RetrogeneDB ID: retro_ocun_364

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 1:56032379..56033113(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RAP1GAP2
• Ensembl ID: ENSOCUG00000000200
• Aliases: None
• Description: RAP1 GTPase activating protein 2 [Source:HGNC Symbol;Acc:29176]

Sequence

>retro_ocun_364
AGACAACAAGATGAACTAAATCAAGCTATAGCAGGGTATCATTATTCAAGTGGCTAAGAAGAGGCACATGAAGCTTTTAA
AAAGGAAACTGAACTAGATATAAATGAGGAATTAAATAAGAAGCATACTGGTCTTCTGGAAAAAAATGGAATTCTGTTAC
TAGATTGCAAAAGAAGGTTATGGAATTAGAATCAAAACTAAATGAAGCAAAAGAAGAATATACATCGGGTGGACCTCTTG
GTCAGAAAAGAGACCCAAAAGAATGGATTCCCCATCCACCAGAAAAATGCACTTTGCGTGGTCACAGGAGTCCAGTCAAC
TTGAGTCATATTCCATCCTGTGTTCAGTGTTATGGTCTCTGTGTCTGAGGATGCTACAATTTAGGTGTGGGATTATGAGA
TTGGTGATTTTGAATGAAGTATTAAGGGGCATATAGATTCTGTACTGGACATTTCTTTTGACCCCAGAGGCAAGCTATGG
CTTCCTGTTCTGCATAGAGGACCACAAAACTATAAAATTTTCAGGGCTTTGAAGGCATCAGAACTATGCATGAGCACAAC
CACAATGTCTCTTCAGTAGCCATCGTGCCCAGTGGAGATCATGTAGTGTCTACTTCAAGAGATAAAACTATACAAATGTG
GAAAGTGCAAACTGGCTACTGTGTGAAGACATTCACAGGACACAGAGAATGGACACATACAATACAGCCAAGTCAGGATG
GCACTCTGATAGCT

Alignment

ORF - retro_ocun_364 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.02 %
• Parental protein coverage: 59.76 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  RQRDELNRAIADYLRSNGYEEAYSVFKKEAELDMNEELDKKYAGLLEK-KWTSVIRLQKKVMELESKLNE
          RQ.DELN.AIA.Y..S.G.EEA...FKKE.ELD.NEEL.KK..GLLEK.KW.SV.RLQKKVMELESKLNE
Retrocopy RQQDELNQAIAGYHYSSG*EEAHEAFKKETELDINEELNKKHTGLLEK<KWNSVTRLQKKVMELESKLNE

Parental  AKEEFTSGGPLGQKRDPKEWIPRPPEKYALSGHRSPV-TRVIFHPVFSVMVSASEDATIKVWDYETGDFE
          AKEE.TSGGPLGQKRDPKEWIP.PPEK..L.GHRSPV.T.VIFHPVFSVMVS.SEDATI.VWDYE.GDFE
Retrocopy AKEEYTSGGPLGQKRDPKEWIPHPPEKCTLRGHRSPV>T*VIFHPVFSVMVSVSEDATI*VWDYEIGDFE

Parental  RTLKGHTDSVQDISFDHSGKL-LASCSADMTIKLWDFQGFECIRTMHGHDHNVSSVAIMPNGDHIVSASR
          ...KGH.DSV.DISFD..GKL..ASCSA..T.KL..FQGFE.IRTMH.H.HNVSSVAI.P.GDH.VS.SR
Retrocopy *SIKGHIDSVLDISFDPRGKL<MASCSA*RTTKL*NFQGFEGIRTMHEHNHNVSSVAIVPSGDHVVSTSR

Parental  DKTIKMWEVQTGYCVKTFTGHREWVRMVRPNQDGTLIA
          DKTI.MW.VQTGYCVKTFTGHREW.....P.QDGTLIA
Retrocopy DKTIQMWKVQTGYCVKTFTGHREWTHTIQPSQDGTLIA

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	312.26 RPM
SRP017611_kidney	0.00 RPM	104.90 RPM
SRP017611_liver	0.00 RPM	35.30 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_364 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_364 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_364 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Oryctolagus cuniculus	ENSOCUG00000000200	1 retrocopy	retro_ocun_364 ,