RetrogeneDB ID: retro_fcat_1924

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: X:63974934..63975720(+)
• Located in intron of: ENSFCAG00000022051

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSFCAG00000001625
• Aliases: None
• Description: None

Sequence

>retro_fcat_1924
CTCAGTCAGGACATCCAGGAGATGAAAGATGAGAGTGCTAGGATGGCGCAAGAAAGGCAAGTCACTATGCTGGAGCTATT
CAGAGTGTCCAGTTACTGACAACATATTGTCATTTCCACCATACTCCAGCTCTCCCAGCAGCTCTCTCAAATCAATGCTA
TGTTCTGTTACTCAATAGGAATCTTCAAAGATGCAGATGTTGGGGAGCCAGTCTATACCACCATTGGTGCGGGTATGGTT
AATACTGTCTTCACTGCAGTTTCTCTGTTTCTGGTCAAAAGAGCAGGGAGGAAGACTCTACTTCTGATTAGCCTTGGATA
CATGGCATTTTGTTCCATCCTCATGACTGTTTCTTTGTTATTAAAGGACAAGTATAATTGGAAGAGCTTTGTCTGTATTG
TGTCTGTCTTGGTCTTTGTGCCGTTTTTTGAAATTGGCCCAGGCTCCATGCCCTGGTTTATTGTGTCGAAACTCTTCATC
CATGTACTCCACCCAGCTGCAATGGCAGAGGCTGGTTATTCCAATGGGACCTCCAACTTTTTGGTTGGGCTGCTCTTCCC
CCTCAGCTGCATTCTATTTAGGAACCTACATTTTTATTGTATTCACTGGCTTCCTTGTTATCTTCTTTGTCTTCATCTTT
TCAAAGTCCCTGATACCTATGGCAGGACTTTTGAGGAAATTACATGAGCCTTTGAAGGGCAGGTTAAGGAGGCCGGTCGA
GCTGACAAAGGCCTCATTGTGGAGATTAATAGCATCCAACCCGTTAAGGAGACCACCACCAATGTC

Alignment

ORF - retro_fcat_1924 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.24 %
• Parental protein coverage: 52.61 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VTQDIQEMKDESARMAQEKQPTVLELFRSPSYQQPIIISIMLQLSQQLSGINAVFYYSTGIFKDAGVEEP
          ..QDIQEMKDESARMAQE.Q.T.LELFR..SY.Q.I.IS..LQLSQQLS.INA.F.YS.GIFKDA.V.EP
Retrocopy LSQDIQEMKDESARMAQERQVTMLELFRVSSY*QHIVISTILQLSQQLSQINAMFCYSIGIFKDADVGEP

Parental  IYATIGAGVVNTIFTVVSLFLVERAGRRTLHMIGLGGMAFCSILMTISLLLKDNYNWMSFVCIAAILVFV
          .Y.TIGAG.VNT.FT.VSLFLV.RAGR.TL..I.LG.MAFCSILMT.SLLLKD.YNW.SFVCI...LVFV
Retrocopy VYTTIGAGMVNTVFTAVSLFLVKRAGRKTLLLISLGYMAFCSILMTVSLLLKDKYNWKSFVCIVSVLVFV

Parental  AFFEIGPGPIPWFIVAELFSQGPRPAAMAVAGCSNWTSNFLVGLLF-PSAAFYLGAYVFIIFTGFLVIFL
          .FFEIGPG..PWFIV..LF.....PAAMA.AG.SN.TSNFLVGLLF.PSAAFYLG.Y.FI.FTGFLVIF.
Retrocopy PFFEIGPGSMPWFIVSKLFIHVLHPAAMAEAGYSNGTSNFLVGLLF>PSAAFYLGTYIFIVFTGFLVIFF

Parental  IFTF-FKVPETRGRTFEEITRAFEGQAREAVRGEKGPIVEMNSIQPVKETATSV
          .F.F.FKVP.T.GRTFEEIT.AFEGQ..EA.R..KG.IVE.NSIQPVKET.T.V
Retrocopy VFIF<FKVPDTYGRTFEEIT*AFEGQVKEAGRADKGLIVEINSIQPVKETTTNV

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	0.11 RPM	86.77 RPM
SRP017611_kidney	0.00 RPM	5.26 RPM
SRP017611_liver	0.00 RPM	1.72 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_1924 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_1924 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 15 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000004556	2 retrocopies	retro_btau_708, retro_btau_709,
Callithrix jacchus	ENSCJAG00000018988	1 retrocopy	retro_cjac_446,
Cavia porcellus	ENSCPOG00000003074	1 retrocopy	retro_cpor_761,
Cavia porcellus	ENSCPOG00000009834	1 retrocopy	retro_cpor_760,
Cavia porcellus	ENSCPOG00000011295	1 retrocopy	retro_cpor_587,
Felis catus	ENSFCAG00000001625	1 retrocopy	retro_fcat_1924 ,
Homo sapiens	ENSG00000059804	2 retrocopies	retro_hsap_3983, retro_hsap_401,
Gorilla gorilla	ENSGGOG00000016813	1 retrocopy	retro_ggor_398,
Macaca mulatta	ENSMMUG00000000439	2 retrocopies	retro_mmul_2301, retro_mmul_502,
Nomascus leucogenys	ENSNLEG00000026903	2 retrocopies	retro_nleu_1572, retro_nleu_1904,
Oryctolagus cuniculus	ENSOCUG00000008575	1 retrocopy	retro_ocun_352,
Pongo abelii	ENSPPYG00000004234	1 retrocopy	retro_pabe_3274,
Pongo abelii	ENSPPYG00000004235	1 retrocopy	retro_pabe_315,
Pan troglodytes	ENSPTRG00000004624	1 retrocopy	retro_ptro_2703,
Pan troglodytes	ENSPTRG00000004626	1 retrocopy	retro_ptro_307,