RetrogeneDB ID: retro_fcat_339

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: A2:100951083..100951776(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TS
• Ensembl ID: ENSFCAG00000009230
• Aliases: None
• Description: Thymidylate synthase [Source:UniProtKB/TrEMBL;Acc:Q9N1D4]

Sequence

>retro_fcat_339
GTGAGAGATTAATTTCCTCTGCTGACAACAAAACGTGTATTCTGAAAGGGTGTTTTGGAGAAGTTGCTGTGGTTTTACCA
AGAGACCTACAAACGCTAGGGAACTGTCCTCCAAGGGAGTGAATATCCGGGATGCCGGTGCACCCTGAGATTTCTTGGAC
AGCCTGGGATTCTCCAACAGAGAAGGGGATTTAGGCCCAGTTTGTGGCTATCAGTAGAGAGGCATTTGGGGGCAGAATAC
AAAGATAAGGATTCAGATTATTCAGGTCAAGGAGTAGACCAAAAGGTCTGCAAAAGGTGACTGACACAACCAAAACCATC
ACCTTTCCTGTGTGGATGGAATCCAAAAGAGCCTCGTCTTATGGCCCTACTTCCATGCCATGCCCTTTGCCAGTCCTACA
CGGTGAACGGTAAGCTGTCCTGACAGCTGTACTGAAGGTCAGGAGACCTGGACCTGGGTGTGCCCTTCCACACCGCCAGC
TCCACCCTGCCCACCTACATACATGATAGTACTGCCCCGAAGCCAGGTGACTTCGTATATACTTTGGGAGATGCACGTAT
TTACCTGAAAATGCAGCTACAGCAAGAACCACTGCCTTTACCCAAGCTCAAAATCCCTCCAAAAGTTGAGACAATTGATG
ACTTCAAGGCTGAGGGCTTTCAGATTGAAGGGTACAATCCTCACTGGACTATT

Alignment

ORF - retro_fcat_339 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.73 %
• Parental protein coverage: 76.27 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LRDEFPLLTTKRVFWKGVLEELLWFI-KGSTNAKELSSKGVKIWDANGSRNFLDSL-GFSNREEGDLGPV
          .RD.FPLLTTKRVF.KGVLE.LLWF..K..TNA.ELSSKGV.I.DA.....FLDSL.G......G.....
Retrocopy VRD*FPLLTTKRVF*KGVLEKLLWFY>KRPTNARELSSKGVNIRDAGAP*DFLDSL<GILQQRRGFRPSL

Parental  YGFQWRHFGAEYKDKDSDYSGQGVDQLQKVIDTIKTNPNDRRIILCGWNPKDLPLMALPPCHALCQFYVV
          .....RH.GAEYKDKDSDYSGQGVDQ..KV.....T.P......LCGWNPK...LMAL.PCHALCQ.Y.V
Retrocopy WLSVERHLGAEYKDKDSDYSGQGVDQ--KVCKR*LTQPKPSPF-LCGWNPKEPRLMALLPCHALCQSYTV

Parental  NGELSCQLYQRSGDMGLGVPFNIASYSLLTYMIAHITGLKPGDFIHTLGDAHIYLNHIEPLKMQLQREPR
          NG.LS.QLY.RSGD..LGVPF..AS..L.TY.I...T..KPGDF..TLGDA.IYL........Q....P.
Retrocopy NGKLS*QLY*RSGDLDLGVPFHTASSTLPTY-IHDSTAPKPGDFVYTLGDARIYLK----MQLQQEPLPL

Parental  PFPKLRILRKVETIDDFKAEDFQIEGYNPHPTI
          P..KL.I..KVETIDDFKAE.FQIEGYNPH.TI
Retrocopy P--KLKIPPKVETIDDFKAEGFQIEGYNPHWTI

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	4.59 RPM
SRP017611_kidney	0.00 RPM	27.10 RPM
SRP017611_liver	0.00 RPM	9.50 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_339 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_339 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 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Felis catus	ENSFCAG00000009230	2 retrocopies	retro_fcat_1107, retro_fcat_339 ,
Loxodonta africana	ENSLAFG00000014910	2 retrocopies	retro_lafr_1030, retro_lafr_635,
Macropus eugenii	ENSMEUG00000009507	1 retrocopy	retro_meug_175,
Monodelphis domestica	ENSMODG00000021479	2 retrocopies	retro_mdom_1084, retro_mdom_1186,
Mustela putorius furo	ENSMPUG00000005419	2 retrocopies	retro_mputfur_1155, retro_mputfur_860,
Mus musculus	ENSMUSG00000025747	1 retrocopy	retro_mmus_584,
Otolemur garnettii	ENSOGAG00000024349	2 retrocopies	retro_ogar_2956, retro_ogar_3211,
Sarcophilus harrisii	ENSSHAG00000003102	1 retrocopy	retro_shar_424,