RetrogeneDB ID: retro_fcat_1107

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: C1:102125555..102126077(+)
• 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_1107
CAGTTTATAACTTTCAGTGGAAAATACAAAGATAAGAATTCAGATTATTCTGGTCAAGGAGTAGACCAACTGCAAAAGGT
GACTGACACAATCAAAACCAACTGTGATGACAGAAGAATCATCCTGTGTGGGTGGAATCCAAAAGATCTCCCTTTAATGG
CTCCTCTCTGCCATTCCCTTTGCCAGTTCTACCTGGAAAATGGTGAGCTGTCCTGTCAGCTGTACCGGAGCTCAGGAGAC
ATGGGCCTGGTTGTGCCCTCCAGTGTCACCAGCTATGCCCTGCTCACCTACAGGATGGTACACATCACAGGCCTGAAGCC
CAATGACTTCATACATACTTTGGGAGATGCACATATTTACCTGAGTCATGTTGAGCTGCTGAAAATGCAGCTTCAGTGAG
AACCAAGGCCTTTCCCGAAGCTTAAGGTCCTTTGAAAAGTTGAGACAATTGATGACTTCAAGGTTAAAGACTTTCAGATT
GAGGGGTACAATCCTCACCTTACTATAAAAATGGAAATGGCT

Alignment

ORF - retro_fcat_1107 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.29 %
• Parental protein coverage: 55.38 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QWRHFGAEYKDKDSDYSGQGVDQLQKVIDTIKTNPNDRRIILCGWNPKDLPLMALPPCHALCQFYVVNGE
          Q...F...YKDK.SDYSGQGVDQLQKV.DTIKTN..DRRIILCGWNPKDLPLMA.P.CH.LCQFY..NGE
Retrocopy QFITFSGKYKDKNSDYSGQGVDQLQKVTDTIKTNCDDRRIILCGWNPKDLPLMA-PLCHSLCQFYLENGE

Parental  LSCQLYQRSGDMGLGVPFNIASYSLLTYMIAHITGLKPGDFIHTLGDAHIYLNHIEPLKMQLQREPRPFP
          LSCQLY..SGDMGL.VP....SY.LLTY...HITGLKP.DFIHTLGDAHIYL.H.E.LKMQLQ.EPRPFP
Retrocopy LSCQLYRSSGDMGLVVPSSVTSYALLTYRMVHITGLKPNDFIHTLGDAHIYLSHVELLKMQLQ*EPRPFP

Parental  KLRILRKVETIDDFKAEDFQIEGYNPHPTIKMDMA
          KL..L.KVETIDDFK..DFQIEGYNPH.TIKM.MA
Retrocopy KLKVL*KVETIDDFKVKDFQIEGYNPHLTIKMEMA

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_1107 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_1107 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,