RetrogeneDB ID: retro_fcat_387

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: A2:91906046..91906550(-)
• Located in intron of: ENSFCAG00000027959

Retrocopy information

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

Parental gene information

• Parental gene symbol: THEM4
• Ensembl ID: ENSFCAG00000003443
• Aliases: None
• Description: thioesterase superfamily member 4 [Source:HGNC Symbol;Acc:17947]

Sequence

>retro_fcat_387
CTGCGTGGCCCACAGGGAGATGAGTCCTCACCGTCAAGGGATCCACGGCCACTTCCAAGGTTGTTTTATTCTGAGAAGGT
CATTTATAAGGACCATGCTCTTCCTAGCCCCAGCTGGAGCAAGGACATGAGCCTCCTCTTTGACCAGCTCCTGAGGAAAG
GTGCAGACAGCTCCTGGAAACATTTGCCTTCATATACAAATGTAAATCTACTGGAAAGATCAAAGACTTCAAAACCTTTT
TTCCTCACACAAAGCCTATAAAAGAACAAATGTCACAGACCCCACTCTTTCCCAGAAGTTTTGAGGAAGGCCTGAGCTTT
GAATATGCAATGTTTCATAGTCATGCTGAAGAAAAGATATTTGCATATTTCAATGAGATACTTACTTGCAAGGAGCACGT
AGATTCCTTCGTGGAGGTGCATTGCCACCATGATTACAGCTGCTGTTGGTATGTCTGCAGTTACAGCCAGGGGAATTGCC
CTGGCTGCCAATCTCAACATCAGC

Alignment

ORF - retro_fcat_387 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.23 %
• Parental protein coverage: 70.76 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  LRGQPGVAPLPAKDPWS-PRRSFSSEVIHMDLSLPNPSWNEDMRLLFDQFMKKSEDGSWKHLPSYKS-KF
          LRG..G....P..DP...PR...S..VI..D..LP.PSW..DM.LLFDQ...K..D.SWKHLPSY.....
Retrocopy LRGPQGDESSPSRDPRPLPRLFYSEKVIYKDHALPSPSWSKDMSLLFDQLLRKGADSSWKHLPSYTNVNL

Parental  TQRTE-DIKIYFPDAKLMKEKLSQAQLFPRSLEEGLGFEYAMFHNCVEDRI-VCIFQGGPYLQGAPGFLH
          ..R...D.K..FP..K..KE..SQ..LFPRS.EEGL.FEYAMFH...E..I..CIFQ...YLQGA..FL.
Retrocopy LERSK<DFKTFFPHTKPIKEQMSQTPLFPRSFEEGLSFEYAMFHSHAEEKI<ICIFQ*DTYLQGARRFLR

Parental  GGA-IATMIDATLGMCAVVAVGVAMTASLNIS
          GGA.IATMI.A..GM.AV.A.G.A..A.LNIS
Retrocopy GGA<IATMITAAVGMSAVTARGIALAANLNIS

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	1.26 RPM
SRP017611_kidney	0.00 RPM	10.31 RPM
SRP017611_liver	0.00 RPM	9.40 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_387 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_387 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 13 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000000355	1 retrocopy	retro_amel_1301,
Choloepus hoffmanni	ENSCHOG00000000818	1 retrocopy	retro_chof_841,
Dasypus novemcinctus	ENSDNOG00000005970	1 retrocopy	retro_dnov_710,
Felis catus	ENSFCAG00000003443	1 retrocopy	retro_fcat_387 ,
Homo sapiens	ENSG00000159445	2 retrocopies	retro_hsap_1569, retro_hsap_978,
Gorilla gorilla	ENSGGOG00000008114	2 retrocopies	retro_ggor_1195, retro_ggor_782,
Microcebus murinus	ENSMICG00000010696	4 retrocopies	retro_mmur_1241, retro_mmur_1436, retro_mmur_1505, retro_mmur_1574,
Nomascus leucogenys	ENSNLEG00000010322	1 retrocopy	retro_nleu_1737,
Oryctolagus cuniculus	ENSOCUG00000005194	1 retrocopy	retro_ocun_1341,
Pongo abelii	ENSPPYG00000000851	1 retrocopy	retro_pabe_1295,
Pan troglodytes	ENSPTRG00000001301	2 retrocopies	retro_ptro_1056, retro_ptro_768,
Tupaia belangeri	ENSTBEG00000003352	2 retrocopies	retro_tbel_2412, retro_tbel_3266,
Tarsius syrichta	ENSTSYG00000005739	1 retrocopy	retro_tsyr_579,