RetrogeneDB ID: retro_fcat_348

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: A2:124436842..124437521(+)
• Located in intron of: ENSFCAG00000012600

Retrocopy information

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

Parental gene information

• Parental gene symbol: RAB3IL1
• Ensembl ID: ENSFCAG00000007376
• Aliases: None
• Description: RAB3A interacting protein (rabin3)-like 1 [Source:HGNC Symbol;Acc:9780]

Sequence

>retro_fcat_348
CAGGGCTCTGAGCTCCTGAAGGAGGAGCTCACATAACCCAGAAGGAACAGAATCTGAAAGATGAGGACCATGAGCAGTGG
TAGGAGGTGTGGGAACCACAGGAACAGGAGCTGGAGGTGTGGCTGATGGCCATCCTCTTTGAGGAAGCCCACAAGATGGT
GTGAGAAGCTCACACGAAGTAGGTGGCATCAGAAAAAACTGCTGAAGCAAGTAGGGGGCAGGATCGACATGCTGCAGGTG
GAGGTGACATCCTTGAAGACATCAGTCATCACGTCCACACCCAGCCTATCTCAAGCATGAGCTCCACCTGCAGCTGCTGT
ACCCTACTAAGCCTGGGCCCCATAAAGGCCAGGAATACCAGCAGCTCCCTCTGCCAGGCTGTGTGCCCCACTGTGAGACA
TGCCCTTTCCTTGGACGAAGAGGACAAGGAGATGGGTATGACCTTTTCTGCAGAATTCTATGCCTGGAGGGAATTACTTA
TCCTGGACAAGCCCTGTTCCTTCCTTGGAAGGGTATACCCAGAGGATGTGGGCCCTTGCCTGGACTTTATAATGCAAAAG
TTCTTGATGCTGTTGTAAGCTGGAGGACAGCGAATGCTCACCGTCTAGCCTGTGGCTCTACGGATGCTGCTGCAGTAAGA
GTGGACACAGTAAAGTTGGGCAGTGCCGACTTATGTGCA

Alignment

ORF - retro_fcat_348 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 53.39 %
• Parental protein coverage: 60.05 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  KGSEFLKEEL-HKAQKELKLKDEECERLSRVREQLERELEE-LTASLFEEAHKMVRAANMKQAASEKQ-L
          .GSE.LKEEL.H..QKE..LKDE..E....V.E..E.ELE..L.A.LFEEAHKMV..A..K..ASEK..L
Retrocopy QGSELLKEEL<HITQKEQNLKDEDHEQW*EVWEPQEQELEVWLMAILFEEAHKMV*EAHTK*VASEKT>L

Parental  KEARGKIDMLQAEVTALKTLVLTST-PASPNRELHPQLLSPTKAGPRKGHLRHK-STSSTLCPTVCPAAG
          K...G.IDMLQ.EVT.LKT.V.TST.PA....ELH.QLL.PTK.GP.KG......S.....CPTV..A..
Retrocopy KQVGGRIDMLQVEVTSLKTSVITST>PAYLKHELHLQLLYPTKPGPHKGQEYQQ>SLCQAVCPTVRHA--

Parental  HTLTPDKEGKEVDTTLFAEFQAWRESPTLDKSCPFLERVYREDVGPCLDFTMQELSALVRAAVEDNTLTI
          ..L..D.E.KE...T..AEF.AWRE...LDK.C.FL.RVY.EDVGPCLDF.MQ....L..A......LT.
Retrocopy --LSLDEEDKEMGMTFSAEFYAWRELLILDKPCSFLGRVYPEDVGPCLDFIMQKFLMLL*AGGQ-RMLTV

Parental  EPVA-SQTPPTAKVAAVECGSTNTCA
          .PVA.S.......V..V..GS...CA
Retrocopy *PVA<STDAAAVRVDTVKLGSADLCA

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	2.52 RPM
SRP017611_kidney	0.00 RPM	9.17 RPM
SRP017611_liver	0.00 RPM	2.22 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_348 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_348 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 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Felis catus	ENSFCAG00000007376	1 retrocopy	retro_fcat_348 ,
Homo sapiens	ENSG00000167994	1 retrocopy	retro_hsap_3716,
Gorilla gorilla	ENSGGOG00000012399	1 retrocopy	retro_ggor_2513,
Macaca mulatta	ENSMMUG00000015148	1 retrocopy	retro_mmul_1698,
Nomascus leucogenys	ENSNLEG00000003273	1 retrocopy	retro_nleu_2858,
Pongo abelii	ENSPPYG00000003175	1 retrocopy	retro_pabe_3140,
Pan troglodytes	ENSPTRG00000003755	1 retrocopy	retro_ptro_2518,