RetrogeneDB ID:

retro_hsap_3710

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:7:26315814..26316230(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000232383
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:RPL23
Ensembl ID:ENSG00000125691
Aliases:None
Description:ribosomal protein L23 [Source:HGNC Symbol;Acc:10316]


Retrocopy-Parental alignment summary:






>retro_hsap_3710
ATGTCGAAGCAAGGATGTGGTGAGTCCTCTGGTGCAAAATTCTGGATTTCCTTGGGTCTTCTGGTAGGATCCCTGATCAA
CAATGCTGACAATACAGGAGCCAAAAATCTGTATATCATCTCCGTGAAGAGGATCAGGGACGGCTGAACAGACTTCCCTG
CCAGTGTGGGTGACATGGGGATGGCCACAGTCAAGAAAGACAAACCAGAGCTCAGAAAAAAGGTACATCCAGCAGTGGTC
ACTTGACAACAAAAGTCATATGGAGAAAAGACGGTGTGTTTCTTTATTTTGAAGGTAATGCAGGGGTCATAATAAAAAAC
AAAGACGAGATGAAGGGTTCTGCCATTACAGGACCAGTAGCAAAGGAGTGTGCAGACTTGTGGCCCCGGATTGCGTTCAA
TACTGGCAGCATTGCA

ORF - retro_hsap_3710 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 81.12 %
Parental protein coverage: 100. %
Number of stop codons detected: 1
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalMSKRGRGGSSGAKFRISLGLPVGAVINCADNTGAKNLYIISVKGIK-GRLNRL-PAAGVGDMVMATVKKG
MSK.G.G.SSGAKF.ISLGL.VG..IN.ADNTGAKNLYIISVK.I..GRLNRL.PA..VGDM.MATVKK.
RetrocopyMSKQGCGESSGAKFWISLGLLVGSLINNADNTGAKNLYIISVKRIR<GRLNRL>PAS-VGDMGMATVKKD
ParentalKPELRKKVHPAVVIRQRKSYR-RKDGVFLYFEDNAGVIVNNKGEMKGSAITGPVAKECADLWPRIASNAG
KPELRKKVHPAVV..Q.KSY..RKDGVFLYFE.NAGVI..NK.EMKGSAITGPVAKECADLWPRIA.N.G
RetrocopyKPELRKKVHPAVVT*QQKSYG<RKDGVFLYFEGNAGVIIKNKDEMKGSAITGPVAKECADLWPRIAFNTG
ParentalSIA
SIA
RetrocopySIA

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 648 .40 RPM
bodymap2_adrenal 0 .00 RPM 671 .03 RPM
bodymap2_brain 0 .00 RPM 181 .66 RPM
bodymap2_breast 0 .12 RPM 478 .08 RPM
bodymap2_colon 0 .14 RPM 795 .05 RPM
bodymap2_heart 0 .02 RPM 211 .75 RPM
bodymap2_kidney 0 .06 RPM 330 .39 RPM
bodymap2_liver 0 .00 RPM 243 .03 RPM
bodymap2_lung 0 .00 RPM 749 .49 RPM
bodymap2_lymph_node 0 .02 RPM 752 .78 RPM
bodymap2_ovary 0 .00 RPM 891 .59 RPM
bodymap2_prostate 0 .03 RPM 911 .16 RPM
bodymap2_skeletal_muscle 0 .02 RPM 556 .95 RPM
bodymap2_testis 0 .70 RPM 483 .20 RPM
bodymap2_thyroid 0 .00 RPM 340 .24 RPM
bodymap2_white_blood_cells 0 .00 RPM 835 .22 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_3710 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_3710 retrocopy.

TSS - click to see more details



TSS No. TSS Name TSS expression level (Expr) in TPM range:
no expression 0 < Expr ≤ 1 1 < Expr ≤ 5 5 < Expr ≤ 10 Expr > 10
TSS #1 TSS_174239151 libraries108 libraries531 libraries476 libraries563 libraries

The graphical summary, for retro_hsap_3710 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1829 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)

Display detail expression values in each library
... or ...
Directly download all expression values

Lab - click to see more details

retro_hsap_3710 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_3710 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_2513
Gorilla gorilla retro_ggor_2508
Pongo abelii retro_pabe_3145
Parental genes homology:
Parental genes homology involve 13 parental genes, and 89 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000042686 retrocopies
retro_amel_1791, retro_amel_226, retro_amel_308, retro_amel_880, retro_amel_918, retro_amel_990,
Callithrix jacchus ENSCJAG000000083119 retrocopies
retro_cjac_1129, retro_cjac_1483, retro_cjac_2283, retro_cjac_2598, retro_cjac_2639, retro_cjac_2772, retro_cjac_2885, retro_cjac_3128, retro_cjac_3831,
Dipodomys ordii ENSDORG000000013723 retrocopies
retro_dord_366, retro_dord_475, retro_dord_530,
Felis catus ENSFCAG0000001450210 retrocopies
retro_fcat_1022, retro_fcat_1431, retro_fcat_1707, retro_fcat_1708, retro_fcat_1959, retro_fcat_242, retro_fcat_296, retro_fcat_716, retro_fcat_756, retro_fcat_859,
Homo sapiens ENSG00000125691 9 retrocopies
retro_hsap_2211, retro_hsap_2213, retro_hsap_2522, retro_hsap_3581, retro_hsap_3708, retro_hsap_3710 , retro_hsap_4042, retro_hsap_4106, retro_hsap_556,
Latimeria chalumnae ENSLACG000000044301 retrocopy
retro_lcha_16,
Macaca mulatta ENSMMUG000000045029 retrocopies
retro_mmul_1598, retro_mmul_1705, retro_mmul_1955, retro_mmul_2366, retro_mmul_2391, retro_mmul_384, retro_mmul_928, retro_mmul_930, retro_mmul_935,
Nomascus leucogenys ENSNLEG000000006427 retrocopies
retro_nleu_1506, retro_nleu_181, retro_nleu_2056, retro_nleu_2337, retro_nleu_2988, retro_nleu_574, retro_nleu_8,
Oryctolagus cuniculus ENSOCUG000000139156 retrocopies
retro_ocun_1027, retro_ocun_1196, retro_ocun_1270, retro_ocun_1919, retro_ocun_251, retro_ocun_482,
Otolemur garnettii ENSOGAG000000124457 retrocopies
retro_ogar_1050, retro_ogar_1645, retro_ogar_1695, retro_ogar_2250, retro_ogar_277, retro_ogar_3145, retro_ogar_539,
Ochotona princeps ENSOPRG0000000195710 retrocopies
retro_opri_1079, retro_opri_1216, retro_opri_137, retro_opri_14, retro_opri_178, retro_opri_202, retro_opri_224, retro_opri_481, retro_opri_639, retro_opri_684,
Rattus norvegicus ENSRNOG0000000410710 retrocopies
retro_rnor_1195, retro_rnor_1539, retro_rnor_1622, retro_rnor_2445, retro_rnor_2483, retro_rnor_2688, retro_rnor_2981, retro_rnor_347, retro_rnor_498, retro_rnor_941,
Ictidomys tridecemlineatus ENSSTOG000000142792 retrocopies
retro_itri_122, retro_itri_1577,

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 = 0.06 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 .03 RPM
FIN_HG00277 0 .00 RPM
FIN_HG00315 0 .00 RPM
FIN_HG00321 0 .00 RPM
FIN_HG00328 0 .02 RPM
FIN_HG00338 0 .02 RPM
FIN_HG00349 0 .00 RPM
FIN_HG00375 0 .02 RPM
FIN_HG00377 0 .03 RPM
FIN_HG00378 0 .02 RPM
GBR_HG00099 0 .00 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 .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 .03 RPM
TSI_NA20532 0 .00 RPM
TSI_NA20538 0 .00 RPM
TSI_NA20756 0 .00 RPM
TSI_NA20765 0 .00 RPM
TSI_NA20771 0 .06 RPM
TSI_NA20786 0 .03 RPM
TSI_NA20798 0 .00 RPM
YRI_NA18870 0 .03 RPM
YRI_NA18907 0 .00 RPM
YRI_NA18916 0 .00 RPM
YRI_NA19093 0 .03 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).





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