RetrogeneDB ID: retro_fcat_1017

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: B4:32559504..32560153(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NT5C3B
• Ensembl ID: ENSFCAG00000023499
• Aliases: NT5C3B, NT5C3L
• Description: 5'-nucleotidase, cytosolic IIIB [Source:HGNC Symbol;Acc:28300]

Sequence

>retro_fcat_1017
AGGGGCAGGGGAGACCATTTACAGGTCATTTCTGATTGTCACATGATCTGGAGCACATTTGCGTATAATGGGAAAGTGAT
GCCCTCCCTTCTTATGACATTTTAGATAACAGCAAGATTATCAGTGAGCAGTCCTGGAAGGAACTCAAAGTGTGCCCTCC
CCACTATTACCCGGTTGAGACTGACCTACGCTGACCATCAAAGTTACCTCATATGGTGGAATGGTGGGCCAAAGCACAGG
ATCTCCCATGCCAGCAGAAGATTTAGAAGTTTCAGATCGCCCAGGTGTTTACAGTACAATGCAGTGCTTAGGGAGGGATA
CAAGACTTTCTTTAACACCCTTTACCAAAACTACATTCCCTTTTTTTTCTTTTTGGCAGGCATTGGTGATACCATGGAGG
AGATTATCTGACAAATAAAGGTGTTCCGCCCCAGCATCTACATTGTGTCTAACTACACGGACTTTGACGAAGACAGTTTT
GGACAGGGATTCAAGGAGTCAGCTCATACACACATACAACAAAAACAGCTCCATTTGTAAGAACTCCAGGTACTTCCAGC
AGCTTCTGGACAAAACCAACATCCTCCTGCTGGAAGACTTCATGGAGGACCTCACTATGGCTGATAAGGTTACCAGTGTG
GAGAGCATT

Alignment

ORF - retro_fcat_1017 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.06 %
• Parental protein coverage: 80.44 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  KGLPRKLQVISDFDMTLSRFAYNGKR-CPS-SYNILDNSKIISEECRNELKALLHHYYPIEIDPHRTVKE
          .G....LQVISD..M..S.FAYNGK..CP..SY.ILDNSKIISE....ELK....HYYP...........
Retrocopy RGRGDHLQVISDCHMIWSTFAYNGKV>CPP>SYDILDNSKIISEQSWKELKVCPPHYYP--VETDLR*PS

Parental  KLPHMVEWWTKAHDLLCQQ-KIQKFQIAQVVRESNAMLREGYKTFFNTLYQNNIPLFIFSAGIGDILEEI
          KLPHMVEWW.KA.DL.CQQ.....F.........NA.LREGYKTFFNTLYQN.IP.....AGIGD..EEI
Retrocopy KLPHMVEWWAKAQDLPCQQ>RFRSFRSPRCL-QYNAVLREGYKTFFNTLYQNYIPXXXXXAGIGDTMEEI

Parental  IRQMKVFHPNIHIVSNYMDFDEDGFLQGFK-GQLIHTYNKNSSVCENSGYFQQLQGKTNILLLGDSMGDL
          I.Q.KVF.P.I.IVSNY.DFDED.F.QGFK..QLIHTYNKNSS.C.NS.YFQQL..KTNILLL.D.M.DL
Retrocopy I*QIKVFRPSIYIVSNYTDFDEDSFGQGFK>SQLIHTYNKNSSICKNSRYFQQLLDKTNILLLEDFMEDL

Parental  TMADGVPGVENI
          TMAD.V..VE.I
Retrocopy TMADKVTSVESI

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	39.02 RPM
SRP017611_kidney	0.00 RPM	19.68 RPM
SRP017611_liver	0.00 RPM	6.57 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_1017 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_1017 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 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000005754	1 retrocopy	retro_amel_1542,
Erinaceus europaeus	ENSEEUG00000013493	1 retrocopy	retro_eeur_413,
Felis catus	ENSFCAG00000023499	1 retrocopy	retro_fcat_1017 ,
Mustela putorius furo	ENSMPUG00000010759	2 retrocopies	retro_mputfur_1354, retro_mputfur_1594,
Pteropus vampyrus	ENSPVAG00000010634	1 retrocopy	retro_pvam_233,
Sorex araneus	ENSSARG00000006434	1 retrocopy	retro_sara_505,