RetrogeneDB ID:

retro_hsap_1594

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:15:73775735..73776166(-)
Located in intron of:ENSG00000183324
Retrocopy
information
Ensembl ID:ENSG00000259186
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:MRPS15
Ensembl ID:ENSG00000116898
Aliases:MRPS15, MPR-S15, RPMS15, S15mt
Description:mitochondrial ribosomal protein S15 [Source:HGNC Symbol;Acc:14504]


Retrocopy-Parental alignment summary:






>retro_hsap_1594
AGTCTCCTCCTCCAGGCTGCAGCAGATACACCATCCAGAAACCAGTCTGGCCTAGACAGGACCATGACCTTCCCCTTTCC
ATGCTGCTCAAAGACCACCAGACCATCCCTGGAATTGAGAAGGGCAATGATACAGTGAAAAGATCCTTGTCTTTGGAAAT
GACCAACCAAAAGGAGAAGCTAAATATCAAGTAAGAACATCTGATGAACAAAGTCGTGGCAAACCCTAAGGACACCAGCT
TCCTGGAGGCTCGAATTATTCCCTTGACCAAAGCCCACAATTATGAAGAACACAGCAGAAACACTGAAATAACAAAACCC
ACAAATACTATTGGTGATGGGCACTGTCCAGAGGAAAAAGATGCTCAAAAACCTTCGTTAGACCAATATGATGTCTCTGA
GAAGACACACTGGGGACTGAGCACATCTTTT

ORF - retro_hsap_1594 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 59.33 %
Parental protein coverage: 56.81 %
Number of stop codons detected: 3
Number of frameshifts detected 4


Retrocopy - Parental Gene Alignment:

ParentalSLLLQAARG-YVVRKPAQSRLDDDPPPSTLLKDYQNVPGIEKVDDVVKRLLSLEMANKKEMLKIKQEQFM
SLLLQAA...Y...KP...R.D.D.P.S.LLKD.Q..PGIEK..D.VKR.LSLEM.N.KE.L.IK.E..M
RetrocopySLLLQAAAD<YTIQKPVWPRQDHDLPLSMLLKDHQTIPGIEKGNDTVKRSLSLEMTNQKEKLNIK*EHLM
ParentalKKIVANPEDTRSLEARIIALSVKIRSYEEH-LEKHRKDKAHKRY-LLMSIDQRKKMLKNLRNTN-YDVFE
.K.VANP.DT..LEARII.L..K...YEEH...KH...K.HK.Y.L.M...QRKKMLKNLR.TN.YDV.E
RetrocopyNKVVANPKDTSFLEARIIPLT-KAHNYEEH<QQKH*NNKTHKYY<LVMGTVQRKKMLKNLR*TN<YDVSE
ParentalKICWGLGIEY
K..WGL....
RetrocopyKTHWGLSTSF

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 .04 RPM 32 .38 RPM
bodymap2_adrenal 0 .00 RPM 39 .85 RPM
bodymap2_brain 0 .00 RPM 15 .78 RPM
bodymap2_breast 0 .04 RPM 40 .95 RPM
bodymap2_colon 0 .00 RPM 26 .30 RPM
bodymap2_heart 0 .00 RPM 38 .93 RPM
bodymap2_kidney 0 .00 RPM 42 .29 RPM
bodymap2_liver 0 .00 RPM 51 .90 RPM
bodymap2_lung 0 .00 RPM 25 .47 RPM
bodymap2_lymph_node 0 .00 RPM 28 .32 RPM
bodymap2_ovary 0 .00 RPM 20 .86 RPM
bodymap2_prostate 0 .00 RPM 35 .96 RPM
bodymap2_skeletal_muscle 0 .00 RPM 54 .36 RPM
bodymap2_testis 0 .00 RPM 74 .90 RPM
bodymap2_thyroid 0 .00 RPM 31 .60 RPM
bodymap2_white_blood_cells 0 .00 RPM 18 .15 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_1594 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_1594 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_1594 retrocopy 5' end.

Lab - click to see more details

retro_hsap_1594 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_1594 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_1071
Pongo abelii retro_pabe_1310
Callithrix jacchus retro_cjac_761
Parental genes homology:
Parental genes homology involve 19 parental genes, and 26 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000014631 retrocopy
retro_amel_1564,
Canis familiaris ENSCAFG000000303901 retrocopy
retro_cfam_1939,
Callithrix jacchus ENSCJAG000000018523 retrocopies
retro_cjac_3095, retro_cjac_761, retro_cjac_859,
Cavia porcellus ENSCPOG000000108771 retrocopy
retro_cpor_430,
Dipodomys ordii ENSDORG000000075811 retrocopy
retro_dord_118,
Felis catus ENSFCAG000000052651 retrocopy
retro_fcat_915,
Homo sapiens ENSG00000116898 1 retrocopy
retro_hsap_1594 ,
Myotis lucifugus ENSMLUG000000064751 retrocopy
retro_mluc_1945,
Monodelphis domestica ENSMODG000000178131 retrocopy
retro_mdom_1094,
Mus musculus ENSMUSG000000288611 retrocopy
retro_mmus_3447,
Nomascus leucogenys ENSNLEG000000114671 retrocopy
retro_nleu_615,
Otolemur garnettii ENSOGAG000000026562 retrocopies
retro_ogar_1327, retro_ogar_16,
Pongo abelii ENSPPYG000000015371 retrocopy
retro_pabe_1310,
Pan troglodytes ENSPTRG000000005411 retrocopy
retro_ptro_1071,
Sus scrofa ENSSSCG000000263931 retrocopy
retro_sscr_1190,
Ictidomys tridecemlineatus ENSSTOG000000006081 retrocopy
retro_itri_454,
Tupaia belangeri ENSTBEG000000009584 retrocopies
retro_tbel_1633, retro_tbel_4438, retro_tbel_845, retro_tbel_882,
Tarsius syrichta ENSTSYG000000089482 retrocopies
retro_tsyr_1612, retro_tsyr_372,
Tursiops truncatus ENSTTRG000000023451 retrocopy
retro_ttru_1500,

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 = 0.05 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 .05 RPM
CEU_NA12872 0 .00 RPM
CEU_NA12873 0 .03 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 .02 RPM
GBR_HG00137 0 .00 RPM
GBR_HG00142 0 .03 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 .02 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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