RetrogeneDB ID: retro_fcat_1650

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: E1:22409088..22409479(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSFCAG00000006383
• Aliases: None
• Description: None

Sequence

>retro_fcat_1650
TGCTCCTGGCTGCACAGCAAACCGACTTTCAGCCTGCCCACAGTGTTGCTTAACCTGTACAGGAATCCACAGAACACAGC
CCAAACCACGGATCGACTGCACTGTCACAGGAGTGACGTGCAGGCACTAGAACCCTAGGATGACTTCTCGGAGGAAGTGT
TCCCGGAGCTGCAGGAGAAGTAGGCAGAGATGGAAGAGATAAATGTGTGCTGAGGGGCAGGGGGAGGGGACCACCTCGAG
GGCTATGTCTAGGTGAAGTTTCCATGGCTAGAGGAGGAGGCAGCACAAACAGGGGCTGAAGTCAATAACCGCTGGTTCAA
CTGGCTGCCCATGCTTCATGGGGAGCTGTCTCCTGTCAACGACTTCCTGGGAGTCTCCCTGTGGGCAGTAT

Alignment

ORF - retro_fcat_1650 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.6 %
• Parental protein coverage: 50.81 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  CSRLHNKPTFSQTIVLLNLYRNPQNTAQTADGSHCHVSDVEVQEHYDNFFEEVFTELQEKYGEIEEMNVC
          CS.LH.KPTFS...VLLNLYRNPQNTAQT.D..HCH.SDV...E..D.F.EEVF.ELQEK..E.EE.NVC
Retrocopy CSWLHSKPTFSLPTVLLNLYRNPQNTAQTTDRLHCHRSDVQALEP*DDFSEEVFPELQEK*AEMEEINVC

Parental  DNL--GDHLVGNVYVKFR-REEDAERAVAELNNRWFNG-QAVHAELSPVTDFR-ESCCRQY
          .....GDHL.G.V.VKF...EE.A....AE.NNRWFN.....H.ELSPV.DF..ES.C.QY
Retrocopy *GAGGGDHLEGYV*VKFPWLEEEAAQTGAEVNNRWFNWLPMLHGELSPVNDFL>ESPCGQY

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	18.55 RPM
SRP017611_liver	0.00 RPM	9.00 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_1650 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_1650 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
Felis catus	ENSFCAG00000006383	1 retrocopy	retro_fcat_1650 ,
Felis catus	ENSFCAG00000009333	1 retrocopy	retro_fcat_44,
Gorilla gorilla	ENSGGOG00000016828	1 retrocopy	retro_ggor_150,
Loxodonta africana	ENSLAFG00000012923	1 retrocopy	retro_lafr_1090,
Mus musculus	ENSMUSG00000078765	1 retrocopy	retro_mmus_540,
Oryctolagus cuniculus	ENSOCUG00000013434	1 retrocopy	retro_ocun_1184,
Sus scrofa	ENSSSCG00000002896	1 retrocopy	retro_sscr_543,