RetrogeneDB ID:

retro_hsap_2911

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:4:11373598..11374513(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000250896
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:RNPS1
Ensembl ID:ENSG00000205937
Aliases:RNPS1, E5.1
Description:RNA binding protein S1, serine-rich domain [Source:HGNC Symbol;Acc:10080]


Retrocopy-Parental alignment summary:






>retro_hsap_2911
ATGGATTTATCAGGAGTGAAAAAGAAGAGCTTGCTGGGAGTCAAAGAAAATAATAAAAAGTCCAGCACTAGGGCCCCTTC
ACCTACCAAACGCAAAGACCGCTCAGATGAGAAGTCCAAGGATCGCTCAAAAGATAAAGGGGCCACCAAGGAGTCGAGTG
AGAAGGATCGCGGCCGGGACAAAACGCGAAAGAGGCACAGCGCTTCCAGTGGTAGCAGCAGTACCAGGTCTCGGTCCAGC
TCGACTTCCAGCTCAGGCTCCAGCACCAGCACTGGCTCAAGCAGTGGCTCCAGCTCTTCCTCAGCCTCCAGCCGCTCAGG
AAGCTCCAGCACCTCCCGCAGCTCCAGCTCTAGCAGCTCTTCTGGCTCTCCAAGTCCTTCTCGGCGCAGACACGACAACA
GGAGGCGCTCCCGCTCCAAATCCAAACCACCTAAAAGAGATGAAAAGGAGAGGAAAAGGCGGAGCCCATCTCCTAAGCCC
ACCAAAGTGCACATTGGGAGACTCACCAGGAATGTGACAAAGGATCACATCATGGAGATATTTTCCACCTATGGGAAAAT
TAAAATGATTGACATGCCCGTGGAAAGGATGCATCCCCATCTGTCCAAAGGCTATGCGTGCGTAGAGTTTGAGAATCCAG
ATGAAGCTGAGAAGGCGCTGAAGCACATGGATGGAGGACAAATTGATGGCCAGGAGATCACTGCCACCGTCGTGCTGGCC
CCCTGGCCTAGGCCAACCCCCAGGAGATTCAGCCCTCCCAGGAGAATGTTGCCACCACCGCCTATGTGGCTCAGGTCTCC
CCCACGGATGAGGAGAAGGTCCCGCTCCCCGAGGCGCAGGTCCCCCGTGCGCCGGAGATCACGGTCCCCGGGCCGCCGCC
GCCACAGGAGCCGCTCCAGCTCCAACTCCTCCCAA

ORF - retro_hsap_2911 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 88.85 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMDLSGVKKKSLLGVKENNKKSSTRAPSPTKRKDRSDEKSKDRSKDKGATKESSEKDRGRDKTRKRRSASS
MDLSGVKKKSLLGVKENNKKSSTRAPSPTKRKDRSDEKSKDRSKDKGATKESSEKDRGRDKTRKR.SASS
RetrocopyMDLSGVKKKSLLGVKENNKKSSTRAPSPTKRKDRSDEKSKDRSKDKGATKESSEKDRGRDKTRKRHSASS
ParentalGSSSTRSRSSSTSSSGSSTSTGSSSGSSSSSASSRSGSSSTSRSSSSSSSSGSPSPSRRRHDNRRRSRSK
GSSSTRSRSSST.............GSSSSS...............SSSSSGSPSPSRRRHDNRRRSRSK
RetrocopyGSSSTRSRSSSTXXXXXXXXXXXXXGSSSSSXXXXXXXXXXXXXXXSSSSSGSPSPSRRRHDNRRRSRSK
ParentalSKPPKRDEKERKRRSPSPKPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEF
SKPPKRDEKERKRRSPSPKPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYA.VEF
RetrocopySKPPKRDEKERKRRSPSPKPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYACVEF
ParentalENPDEAEKALKHMDGGQIDGQEITATAVLAPWPRPPPRRFSPPRRMLPPPPMWRRSPPRMRRRSRSPRRR
ENPDEAEKALKHMDGGQIDGQEITAT.VLAPWPRP.PRRFSPPRRMLPPPPMW.RSPPRMRRRSRSPRRR
RetrocopyENPDEAEKALKHMDGGQIDGQEITATVVLAPWPRPTPRRFSPPRRMLPPPPMWLRSPPRMRRRSRSPRRR
ParentalSPVRRRSRSPGRRRHRSRSSSNSSR
SPVRRRSRSPGRRRHRSRSSSNSS.
RetrocopySPVRRRSRSPGRRRHRSRSSSNSSQ

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 .08 RPM 46 .12 RPM
bodymap2_adrenal 0 .27 RPM 69 .64 RPM
bodymap2_brain 0 .00 RPM 50 .54 RPM
bodymap2_breast 0 .02 RPM 35 .06 RPM
bodymap2_colon 0 .02 RPM 52 .38 RPM
bodymap2_heart 0 .02 RPM 30 .22 RPM
bodymap2_kidney 0 .04 RPM 47 .52 RPM
bodymap2_liver 0 .00 RPM 17 .93 RPM
bodymap2_lung 0 .02 RPM 58 .03 RPM
bodymap2_lymph_node 0 .04 RPM 78 .41 RPM
bodymap2_ovary 0 .10 RPM 63 .17 RPM
bodymap2_prostate 0 .03 RPM 77 .16 RPM
bodymap2_skeletal_muscle 0 .22 RPM 95 .32 RPM
bodymap2_testis 0 .11 RPM 99 .24 RPM
bodymap2_thyroid 0 .00 RPM 60 .24 RPM
bodymap2_white_blood_cells 0 .00 RPM 56 .70 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_2911 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_2911 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_2911 retrocopy 5' end.

Lab - click to see more details

retro_hsap_2911 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_2911 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_1967
Gorilla gorilla retro_ggor_2016
Parental genes homology:
Parental genes homology involve 19 parental genes, and 43 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000178611 retrocopy
retro_amel_194,
Bos taurus ENSBTAG000000099697 retrocopies
retro_btau_1187, retro_btau_1239, retro_btau_1283, retro_btau_1515, retro_btau_764, retro_btau_776, retro_btau_85,
Canis familiaris ENSCAFG000000193971 retrocopy
retro_cfam_449,
Equus caballus ENSECAG000000232881 retrocopy
retro_ecab_524,
Felis catus ENSFCAG000000076901 retrocopy
retro_fcat_248,
Homo sapiens ENSG00000205937 1 retrocopy
retro_hsap_2911 ,
Gorilla gorilla ENSGGOG000000142751 retrocopy
retro_ggor_2016,
Macropus eugenii ENSMEUG000000088821 retrocopy
retro_meug_1996,
Myotis lucifugus ENSMLUG000000168083 retrocopies
retro_mluc_2237, retro_mluc_2618, retro_mluc_643,
Macaca mulatta ENSMMUG000000192381 retrocopy
retro_mmul_794,
Monodelphis domestica ENSMODG000000158911 retrocopy
retro_mdom_1171,
Mus musculus ENSMUSG000000346811 retrocopy
retro_mmus_173,
Otolemur garnettii ENSOGAG000000315821 retrocopy
retro_ogar_3241,
Rattus norvegicus ENSRNOG000000087034 retrocopies
retro_rnor_1537, retro_rnor_2135, retro_rnor_2988, retro_rnor_649,
Sarcophilus harrisii ENSSHAG000000169511 retrocopy
retro_shar_390,
Ictidomys tridecemlineatus ENSSTOG000000132001 retrocopy
retro_itri_1160,
Tupaia belangeri ENSTBEG000000090988 retrocopies
retro_tbel_1262, retro_tbel_1851, retro_tbel_2132, retro_tbel_2154, retro_tbel_2216, retro_tbel_3193, retro_tbel_3286, retro_tbel_4688,
Tarsius syrichta ENSTSYG000000016291 retrocopy
retro_tsyr_957,
Tursiops truncatus ENSTTRG000000082207 retrocopies
retro_ttru_1010, retro_ttru_1033, retro_ttru_1558, retro_ttru_1808, retro_ttru_1809, retro_ttru_203, retro_ttru_986,

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 = 0.34 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .15 RPM
CEU_NA11843 0 .11 RPM
CEU_NA11930 0 .16 RPM
CEU_NA12004 0 .08 RPM
CEU_NA12400 0 .11 RPM
CEU_NA12751 0 .12 RPM
CEU_NA12760 0 .22 RPM
CEU_NA12827 0 .14 RPM
CEU_NA12872 0 .03 RPM
CEU_NA12873 0 .03 RPM
FIN_HG00183 0 .11 RPM
FIN_HG00277 0 .07 RPM
FIN_HG00315 0 .06 RPM
FIN_HG00321 0 .12 RPM
FIN_HG00328 0 .09 RPM
FIN_HG00338 0 .09 RPM
FIN_HG00349 0 .31 RPM
FIN_HG00375 0 .07 RPM
FIN_HG00377 0 .13 RPM
FIN_HG00378 0 .19 RPM
GBR_HG00099 0 .17 RPM
GBR_HG00111 0 .00 RPM
GBR_HG00114 0 .05 RPM
GBR_HG00119 0 .10 RPM
GBR_HG00131 0 .03 RPM
GBR_HG00133 0 .10 RPM
GBR_HG00134 0 .04 RPM
GBR_HG00137 0 .14 RPM
GBR_HG00142 0 .08 RPM
GBR_HG00143 0 .03 RPM
TSI_NA20512 0 .08 RPM
TSI_NA20513 0 .05 RPM
TSI_NA20518 0 .31 RPM
TSI_NA20532 0 .17 RPM
TSI_NA20538 0 .32 RPM
TSI_NA20756 0 .15 RPM
TSI_NA20765 0 .04 RPM
TSI_NA20771 0 .34 RPM
TSI_NA20786 0 .10 RPM
TSI_NA20798 0 .16 RPM
YRI_NA18870 0 .27 RPM
YRI_NA18907 0 .03 RPM
YRI_NA18916 0 .13 RPM
YRI_NA19093 0 .05 RPM
YRI_NA19099 0 .16 RPM
YRI_NA19114 0 .03 RPM
YRI_NA19118 0 .10 RPM
YRI_NA19213 0 .05 RPM
YRI_NA19214 0 .02 RPM
YRI_NA19223 0 .18 RPM

Indel association:

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



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