RetrogeneDB ID: retro_fcat_1392

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: D1:22542485..22542943(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FAM3C
• Ensembl ID: ENSFCAG00000023087
• Aliases: None
• Description: family with sequence similarity 3, member C [Source:HGNC Symbol;Acc:18664]

Sequence

>retro_fcat_1392
GCAAAGTTGGTGGTAGCGGCCACAGCATGGTTACCACACATTATGTTACTTCTCAAGTATTTGGAATACAGATGGATGCA
AGTTTTGGAAATCTCTTTGTAAGGTCAGCATGGGTCATGGCTGCATGATCTACAGACCTTTCTGGATATAACTGTGAGAT
GTCAAAAGCTTGCCCTGAGAATCAGTTTGCCTTTAAAAATGGTAAGTAGAGCAGCCAATGTGGTGGGACCCAAAATCTGC
CTAACGAGCGTTCTAATGAGTGGTGTTATGATAATGTTAGGAGAGGAGCCAGTGTTGCCTCGGTAGAGGGAAAAATAGAA
GAAGTATTAGGCACCCAATATTTTGACACGTGGGGAAAAGATGTGGCCCCGTTTATGGAGTTTGTGAAGTCCATGCCAGA
TGGGAAAATAGTCTTAACCGGAACATACGATGACGGAGCAGCCAGACTCAGTGATGAG

Alignment

ORF - retro_fcat_1392 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.33 %
• Parental protein coverage: 67.84 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  AKLVVAVAVFL-LTFYVISQVFEIKMDASLGNLFARSALDTAVRSTKPPRYKCGISKACPEKHFAFK-MA
          AKLVVA....L..T.YV.SQVF.I.MDAS.GNLF.RSA...A..ST....Y.C..SKACPE..FAFK.M.
Retrocopy AKLVVAATAWL<TTHYVTSQVFGIQMDASFGNLFVRSAWVMAA*STDLSGYNCEMSKACPENQFAFK>MV

Parental  SGAANVVGPKICLEDNVLMSGVK-NNVGRGINVALANGKTGEVLDTKYFDMWGGDVAPFIEFLKSIQDGT
          S.AANVVGPKICL...VLMSGV...NV.RG..VA...GK..EVL.T.YFD.WG.DVAPF.EF.KS..DG.
Retrocopy SRAANVVGPKICLT-SVLMSGVM<DNVRRGASVASVEGKIEEVLGTQYFDTWGKDVAPFMEFVKSMPDGK

Parental  IVLMGTYDDGATKLNDE
          IVL.GTYDDGA..L.DE
Retrocopy IVLTGTYDDGAARLSDE

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	266.50 RPM
SRP017611_kidney	0.10 RPM	28.34 RPM
SRP017611_liver	0.00 RPM	46.70 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_1392 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_1392 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 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000003224	1 retrocopy	retro_chof_1467,
Felis catus	ENSFCAG00000023087	1 retrocopy	retro_fcat_1392 ,
Homo sapiens	ENSG00000196937	1 retrocopy	retro_hsap_4657,
Loxodonta africana	ENSLAFG00000010029	1 retrocopy	retro_lafr_1169,
Macropus eugenii	ENSMEUG00000006906	2 retrocopies	retro_meug_2057, retro_meug_536,
Monodelphis domestica	ENSMODG00000015478	1 retrocopy	retro_mdom_1392,
Sarcophilus harrisii	ENSSHAG00000015103	1 retrocopy	retro_shar_6,
Tursiops truncatus	ENSTTRG00000016229	2 retrocopies	retro_ttru_1219, retro_ttru_855,