RetrogeneDB ID: retro_ocun_449

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 11:49453564..49454142(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ISOC1
• Ensembl ID: ENSOCUG00000017498
• Aliases: None
• Description: isochorismatase domain containing 1 [Source:HGNC Symbol;Acc:24254]

Sequence

>retro_ocun_449
CTCATCACTCTGGGAAATCTTACACCTTCCAGCACTGGGTTTTTCTTTTGTGATATGCACAATAAATTCAGAACATCCAT
CAAGTATTTTGTGGATATTATTAGTGTGGGCAGAGAACTGTTGCAAGAGGTCCAGATTTTATAAAGTCCGGTTACCGAAA
CAGAACACTATTCTAATGGTCTTGGTAGCACATTCAAGAAATCGATTTGACAAGTGCAAAACTGGTACTTCCAAGGATCA
AATTTCCTTTGGTATTACCAGAAGCAGAAGCATCATTATCAGAGATTCCTGGAGTCAGGAATGTTGTACTTGTTGGAGCA
GAAAATCATATATGCATCCAACAATCGGCTCTGAAGCCCATTGGCCATGGTATCAAGACTCACATTGCTGCTGACACCAC
CTAAAGAAGCATGATGGACGGGATGATTGCTCATGAGTGTCTTCCTCAAATCAGTGTCGTGGTGCCCTTGAGTGAGGCTG
TCCTGCTGTAGCTGGTGGCTGATAAAGACCATCCTAAATTCAAAGACATTCAGAAACTAATTAAAGTGCATACTGCAGAG
TCAGGTCTGCTTTCCAAA

Alignment

ORF - retro_ocun_449 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.64 %
• Parental protein coverage: 98.98 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LTTLGNLTPSSTVFFCCDMQERFRPAIKYFGDIISVGQRLLQGARILGIPVIVTEQYPKGLGST-VQEID
          L.TLGNLTPSST.FF.CDM...FR..IKYF.DIISVG..LLQ...IL..PV..TE.Y..GLGST..QEID
Retrocopy LITLGNLTPSSTGFFFCDMHNKFRTSIKYFVDIISVGRELLQEVQIL*SPVTETEHYSNGLGST<IQEID

Parental  LTGVKLVLPKTKFSMVLPEVEAALAEIPGVRSVVLFGVETHVCIQQTALELVGRGIEVHIVADATSSRSM
          LT..KLVLP..KF..VLPE.EA.L.EIPGVR.VVL.G.E.H.CIQQ.AL...G.GI..HI.AD.T..RSM
Retrocopy LTSAKLVLPRIKFPLVLPEAEASLSEIPGVRNVVLVGAENHICIQQSALKPIGHGIKTHIAAD-TT*RSM

Parental  MDRMFALERLARTGIIVTTSEAVLLQLVADKDHPKFKEIQNLIKASAPESGLLSK
          MD.M.A.E.L......V..SEAVLL.LVADKDHPKFK.IQ.LIK....ESGLLSK
Retrocopy MDGMIAHECLPQISVVVPLSEAVLL*LVADKDHPKFKDIQKLIKVHTAESGLLSK

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	24.50 RPM
SRP017611_kidney	0.00 RPM	58.48 RPM
SRP017611_liver	0.00 RPM	33.91 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_449 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_449 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_449 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000006851	1 retrocopy	retro_chof_1203,
Oryctolagus cuniculus	ENSOCUG00000017498	1 retrocopy	retro_ocun_449 ,
Sus scrofa	ENSSSCG00000014258	2 retrocopies	retro_sscr_421, retro_sscr_443,