RetrogeneDB ID:

retro_hsap_712

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:10:94356617..94357035(-)
Located in intron of:ENSG00000138160
Retrocopy
information
Ensembl ID:ENSG00000184111
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:RPL11
Ensembl ID:ENSG00000142676
Aliases:RPL11, DBA7, GIG34, L11
Description:ribosomal protein L11 [Source:HGNC Symbol;Acc:10301]


Retrocopy-Parental alignment summary:






>retro_hsap_712
ATCTGTATGGAGGAGACTGGAGATGACTGACCCCAGCAGCCAAGGTGTTGGAGCAGCTCATAGGCCAGACCCCTGTGTTC
TCCAAAGTCAAATACATTGTCAGATCCTTTGGCATCAGGAGAAGTGAAGATTGCCACCCACTGCACAAAGGGCCAAAGCA
GAAGAAACCCTGAAGAAAGGTCTAAAGATGCAGGAGTGTGAATCAAGAAAGAACAACTTCTCAGATACTGGAAACTTTGG
TTTGGAGATCCAGGAACACACAGATTTGGGTATCAAATGTGACCCATGCATTGGTATCTACAGCCTGGACTTCTGTATGG
TGCTGGGTAGGCCTGGTTTCAGCACTGCAGACACATAGCACAGAACAGGCTGCACTGGGGCCAAACACAGAATCAACAAA
GAGGCCATGCACTGGTTC

ORF - retro_hsap_712 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 70.34 %
Parental protein coverage: 80.34 %
Number of stop codons detected: 1
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalICVGESGDR-LTRAAKVLEQLTGQTPVFSKARYTVRSFGIRRNEKIAVHCTVRGAK-AEEILEKGLKVRE
IC..E.GD..LT.AAKVLEQL.GQTPVFSK..Y.VRSFGIRR.E....H....G.K.AEE.L.KGLK..E
RetrocopyICMEETGDD<LTPAAKVLEQLIGQTPVFSKVKYIVRSFGIRRSED--CHPLHKGPK<AEETLKKGLKMQE
ParentalYELRKNNFSDTGNFGFGIQEHIDLGIKYDPSIGIYGLDFYVVLGRPGFSIADKKRRTGCIGAKHRISKEE
.E.RKNNFSDTGNFG..IQEH.DLGIK.DP.IGIY.LDF..VLGRPGFS.AD...RTGC.GAKHRI.K.E
RetrocopyCESRKNNFSDTGNFGLEIQEHTDLGIKCDPCIGIYSLDFCMVLGRPGFSTADT*HRTGCTGAKHRINK-E
ParentalAMRWF
AM.WF
RetrocopyAMHWF

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 970 .38 RPM
bodymap2_adrenal 0 .08 RPM 1130 .92 RPM
bodymap2_brain 0 .00 RPM 214 .62 RPM
bodymap2_breast 0 .00 RPM 661 .00 RPM
bodymap2_colon 0 .00 RPM 947 .57 RPM
bodymap2_heart 0 .00 RPM 210 .62 RPM
bodymap2_kidney 0 .00 RPM 373 .41 RPM
bodymap2_liver 0 .00 RPM 317 .51 RPM
bodymap2_lung 0 .00 RPM 912 .03 RPM
bodymap2_lymph_node 0 .00 RPM 994 .96 RPM
bodymap2_ovary 0 .10 RPM 1227 .26 RPM
bodymap2_prostate 0 .00 RPM 1177 .85 RPM
bodymap2_skeletal_muscle 0 .00 RPM 396 .86 RPM
bodymap2_testis 0 .00 RPM 630 .41 RPM
bodymap2_thyroid 0 .00 RPM 607 .33 RPM
bodymap2_white_blood_cells 0 .00 RPM 1137 .36 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_712 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_712 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_712 retrocopy 5' end.

Lab - click to see more details

retro_hsap_712 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_712 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Gorilla gorilla retro_ggor_603
Pongo abelii retro_pabe_615
Macaca mulatta retro_mmul_2462
Parental genes homology:
Parental genes homology involve 18 parental genes, and 58 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000209051 retrocopy
retro_btau_267,
Canis familiaris ENSCAFG000000132322 retrocopies
retro_cfam_1059, retro_cfam_543,
Callithrix jacchus ENSCJAG000000209531 retrocopy
retro_cjac_790,
Dasypus novemcinctus ENSDNOG000000112302 retrocopies
retro_dnov_1453, retro_dnov_605,
Homo sapiens ENSG00000142676 6 retrocopies
retro_hsap_1159, retro_hsap_1801, retro_hsap_2272, retro_hsap_3238, retro_hsap_606, retro_hsap_712 ,
Gorilla gorilla ENSGGOG000000146286 retrocopies
retro_ggor_1192, retro_ggor_1325, retro_ggor_1690, retro_ggor_2204, retro_ggor_533, retro_ggor_603,
Loxodonta africana ENSLAFG000000308532 retrocopies
retro_lafr_371, retro_lafr_434,
Macropus eugenii ENSMEUG000000137383 retrocopies
retro_meug_488, retro_meug_517, retro_meug_633,
Macaca mulatta ENSMMUG000000024453 retrocopies
retro_mmul_2039, retro_mmul_2415, retro_mmul_2462,
Monodelphis domestica ENSMODG000000128281 retrocopy
retro_mdom_641,
Mus musculus ENSMUSG000000592913 retrocopies
retro_mmus_144, retro_mmus_146, retro_mmus_78,
Ornithorhynchus anatinus ENSOANG000000003211 retrocopy
retro_oana_49,
Oryctolagus cuniculus ENSOCUG000000229281 retrocopy
retro_ocun_1387,
Pongo abelii ENSPPYG000000017366 retrocopies
retro_pabe_1478, retro_pabe_1946, retro_pabe_2686, retro_pabe_612, retro_pabe_615, retro_pabe_964,
Pteropus vampyrus ENSPVAG000000042821 retrocopy
retro_pvam_1068,
Rattus norvegicus ENSRNOG000000262609 retrocopies
retro_rnor_1735, retro_rnor_2287, retro_rnor_2314, retro_rnor_2690, retro_rnor_271, retro_rnor_2725, retro_rnor_668, retro_rnor_795, retro_rnor_919,
Sus scrofa ENSSSCG000000242604 retrocopies
retro_sscr_1048, retro_sscr_1049, retro_sscr_1074, retro_sscr_819,
Tarsius syrichta ENSTSYG000000013496 retrocopies
retro_tsyr_1138, retro_tsyr_127, retro_tsyr_1583, retro_tsyr_1605, retro_tsyr_516, retro_tsyr_520,

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 = 0.11 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .00 RPM
CEU_NA11843 0 .06 RPM
CEU_NA11930 0 .00 RPM
CEU_NA12004 0 .00 RPM
CEU_NA12400 0 .00 RPM
CEU_NA12751 0 .05 RPM
CEU_NA12760 0 .04 RPM
CEU_NA12827 0 .00 RPM
CEU_NA12872 0 .00 RPM
CEU_NA12873 0 .00 RPM
FIN_HG00183 0 .00 RPM
FIN_HG00277 0 .11 RPM
FIN_HG00315 0 .00 RPM
FIN_HG00321 0 .03 RPM
FIN_HG00328 0 .00 RPM
FIN_HG00338 0 .00 RPM
FIN_HG00349 0 .00 RPM
FIN_HG00375 0 .02 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 .02 RPM
GBR_HG00131 0 .00 RPM
GBR_HG00133 0 .02 RPM
GBR_HG00134 0 .04 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 .10 RPM
TSI_NA20538 0 .00 RPM
TSI_NA20756 0 .00 RPM
TSI_NA20765 0 .02 RPM
TSI_NA20771 0 .00 RPM
TSI_NA20786 0 .03 RPM
TSI_NA20798 0 .03 RPM
YRI_NA18870 0 .03 RPM
YRI_NA18907 0 .03 RPM
YRI_NA18916 0 .04 RPM
YRI_NA19093 0 .03 RPM
YRI_NA19099 0 .00 RPM
YRI_NA19114 0 .00 RPM
YRI_NA19118 0 .02 RPM
YRI_NA19213 0 .00 RPM
YRI_NA19214 0 .00 RPM
YRI_NA19223 0 .06 RPM

Indel association:

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



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