RetrogeneDB ID:

retro_hsap_1895

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:18:61739397..61739882(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000237314
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:RPL12
Ensembl ID:ENSG00000197958
Aliases:RPL12, L12
Description:ribosomal protein L12 [Source:HGNC Symbol;Acc:10302]


Retrocopy-Parental alignment summary:






>retro_hsap_1895
CCTCAGTTCAACCCCAAGAAGATCATAGATGTATACCTGAGGTGTACTGGTGGAAAACTCATGCCACATCTGGTGAGGTC
CCAAAATTAGTCTTCTGGATCTGTCTCCAAAAAAAGCTGCTGATGACATCATCAGAGTAACTGGAGACTGGAAGGGTCTA
AAGATTATAGTGAAACTGACCATTCAAAACAGACAGAAACAGAGGGAATGGGTAACTTCTGCCTCTGCCCTGATTATCAA
AGCCCTCAACGATCTGCCAAGAGACAGAAGAAAGTAGAAAATCACTAAACACTGTGGGAATATCACTTTTGATGAGATTG
TCAACATCTCCTGACAGGTCACTACTGATCTTTGGCAGAGAACGCTGTGGAACCAATAAGGAGATCCTAGGGACTGCCCA
ATCTGTGGTCTGTCGGCTGCAGAGTTGATGCTTCCACCCTCATGATATCACAGATGACATCAACGGTGCTGCGGTGAAAT
TCCCA

ORF - retro_hsap_1895 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 64.07 %
Parental protein coverage: 97.58 %
Number of stop codons detected: 4
Number of frameshifts detected 4


Retrocopy - Parental Gene Alignment:

ParentalPKFDPNEIKVVYLRCTGGEV-GATSALAP-KIGPLGLSPKKVGDDIAKATGDWKGLRITVKLTIQNRQAQ
P.F.P..I..VYLRCTGG....ATS...P.KI..L.LSPKK..DDI...TGDWKGL.I.VKLTIQNRQ.Q
RetrocopyPQFNPKKIIDVYLRCTGGKL<HATSGEVP<KISLLDLSPKKAADDIIRVTGDWKGLKIIVKLTIQNRQKQ
ParentalIEVVPSASALIIKALKEPPRDRKKQKNIKHSGNITFDEIVNIARQM-RHRSLA-RELSGTIKEILGTAQS
.E.V.SASALIIKAL...PRDR.K.K..KH.GNITFDEIVNI..Q.....SLA.RE..GT.KEILGTAQS
RetrocopyREWVTSASALIIKALNDLPRDRRK*KITKHCGNITFDEIVNIS*QV<HY*SLA<RERCGTNKEILGTAQS
ParentalVGCNVDG--RHPHDIIDDINSGAVECP
V.C.......HPHDI.DDIN..AV..P
RetrocopyVVCRLQS*CFHPHDITDDINGAAVKFP

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 334 .37 RPM
bodymap2_adrenal 0 .04 RPM 375 .59 RPM
bodymap2_brain 0 .00 RPM 87 .48 RPM
bodymap2_breast 0 .00 RPM 274 .19 RPM
bodymap2_colon 0 .00 RPM 494 .79 RPM
bodymap2_heart 0 .00 RPM 91 .33 RPM
bodymap2_kidney 0 .00 RPM 286 .03 RPM
bodymap2_liver 0 .00 RPM 146 .20 RPM
bodymap2_lung 0 .00 RPM 420 .61 RPM
bodymap2_lymph_node 0 .00 RPM 493 .85 RPM
bodymap2_ovary 0 .00 RPM 470 .84 RPM
bodymap2_prostate 0 .00 RPM 765 .31 RPM
bodymap2_skeletal_muscle 0 .00 RPM 532 .70 RPM
bodymap2_testis 0 .08 RPM 314 .22 RPM
bodymap2_thyroid 0 .00 RPM 203 .98 RPM
bodymap2_white_blood_cells 0 .00 RPM 691 .71 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_1895 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_1895 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_1895 retrocopy 5' end.

Lab - click to see more details

retro_hsap_1895 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_1895 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Gorilla gorilla retro_ggor_1389
Pongo abelii retro_pabe_1577
Parental genes homology:
Parental genes homology involve 13 parental genes, and 151 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000069633 retrocopies
retro_btau_102, retro_btau_2, retro_btau_5,
Callithrix jacchus ENSCJAG000000180821 retrocopy
retro_cjac_221,
Homo sapiens ENSG00000197958 41 retrocopies
retro_hsap_1064, retro_hsap_117, retro_hsap_1210, retro_hsap_127, retro_hsap_1311, retro_hsap_1359, retro_hsap_137, retro_hsap_1401, retro_hsap_1592, retro_hsap_1644, retro_hsap_1790, retro_hsap_1850, retro_hsap_1880, retro_hsap_1895 , retro_hsap_2005, retro_hsap_2031, retro_hsap_2099, retro_hsap_2123, retro_hsap_2202, retro_hsap_2311, retro_hsap_2381, retro_hsap_2428, retro_hsap_2436, retro_hsap_2456, retro_hsap_2642, retro_hsap_3388, retro_hsap_3405, retro_hsap_3458, retro_hsap_3544, retro_hsap_3578, retro_hsap_3709, retro_hsap_4107, retro_hsap_4121, retro_hsap_4746, retro_hsap_584, retro_hsap_643, retro_hsap_705, retro_hsap_719, retro_hsap_768, retro_hsap_868, retro_hsap_983,
Latimeria chalumnae ENSLACG000000153733 retrocopies
retro_lcha_31, retro_lcha_87, retro_lcha_92,
Macropus eugenii ENSMEUG0000000738012 retrocopies
retro_meug_1102, retro_meug_1107, retro_meug_1199, retro_meug_1357, retro_meug_1426, retro_meug_1611, retro_meug_1634, retro_meug_1691, retro_meug_1953, retro_meug_265, retro_meug_479, retro_meug_493,
Macaca mulatta ENSMMUG000000004222 retrocopies
retro_mmul_1823, retro_mmul_53,
Monodelphis domestica ENSMODG000000045719 retrocopies
retro_mdom_1061, retro_mdom_1177, retro_mdom_1192, retro_mdom_1526, retro_mdom_1719, retro_mdom_1871, retro_mdom_1947, retro_mdom_309, retro_mdom_925,
Mus musculus ENSMUSG000000389001 retrocopy
retro_mmus_28,
Oryctolagus cuniculus ENSOCUG000000049029 retrocopies
retro_ocun_1246, retro_ocun_1632, retro_ocun_1895, retro_ocun_318, retro_ocun_329, retro_ocun_520, retro_ocun_556, retro_ocun_677, retro_ocun_880,
Ochotona princeps ENSOPRG0000001107821 retrocopies
retro_opri_100, retro_opri_1018, retro_opri_1066, retro_opri_1110, retro_opri_1210, retro_opri_1217, retro_opri_221, retro_opri_265, retro_opri_336, retro_opri_353, retro_opri_418, retro_opri_461, retro_opri_479, retro_opri_576, retro_opri_638, retro_opri_648, retro_opri_658, retro_opri_672, retro_opri_835, retro_opri_905, retro_opri_986,
Pongo abelii ENSPPYG0000001962244 retrocopies
retro_pabe_1009, retro_pabe_1084, retro_pabe_1095, retro_pabe_1127, retro_pabe_1159, retro_pabe_1223, retro_pabe_1246, retro_pabe_1309, retro_pabe_1361, retro_pabe_1471, retro_pabe_1509, retro_pabe_1577, retro_pabe_1659, retro_pabe_1660, retro_pabe_1736, retro_pabe_1794, retro_pabe_1806, retro_pabe_1820, retro_pabe_1969, retro_pabe_1982, retro_pabe_2000, retro_pabe_2149, retro_pabe_2328, retro_pabe_2531, retro_pabe_2802, retro_pabe_2859, retro_pabe_2928, retro_pabe_2947, retro_pabe_3002, retro_pabe_3146, retro_pabe_3185, retro_pabe_3276, retro_pabe_3363, retro_pabe_3405, retro_pabe_3482, retro_pabe_3693, retro_pabe_488, retro_pabe_521, retro_pabe_604, retro_pabe_620, retro_pabe_757, retro_pabe_815, retro_pabe_831, retro_pabe_904,
Pan troglodytes ENSPTRG000000228081 retrocopy
retro_ptro_21,
Rattus norvegicus ENSRNOG000000162204 retrocopies
retro_rnor_166, retro_rnor_236, retro_rnor_247, retro_rnor_312,

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 ) 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 .00 RPM
CEU_NA12760 0 .00 RPM
CEU_NA12827 0 .00 RPM
CEU_NA12872 0 .00 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 .00 RPM
GBR_HG00111 0 .00 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 .00 RPM
GBR_HG00142 0 .00 RPM
GBR_HG00143 0 .00 RPM
TSI_NA20512 0 .00 RPM
TSI_NA20513 0 .00 RPM
TSI_NA20518 0 .00 RPM
TSI_NA20532 0 .00 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 .00 RPM
YRI_NA19099 0 .00 RPM
YRI_NA19114 0 .00 RPM
YRI_NA19118 0 .00 RPM
YRI_NA19213 0 .00 RPM
YRI_NA19214 0 .00 RPM
YRI_NA19223 0 .00 RPM

Indel association:

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



Copyright © RetrogeneDB 2014-2017