RetrogeneDB ID: retro_ocun_668

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 13:119550474..119551509(-)
• 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_668
AAGGCTGCTATTACTATACGATCTTTAATAAACCCAGATAGGTACATCACTGTTGTGGAGCATGATCTAAGTGTATTAGA
CTATCTCTCTGACTCCTCATGCTGTTTGTATGGTGTGCCAAGTGCTTATGGTGTTGTAACTATGCCTTGTAGTGTTAGAG
AAGGCATAAACACTTTCTTGGATGGCTATGTTCCAACAGAAAACTTGAGATTCAGAGATGCATCGCTTGTTTTTAAAGTG
GCTGAGACAGCAAATGAAGAAGTTAAAAAGATGTGTATGTATAACTACCCAGGGATGAAGAAAAAGATGGGAGAGTTTGA
GCTAGCAATTGTAGCTGGAGAGTTTACGGATTCTGAAATTATGGGGATGCTTCGGGAAAATGGTACAGGCAAAACGACAT
TCATCAGAATGCTTGCTGGAAGGCTTAAACCTAATGAAGGAGGAGAAGTGCCAGTTCTAAATGTCAGTTATAAGCCACAA
AAGATCAGTCCCAAATCAACTGGAAGTGTTCGCCAGTTATTACATGAAAAGATAAGCGATGCTTACACTCATCCACAGTT
TGTGACTGATGTAATGAAGCCTCTGCAGATTGAAAACATCACTGATCAAGAGGTACAAACATTATCTGGAGGAGAACTAC
AGCGAGTAGCTTTAGCTCTTTGCTTGGGCAAACCTGCTGATGTCTATTTAATTGATGAGCCATCTGCATATTTGGATTCT
GAGCAAAGATTGATGGCAGCTGGAGTTGTCAAACGTTTCATACTCCATACGAAGAAGACGGCCTTTGTTGTGGAACATGA
CTTCATCATGGCCACCTATCTAGCAGATCGAGTCACTGTTTTTGATGGTGTCCCATCTAAGAACACTGTTGCAAATAGTC
CTCAAACCCTTTTGGCCGGCATGAATAAATGTTTGTCTCAGCTTGAAATTACATTCAGAAGAGATCCAAACAACTATAGA
CCACGAATAAACAAACTCAACTCAATTAAGGATGTAGAACAGAAGAAGAGTGGAAACTACTTTTTCTTGGATGAT

Alignment

ORF - retro_ocun_668 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.38 %
• Parental protein coverage: 57.76 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KAAITIRSLINPDRYIIVVEHDLSVLDYLSDFICCLYGVPSAYGVVTMPFSVREGINIFLDGYVPTENLR
          KAAITIRSLINPDRYI.VVEHDLSVLDYLSD..CCLYGVPSAYGVVTMP.SVREGIN.FLDGYVPTENLR
Retrocopy KAAITIRSLINPDRYITVVEHDLSVLDYLSDSSCCLYGVPSAYGVVTMPCSVREGINTFLDGYVPTENLR

Parental  FRDASLVFKVAETANEEEVKKMCMYKYPGMKKKMGEFELAIVAGEFTDSEIMVMLGENGTGKTTFIRMLA
          FRDASLVFKVAETANEE.VKKMCMY.YPGMKKKMGEFELAIVAGEFTDSEIM.ML.ENGTGKTTFIRMLA
Retrocopy FRDASLVFKVAETANEE-VKKMCMYNYPGMKKKMGEFELAIVAGEFTDSEIMGMLRENGTGKTTFIRMLA

Parental  GRLKPDEGGEVPVLNVSYKPQKISPKSTGSVRQLLHEKIRDAYTHPQFVTDVMKPLQIENIIDQEVQTLS
          GRLKP.EGGEVPVLNVSYKPQKISPKSTGSVRQLLHEKI.DAYTHPQFVTDVMKPLQIENI.DQEVQTLS
Retrocopy GRLKPNEGGEVPVLNVSYKPQKISPKSTGSVRQLLHEKISDAYTHPQFVTDVMKPLQIENITDQEVQTLS

Parental  GGELQRVALALCLGKPADVYLIDEPSAYLDSEQRLMAARVVKRFILHAKKTAFVVEHDFIMATYLADRVI
          GGELQRVALALCLGKPADVYLIDEPSAYLDSEQRLMAA.VVKRFILH.KKTAFVVEHDFIMATYLADRV.
Retrocopy GGELQRVALALCLGKPADVYLIDEPSAYLDSEQRLMAAGVVKRFILHTKKTAFVVEHDFIMATYLADRVT

Parental  VFDGVPSKNTVANSPQTLLAGMNKFLSQLEITFRRDPNNYRPRINKLNSIKDVEQKKSGNYFFLDD
          VFDGVPSKNTVANSPQTLLAGMNK.LSQLEITFRRDPNNYRPRINKLNSIKDVEQKKSGNYFFLDD
Retrocopy VFDGVPSKNTVANSPQTLLAGMNKCLSQLEITFRRDPNNYRPRINKLNSIKDVEQKKSGNYFFLDD

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	0.06 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_668 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_668 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_668 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,