RetrogeneDB ID: retro_ocun_201

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: GL018719:143131..144598(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000023851
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOCUG00000021090
• Aliases: None
• Description: None

Sequence

>retro_ocun_201
TTCTGGCCGGCCCCACAGGCGCACATGGAATCATTCCGCTGGCTACAAGCTGCCCCCCGGCCGCCTGAGGAGCCTTACTC
GGTCTACATCTCAGCCCCCGGTGAGAAAAGGAGGACTGCCTATGTCGCCAAGCCCGGCTCGTCCGCAGTGCCTATAGGTG
CCAAGAGGCCCCTCGCGGCCAGCAGCAGCCTGCCCGTCCCAGTCCCCGAGCCTGGCAGCCGGCCACCCAAGGCGCGCACG
TGGTCGGGGATGGTGCCCAAGACCACCACCACGATCCCGTCCAAGCGGATCGCTTCCAGCCCCGCCTCCCAGGGTTTCAA
CAAACCCATCGTCTCCAAAGAGCGTGAGGGCAAAGTCCCCTCTGTGGTCCGCCAACGTTACCTCAGCTTGTTTATCGAGG
AATGTCTCAAGTTCTGCTCTTCCAATCAGGAGGCCACAGAGAAAGCGCTGAACGAGGAGAAGGTGGCCTACGACTGCAGC
CCCAGCAAAAGAATCTACGTGGACGTCGCCGCGAGCACCCTCCGGAGGCTCAGGGGCCTAGTGCCCAGCGCCGCGCCAAG
TCCCAACAGCGCCTCCCTGTACAGGCACCTCGGCCGCTACCTGCTCACCGAAGACCAGCTCAAGGAGAACGGCTACCCCT
TCCCGCACCCTGAACGGCCAGGGGGAGCCATCCTCTTCAAAGGCCAGGAGAAGCTGCCCAAAGACGCCTCCTGCAGAATC
TGCTGCCGCTGTGGCACCAAGTACCCGGTGTTGCCTTCGGGCCTCAGTGCTGGCGACCAGGAGTGTCGCTACCACTGGGG
GCGGCTTCGGCCGGCAGAGGCGGCTGGCGGCTGGGAGACCAGGTACATATGCTGCGCGGAGGCTTTGGGCTCTGCCGGCT
GCCGGGTCGCCAAGCGGCATGTCCAAGACGGCCGGAAGGAAAACCTCCAAGGGTTTGTGAAGACCCCGGAGAGGGCGCGG
TCTCACCCCGCCCAGCCTGGCGTCTACGCCCTTGACTGCGAAATGTCTTACACAACGCTGGGGCTGGAGCTGACGCGGGT
CACGGTGGTGGACCCCGAAATGCGAGTGGTGTACGACACCTTCGTCAAGCCCGATAACGAGATCGTGGACTATAACACCA
AGTTTTCCGGGGTGACCGAGGCCGACCTCGCCCACACCAACGTCACGCTGCGCGACGTCCAGGCCGTCCTGCTGAGCCTG
TTCAGCGCCGACACCATCCTCATCGGGCACAGCCTGGAGAGCGACCTGTTGACCCTGAAGGTCATCCACTGCACGGTGGT
GGACACATCTGTGCTCTTCCCCCATCACTTGGGCCTCCCGTTCAAGCGCTCGCTGCGGAATCTCATGGCCGACTACCTCC
ACAAGGTCATCCAGGATGACGTGCGTGGGCACAACTCCCAGGAGGACGCCAGTTCCTGCATGAGTCTGGTGTTGTGGAAG
ATCGAGGAAGACACCAAGGCCAGCGAC

Alignment

ORF - retro_ocun_201 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.58 %
• Parental protein coverage: 70.64 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TLYRHLRNHLLTEEQLRENNYPRPNPDKPGCVLLNPCMTKTSVNDASKKICCRCGKIYDVTPSGKHSRVE
          .LYRHL...LLTE.QL.EN.YP.P.P..PG...L.....K....DAS..ICCRCG..Y.V.PSG......
Retrocopy SLYRHLGRYLLTEDQLKENGYPFPHPERPGGAILFKGQEKLP-KDASCRICCRCGTKYPVLPSGLSAGDQ

Parental  ECYYHFGQVRSHKVLDGLESRYSCCGGVLGSPGCQESKLHVHD-QKENLEGFVKTSVKIPPADGNYGVFA
          EC.YH.G..R......G.E.RY.CC...LGS.GC...K.HV.D..KENL.GFVKT...........GV.A
Retrocopy ECRYHWGRLRPAEAAGGWETRYICCAEALGSAGCRVAKRHVQDGRKENLQGFVKTPERARSHPAQPGVYA

Parental  VNCEMCYTVKGLELTRVTVVDSSFQMVCDTFVKPDEEIIDYNTRFSGVVEDDLKNIRTSIRDVQAILLNL
          ..CEM.YT..GLELTRVTVVD.....V.DTFVKPD.EI.DYNT.FSGV.E.DL.......RDVQA.LL.L
Retrocopy LDCEMSYTTLGLELTRVTVVDPEMRVVYDTFVKPDNEIVDYNTKFSGVTEADLAHTNVTLRDVQAVLLSL

Parental  FSADTILIGHSFEQCLYALKLIHTCVVDTTVMFPHRLGLPHKRSLGSLVADYLQRIIQDDVFEGHNTSEK
          FSADTILIGHS.E..L..LK.IH..VVDT.V.FPH.LGLP.KRSL..L.ADYL...IQDDV..GHN..E.
Retrocopy FSADTILIGHSLESDLLTLKVIHCTVVDTSVLFPHHLGLPFKRSLRNLMADYLHKVIQDDV-RGHNSQED

Parental  AKACMELVLWKVKEDLK
          A..CM.LVLWK..ED.K
Retrocopy ASSCMSLVLWKIEEDTK

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	0.50 RPM
SRP017611_kidney	0.00 RPM	0.51 RPM
SRP017611_liver	0.00 RPM	0.00 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_201 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_201 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_201 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryctolagus cuniculus	ENSOCUG00000021090	3 retrocopies	retro_ocun_123, retro_ocun_1327, retro_ocun_201 ,