RetrogeneDB ID: retro_ocun_1159

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 3:23221573..23223271(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOCUG00000010930
• Aliases: None
• Description: None

Sequence

>retro_ocun_1159
GTGCTGATGGAAAAACCCTTAGAGATAATTCAGGCTGAACTGAGGGTGGCAGACATAAACGACCATGCCCCTGTGTTCTC
CGAAAGAGAAATGATTCTAAAAATACCAGAAAACAGCCCTCTAGGAAGCGCGTACCCCCTGAATAATGCTCTGGATTTGG
ACGTAGGAAGCAACAACGTTCAAAACTATAAAATCAGCTCCAATTCCCATTTTTGCGTTCTAACCCGCGAACGCAGCGAT
GGCAGGAAATACCCTGAGCTGGTGTTGGATAAAGAGCTGGACCGGGAGGAGGAGCCTGAACTGAGATTAACTCTGACGGC
GCTGGATGGCGGCTCTCCGCCCCGCTCTGGCTCCGCAGAGGTGCTCATTGAAGTTGTGGACACGAATGATAACGCCCCCG
AGTTTGCGCAACCGCTCTACAGGGTTCAGGTTCCGGAGGACAGCCCCGAGGGCTCCTTGGCTGTCACGGTATTCGCCACT
GATTTAGACAGTGGGGACTATGGGAAAATATCGTACACGCTCGTTCAGCCTTCAGAAGGTATCAGCGACACTTTGGAGGT
AAATCCTGTGACAGGAGCAGTTCGACTGAGAAAACAAATAGACTTTGAAAGAGTCCAGTCTTATGAAGTGGACATCAAGG
CCACGGACGGGGGAGGTCTTTCAGGAAAATGCACTCTGCTCCTGCAGGTGGTGGACGTGAACGACAATCCGCCAGAGGTG
ACGATGTCTGCACTCAACAGCCCCATCCCGGAGAACGCGCCCGAGACTGTAGTTGCTGTTTTCAGCGTCTCGGATCCTGA
TTCCGGGGACAACGGGAGGACCATTTCCTCCATCCAGGAAGACCTCCCATTCATTCTGAAACCGTCAGTTAAGAACTTCT
ACACCCTGGTAACTGAGAGCCCGCTGGACAGGGAGACCAGGGCCGAGTACAACATCACCATCACCGTGTCCGACCTGGGC
ACGCCCAGGCTGACCACCCGGCACCACGTCGCGGTGCAGGTGTCTGACGTGAACGACAACGCCCCGGCCTTCAGCCAGGC
CGCCTACACCCTGCTGGTGCGCGAGAACAACAGCCCCGGGCTGCTCATCGGCTCCGTGAGCGCCAGCGACAGGGACGCGG
GCGCCAACGCTCAGGTGACCTACTCGCTGCTGCCGCCGCCACAGCAGCCCGACGTGGCGGCGCTCGTGTCGGTGCACGCG
GACAGCGGGCAGCTGTACGCGCTGCGCGCGCTGGACTACGAGGCCCTGCGCGCCTTCGAGTTCGGCGTGCGCGCCGCCGA
CCGCGGCTCCCCGGCGCTGAGCAGCGAGGCGCGCGTGCGCGTGCAGCTGCTGGACGCCAACGACCACGCGCCGGCCGTGC
TGTACCCGCCGGCCAACGGCTCGGCCGCCTGCCCCGAGCTGGTGCCGCGCGCGGCCGACGCGGGCTACCTGGTGACCAAG
GTGGTGGCGGTGGACGGCGACGCGGGCCAGAACGCCTGGCTGTCGTTCGAGCTGCTCAAGGCCACGGAGCCCGGGCTGTT
CGGCGTGTGGGCGCACAGCGGCGAGGTGCGCACGGCGCGGCCGCTGAGCGAGCGCGACGCGCCCAGGCAGCGGCTGCTGG
TGCTGGTGCGCGACCACGGCGAGCCGCCGCTGTCGGCCAGCGTCACGCTGCACGTGCTGCTGGTGGACGGCTTCTCGCAG
CCCTACCTGGCGCTGCCC

Alignment

ORF - retro_ocun_1159 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.33 %
• Parental protein coverage: 72.48 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VLFENPLQFFWAELLVKDINDHAPTFLDKNILLKILEGTTSETSFPMDSAQDLDVGKNGVQNYTITPNPH
          VL.E.PL....AEL.V.DINDHAP.F......LKI.E........P...A.DLDVG.N.VQNY.I..N.H
Retrocopy VLMEKPLEIIQAELRVADINDHAPVFSEREMILKIPENSPLGSAYPLNNALDLDVGSNNVQNYKISSNSH

Parental  FHLKLQDNDDGSKYPELILDRPLDREKEPELSLMLTALDGGSPPRSGTALIRVVVLDINDNAPEFEKPVY
          F........DG.KYPEL.LD..LDRE.EPEL.L.LTALDGGSPPRSG.A.....V.D.NDNAPEF..P.Y
Retrocopy FCVLTRERSDGRKYPELVLDKELDREEEPELRLTLTALDGGSPPRSGSAEVLIEVVDTNDNAPEFAQPLY

Parental  EVQVPENSPVDSLIIKVSASDLDAGINGELSYSFSHVSRDARKTFEIHPISGEVHLKALLDFETIQSYTI
          .VQVPE.SP..SL...V.A.DLD.G..G..SY.....S.....T.E..P..G.V.L....DFE..QSY..
Retrocopy RVQVPEDSPEGSLAVTVFATDLDSGDYGKISYTLVQPSEGISDTLEVNPVTGAVRLRKQIDFERVQSYEV

Parental  NIQAIDGGSLSGKATILVRVVDVNDNPPEIAMTSLISPIPENSSPEMVVAVFSVRDPDSGDNGRMVCSIQ
          .I.A.DGG.LSGK.T.L..VVDVNDNPPE..M..L.SPIPEN..PE.VVAVFSV.DPDSGDNGR...SIQ
Retrocopy DIKATDGGGLSGKCTLLLQVVDVNDNPPEVTMSALNSPIPENA-PETVVAVFSVSDPDSGDNGRTISSIQ

Parental  NDLPFLLKPTFKNFYTLLTITEGPLDRETRAEYNITITVSDLGTPRLTTRHHIAVQVSDVNDNAPTFSQA
          .DLPF.LKP..KNFYTL...TE.PLDRETRAEYNITITVSDLGTPRLTTRHH.AVQVSDVNDNAP.FSQA
Retrocopy EDLPFILKPSVKNFYTL--VTESPLDRETRAEYNITITVSDLGTPRLTTRHHVAVQVSDVNDNAPAFSQA

Parental  AYTLLVRENNSPGLLIGSVSASDRDAGANAQVTYSLLPPPQQPDVAALVSVHADSGQLYALRALDYEALR
          AYTLLVRENNSPGLLIGSVSASDRDAGANAQVTYSLLPPPQQPDVAALVSVHADSGQLYALRALDYEALR
Retrocopy AYTLLVRENNSPGLLIGSVSASDRDAGANAQVTYSLLPPPQQPDVAALVSVHADSGQLYALRALDYEALR

Parental  AFEFGVRAADRGSPALSSEARVRVQLLDANDHAPAVLYPPANGSAACPELVPRAADAGYLVTKVVAVDGD
          AFEFGVRAADRGSPALSSEARVRVQLLDANDHAPAVLYPPANGSAACPELVPRAADAGYLVTKVVAVDGD
Retrocopy AFEFGVRAADRGSPALSSEARVRVQLLDANDHAPAVLYPPANGSAACPELVPRAADAGYLVTKVVAVDGD

Parental  AGQNAWLSFELLKATEPGLFGVWAHSGEVRTARPLSERDAPRQRLLVLVRDHGEPPLSASVTLHVLLVDG
          AGQNAWLSFELLKATEPGLFGVWAHSGEVRTARPLSERDAPRQRLLVLVRDHGEPPLSASVTLHVLLVDG
Retrocopy AGQNAWLSFELLKATEPGLFGVWAHSGEVRTARPLSERDAPRQRLLVLVRDHGEPPLSASVTLHVLLVDG

Parental  FSQPYLALP
          FSQPYLALP
Retrocopy FSQPYLALP

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	1.27 RPM	5.91 RPM
SRP017611_kidney	0.30 RPM	0.91 RPM
SRP017611_liver	0.00 RPM	0.31 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1159 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1159 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1159 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000016152	1 retrocopy	retro_cjac_1774,
Oryctolagus cuniculus	ENSOCUG00000010930	1 retrocopy	retro_ocun_1159 ,
Oryctolagus cuniculus	ENSOCUG00000010938	1 retrocopy	retro_ocun_262,