RetrogeneDB ID:

retro_hsap_3371

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:5:115387609..115387981(-)
Located in intron of:ENSG00000268714
Retrocopy
information
Ensembl ID:ENSG00000185641
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:RPS25
Ensembl ID:ENSG00000118181
Aliases:None
Description:ribosomal protein S25 [Source:HGNC Symbol;Acc:10413]


Retrocopy-Parental alignment summary:






>retro_hsap_3371
ATGCCGCCCAAGGACGACGAGAAGAAGGACGCTGGAAAGTCAGCCAAGAAAAACAAAGACCCAGTGAACAAATCCGGGGG
CAAGGCCAAAAAGAAGAAGTGGTCCAAAGGCAAAGTTCGGGACAAGCTCAATAACTTAGTCTTGTTTGACAAAGCTACCT
ATGACAAACTCTGTAAGGAAGTTCCCAACTATAAACTTATAACCCCAGCTGTGGTCTCTGAGAGACTGAAGATTCGAGGC
TCCCTGGCCAGGGCAGCCCTTCAGGAGCTCCTTAGTAAAGGACTTATCAAACTGGTTTCAAAGCACAGAGCTCAAGTAAT
TTACACCAGAAATACCAAGGGTGGAGATGCTCCAGCTGCTGGTGAAGATGCA

ORF - retro_hsap_3371 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 97.6 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMPPKDDKKKKDAGKSAKKDKDPVNKSGGKAKKKKWSKGKVRDKLNNLVLFDKATYDKLCKEVPNYKLITP
MPPKDD.KK.DAGKSAKK.KDPVNKSGGKAKKKKWSKGKVRDKLNNLVLFDKATYDKLCKEVPNYKLITP
RetrocopyMPPKDDEKK-DAGKSAKKNKDPVNKSGGKAKKKKWSKGKVRDKLNNLVLFDKATYDKLCKEVPNYKLITP
ParentalAVVSERLKIRGSLARAALQELLSKGLIKLVSKHRAQVIYTRNTKGGDAPAAGEDA
AVVSERLKIRGSLARAALQELLSKGLIKLVSKHRAQVIYTRNTKGGDAPAAGEDA
RetrocopyAVVSERLKIRGSLARAALQELLSKGLIKLVSKHRAQVIYTRNTKGGDAPAAGEDA

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 2 .48 RPM 320 .89 RPM
bodymap2_adrenal 4 .36 RPM 469 .20 RPM
bodymap2_brain 1 .55 RPM 161 .29 RPM
bodymap2_breast 2 .82 RPM 271 .17 RPM
bodymap2_colon 6 .42 RPM 629 .09 RPM
bodymap2_heart 0 .31 RPM 132 .61 RPM
bodymap2_kidney 1 .08 RPM 237 .68 RPM
bodymap2_liver 0 .30 RPM 130 .82 RPM
bodymap2_lung 1 .28 RPM 384 .44 RPM
bodymap2_lymph_node 1 .86 RPM 435 .74 RPM
bodymap2_ovary 4 .80 RPM 467 .37 RPM
bodymap2_prostate 2 .68 RPM 535 .68 RPM
bodymap2_skeletal_muscle 1 .42 RPM 327 .14 RPM
bodymap2_testis 2 .98 RPM 380 .49 RPM
bodymap2_thyroid 1 .73 RPM 251 .51 RPM
bodymap2_white_blood_cells 2 .11 RPM 539 .51 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_3371 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_3371 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_147856239 libraries395 libraries1071 libraries106 libraries18 libraries
TSS #2 TSS_147857264 libraries404 libraries1075 libraries81 libraries5 libraries

The graphical summary, for retro_hsap_3371 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_3371 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_3371 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_2291
Parental genes homology:
Parental genes homology involve 12 parental genes, and 90 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000277722 retrocopies
retro_btau_203, retro_btau_9,
Callithrix jacchus ENSCJAG000000136911 retrocopy
retro_cjac_208,
Dasypus novemcinctus ENSDNOG000000078807 retrocopies
retro_dnov_1092, retro_dnov_1566, retro_dnov_2219, retro_dnov_2593, retro_dnov_346, retro_dnov_877, retro_dnov_973,
Homo sapiens ENSG00000118181 3 retrocopies
retro_hsap_3371 , retro_hsap_3547, retro_hsap_4310,
Gorilla gorilla ENSGGOG000000255407 retrocopies
retro_ggor_1601, retro_ggor_1666, retro_ggor_1979, retro_ggor_2395, retro_ggor_2880, retro_ggor_337, retro_ggor_634,
Mus musculus ENSMUSG0000000992715 retrocopies
retro_mmus_128, retro_mmus_1368, retro_mmus_1455, retro_mmus_1760, retro_mmus_1769, retro_mmus_1788, retro_mmus_2375, retro_mmus_2393, retro_mmus_2641, retro_mmus_2700, retro_mmus_2797, retro_mmus_3218, retro_mmus_336, retro_mmus_3523, retro_mmus_880,
Oryctolagus cuniculus ENSOCUG0000001725611 retrocopies
retro_ocun_1166, retro_ocun_1231, retro_ocun_1319, retro_ocun_1553, retro_ocun_1761, retro_ocun_291, retro_ocun_298, retro_ocun_548, retro_ocun_623, retro_ocun_856, retro_ocun_978,
Otolemur garnettii ENSOGAG000000072653 retrocopies
retro_ogar_220, retro_ogar_257, retro_ogar_32,
Pongo abelii ENSPPYG000000259156 retrocopies
retro_pabe_1889, retro_pabe_1971, retro_pabe_2930, retro_pabe_3507, retro_pabe_71, retro_pabe_94,
Sorex araneus ENSSARG000000022844 retrocopies
retro_sara_21, retro_sara_212, retro_sara_43, retro_sara_542,
Tupaia belangeri ENSTBEG0000001024416 retrocopies
retro_tbel_1592, retro_tbel_1823, retro_tbel_1849, retro_tbel_22, retro_tbel_2651, retro_tbel_2744, retro_tbel_3106, retro_tbel_3107, retro_tbel_3499, retro_tbel_374, retro_tbel_3871, retro_tbel_3877, retro_tbel_4239, retro_tbel_4434, retro_tbel_444, retro_tbel_4464,
Tarsius syrichta ENSTSYG0000000542215 retrocopies
retro_tsyr_1050, retro_tsyr_1098, retro_tsyr_1125, retro_tsyr_1230, retro_tsyr_1252, retro_tsyr_1454, retro_tsyr_154, retro_tsyr_1558, retro_tsyr_2081, retro_tsyr_358, retro_tsyr_414, retro_tsyr_428, retro_tsyr_570, retro_tsyr_859, retro_tsyr_873,

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 = 4.63 RPM Legend:


Library Retrogene expression
CEU_NA11831 4 .11 RPM
CEU_NA11843 3 .75 RPM
CEU_NA11930 4 .63 RPM
CEU_NA12004 2 .58 RPM
CEU_NA12400 3 .40 RPM
CEU_NA12751 1 .99 RPM
CEU_NA12760 4 .58 RPM
CEU_NA12827 3 .68 RPM
CEU_NA12872 2 .01 RPM
CEU_NA12873 2 .97 RPM
FIN_HG00183 3 .73 RPM
FIN_HG00277 2 .99 RPM
FIN_HG00315 1 .93 RPM
FIN_HG00321 1 .60 RPM
FIN_HG00328 1 .92 RPM
FIN_HG00338 2 .30 RPM
FIN_HG00349 4 .13 RPM
FIN_HG00375 2 .59 RPM
FIN_HG00377 2 .32 RPM
FIN_HG00378 1 .85 RPM
GBR_HG00099 2 .62 RPM
GBR_HG00111 2 .86 RPM
GBR_HG00114 2 .76 RPM
GBR_HG00119 2 .20 RPM
GBR_HG00131 1 .93 RPM
GBR_HG00133 2 .22 RPM
GBR_HG00134 1 .59 RPM
GBR_HG00137 3 .57 RPM
GBR_HG00142 4 .03 RPM
GBR_HG00143 2 .87 RPM
TSI_NA20512 2 .43 RPM
TSI_NA20513 1 .33 RPM
TSI_NA20518 2 .72 RPM
TSI_NA20532 2 .07 RPM
TSI_NA20538 2 .21 RPM
TSI_NA20756 2 .79 RPM
TSI_NA20765 1 .14 RPM
TSI_NA20771 3 .49 RPM
TSI_NA20786 1 .15 RPM
TSI_NA20798 2 .00 RPM
YRI_NA18870 3 .45 RPM
YRI_NA18907 1 .59 RPM
YRI_NA18916 1 .18 RPM
YRI_NA19093 1 .69 RPM
YRI_NA19099 1 .78 RPM
YRI_NA19114 1 .70 RPM
YRI_NA19118 2 .11 RPM
YRI_NA19213 1 .77 RPM
YRI_NA19214 1 .16 RPM
YRI_NA19223 1 .71 RPM

Indel association:

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



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