RetrogeneDB ID:

retro_ocun_1205

Retrocopy
location
Organism:Rabbit (Oryctolagus cuniculus)
Coordinates:3:105620130..105621033(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSOCUG00000021479
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:HNRNPA2B1
Ensembl ID:ENSOCUG00000026859
Aliases:None
Description:heterogeneous nuclear ribonucleoprotein A2/B1 [Source:HGNC Symbol;Acc:5033]


Retrocopy-Parental alignment summary:






>retro_ocun_1205
GAGAGAGAAAAGGAACAGTTCCATAAACTCTTTATTGGGGGCTTAAGGTTTGAAATCACAGAAGAAAGTTTGAGGAACTA
CTATGAGCAATGGGGAAAACTTACAGATTGTGTGGTAATGAGGGATCCTGCAAGCAAAAGATCAAGAGGATTTGGTTTTG
TAACTTTCTCATCCATGGATGAGGTTGATGCTGCCATGGCTACAAGACCTCATTCAATTGATGGGAGAGTGATTGAGCCA
AAGCGTGCTGTAGCAAGAGAAGAATCTGGAAAACCTGGGGTTCACGTAACTGTAAAGAAGCTGTTTGATGGTAGAATTAA
AGAAGATACTGAGGAATATCACCTTAGAGATTACTTTGAAGAACATGGAAAAATTGATACCCTTGAAATAATTACTGATA
GGCAGACTGGGAAGAAAAGAGGCTTTGTTACTTTTGATGACCATGATCTTGTGGATAAAATGGTATTGCAAAAATACCAC
ACCATCAATGGTCATAATGCACAAGTAAGAAAGGCTTTGTCTAGAAATGCAAGAAGTCCAGAGTTCTAAGAGTGGAAGAG
GAGGTAATTTCGGTTTTGGAGATTCACATGGTGGTGGTGGGAATTTGGGACCAGGGCCAGGAAGTAATTGTAGAGGAGGA
TCTGATGGATATGGACATGGACGTGGATTTGGGGAAGGCTATAATGGGTATGGAGGAGGACCTGGAGGTGGCAATTTAGG
AGGTAGCCCTGGTTATGGAGGAGGAAGAGGAGGATATGGTGGTGGAGGACCTGGAGATGGCAACCAGGGTGGGGCTACGG
AGGTGGTTATGACAACTATGCAGGAGGAAACTATGAAAGTGGAAATTACAATGATTTTGGAAATTACAATCAGCAACCCT
CTAACTACGGTCCAATGGAAACT

ORF - retro_ocun_1205 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 83.71 %
Parental protein coverage: 86.4 %
Number of stop codons detected: 0
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalKREKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAARP
.REKEQF.KLFIGGL.FE.TEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSM.EVDAAMA.RP
RetrocopyEREKEQFHKLFIGGLRFEITEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMDEVDAAMATRP
ParentalHSIDGRVVEPKRAVAREESGKPGAHVTVKKLFVGGIKEDTEEHHLRDYFEEYGKIDTIEIITDRQSGKKR
HSIDGRV.EPKRAVAREESGKPG.HVTVKKLF.G.IKEDTEE.HLRDYFEE.GKIDT.EIITDRQ.GKKR
RetrocopyHSIDGRVIEPKRAVAREESGKPGVHVTVKKLFDGRIKEDTEEYHLRDYFEEHGKIDTLEIITDRQTGKKR
ParentalGFGFVTFDDHDPVDKIVLQKYHTINGHNAEVRKALSR-QEMQEVQSSRSGRGGNFGFGDSRGGGGNFGPG
..GFVTFDDHD.VDK.VLQKYHTINGHNA.VRKALSR.........S..G....FG..DS.GGGGN.GPG
Retrocopy--GFVTFDDHDLVDKMVLQKYHTINGHNAQVRKALSR>MQEVQSSKSGRGGNFGFG--DSHGGGGNLGPG
ParentalPGSNFRGSADGYGSGRGFGDGYNGYGGGPGGGNFGGSPGYGGGRGGYGGGGPGYGNQGG-GYGGGYDNYG
PGSN.RG..DGYG.GRGFG.GYNGYGGGPGGGN.GGSPGYGGGRGGYGGGGPG.GNQGG.GYGGGYDNY.
RetrocopyPGSNCRGGSDGYGHGRGFGEGYNGYGGGPGGGNLGGSPGYGGGRGGYGGGGPGDGNQGG<GYGGGYDNYA
ParentalGGNYGSGNYNDFGNYNQQPSNYGPMKS
GGNY.SGNYNDFGNYNQQPSNYGPM..
RetrocopyGGNYESGNYNDFGNYNQQPSNYGPMET

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






RNA-Seq - click to see more details

(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)

Expression validation based on RNA-Seq data:
Library Retrocopy expression Parental gene expression
SRP017611_brain 0 .22 RPM 108 .28 RPM
SRP017611_kidney 0 .41 RPM 109 .67 RPM
SRP017611_liver 0 .23 RPM 57 .73 RPM

ChIP-Seq - click to see more details

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_ocun_1205 retrocopy.

TSS - click to see more details

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab - click to see more details

retro_ocun_1205 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ocun_1205 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 20 parental genes, and 47 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000057264 retrocopies
retro_btau_1330, retro_btau_1535, retro_btau_193, retro_btau_228,
Choloepus hoffmanni ENSCHOG0000001383215 retrocopies
retro_chof_1060, retro_chof_1191, retro_chof_1413, retro_chof_1460, retro_chof_1507, retro_chof_2062, retro_chof_2135, retro_chof_2235, retro_chof_2263, retro_chof_2404, retro_chof_2425, retro_chof_2473, retro_chof_2574, retro_chof_499, retro_chof_853,
Ciona intestinalis ENSCING000000040621 retrocopy
retro_cint_7,
Ciona savignyi ENSCSAVG000000004721 retrocopy
retro_csav_26,
Dasypus novemcinctus ENSDNOG000000129281 retrocopy
retro_dnov_1978,
Dipodomys ordii ENSDORG000000054821 retrocopy
retro_dord_489,
Echinops telfairi ENSETEG000000185771 retrocopy
retro_etel_1368,
Felis catus ENSFCAG000000277651 retrocopy
retro_fcat_692,
Macropus eugenii ENSMEUG000000010842 retrocopies
retro_meug_1897, retro_meug_214,
Myotis lucifugus ENSMLUG000000075781 retrocopy
retro_mluc_34,
Mus musculus ENSMUSG000000049801 retrocopy
retro_mmus_573,
Oryctolagus cuniculus ENSOCUG000000027432 retrocopies
retro_ocun_994, retro_ocun_995,
Oryctolagus cuniculus ENSOCUG000000133501 retrocopy
retro_ocun_1675,
Oryctolagus cuniculus ENSOCUG000000138051 retrocopy
retro_ocun_505,
Oryctolagus cuniculus ENSOCUG000000264243 retrocopies
retro_ocun_1800, retro_ocun_1811, retro_ocun_950,
Oryctolagus cuniculus ENSOCUG00000026859 2 retrocopies
retro_ocun_1205 , retro_ocun_642,
Ochotona princeps ENSOPRG000000116982 retrocopies
retro_opri_165, retro_opri_893,
Ictidomys tridecemlineatus ENSSTOG000000062023 retrocopies
retro_itri_1723, retro_itri_448, retro_itri_717,
Tursiops truncatus ENSTTRG000000007093 retrocopies
retro_ttru_1066, retro_ttru_1204, retro_ttru_1788,
Vicugna pacos ENSVPAG000000104171 retrocopy
retro_vpac_616,


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