RetrogeneDB ID: retro_fcat_848

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: B3:72713958..72714459(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: VPS29
• Ensembl ID: ENSFCAG00000004135
• Aliases: None
• Description: vacuolar protein sorting 29 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:14340]

Sequence

>retro_fcat_848
TTGGTGTTGGTATTAGGAGACCTACACATTCCATACCAGTCCAACAAGTTTGCTGCCTACATTTAAAAAAACTGCAGGTC
CCAGGAAAGAGTCAACACATTCTCTGTACTGGAAACCTTTGCCCCAAAGAGAGTTAAGACTATCTCAAGACTCTGGTCAG
TGATGTTCATGTTGTGAGAGAAGACTTCAATGAGAATCTGAATTATCCAGAACAGAAAGTTGTGACTGTTGGCACTTCAA
AATTAATTTGATCCATGGGTATCATGTTACTCTATGGGGAATGTGGCCACATTAGCCCTGTTGCAGAGGGAGTTTGATGT
GAATATTCATATCTTGAGACACACACACAAATTTGAAGCATTTGAGCATGAAAATAAATTTTACAATAACTCAGGTTCTG
CCACTGGGGCATATAATGCCTTGGAAGCAAACATTATTCCTTCATTTGTGTTGATGGATATCCAGGCTTCTACAGTTGTC
ACTTATGTGTATCAGCTAATT

Alignment

ORF - retro_fcat_848 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.95 %
• Parental protein coverage: 89.78 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  LVLVLGDLHIPHRCN-SLPAKFK-KLLVPGKIQHILCTGNLCTKESYDYLKTLAGDVHIVRGDFDENLNY
          LVLVLGDLHIP...N.SL...FK.KL.VPGK.QHILCTGNLC.KES.DYLKTL..DVH.VR.DF.ENLNY
Retrocopy LVLVLGDLHIPYQSN>SLLPTFK>KLQVPGKSQHILCTGNLCPKES*DYLKTLVSDVHVVREDFNENLNY

Parental  PEQKVVTVG-QFKIGLIHGHQVIPW-GDMASLALLQRQFDVDILISGHTHKFEAFEHENKFYINPGSATG
          PEQKVVTVG..FKI.LIHG..V..W.G..A.LALLQR.FDV.I.I..HTHKFEAFEHENKFY.N.GSATG
Retrocopy PEQKVVTVG<HFKINLIHGYHVTLW<GNVATLALLQREFDVNIHILRHTHKFEAFEHENKFYNNSGSATG

Parental  AYNALETNIIPSFVLMDIQASTVVTYVYQLI
          AYNALE.NIIPSFVLMDIQASTVVTYVYQLI
Retrocopy AYNALEANIIPSFVLMDIQASTVVTYVYQLI

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	43.15 RPM
SRP017611_kidney	0.00 RPM	73.27 RPM
SRP017611_liver	0.00 RPM	34.47 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_848 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_848 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 6 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000001891	1 retrocopy	retro_acar_30,
Felis catus	ENSFCAG00000004135	2 retrocopies	retro_fcat_165, retro_fcat_848 ,
Loxodonta africana	ENSLAFG00000006176	1 retrocopy	retro_lafr_1115,
Oryctolagus cuniculus	ENSOCUG00000011924	1 retrocopy	retro_ocun_1611,
Tupaia belangeri	ENSTBEG00000012756	4 retrocopies	retro_tbel_1121, retro_tbel_2187, retro_tbel_330, retro_tbel_4424,
Tursiops truncatus	ENSTTRG00000015090	2 retrocopies	retro_ttru_1404, retro_ttru_1492,