATCCAAAGCTGAAAGAAGTGGATGATGTGCTTGGTGGAGC
ACCTGCCTGGGAGAATGTTGACTCCACTGCAGAGTCATGTCCTAAATGCGACCATCCTCTTGCCTATTTCAAGCAGCTTC
TGCAGACTAGCCAATGACCACCT

Alignment

ORF - retro_fcat_1978 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.28 %
• Parental protein coverage: 81.48 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LFCPGCGNGLIVEEGQRCHRFACNTCPYVHNITRKVTNR-KYPKLKEVDDVLGGAAAWENVDSTAESCPK
          LF.P...NGLIVEEGQ...RFACNTCPY.HNIT.KVT...KYPKLKEVDDVLGGA.AWENVDSTAESCPK
Retrocopy LFHPD*RNGLIVEEGQCSRRFACNTCPYLHNITCKVTKQ<KYPKLKEVDDVLGGAPAWENVDSTAESCPK

Parental  CEHPRAYFMQLQTRSADEP
          C.HP.AYF.QL...S...P
Retrocopy CDHPLAYFKQLLQTSQ*PP

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	5.16 RPM
SRP017611_kidney	0.00 RPM	6.08 RPM
SRP017611_liver	0.00 RPM	3.54 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_1978 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_1978 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 11 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000019715	1 retrocopy	retro_cfam_1881,
Callithrix jacchus	ENSCJAG00000011568	1 retrocopy	retro_cjac_2660,
Echinops telfairi	ENSETEG00000009989	2 retrocopies	retro_etel_1166, retro_etel_1543,
Felis catus	ENSFCAG00000009110	2 retrocopies	retro_fcat_1978 , retro_fcat_409,
Homo sapiens	ENSG00000161980	1 retrocopy	retro_hsap_1861,
Myotis lucifugus	ENSMLUG00000015593	3 retrocopies	retro_mluc_1565, retro_mluc_1943, retro_mluc_341,
Oryctolagus cuniculus	ENSOCUG00000013608	1 retrocopy	retro_ocun_145,
Otolemur garnettii	ENSOGAG00000002526	2 retrocopies	retro_ogar_1101, retro_ogar_254,
Pan troglodytes	ENSPTRG00000007525	1 retrocopy	retro_ptro_1241,
Pteropus vampyrus	ENSPVAG00000000530	1 retrocopy	retro_pvam_928,
Sus scrofa	ENSSSCG00000007970	1 retrocopy	retro_sscr_1141,