RetrogeneDB ID: retro_fcat_1898

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: X:18836026..18836862(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSFCAG00000027648
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PTGR1
• Ensembl ID: ENSFCAG00000004339
• Aliases: None
• Description: prostaglandin reductase 1 [Source:HGNC Symbol;Acc:18429]

Sequence

>retro_fcat_1898
AGAGTGACAGCCTAAAGACTGAACGAGGGTAATATGATGATGGGGCAACAAGTGGCCACAGTTGTGCAAAGTAAAAACTC
AGCCTTCCCAACAGGAACTATGGTAGTGGCTTCTTCAGGCTGGACAACTCACTCCGTTTCTGATGGGAAAGATCTGGAAA
AACTGCCTGCAGAGTGGCCAGACACGTTACCACTATCTTTGGCTCTGGGAATGATTGGCATGACAGGGCTAACAGCCTAC
TTTGGCTTACCTGACATCTGTGGTGTGAAGAGTGGAGAAATGGTGCAGGTTAATGCAGCACTGGGAGCATGGGGCTCTGC
TGTGGGCCAGACAGCTAAGCTCAGAACCGCAAAGTTGTTGGCGCAGCAGGGTCTGGTGAAAAGCTCGCCTACCTTAAAAT
GCTTGGATGTGATGGTGCCTTTAACTACAAAACAGTAGAGTCTTTGGAAGAAAACTTTGAAAAAGCCTCTCCTGATGGTT
ATGATTGTTATTTTGATAATGTAGGTGGAGAGTTTTCAAACATTGTTATCTCCCAGACGAAGAAATTTGGAAGAACTGCT
ATATGTGGGGCCATCTCTGTATATAATCCTACTCGCCCACTTCCCCCAGGCCCACCCCCAGAGAATATTCTCTATCAGCA
ACACCGCATGGAAGGGTTCATCATCACCCGCTGGCAAGGAGATGTCTGCCAGAAGGCTCTGAAAGACTTGCTGAGATGGG
TATTAGAGGGTAAAATCCAGTCCCATGAAAACATCACTGAAGAGTTTGAAACCATGCCAGCTGCATTTATGGGAATGCTG
AAAGGCGCTAATTTGGGGAAAACAATAGTGAAAGCA

Alignment

ORF - retro_fcat_1898 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.93 %
• Parental protein coverage: 84.8 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RVAAKRLKEGDTMMGQQVARVVESKNSAFPTGTMVVASSGWTTHSISDGKDLEKLPAEWPDTLPVSLALG
          RV.A.RL.EG..MMGQQVA.VV.SKNSAFPTGTMVVASSGWTTHS.SDGKDLEKLPAEWPDTLP.SLALG
Retrocopy RVTA*RLNEGNMMMGQQVATVVQSKNSAFPTGTMVVASSGWTTHSVSDGKDLEKLPAEWPDTLPLSLALG

Parental  TVGMTGLTAYFGLLDICGVKGGETVMVNAAAGAVGSAVGQIAKLKGCK-VVGAAGSDEKVAYLKKLGYDV
          ..GMTGLTAYFGL.DICGVK.GE.V.VNAA.GA.GSAVGQ.AKL...K.VVGAAGS.EK.AYLK.LG.D.
Retrocopy MIGMTGLTAYFGLPDICGVKSGEMVQVNAALGAWGSAVGQTAKLRTAK<VVGAAGSGEKLAYLKMLGCDG

Parental  AFNYKTVESLEETLKKASPDGYDCYFDNVGGEFSNIVIPQMKKFGRIAICGAISVYNTTRPLPPGPPPEN
          AFNYKTVESLEE...KASPDGYDCYFDNVGGEFSNIVI.Q.KKFGR.AICGAISVYN.TRPLPPGPPPEN
Retrocopy AFNYKTVESLEENFEKASPDGYDCYFDNVGGEFSNIVISQTKKFGRTAICGAISVYNPTRPLPPGPPPEN

Parental  IIYQQLRMEGFIVTRWQGDVRQKALKDLLTWVLEGKIQYREYITEGFENMPAAFMGMLKGENLGKTIVKA
          I.YQQ.RMEGFI.TRWQGDV.QKALKDLL.WVLEGKIQ..E.ITE.FE.MPAAFMGMLKG.NLGKTIVKA
Retrocopy ILYQQHRMEGFIITRWQGDVCQKALKDLLRWVLEGKIQSHENITEEFETMPAAFMGMLKGANLGKTIVKA

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	1.72 RPM
SRP017611_kidney	0.00 RPM	44.62 RPM
SRP017611_liver	0.00 RPM	23.35 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_1898 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_1898 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 8 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000003000	2 retrocopies	retro_cfam_1290, retro_cfam_1876,
Callithrix jacchus	ENSCJAG00000017571	1 retrocopy	retro_cjac_1653,
Echinops telfairi	ENSETEG00000006136	1 retrocopy	retro_etel_358,
Felis catus	ENSFCAG00000004339	1 retrocopy	retro_fcat_1898 ,
Homo sapiens	ENSG00000106853	1 retrocopy	retro_hsap_219,
Nomascus leucogenys	ENSNLEG00000017487	1 retrocopy	retro_nleu_2424,
Otolemur garnettii	ENSOGAG00000011144	1 retrocopy	retro_ogar_2834,
Pongo abelii	ENSPPYG00000019499	1 retrocopy	retro_pabe_283,