RetrogeneDB ID: retro_fcat_1454

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: D1:76473275..76473724(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSFCAG00000005760
• Aliases: None
• Description: None

Sequence

>retro_fcat_1454
ACCGCTTTGTATAAGTTGACCTTTACACCAACAGGCACCATTGAGTTGGACAATAGATGTTACAAGTGACATCTCAATCT
TCTAAAGGTGAAGCCTCCAATGGAGCCTACAGATACTCTCATATGCCCAGCAGGGCCTTTGTCTTTCCCCTGCCAATTAC
AAACAGAATATGCCCTTACCCTCCTGGCTACTTCTATCCATCACCCCCATCTGACTTCTATCCAGAACTTCCCATGATGA
ACATGGAATAGTTGCAACCATGGCAACCACCCTATTCTGGGCTTATGGAACCTCCAGCCAGCAGCCCTGATGTTCCCTCT
ACTCCTGTAGCTGAAGCCAAGGCCACAGAAGCAGCTGCCGGAGCCAGTTACAACCGGGACAACAAACACAATGCCTACAT
GCCCAGAAACCAGTTTCTGCCACCTTCCTACTACCCCATGGAAGATAAG

Alignment

ORF - retro_fcat_1454 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.05 %
• Parental protein coverage: 58.24 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SAPYKLTFTAGGAIEF-GQRMLQVASQASRGEAPNGAYGYSYMPSGAYVFPPPVANGMYPCPPGYPYPPP
          .A.YKLTFT..G.IE..GQ.MLQV.SQ.S.GEA.NGAY.YS.MPS.A.VFP.P..N...P.PPGY.YP.P
Retrocopy TALYKLTFTPTGTIEL<GQ*MLQVTSQSSKGEASNGAYRYSHMPSRAFVFPLPITNRICPYPPGYFYPSP

Parental  PPEFYPGPPMMDGAMGYVQPPPPPYPGPMEPPVSGPDVPSTPAAEAKAAEAAASAYYNPGNPHNVYMPTT
          P..FYP..PMM...M...QP..PPY.G.MEPP.S.PDVPSTP.AEAKA.EAAA.A.YN..N.HN.YMP..
Retrocopy PSDFYPELPMMN--ME*LQPWQPPYSGLMEPPASSPDVPSTPVAEAKATEAAAGASYNRDNKHNAYMPRN

Parental  QPPPPPYYPPEDK
          Q..PP.YYP.EDK
Retrocopy QFLPPSYYPMEDK

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	178.47 RPM
SRP017611_kidney	0.00 RPM	90.90 RPM
SRP017611_liver	0.00 RPM	31.54 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_1454 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_1454 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 12 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000037619	1 retrocopy	retro_cjac_575,
Felis catus	ENSFCAG00000005760	1 retrocopy	retro_fcat_1454 ,
Homo sapiens	ENSG00000132471	1 retrocopy	retro_hsap_1926,
Gorilla gorilla	ENSGGOG00000009241	2 retrocopies	retro_ggor_1404, retro_ggor_698,
Macropus eugenii	ENSMEUG00000000070	1 retrocopy	retro_meug_579,
Macaca mulatta	ENSMMUG00000009381	2 retrocopies	retro_mmul_1062, retro_mmul_854,
Monodelphis domestica	ENSMODG00000007725	3 retrocopies	retro_mdom_1410, retro_mdom_1847, retro_mdom_375,
Nomascus leucogenys	ENSNLEG00000001625	1 retrocopy	retro_nleu_1214,
Ochotona princeps	ENSOPRG00000006045	2 retrocopies	retro_opri_301, retro_opri_851,
Pongo abelii	ENSPPYG00000008640	3 retrocopies	retro_pabe_693, retro_pabe_75, retro_pabe_913,
Pan troglodytes	ENSPTRG00000009660	1 retrocopy	retro_ptro_15,
Ictidomys tridecemlineatus	ENSSTOG00000021421	2 retrocopies	retro_itri_1585, retro_itri_660,