RetrogeneDB ID: retro_fcat_223

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: A1:36400273..36401192(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSFCAG00000026530
• Aliases: None
• Description: None

Sequence

>retro_fcat_223
TCAAAAAGCCTGGGAGGGCCGCTGAGCGACCCCCGGAGCAGGAGCCAGTCCGAGCCCAGGGCGCCACCACCGCAGGAGCA
ATGTGCAACAGCGTTGCTTTCGTGGCCTGCTCACAGGGGACTGTCCAAGTTCCCGGGATGCAGAATAACACAGCCCATCC
AGAAGAACTAGTCACAAAACTAAAACACATCGGGAAAGTCTCCTTTGGAGAAGTTTTCAAAGGAATTTGATACTGCACCC
AGCAGGTGCTTGCTATTAAAGTCCCAGGCCCCGAGGGAGCCAAAGAAGAAACTGCAGGCATTCAGCAAGAAATCGCTGTT
TTGAGTCAGCGTGACAGCTCATATGTAACAAAATGCTATGGAGCATATTTAGAGCGTTCAAAATTAACAATGGAATACCC
GGGTGGTGGTGGTTCATCCCTGGCTCTTCCTCAAGCTGGTCCATTTGATGAGTGCCAGATCGCTACCCTGCTAAAGGAAA
TGTTGAAAGGTCTGCACTGTCTCCGTTCAGAAAAGAAAATTCACTGAGACAGAAAAAGCTGCCAGCATCTTGCTGTCAGA
ACAAGGAGATGTTAAACCTGCTGACTTTGGAGTTACTGTCCAGCTGACAGATACACAAATTAAAAGAAATACCTTTGTGG
GAATACCATTTCGGATGGTTCCTGAACTTCTTCAACGGTGGGCTTGTAACTCAAAAGCTGACATTTGGTCATTGGGAATT
ACTGCTATTGAACCATCCAAGGCAGAGCCACCTAACTGTGATGTGCATCCAATGAGAGTTCTGTTTCTTATTCCAAAAAA
ATCCCCCAACTCTTGTTGGAGACTTTACTAAGTCCTTTAAGGAGTTTATTGATGCTTGCCTGAACAAAGAACCATGATTT
TGTCCTACAGCTAAAGAACTCCTGAAACACAAATTCATT

Alignment

ORF - retro_fcat_223 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.72 %
• Parental protein coverage: 68.44 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  SKSLGGPRATPRRRSQSEPRAPPPQEQCGAA-VAFMAHSPVAVQVPGMQNNIADPEELFTKLERIGKGSF
          SKSLGGP...PR.RSQSEPRAPPPQEQC..A.VAF.A.S...VQVPGMQNN.A.PEEL.TKL..IGK.SF
Retrocopy SKSLGGPLSDPRSRSQSEPRAPPPQEQCATA<VAFVACSQGTVQVPGMQNNTAHPEELVTKLKHIGKVSF

Parental  GEVFKGIDNRTQQVVAIKIIDLEEAEDEIEDIQQEITVLSQCDSSYVTKYYGSYLKGSKLWIIMEYLGGG
          GEVFKGI...TQQV.AIK....E.A..E...IQQEI.VLSQ.DSSYVTK.YG.YL..SKL...MEY.GGG
Retrocopy GEVFKGI*YCTQQVLAIKVPGPEGAKEETAGIQQEIAVLSQRDSSYVTKCYGAYLERSKL--TMEYPGGG

Parental  -SALDLLRAGPFDEFQIATMLKEILKGLDYLHSEKKIHRDIK-AANVLLSEQGDVKLADFGVAGQLTDTQ
          .S.L.L..AGPFDE.QIAT.LKE.LKGL..L.SEKKIH.D.K.AA..LLSEQGDVK.ADFGV..QLTDTQ
Retrocopy GSSLALPQAGPFDECQIATLLKEMLKGLHCLRSEKKIH*DRK>AASILLSEQGDVKPADFGVTVQLTDTQ

Parental  IKRNTFVGTPFWMAPEVIQQSAYDSKADIWSLGITAIELAKGEPPNSDMHPMRVL-FLIPKNNPPTLVGD
          IKRNTFVG.PF.M.PE..Q..A..SKADIWSLGITAIE..K.EPPN.D.HPMRVL.FL..K.NPPTLVGD
Retrocopy IKRNTFVGIPFRMVPELLQRWACNSKADIWSLGITAIEPSKAEPPNCDVHPMRVL>FLFQK-NPPTLVGD

Parental  FTKSFKEFIDACLNKDPSFRPTAKELLKHKFI
          FTKSFKEFIDACLNK.P.F.PTAKELLKHKFI
Retrocopy FTKSFKEFIDACLNKEP*FCPTAKELLKHKFI

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	1.95 RPM
SRP017611_kidney	0.00 RPM	3.19 RPM
SRP017611_liver	0.00 RPM	0.10 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_223 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_223 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 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000018826	1 retrocopy	retro_cfam_1067,
Felis catus	ENSFCAG00000026530	1 retrocopy	retro_fcat_223 ,
Macropus eugenii	ENSMEUG00000013597	1 retrocopy	retro_meug_307,
Microcebus murinus	ENSMICG00000009064	1 retrocopy	retro_mmur_527,
Otolemur garnettii	ENSOGAG00000002621	1 retrocopy	retro_ogar_2658,