RetrogeneDB ID: retro_fcat_1199

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: C1:86718412..86718852(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GSTA4
• Ensembl ID: ENSFCAG00000005237
• Aliases: None
• Description: glutathione S-transferase alpha 4 [Source:HGNC Symbol;Acc:4629]

Sequence

>retro_fcat_1199
CGAGAACAGTGGCAGAAACTCCAGGATGGTAACCACCTACTGTTCCAACAAGTGCCAATGGTTGAAATTGATGGAATGAA
GTTGGTGCAGACCAGAAGCATTCTCCAACTACATTGTGGAGACCATCATCTCTTTGGCAAGGACCTCAAGGAGAGAACCT
GATTGACATGACTACGGAGGGGATCCTAGATCTCATGGAACTGATTGCTGTTCATCCTTTCCTAAAACCAGATGATCAAC
AAGAAGACATGATAACATGGCCCAGAAGTCTATAATTAGATACTTGCCCATGTTTGAAAAGGTTTTAAAGGATAATGACC
AAAAGGTTTCTTGTTGGTAATTAGCTAAGCCTTGTGGGTGTGATTCTACTCTAAACCATTCTGTCTCTGGAAGAGGAAGT
CCCCAATATCCTGTCTGAACCTCCCAGAGTTCTACAGTGG

Alignment

ORF - retro_fcat_1199 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.67 %
• Parental protein coverage: 66.22 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  KEQLQKLQDGNHLLFQQVPMVEIDGMKLVQTRSILHYIAEKHHLFGKDLKERT-LIDMYVEGTLDLLELI
          .EQ.QKLQDGNHLLFQQVPMVEIDGMKLVQTRSIL......HHLFGKDLKERT.LIDM..EG.LDL.ELI
Retrocopy REQWQKLQDGNHLLFQQVPMVEIDGMKLVQTRSILQLHCGDHHLFGKDLKERT<LIDMTTEGILDLMELI

Parental  IMHPFLKPDDQQKEVV-NMAQKAIIRYFPVFEKVLRDHGQ-RFLVGNQLSLADVILLQTILALEEKIPNI
          ..HPFLKPDDQQ.....NMAQK.IIRY.P.FEKVL.D..Q.RFLVGN.LSL..VILL.TIL.LEE..PNI
Retrocopy AVHPFLKPDDQQEDMI<NMAQKSIIRYLPMFEKVLKDNDQ>RFLVGN*LSLVGVILL*TILSLEEEVPNI

Parental  LSAFPHLQEF
          LS..P.....
Retrocopy LSEPPRVLQW

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	179.39 RPM
SRP017611_kidney	0.00 RPM	116.04 RPM
SRP017611_liver	0.00 RPM	172.86 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_1199 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_1199 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 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000005658	1 retrocopy	retro_amel_787,
Bos taurus	ENSBTAG00000004288	1 retrocopy	retro_btau_670,
Canis familiaris	ENSCAFG00000024066	1 retrocopy	retro_cfam_1440,
Felis catus	ENSFCAG00000005237	1 retrocopy	retro_fcat_1199 ,
Monodelphis domestica	ENSMODG00000018810	1 retrocopy	retro_mdom_954,
Mustela putorius furo	ENSMPUG00000008911	1 retrocopy	retro_mputfur_1383,
Sorex araneus	ENSSARG00000009989	1 retrocopy	retro_sara_769,