RetrogeneDB ID: retro_fcat_1622

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: D4:39790014..39790686(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: C6orf136
• Ensembl ID: ENSFCAG00000007692
• Aliases: None
• Description: chromosome 6 open reading frame 136 [Source:HGNC Symbol;Acc:21301]

Sequence

>retro_fcat_1622
CTACCATTCCCGCCACCCTTGGCCCCAGTCCACAACAACCATTTCTCCATCTTCTCTTCCCTGCCCCCACCCCCTCCTAT
CTTGTTGCTTCCTTGGAGATCCCCCACTCCCTCTCCTTCAGATCCAGGCCCTCAGCTCACCATGGGTGGTTCTCCCTCCA
GGGAAGGGGGAAGAGAGACCCAGACGTGAGATGCATAGCGACTACCTGGATGGGCTTAGGAGCTTATTTGAGGGAACTCC
CTGCCCCTTTCCTGGGGCTTTAATACTTTTCCAAGCCCCTCGGATCTCTTGCCCTTCCCCTACCACACCATCAGGAGATA
TGAATATCAAGGACCACCTGGCTATCATGTATGAGAGACTGAGACAAGAGCTCCCCAATCTCTTCCTTCACTTCCATGAC
TATACTCTGTATTCATCGGGTGTGGAATTCATCAATGAGATCCTGAACATATGTACCAAGGGCTGGACATGGTACCTTCT
GTCACTGACCATCTGCCACTTCCTGGCCTGGAACTATTTTGCACAGCTTCAGTTGGAGGTTCTACAGCTGACCTGCAACC
CAGAGAATTAGACCCTGCAAGCCTGCTGGTGGCTTGTGGGGCTGCCCATCCACATAGTCTTTCTGCATTTCTATAAGTGT
GACAAGGAAGAGCTTAACAGACCTATGTTGCC

Alignment

ORF - retro_fcat_1622 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.19 %
• Parental protein coverage: 72.29 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  LPFPPL-WPHSTTTTSPS-SILWSPPLPPPPIWLLPRA-PPLPLPQIQALSSPWVVLPPGKGEEGPGPEM
          LPFPP..WP.S..TT..S.SI..S.P.PPPPI.LLP...PPLPL.QIQALSSPWVVLPPGKGEE.P..EM
Retrocopy LPFPPP>WPQS--TTTIS<SIFSSLP-PPPPILLLPWR>PPLPLLQIQALSSPWVVLPPGKGEERPRREM

Parental  HSGCLDGLRSLFEGPPCPYPGALIPFQAPGTSCPCPATPSGDPSMEEHLAIMYERLRHELPNLFLHSHDY
          HS..LDGLRSLFEG.PCP.PGALI.FQAP..SCP.P.TPSGD.....HLAIMYERLR.ELPNLFLH.HDY
Retrocopy HSDYLDGLRSLFEGTPCPFPGALILFQAPRISCPSPTTPSGDMNIKDHLAIMYERLRQELPNLFLHFHDY

Parental  TLYSSDVEFINEILNIRTKGLTWYILSLTLCRFLAWNYFAQLRLEVLQLTRHPENWTLQARWRLVGLPIH
          TLYSS.VEFINEILNI.TKG.TWY.LSLT.C.FLAWNYFAQL.LEVLQLT..PEN.TLQA.W.LVGLPIH
Retrocopy TLYSSGVEFINEILNICTKGWTWYLLSLTICHFLAWNYFAQLQLEVLQLTCNPEN*TLQACWWLVGLPIH

Parental  MLFLRFYKRDKEELY-QTYDA
          ..FL.FYK.DKEEL..QTY.A
Retrocopy IVFLHFYKCDKEELN<QTYVA

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	22.61 RPM
SRP017611_kidney	0.00 RPM	33.29 RPM
SRP017611_liver	0.00 RPM	12.43 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_1622 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_1622 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Felis catus	ENSFCAG00000007692	1 retrocopy	retro_fcat_1622 ,
Monodelphis domestica	ENSMODG00000015898	1 retrocopy	retro_mdom_1511,