RetrogeneDB ID: retro_ocun_1925

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: X:43504146..43505063(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ABCE1
• Ensembl ID: ENSOCUG00000001821
• Aliases: None
• Description: ATP-binding cassette, sub-family E (OABP), member 1 [Source:HGNC Symbol;Acc:69]

Sequence

>retro_ocun_1925
AAGACTGCTACTTCCATACAAACTCTAACAAATCCAGATAGATATACCATTGTGATAGAACATGATCTAAGTGTATGATA
TTATCTCCATTACTTTAGCTGCTGTTTGTATGGTACACCAAGTGCTTATGGTTTTGTCATCATGCATTTCAGTGTCAGAG
AAGGCATAAACATTTTCTTGGTTGGATATGTTCCAATAGAAAGCTTGAGATTCAGAGATGTATTGCTTGTTTTTAAAGTG
GTTGAGACAGAAAGCTAAGAAGTTAAAAAGATGTGTACTTATAAATATCCAGGGATGTATAAAAAAGATGGGCAAGACTG
AACTAGTAATTGTAGTTGGAGAGATTACAGAAATCTGAAATCATGGTGATGCTGGGGGAAATGGTACAGGCAAAATGACA
TTTATCAGAATGCTTGCTGGAAGACTTAAACCTGATGAAGCAGGAGAAGTGCCAGTTCTAAATGTCACTTACAAGCCACA
GAAAATCATTCCCAAATCAATTGGAAATGTTCACTGTTACTACATGAAAAGATAAGAGAGGATTATACTCAACCCCAGTG
TGTGACTCATGTAATGAAGCCTCTGTGAACTGAAAACATCGTTGATCAAGAGCTGCAGACATTATCCAGTGGTGAACTGC
AGTGAGTAGTTCTAGGTCTTTGTTGGGGCAAACCTGCCAATGTCTATTTAGTTGATGAACCATCTGTATATTTGGATTCC
AGGAAAAGACAGATGGCAGCTTGGGTTGTCAAACATTCCATACTCCATGCAATGAAGAAGGCATTTGTTGTGGACATGAC
TTCATCATGGCCATGTATGTAGCAGATCGAGTCATAGTTTTTGGTGGTGTTCCATCTAAGAACACAGTTGCTGTCCTCAA
ACAATTTTGGCTGGCATGAATAGATTTTTTGTTATCT

Alignment

ORF - retro_ocun_1925 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.12 %
• Parental protein coverage: 51.25 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  KAAITIRSLINPDRYIIVVEHDLSVLDYLSDFICCLYGVPSAYGVVTMPFSVREGINIFLDGYVPTENLR
          K.A..I..L.NPDRY.IV.EHDLSV..YL..F.CCLYG.PSAYG.V.M.FSVREGINIFL.GYVP.E.LR
Retrocopy KTATSIQTLTNPDRYTIVIEHDLSV*YYLHYFSCCLYGTPSAYGFVIMHFSVREGINIFLVGYVPIESLR

Parental  FRDASLVFKVAETANEEEVKKMCMYKYPGMKKK-MGEFELAIVAGEFTD-SEIMVMLGE-NGTGKTTFIR
          FRD..LVFKV.ET...E.VKKMC.YKYPGM.KK.MG..EL.IV.GE.T..SEIMVMLGE.NGTGK.TFIR
Retrocopy FRDVLLVFKVVETES*E-VKKMCTYKYPGMYKK>MGKTELVIVVGEITE>SEIMVMLGE<NGTGKMTFIR

Parental  MLAGRLKPDEGGEVPVLNVSYKPQKISPKSTGSVR-QLLHEKIRDAYTHPQFVTDVMKPLQIENIIDQEV
          MLAGRLKPDE.GEVPVLNV.YKPQKI.PKS.G.V...LLHEKIR..YT.PQ.VT.VMKPL..ENI.DQE.
Retrocopy MLAGRLKPDEAGEVPVLNVTYKPQKIIPKSIGNVH<LLLHEKIREDYTQPQCVTHVMKPL*TENIVDQEL

Parental  QTLSGGELQRVALALCLGKPADVYLIDEPSAYLDSEQRLMAARVVKRFILHAKKTAFVVE-HDFIMATYL
          QTLS.GELQ.V.L.LC.GKPA.VYL.DEPS.YLDS..R.MAA.VVK..ILHA.K.AFVV..HDFIMA.Y.
Retrocopy QTLSSGELQ*VVLGLCWGKPANVYLVDEPSVYLDSRKRQMAAWVVKHSILHAMKKAFVVD<HDFIMAMYV

Parental  ADRVIVFDGVPSKNTVANSPQTLLAGMNKFLS
          ADRVIVF.GVPSKNTVA...Q..LA.....LS
Retrocopy ADRVIVFGGVPSKNTVAVLKQFWLA*IDFLLS

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	61.37 RPM
SRP017611_kidney	0.00 RPM	71.76 RPM
SRP017611_liver	0.00 RPM	24.74 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1925 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1925 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1925 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000004534	1 retrocopy	retro_chof_1280,
Cavia porcellus	ENSCPOG00000007367	1 retrocopy	retro_cpor_289,
Homo sapiens	ENSG00000164163	1 retrocopy	retro_hsap_3826,
Macaca mulatta	ENSMMUG00000004433	1 retrocopy	retro_mmul_1628,
Mus musculus	ENSMUSG00000058355	1 retrocopy	retro_mmus_1503,
Nomascus leucogenys	ENSNLEG00000005460	1 retrocopy	retro_nleu_2125,
Oryctolagus cuniculus	ENSOCUG00000001821	2 retrocopies	retro_ocun_1925 , retro_ocun_668,
Procavia capensis	ENSPCAG00000006183	1 retrocopy	retro_pcap_90,
Pongo abelii	ENSPPYG00000015097	1 retrocopy	retro_pabe_3067,
Pan troglodytes	ENSPTRG00000016481	1 retrocopy	retro_ptro_2603,