RetrogeneDB ID: retro_fcat_1009

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: B4:4417315..4417858(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSFCAG00000029331
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: MCTS1
• Ensembl ID: ENSFCAG00000008448
• Aliases: None
• Description: malignant T cell amplified sequence 1 [Source:HGNC Symbol;Acc:23357]

Sequence

>retro_fcat_1009
ATGTTCAAGAAATTTGACGAGAAAGAAAATGTGTCGAACTGCATCCAGTTGAAAACCTCCGTTATTAAGGGCATTAAGAA
CCAGTTGATAGAGCAATTTCCAGGTATTGAACCATGGCTTAATCAGATCTTGCCTAAGAAAGATCCGGTCAAAATAGTGC
GATGCCACGAACACATAGAGATCCTTACGGTAAACGGAGAGTTACTGTTCTTTAGGCAAAGAGAAGGCCCTTTTTATCCG
ACCCTGAGGCTACTGCACAAATACCCTTTCATCCTGCCGCACCAGCAGGTCGATAAAGGAGCCATCAAGTTTGTACTCAG
TGGAGCCAATATCATGTGTCCAGGCTTAACCTCTCCGGGAGCTAAGCTCTACCCGGCCGCGGTAGATACGGTTGTGGCAA
TCATGGCCGAGGGGAAGCAGCATGCGCTGTGTGTCGGGGTCATGAAGATGTCCGCAGAAGATATTGAGAAAGTCAACAAA
GGCATCGGCATCGAGAACATCCATTACCTAAACGACGGGCTGTGGCACATGAAGACCTACAAA

Alignment

ORF - retro_fcat_1009 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.34 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MFKKFDEKENVSNCIQLKTSVIKGIKNQLIEQFPGIEPWLNQIMPKKDPVKMVRCHEHIEILTVNGELLF
          MFKKFDEKENVSNCIQLKTSVIKGIKNQLIEQFPGIEPWLNQI.PKKDPVK.VRCHEHIEILTVNGELLF
Retrocopy MFKKFDEKENVSNCIQLKTSVIKGIKNQLIEQFPGIEPWLNQILPKKDPVKIVRCHEHIEILTVNGELLF

Parental  FRQREGPFYPTLRLLHKYPFILPHQQVDKGAIKFVLSGANIMCPGLTSPGAQLYPAAVDTVVAIMAEGKQ
          FRQREGPFYPTLRLLHKYPFILPHQQVDKGAIKFVLSGANIMCPGLTSPGA.LYPAAVDTVVAIMAEGKQ
Retrocopy FRQREGPFYPTLRLLHKYPFILPHQQVDKGAIKFVLSGANIMCPGLTSPGAKLYPAAVDTVVAIMAEGKQ

Parental  HALCVGVMKMSAEDIEKVNKGIGIENIHYLNDGLWHMKTYK
          HALCVGVMKMSAEDIEKVNKGIGIENIHYLNDGLWHMKTYK
Retrocopy HALCVGVMKMSAEDIEKVNKGIGIENIHYLNDGLWHMKTYK

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	23.30 RPM	3.44 RPM
SRP017611_kidney	33.08 RPM	2.89 RPM
SRP017611_liver	18.70 RPM	2.53 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_1009 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_1009 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 10 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000034992	1 retrocopy	retro_btau_116,
Canis familiaris	ENSCAFG00000018545	1 retrocopy	retro_cfam_94,
Echinops telfairi	ENSETEG00000015462	1 retrocopy	retro_etel_19,
Felis catus	ENSFCAG00000008448	2 retrocopies	retro_fcat_1009 , retro_fcat_310,
Myotis lucifugus	ENSMLUG00000015101	1 retrocopy	retro_mluc_16,
Mustela putorius furo	ENSMPUG00000001407	1 retrocopy	retro_mputfur_98,
Mus musculus	ENSMUSG00000000355	3 retrocopies	retro_mmus_2504, retro_mmus_2505, retro_mmus_69,
Oryctolagus cuniculus	ENSOCUG00000014315	1 retrocopy	retro_ocun_212,
Pongo abelii	ENSPPYG00000020687	2 retrocopies	retro_pabe_1786, retro_pabe_1833,
Ictidomys tridecemlineatus	ENSSTOG00000011496	2 retrocopies	retro_itri_1136, retro_itri_1468,