RetrogeneDB ID: retro_fcat_165

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: A1:100662492..100663031(+)
• 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_165
GTGTTAGTATCCGGAGACTTTACAACCCACACTGGTGCAACAGGTTGCCAGCTACATTCAAGAAACTGCTGGTGCCAGGA
AAGATTCAGCCCCTTCTCTGTCCGGGAAACCTTTGGAGCAAAGAGAGTTATGACTATCTCAAAACTCAGATCAGTGAGGT
TCGTATTGTGAGAGGAGATGTTCGTGGGAATCTGAATTATCCAGAACAGAAAGGGCTGACTGGTAGGCAGTTTAGAATTG
GCTGGTTCCCTGGGCATCCAGTTATTCCTTGGGGAGGCACAGCCAGCTTAGCCCTGTTGCACAGTGAGTCTGATGTGGAC
ATTCTTATCTCGGGACACACACACAAATTCGAAGCATTCGAGCATGAAAATAAATTTTATGTTAACCCAGGTCCTGCCAC
TGGAGCACATAATGCCTTGGAAACAAACATGATTCCTTCATTCATGTTGATGGATAGCCAGGCTTCCACAGCTGTCACTT
ATGTGTAGCAGCTAATTGGAGATGATGTGAAAGTCGCATGAATTGAATACAAAAAATCT

Alignment

ORF - retro_fcat_165 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.14 %
• Parental protein coverage: 96.77 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VLVLGD-LHIPHRCNSLPAKFKKLLVPGKIQHILCTGNLCTKESYDYLKTLAGDVHIVRGDFDENLNYPE
          VLV.GD.L..PH.CN.LPA.FKKLLVPGKIQ..LC.GNL..KESYDYLKT....V.IVRGD...NLNYPE
Retrocopy VLVSGD<LYNPHWCNRLPATFKKLLVPGKIQPLLCPGNLWSKESYDYLKTQISEVRIVRGDVRGNLNYPE

Parental  QKVVTVGQFKIGLIHGHQVIPWGDMASLALLQRQFDVDILISGHTHKFEAFEHENKFYINPGSATGAYNA
          QK..T..QF.IG...GH.VIPWG..ASLALL....DVDILISGHTHKFEAFEHENKFY.NPG.ATGA.NA
Retrocopy QKGLTGRQFRIGWFPGHPVIPWGGTASLALLHSESDVDILISGHTHKFEAFEHENKFYVNPGPATGAHNA

Parental  LETNIIPSFVLMDIQASTVVTYVYQLIGDDVKVERIEYKKS
          LETN.IPSF.LMD.QAST.VTYV.QLIGDDVKV..IEYKKS
Retrocopy LETNMIPSFMLMDSQASTAVTYV*QLIGDDVKVA*IEYKKS

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_165 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_165 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,