RetrogeneDB ID:

retro_hsap_2204

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:2:206905155..206905566(+)
Located in intron of:ENSG00000114933
Retrocopy
information
Ensembl ID:ENSG00000237041
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:RPL27
Ensembl ID:ENSG00000131469
Aliases:RPL27, L27
Description:ribosomal protein L27 [Source:HGNC Symbol;Acc:10328]


Retrocopy-Parental alignment summary:






>retro_hsap_2204
ATGGGCAAGTGCATGAAACCTGGGAAAGTGGTGCTGGTCCTGGCCAGCAGTATTCTGGCTGAACACAAAGCTGTCATCGT
AAAGAACATTAATGATGGCACCTCAGACTGCCCCTACATCCAAGCTCTCGTGGTTGGAATTGATCGCTATCCCTGCAAAG
TGACAGCTGCCATGGGCAAAAAGAAGATTACCAGGAGGTCAAAGATCGAGTCTTTTGTGAAGGTTTATAACTACAATCAT
CTTACGCCTACAGTGCACTCTGTGGATATCCTCTTACACAAAACTGTCATCCACAAGGATGTCTTCAGAGATCCTGCTCT
TAAACACAAGTCCCAATGGGAGGCCAAGGTCAAGCTCAAAGAGAGATACAAAACGGGCAAGAACAAGCAGTTCTTCCAGA
AGCTACAGTTT

ORF - retro_hsap_2204 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 76.64 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMGKFMKPGKVVLVLAGRY-SGRKAVIVKNIDDGTSDRPYSHALVAGIDRYPRKVTAAMGKKKIAKRSKIK
MGK.MKPGKVVLVLA.......KAVIVKNI.DGTSD.PY..ALV.GIDRYP.KVTAAMGKKKI..RSKI.
RetrocopyMGKCMKPGKVVLVLASSILAEHKAVIVKNINDGTSDCPYIQALVVGIDRYPCKVTAAMGKKKITRRSKIE
ParentalSFVKVYNYNHLMPTRYSVDIPLDKTVVNKDVFRDPALKRKARREAKVKFEERYKTGKNKWFFQKLRF
SFVKVYNYNHL.PT..SVDI.L.KTV..KDVFRDPALK.K...EAKVK..ERYKTGKNK.FFQKL.F
RetrocopySFVKVYNYNHLTPTVHSVDILLHKTVIHKDVFRDPALKHKSQWEAKVKLKERYKTGKNKQFFQKLQF

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 241 .08 RPM
bodymap2_adrenal 0 .04 RPM 363 .66 RPM
bodymap2_brain 0 .00 RPM 121 .72 RPM
bodymap2_breast 0 .00 RPM 201 .25 RPM
bodymap2_colon 0 .00 RPM 427 .75 RPM
bodymap2_heart 0 .00 RPM 164 .32 RPM
bodymap2_kidney 0 .00 RPM 141 .79 RPM
bodymap2_liver 0 .00 RPM 160 .56 RPM
bodymap2_lung 0 .00 RPM 512 .69 RPM
bodymap2_lymph_node 0 .00 RPM 489 .64 RPM
bodymap2_ovary 0 .13 RPM 349 .24 RPM
bodymap2_prostate 0 .00 RPM 572 .27 RPM
bodymap2_skeletal_muscle 0 .00 RPM 321 .43 RPM
bodymap2_testis 0 .00 RPM 320 .22 RPM
bodymap2_thyroid 0 .00 RPM 193 .10 RPM
bodymap2_white_blood_cells 0 .00 RPM 603 .00 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_2204 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_2204 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_2204 retrocopy 5' end.

Lab - click to see more details

retro_hsap_2204 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_2204 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_1673
Gorilla gorilla retro_ggor_1741
Macaca mulatta retro_mmul_925
Parental genes homology:
Parental genes homology involve 21 parental genes, and 112 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000002003 retrocopies
retro_amel_122, retro_amel_37, retro_amel_674,
Bos taurus ENSBTAG000000174416 retrocopies
retro_btau_1113, retro_btau_129, retro_btau_1565, retro_btau_1855, retro_btau_338, retro_btau_394,
Canis familiaris ENSCAFG000000146306 retrocopies
retro_cfam_1193, retro_cfam_2109, retro_cfam_339, retro_cfam_364, retro_cfam_947, retro_cfam_959,
Callithrix jacchus ENSCJAG000000130679 retrocopies
retro_cjac_1345, retro_cjac_1350, retro_cjac_1543, retro_cjac_1630, retro_cjac_2210, retro_cjac_275, retro_cjac_2828, retro_cjac_369, retro_cjac_776,
Felis catus ENSFCAG000000131426 retrocopies
retro_fcat_1026, retro_fcat_1184, retro_fcat_1824, retro_fcat_228, retro_fcat_698, retro_fcat_78,
Homo sapiens ENSG00000131469 6 retrocopies
retro_hsap_1161, retro_hsap_1312, retro_hsap_2112, retro_hsap_2204 , retro_hsap_238, retro_hsap_3787,
Gorilla gorilla ENSGGOG000000260396 retrocopies
retro_ggor_1741, retro_ggor_1852, retro_ggor_2546, retro_ggor_2630, retro_ggor_298, retro_ggor_907,
Loxodonta africana ENSLAFG000000142203 retrocopies
retro_lafr_443, retro_lafr_739, retro_lafr_965,
Microcebus murinus ENSMICG000000142145 retrocopies
retro_mmur_1340, retro_mmur_1498, retro_mmur_1542, retro_mmur_673, retro_mmur_695,
Myotis lucifugus ENSMLUG000000041191 retrocopy
retro_mluc_359,
Macaca mulatta ENSMMUG000000080907 retrocopies
retro_mmul_1646, retro_mmul_1997, retro_mmul_418, retro_mmul_478, retro_mmul_52, retro_mmul_680, retro_mmul_925,
Monodelphis domestica ENSMODG000000151281 retrocopy
retro_mdom_1141,
Mus musculus ENSMUSG000000633162 retrocopies
retro_mmus_223, retro_mmus_277,
Nomascus leucogenys ENSNLEG000000119012 retrocopies
retro_nleu_334, retro_nleu_45,
Oryctolagus cuniculus ENSOCUG000000038721 retrocopy
retro_ocun_263,
Otolemur garnettii ENSOGAG0000000394014 retrocopies
retro_ogar_1091, retro_ogar_1297, retro_ogar_1478, retro_ogar_1692, retro_ogar_1887, retro_ogar_2189, retro_ogar_2354, retro_ogar_2625, retro_ogar_2687, retro_ogar_2915, retro_ogar_3207, retro_ogar_3294, retro_ogar_3381, retro_ogar_618,
Pan troglodytes ENSPTRG000000092326 retrocopies
retro_ptro_127, retro_ptro_1673, retro_ptro_208, retro_ptro_2569, retro_ptro_794, retro_ptro_900,
Pteropus vampyrus ENSPVAG000000088174 retrocopies
retro_pvam_1084, retro_pvam_1231, retro_pvam_25, retro_pvam_509,
Rattus norvegicus ENSRNOG000000206748 retrocopies
retro_rnor_1150, retro_rnor_125, retro_rnor_1257, retro_rnor_1968, retro_rnor_2594, retro_rnor_2989, retro_rnor_386, retro_rnor_414,
Sarcophilus harrisii ENSSHAG000000120424 retrocopies
retro_shar_10, retro_shar_253, retro_shar_730, retro_shar_741,
Tarsius syrichta ENSTSYG0000000316712 retrocopies
retro_tsyr_1032, retro_tsyr_1154, retro_tsyr_1711, retro_tsyr_2036, retro_tsyr_381, retro_tsyr_476, retro_tsyr_602, retro_tsyr_787, retro_tsyr_816, retro_tsyr_822, retro_tsyr_95, retro_tsyr_989,

Expression level across human populations :
image/svg+xml GBR_HG00142 GBR_HG00099 GBR_HG00114 GBR_HG00143 GBR_HG00131 GBR_HG00137 GBR_HG00133 GBR_HG00119 GBR_HG00111 GBR_HG00134 FIN_HG00378 FIN_HG00338 FIN_HG00349 FIN_HG00375 FIN_HG00315 FIN_HG00277 FIN_HG00328 FIN_HG00321 FIN_HG00377 FIN_HG00183 TSI_NA20756 TSI_NA20538 TSI_NA20798 TSI_NA20532 TSI_NA20765 TSI_NA20518 TSI_NA20513 TSI_NA20512 TSI_NA20771 TSI_NA20786 YRI_NA19114 YRI_NA19099 YRI_NA18870 YRI_NA18907 YRI_NA19223 YRI_NA19214 YRI_NA18916 YRI_NA19093 YRI_NA19118 YRI_NA19213 Toscaniin Italia: Finnish inFinland: British in England and Scotland: Utah Residents (CEPH) with Northernand Western European Ancestry: Yoruba in Ibadan, Nigeria: CEU_NA12760 CEU_NA12827 CEU_NA12872 CEU_NA12751 CEU_NA12873 CEU_NA12400 CEU_NA11930 CEU_NA12004 CEU_NA11831 CEU_NA11843 No expression ( = 0 RPM ) > 0 RPM = 0.05 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .00 RPM
CEU_NA11843 0 .00 RPM
CEU_NA11930 0 .00 RPM
CEU_NA12004 0 .00 RPM
CEU_NA12400 0 .00 RPM
CEU_NA12751 0 .02 RPM
CEU_NA12760 0 .00 RPM
CEU_NA12827 0 .05 RPM
CEU_NA12872 0 .03 RPM
CEU_NA12873 0 .00 RPM
FIN_HG00183 0 .00 RPM
FIN_HG00277 0 .00 RPM
FIN_HG00315 0 .00 RPM
FIN_HG00321 0 .00 RPM
FIN_HG00328 0 .00 RPM
FIN_HG00338 0 .00 RPM
FIN_HG00349 0 .00 RPM
FIN_HG00375 0 .00 RPM
FIN_HG00377 0 .00 RPM
FIN_HG00378 0 .00 RPM
GBR_HG00099 0 .03 RPM
GBR_HG00111 0 .02 RPM
GBR_HG00114 0 .00 RPM
GBR_HG00119 0 .00 RPM
GBR_HG00131 0 .00 RPM
GBR_HG00133 0 .00 RPM
GBR_HG00134 0 .00 RPM
GBR_HG00137 0 .03 RPM
GBR_HG00142 0 .00 RPM
GBR_HG00143 0 .03 RPM
TSI_NA20512 0 .03 RPM
TSI_NA20513 0 .00 RPM
TSI_NA20518 0 .00 RPM
TSI_NA20532 0 .03 RPM
TSI_NA20538 0 .00 RPM
TSI_NA20756 0 .00 RPM
TSI_NA20765 0 .00 RPM
TSI_NA20771 0 .00 RPM
TSI_NA20786 0 .00 RPM
TSI_NA20798 0 .00 RPM
YRI_NA18870 0 .00 RPM
YRI_NA18907 0 .00 RPM
YRI_NA18916 0 .00 RPM
YRI_NA19093 0 .03 RPM
YRI_NA19099 0 .03 RPM
YRI_NA19114 0 .00 RPM
YRI_NA19118 0 .00 RPM
YRI_NA19213 0 .00 RPM
YRI_NA19214 0 .00 RPM
YRI_NA19223 0 .04 RPM

Indel association:

No indels were associated with its genomic coordinates. Based on Kabza et al. 2015 (PubMed).



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