RetrogeneDB ID: retro_fcat_1143

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: C1:173680569..173681176(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ARL6IP6
• Ensembl ID: ENSFCAG00000005242
• Aliases: None
• Description: ADP-ribosylation-like factor 6 interacting protein 6 [Source:HGNC Symbol;Acc:24048]

Sequence

>retro_fcat_1143
CCCCTGTTGTTTGCCTGGCCTACATTTTCTGCCTTCATTCCGGGAGACAGTAGCAGTGAAGGTGAAGTGGATGATGAGAA
GGACGGATGCGACTCAAGTTGCATGCCACTTGCGGAAGGAGTTCTCGGCTGGGGCGTCATTGGAGCCTAGAAAGGTCTCA
TTGCTCCAGGAGGATGGAGACAGGTCTCCGGTTCTGCCAGATAAGCACAATGACATTTTCTGGGTGGTTGCGGGTGGCTG
AGCCCAGGCTTAGCAGAGGCTGGTACAGGTCCTCTCAATTCTCTGTTTGCTGCTGTTCGCCTTCTTTCTCGCCATCACCT
ACCTGATAGTAAAAGAGTTATATGTTGAGAATTTGAAGAATGAAGAGGATGTAGACACTGGGCTACTAGGATTCTGGACT
CTACTTATCATATCTCTGTCTGCAAGATTCTCCTGCTGTAGCTTTTCTTGCACAGTGACTAATCTTGACTTTTTTGAACC
AGGAAGATTTCCTCCTACTCCTCTTTCACCTGCCAGGTGCAAGAAACTGACCACACATTCTTTCCACATGGGCTGCATAG
CATGGCAGAGTGTTGTAGCTGCTCTTATTGTAACATGGTATCTCATG

Alignment

ORF - retro_fcat_1143 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.86 %
• Parental protein coverage: 91.56 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PVPFARPAFTAFTQGDSWGEGE-GDEEDGCD-QVARDLRAEFSAGASSEPRKGSLLQRDRDGSPVLPDKR
          P..FA.P.F.AF..GDS..EGE..DE.DGCD.QVA..LR.EFSAGAS.EPRK.SLLQ.D.D.SPVLPDK.
Retrocopy PLLFAWPTFSAFIPGDSSSEGEVDDEKDGCD>QVACHLRKEFSAGASLEPRKVSLLQEDGDRSPVLPDKH

Parental  NGIFSTVAGGRAQARRWPVQILSILCSLLFAILLAFLLAIAYLIVKELHAENLKT-EDVDTGLLGFWTLL
          N.IF..VAGG.AQA....VQ.LSILC.LLF....AF.LAI.YLIVKEL..ENLK..EDVDTGLLGFWTLL
Retrocopy NDIFWVVAGG*AQA*QRLVQVLSILCLLLF----AFFLAITYLIVKELYVENLKNEEDVDTGLLGFWTLL

Parental  IISLSAGFSCCSFSWTVTYFDSFEPGMFPPTPLSPARFKKLTGHSFHMGYSMAILNGIVAAFTVAWCLM
          IISLSA.FSCCSFS.TVT..D.FEPG.FPPTPLSPAR.KKLT.HSFHMG.........VAA..V.W.LM
Retrocopy IISLSARFSCCSFSCTVTNLDFFEPGRFPPTPLSPARCKKLTTHSFHMG--CIAWQSVVAALIVTWYLM

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	0.23 RPM	5.85 RPM
SRP017611_kidney	0.10 RPM	9.28 RPM
SRP017611_liver	0.00 RPM	6.07 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_1143 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_1143 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 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Felis catus	ENSFCAG00000005242	1 retrocopy	retro_fcat_1143 ,
Microcebus murinus	ENSMICG00000017157	1 retrocopy	retro_mmur_838,
Mustela putorius furo	ENSMPUG00000000415	1 retrocopy	retro_mputfur_75,