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RetrogeneDB - Retrocopy retro_hsap_239 details

RetrogeneDB ID:

retro_hsap_239

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:1:159990119..159990515(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000237409
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:RPL27A
Ensembl ID:ENSG00000166441
Aliases:RPL27A, L27A
Description:ribosomal protein L27a [Source:HGNC Symbol;Acc:10329]


Retrocopy-Parental alignment summary:






>retro_hsap_239
AGGACCCAGAAATTTTGGAGCCAGGTGAGCCACAGCCTCTGCCGCATCAGCAAGCACTGAAAGCACCCAGGTGGCCGTGG
CAATGCTGGCGGCATGCATCACCACAGGATCGACTTCAGCAAATGTCACCCAGGTTACTTTAGGAAAGTTGGTATGAGGC
ATTACCACCTAAAGAGGAACCTGAGCTTCTACCCAGCTGTCAACCTTGACAAATTGTGGGCTTTGGTCAGGAAGCAGACA
CAGGTGAATGCTGCTAAAAACAAGCCTGGAACAGCTCCCATCACTGATGTGGTGCCATCGGGCTACTATAGAGTTCTGGG
AAGGGAAAAGTTCCCAAACCAGCCTGTCATCGTGAAGGCCAAATTCTTCAGCAGAAGAGCTCAGGAGAAGATTCAG

ORF - retro_hsap_239 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 73.48 %
Parental protein coverage: 89.19 %
Number of stop codons detected: 1
Number of frameshifts detected: 0


Retrocopy - Parental Gene Alignment:

ParentalKTRKLRGHVSHGHGRIGKHRKHPGGRGNAGGLHHHRINFDKYHPGYFGKVGMKHYHLKRNQSFCPTVNLD
.T.K....VSH...RI.KH.KHPGGRGNAGG.HHHRI.F.K.HPGYF.KVGM.HYHLKRN.SF.P.VNLD
RetrocopyRTQKFWSQVSHSLCRISKH*KHPGGRGNAGGMHHHRIDFSKCHPGYFRKVGMRHYHLKRNLSFYPAVNLD
ParentalKLWTLVSEQTRVNAAKNKTGAAPIIDVVRSGYYKVLGKGKLPKQPVIVKAKFFSRRAEEKIK
KLW.LV..QT.VNAAKNK.G.API.DVV.SGYY.VLG..K.P.QPVIVKAKFFSRRA.EKI.
RetrocopyKLWALVRKQTQVNAAKNKPGTAPITDVVPSGYYRVLGREKFPNQPVIVKAKFFSRRAQEKIQ

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
bodymap2_adipose 0 .00 RPM 407 .04 RPM
bodymap2_adrenal 0 .00 RPM 683 .19 RPM
bodymap2_brain 0 .09 RPM 103 .14 RPM
bodymap2_breast 0 .00 RPM 309 .93 RPM
bodymap2_colon 0 .00 RPM 485 .08 RPM
bodymap2_heart 0 .00 RPM 123 .73 RPM
bodymap2_kidney 0 .00 RPM 179 .49 RPM
bodymap2_liver 0 .00 RPM 187 .33 RPM
bodymap2_lung 0 .00 RPM 563 .40 RPM
bodymap2_lymph_node 0 .00 RPM 575 .42 RPM
bodymap2_ovary 0 .00 RPM 534 .80 RPM
bodymap2_prostate 0 .00 RPM 586 .75 RPM
bodymap2_skeletal_muscle 0 .00 RPM 291 .64 RPM
bodymap2_testis 0 .00 RPM 232 .16 RPM
bodymap2_thyroid 0 .00 RPM 324 .56 RPM
bodymap2_white_blood_cells 0 .00 RPM 719 .98 RPM

ChIP-Seq - click to see more details

RNA Polymerase II activity near the 5' end of retro_hsap_239 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_239 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_239 retrocopy 5' end.

Lab - click to see more details

retro_hsap_239 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_239 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 8 parental genes, and 46 retrocopies.

Species Parental gene accession Retrocopies number
Homo sapiens ENSG00000166441 7 retrocopies
retro_hsap_1263, retro_hsap_1908, retro_hsap_2352, retro_hsap_239 , retro_hsap_3335, retro_hsap_3586, retro_hsap_3682,
Gorilla gorilla ENSGGOG000000016602 retrocopies
retro_ggor_155, retro_ggor_1785,
Myotis lucifugus ENSMLUG000000166167 retrocopies
retro_mluc_113, retro_mluc_1253, retro_mluc_164, retro_mluc_2123, retro_mluc_2202, retro_mluc_47, retro_mluc_572,
Macaca mulatta ENSMMUG000000218282 retrocopies
retro_mmul_207, retro_mmul_268,
Mus musculus ENSMUSG000000463641 retrocopy
retro_mmus_40,
Pan troglodytes ENSPTRG000000033331 retrocopy
retro_ptro_33,
Rattus norvegicus ENSRNOG0000001421410 retrocopies
retro_rnor_132, retro_rnor_193, retro_rnor_1996, retro_rnor_2466, retro_rnor_253, retro_rnor_261, retro_rnor_334, retro_rnor_370, retro_rnor_565, retro_rnor_606,
Tarsius syrichta ENSTSYG0000001320716 retrocopies
retro_tsyr_1103, retro_tsyr_155, retro_tsyr_1591, retro_tsyr_1607, retro_tsyr_1623, retro_tsyr_170, retro_tsyr_1725, retro_tsyr_187, retro_tsyr_204, retro_tsyr_283, retro_tsyr_498, retro_tsyr_50, retro_tsyr_550, retro_tsyr_608, retro_tsyr_612, retro_tsyr_716,

Expression level across human populations :

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