RetrogeneDB ID: retro_fcat_18

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: B4:76805494..76806784(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSFCAG00000009338
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: PCED1A
• Ensembl ID: ENSFCAG00000002886
• Aliases: None
• Description: PC-esterase domain containing 1A [Source:HGNC Symbol;Acc:16212]

Sequence

>retro_fcat_18
ACGGCCCACCTGCTGCCTGCCGACGTGCAGCAGCTGCTCCACAACAAGTTCGTGGTCATCCTGGGAGACTCTGTCCAAAG
GGCCGTGTACAAGGACCTGGTGCTCCTGCTGCAGAAGGACCTCCTGCTCACTCCCACCCAGCTCAAGGCCAAGGGGGAGG
AGAGCTTTGAACGGGACAAGCTGGTGGACGGAGGCCAGCGGGGCCCCATGCACAACGGCACCCAGTACCGGGAGGTCCGC
CAGTTCTGCTCCGACCACCACCTGGTGCGCTTCTACTTCCTGACGCGCGTGTACTCCAGCTACCTCGAGGCCATCCTGCA
AGAGCTGCAGTCCAGCCAGCACGGCCCCCCGGACGTGATCATCATGAACTCCTGCCTCTGGGACCTCTCCAGGTACGGTC
CGGACTCCTGGAAGAGCTACCTGGAGAACCTGGAGAGCCTGTTCGAGCGCCTGGGCCAGGTTCTGCCCGAGTCGTGCCTC
CTGGTGTGGAACACAGCCATGCCCGTGGGCAAGAAGATCACCGCGGGCTTCCTCCCGCCGGAGCACCGGCCTGAGGATTC
CTCCCTGAGAGACAGAGTCATCGCGGCCAACTTCCACAGCTCTGTGGAAGCGAAGAAACACGGCTTCGATGTGCTGGACT
TGCACTTCCACTTCCGCCACGCGGGGCGCCACCTGCAGCGGGACGGAGTGCACTGGGACCAGCTCGCGCACCGCCACCTC
TCCCAGCTGCTGCTGGCCCACGTGGCCGACGCCTGGGGCGTGGATCTGCCCCGGCGGTACCCGGTGGGCCCCTGGATCCG
GGATGGCCCCGCGAGGACCGGACCCGGCCGGGGAGTTGAGCGGCAGCCCCAGGCCAGCCCAGATCAACCGTCCTTGCCTC
CTGCCGGGTACCGCCCCCTGCTCCCACTTCCCCATCTACTCCCGCCCCCGCCTCCCCTCCTGCCCTTACCCCCACATCCC
CGCCCTTTTCCCTTTCACCCTGTGATGACCAGATTCCTGTTCGGTCCCCGAGATCACTTTTCTGCCTCAGACCATCCTTT
CCAGTCCGATCAGTTCTCTTCAAACCATTTCCATTCAGATGTCCCCTCACCTACCCAGACAGGATTTTCCTTTGAAGATG
ATCCCCAGCCACCCAGGCCCCCTTTCCCCACACCCTACCTGCAGCGGGCCCCTGTGGTTCATAGGGGGTTTCCCCGGCAT
CTGCCTCGTGGCCCCTATGTGCCCTGGGGTCGGCGGCCCAGATCTTCCAAGAGACAGGCCCCATCCCACCCACAGCCAAG
GCCTCAATAA

Alignment

ORF - retro_fcat_18 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.25 %
• Parental protein coverage: 72.47 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  HFQASEVQQLLHNKFVVILGDSIQRSVYKDLVLLLQRDSLLTAAQLKAKGELSFEQDQLVAGGQLGELHN
          H.....VQQLLHNKFVVILGDS.QR.VYKDLVLLLQ.D.LLT..QLKAKGE.SFE.D.LV.GGQ.G..HN
Retrocopy HLLPADVQQLLHNKFVVILGDSVQRAVYKDLVLLLQKDLLLTPTQLKAKGEESFERDKLVDGGQRGPMHN

Parental  GTQYREVRQFCSGSGHHLVRFYFLTRVYSEYLEGVLEELT---YGPAPDLVIINSCLWDLSRYGRCSMES
          GTQYREVRQFCS...HHLVRFYFLTRVYS.YLE..L.EL.....GP.PD..I.NSCLWDLSRYG..S..S
Retrocopy GTQYREVRQFCSD--HHLVRFYFLTRVYSSYLEAILQELQSSQHGP-PDVIIMNSCLWDLSRYGPDSWKS

Parental  YRENLERVFVRMDQVLPDSCLLVWNMAMPLGERVTGGFLLPELQPLAGSLRRDVVEGNFYSATLAGDHCF
          Y.ENLE..F.R..QVLP.SCLLVWN.AMP.G...T.GFL.PE..P...SLR..V...NF.S...A..H.F
Retrocopy YLENLESLFERLGQVLPESCLLVWNTAMPVGKKITAGFLPPEHRPEDSSLRDRVIAANFHSSVEAKKHGF

Parental  DVLDLHFHFRHAVQHRHRDGVHWDQHAHRHLSHLLLTHVADAWGVELPQRDYPSDPWIEDWPEPDHPFQG
          DVLDLHFHFRHA..H..RDGVHWDQ.AHRHLS.LLL.HVADAWGV.LP.R.YP..PWI.D.P....P..G
Retrocopy DVLDLHFHFRHAGRHLQRDGVHWDQLAHRHLSQLLLAHVADAWGVDLPRR-YPVGPWIRDGPARTGPGRG

Parental  SHGQPPDFGEQLCLPPPQPSPLPPPIPFPYPIPQPSPPPLFPPLPQDTPFFP
          ...QP.....Q..LPP....PL....P.P...P.P.P....PP.P...PF.P
Retrocopy VERQPQASPDQPSLPPAGYRPL---LPLPHLLPPPPPLLPLPPHPRPFPFHP

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	0.34 RPM	24.45 RPM
SRP017611_kidney	0.31 RPM	18.96 RPM
SRP017611_liver	0.10 RPM	8.39 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_18 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_18 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 16 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000003863	1 retrocopy	retro_btau_182,
Cavia porcellus	ENSCPOG00000025475	2 retrocopies	retro_cpor_343, retro_cpor_79,
Equus caballus	ENSECAG00000016497	1 retrocopy	retro_ecab_87,
Felis catus	ENSFCAG00000002886	1 retrocopy	retro_fcat_18 ,
Homo sapiens	ENSG00000132635	2 retrocopies	retro_hsap_2207, retro_hsap_82,
Microcebus murinus	ENSMICG00000016578	2 retrocopies	retro_mmur_163, retro_mmur_278,
Myotis lucifugus	ENSMLUG00000028662	2 retrocopies	retro_mluc_222, retro_mluc_647,
Macaca mulatta	ENSMMUG00000005200	2 retrocopies	retro_mmul_333, retro_mmul_341,
Mus musculus	ENSMUSG00000037773	2 retrocopies	retro_mmus_1001, retro_mmus_332,
Otolemur garnettii	ENSOGAG00000004701	1 retrocopy	retro_ogar_81,
Pongo abelii	ENSPPYG00000010833	2 retrocopies	retro_pabe_192, retro_pabe_2080,
Pan troglodytes	ENSPTRG00000013185	1 retrocopy	retro_ptro_105,
Pteropus vampyrus	ENSPVAG00000006834	1 retrocopy	retro_pvam_9,
Sus scrofa	ENSSSCG00000007168	1 retrocopy	retro_sscr_23,
Ictidomys tridecemlineatus	ENSSTOG00000016356	2 retrocopies	retro_itri_1190, retro_itri_783,
Tursiops truncatus	ENSTTRG00000003464	1 retrocopy	retro_ttru_16,