RetrogeneDB ID:

retro_hsap_2300

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:2:106905261..106905509(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000230353
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:RPS21
Ensembl ID:ENSG00000171858
Aliases:RPS21, HLDF, S21
Description:ribosomal protein S21 [Source:HGNC Symbol;Acc:10409]


Retrocopy-Parental alignment summary:






>retro_hsap_2300
ATGCAGAATGACACTGGTGAGTTCATAGGCCTGTACATGCCATGGAAATGGTCCAATAGCAACTGCATCATCGATGCCAA
GGACCACAAATCCATCCAGATGAACGGGGCCAAGGTTGACAAGGTAGCAGGCAGGTTTAACCACCAGTTTAAAACCTATG
CTATCTGCAGGGCCATTCGCAGGATGGGTAAGTCACATGACTGCATTCTCCAATTGGCCAAGACCGACGGATTGTATTAA
AGAACTTT

ORF - retro_hsap_2300 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 73.81 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMQNDAGEFVDLYVPRKCSASNRIIGAKDHASIQMNVAEVDKVTGRFNGQFKTYAICGAIRRMGESDDSIL
MQND.GEF..LY.P.K.S.SN.II.AKDH.SIQMN.A.VDKV.GRFN.QFKTYAIC.AIRRMG.S.D.IL
RetrocopyMQNDTGEFIGLYMPWKWSNSNCIIDAKDHKSIQMNGAKVDKVAGRFNHQFKTYAICRAIRRMGKSHDCIL
ParentalRLAKADG-IVSKNF
.LAK.DG.IV.KNF
RetrocopyQLAKTDG<IVLKNF

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 128 .53 RPM
bodymap2_adrenal 0 .00 RPM 194 .85 RPM
bodymap2_brain 0 .00 RPM 40 .65 RPM
bodymap2_breast 0 .00 RPM 106 .71 RPM
bodymap2_colon 0 .00 RPM 138 .21 RPM
bodymap2_heart 0 .00 RPM 58 .52 RPM
bodymap2_kidney 0 .00 RPM 78 .69 RPM
bodymap2_liver 0 .00 RPM 83 .75 RPM
bodymap2_lung 0 .00 RPM 279 .38 RPM
bodymap2_lymph_node 0 .00 RPM 323 .61 RPM
bodymap2_ovary 0 .00 RPM 177 .12 RPM
bodymap2_prostate 0 .00 RPM 320 .49 RPM
bodymap2_skeletal_muscle 0 .00 RPM 240 .23 RPM
bodymap2_testis 0 .00 RPM 113 .29 RPM
bodymap2_thyroid 0 .00 RPM 118 .51 RPM
bodymap2_white_blood_cells 0 .00 RPM 338 .08 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_2300 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_2300 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_110767541 libraries788 libraries479 libraries18 libraries3 libraries

The graphical summary, for retro_hsap_2300 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_2300 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_2300 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Gorilla gorilla retro_ggor_131
Parental genes homology:
Parental genes homology involve 16 parental genes, and 70 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000173992 retrocopies
retro_amel_1783, retro_amel_87,
Bos taurus ENSBTAG000000207952 retrocopies
retro_btau_174, retro_btau_1780,
Canis familiaris ENSCAFG000000126764 retrocopies
retro_cfam_1055, retro_cfam_1687, retro_cfam_1896, retro_cfam_28,
Callithrix jacchus ENSCJAG000000141955 retrocopies
retro_cjac_2266, retro_cjac_2572, retro_cjac_629, retro_cjac_82, retro_cjac_884,
Homo sapiens ENSG00000171858 6 retrocopies
retro_hsap_1179, retro_hsap_1883, retro_hsap_2300 , retro_hsap_2949, retro_hsap_3026, retro_hsap_4303,
Gorilla gorilla ENSGGOG000000237457 retrocopies
retro_ggor_131, retro_ggor_1380, retro_ggor_1647, retro_ggor_2043, retro_ggor_2089, retro_ggor_2875, retro_ggor_917,
Latimeria chalumnae ENSLACG000000127531 retrocopy
retro_lcha_124,
Monodelphis domestica ENSMODG000000167691 retrocopy
retro_mdom_464,
Mus musculus ENSMUSG0000003900111 retrocopies
retro_mmus_1100, retro_mmus_1324, retro_mmus_1482, retro_mmus_1510, retro_mmus_1688, retro_mmus_1837, retro_mmus_2039, retro_mmus_2071, retro_mmus_2243, retro_mmus_576, retro_mmus_992,
Ornithorhynchus anatinus ENSOANG000000033612 retrocopies
retro_oana_102, retro_oana_107,
Otolemur garnettii ENSOGAG0000001667312 retrocopies
retro_ogar_1013, retro_ogar_1339, retro_ogar_1742, retro_ogar_2111, retro_ogar_2176, retro_ogar_2532, retro_ogar_2703, retro_ogar_2921, retro_ogar_3119, retro_ogar_3214, retro_ogar_3256, retro_ogar_719,
Pongo abelii ENSPPYG000000112058 retrocopies
retro_pabe_1562, retro_pabe_157, retro_pabe_2446, retro_pabe_2505, retro_pabe_3503, retro_pabe_365, retro_pabe_710, retro_pabe_986,
Pan troglodytes ENSPTRG000000137081 retrocopy
retro_ptro_42,
Rattus norvegicus ENSRNOG000000063252 retrocopies
retro_rnor_128, retro_rnor_172,
Sus scrofa ENSSSCG000000218251 retrocopy
retro_sscr_7,
Ictidomys tridecemlineatus ENSSTOG000000010295 retrocopies
retro_itri_1027, retro_itri_1487, retro_itri_637, retro_itri_82, retro_itri_849,

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).



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