RetrogeneDB ID: retro_fcat_433

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: A3:88144499..88145409(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSFCAG00000028283
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: TMEM59
• Ensembl ID: ENSFCAG00000007737
• Aliases: None
• Description: transmembrane protein 59 [Source:HGNC Symbol;Acc:1239]

Sequence

>retro_fcat_433
ATGGCAGCGCCAAAGGGGAGCCTCTGGGTCAGGGCCCAATTGGGGTTCCCGCCACTGCTGCTGCTGACCATGGCCCTGGC
GGGAGGCTCGAGGACCACTTGGGCTGAAGTGTTTGACTCGGCCTTGGGTGATACGGCATCTTATCACTGGGCCTGTCAGT
TGACCTTCCTCTTACATACCTACCCCAAGGAAGAGGAGTTGTACGCATGTCAGAAAGGTCGCAGGCTGTTTTCAATTTGT
CAATTTGTGGATGATGGAATTGGTTTAAATTGGACCAAAATAGAATGTTGAATCTGCATGTAGAGAAGCACATTCTCAAT
CTGGTAAGCAATATGCTTGACATCTTGGTTGCCAGGACCAGCTGCCATTCGCTGAACTGAGACAAGAACAGCTCATGCTC
CTGATGCCAAAAATGCATCTATTCTTCCCTCTAACTCTGGTAAGGTCATTCTAGAGTGACATGATGGACTCTGAACAGAG
CTTCATAACCTCTCCGTGGACGTTTTATCTTCAAGGTGATGATGGAAAAATAGTTATATTCCAGTCTAAGCCAGAAATCC
AGTATGCACCACAGTTGGAGCAGGAGCCTACAAATTTGAAAGAATTGTGCCTATGCAAAATGTCCTATCTGCAAACGAGA
AGTTCACAAACACATAGGAAGTGTCTTGAAGATGGAGAAAGTGATGGCTTTTTAAGATGTTTCCCTCTTAACTCTGGGTG
GATTTTAACCACAACTCCTGTCCTCTCGGTGATGGTATTGCTCTGGACTTGTTGCGCAACTGTTGCTACAGCTGTGGAGC
AGTATGTTCCCTCTGAGGAGCTGAGTATCTATGGTGACTTGGAATTTGTGAATGCACAAAAGCTAAACAGATATCCAGCT
TCTTCTCTTGTGGTTGTTAGATGGAAAGCT

Alignment

ORF - retro_fcat_433 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.51 %
• Parental protein coverage: 93.81 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAASKGSLWVRAQLGLPPLLLLTMALAGGSGTASAEAFDSILGDTASCHRACQLTFPLHTYPKEEELYAC
          MAA.KGSLWVRAQLG.PPLLLLTMALAGGS.T..AE.FDS.LGDTAS.H.ACQLTF.LHTYPKEEELYAC
Retrocopy MAAPKGSLWVRAQLGFPPLLLLTMALAGGSRTTWAEVFDSALGDTASYHWACQLTFLLHTYPKEEELYAC

Parental  QRGCRLFSICQFVDDGIDLNRTKMEC-ESACTEAYSQSDEQYACHLGCQNQLPFAELRQEQLMSLMPKMH
          Q.G.RLFSICQFVDDGI.LN.TK.EC.ESAC.EA.SQS..QYA.HLGCQ.QLPFAELRQEQLM.LMPKMH
Retrocopy QKGRRLFSICQFVDDGIGLNWTKIEC>ESACREAHSQSGKQYA*HLGCQDQLPFAELRQEQLMLLMPKMH

Parental  LLFPLTLVRSFWSDMMDSAQSFITSSWTFYLQADDGKIVIFQSKPEIQYAPQLEQEPTNLKESSLSKMSY
          L.FPLTLVRSF.SDMMDS.QSFITS.WTFYLQ.DDGKIVIFQSKPEIQYAPQLEQEPTNLKE..L.KMSY
Retrocopy LFFPLTLVRSF*SDMMDSEQSFITSPWTFYLQGDDGKIVIFQSKPEIQYAPQLEQEPTNLKELCLCKMSY

Parental  LQMRSSQTHRNYLEDGESDGFLRCLSLNSGWILTTTLVLSVMVLLWICCATVATAVEQYVPSEKLSIYGD
          LQ.RSSQTHR..LEDGESDGFLRC..LNSGWILTTT.VLSVMVLLW.CCATVATAVEQYVPSE.LSIYGD
Retrocopy LQTRSSQTHRKCLEDGESDGFLRCFPLNSGWILTTTPVLSVMVLLWTCCATVATAVEQYVPSEELSIYGD

Parental  LEFVNEQKLNRYPASSLVVVRSKA
          LEFVN.QKLNRYPASSLVVVR.KA
Retrocopy LEFVNAQKLNRYPASSLVVVRWKA

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	0.11 RPM	77.36 RPM
SRP017611_kidney	0.00 RPM	190.14 RPM
SRP017611_liver	0.00 RPM	142.33 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_433 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_433 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 3 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000009526	1 retrocopy	retro_btau_526,
Felis catus	ENSFCAG00000007737	1 retrocopy	retro_fcat_433 ,
Tursiops truncatus	ENSTTRG00000003198	3 retrocopies	retro_ttru_1079, retro_ttru_1723, retro_ttru_332,