RetrogeneDB ID:

retro_hsap_1495

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:15:50086440..50088221(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000259388
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:RLIM
Ensembl ID:ENSG00000131263
Aliases:RLIM, NY-REN-43, RNF12
Description:ring finger protein, LIM domain interacting [Source:HGNC Symbol;Acc:13429]


Retrocopy-Parental alignment summary:






>retro_hsap_1495
ATGGAAAACTCAGTTTCTAATGACAAAGGAAGTGGTGATCAGTCTGCAGCACAGTGCAGAAGTCAGATGGACCGATTGGA
TCGGGAAGAAGCTTTCTATCCATTTGTAAATAACCTGAGTGAAGAAGATTATAGGCTTATGGAGATAATAATTTGCTAGG
CACCCCAGGTGAAAGTACTGAGGAAGAGTTGCTGAGAAGACTACAGCAAACTAAAGAAGGCCCACCACTGCAAAACTCAG
GTGAAAATAGAGGAGGAGACTCTTCAGATGATGTGTCTAATGGTGACTCTATAATAGACTGGCTTAACTCTGTCAGACAA
ACTGGAAATACAACAAGAAGTGGGCAAAGAGGAAACCAATCTTGGAGAGCAGTGAGCCGGACTAATCCAAACAGCGGTAA
TTTCAGATTCAGTTTAGAGATAAATGTTAACAGTAATAATGGGAGCCAAAATTCAGAGAATGAAAATGAGCCATCTGCAA
GACGTTCTAGTGGAGAAAATGTGGAAAACAACAGCCAAAGGCAAGTGGAAAACCCACGATCTGAATCAACATCTGCAAGG
CCATCTAGATCAGAACGAAATTCAACTGAAGCATTAACAGAAGTCCCACCTACCAGAGGTCGGGGAGGGCAAGAAGCAGG
AGCCCAGACCGTGGGAGAGCCAGAGCAAGAGCTGAGAGAAGTAGGTCACCTCTGCATCCAATGAGTGAAATTCCACGAAG
ATCTCATCATAGTATCTCATCTCAGACTTTTGAACATCCTTTGGTAAATGAGATGGAGGGAAGTTCTAGAACCCGGCCCT
GTGTGACATTGAGACAGCAAATATCTGGGCCTGAGTTGCTAAGTAGAGGTCTTTTTGCAGCTTCTGGAAAAAGAAATGCC
TCTCAAGCAGCAGGTTCTTCAGACACAGCGGCCAATGGTGAATCTACAGGATCAGCACAGAGACCTCTAACCATAGTCCT
TGATCTTCAAGTAAAAAGAGTTAGTCCTGGAGAATATCGGCAGAGAGATAGCATAGCCAGCAGAACTCGGTCTAGGTCTC
AGAGGCCAAACAACACTATCACCTATGAAAGTGAGCGAGGAGGTTTCAGGCGTACGTTTTCACGTTCTGAGTGGGCAGGT
GTGAGAACCTATGTCAGTAGCACCAGAATCCCCATTTGTAGAATCTTAAATACTGGTTTATGTGAGACTACATCTGTTGC
AATTCAGACGATGTTAAGGCAGATAATGACAGGTTTTGGTGAGTTAAGCTATTTTATGTACAGTGATAGCGACTCAGAGC
CTACTGGCTCAGTCCCAAATCAAAATATGGAAAGGGCAGAGTCACGGAGTGGAAGAGGGGGTTCTGGTGGTGGTAATAGT
TCTGGTTCCAGTTCGAGTTCCAGTTCAAGTTCCAGTTCCAGTTCCAGTCCTAGTTCCAGTTCCGGTGGTGAAAGCTCAGA
AACTAGCTCAGATTTATTTGAAGGCAGTAATGAAGGAAGCTTATCATCAGGCTCATCAGGTGCCAGGCGAGAGGGTCGAC
ATACGGCCCCAGTCATATTTCATTAAAGTGGCTCTTTGCCCTTCCTAGCCTGGCTCAGTTTTCCTCTTAAATGAGGATGA
TGATGACCAACCTAGAGGACTCACTAAAGAACAGATTGACAACTTGGCAATGAGAAGTTTTGGTGAAAATGGTGCATTAA
AAACCTGTAGTGTTTGCATTACAGAATATACAGAAAGCAACAAACTTCGTAAACTACCTTGTTCCCATGAGTACCATGTC
CACTGACTGCATCGATCGCTG

ORF - retro_hsap_1495 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 86.94 %
Parental protein coverage: 96.31 %
Number of stop codons detected: 2
Number of frameshifts detected 4


Retrocopy - Parental Gene Alignment:

ParentalMENSDSNDKGSGDQSAAQRRSQMDRLDREEAFYQFVNNLSEEDYRLMR-DNNLLGTPGESTEEELLRRLQ
MENS.SNDKGSGDQSAAQ.RSQMDRLDREEAFY.FVNNLSEEDYRLM..DNNLLGTPGESTEEELLRRLQ
RetrocopyMENSVSNDKGSGDQSAAQCRSQMDRLDREEAFYPFVNNLSEEDYRLME<DNNLLGTPGESTEEELLRRLQ
ParentalQIKEGPPPQNSDENRGGDSSDDVSNGDSIIDWLNSVRQTGNTTRSGQRGNQSWRAVSRTNPNSGDFRFSL
Q.KEGPP.QNS.ENRGGDSSDDVSNGDSIIDWLNSVRQTGNTTRSGQRGNQSWRAVSRTNPNSG.FRFSL
RetrocopyQTKEGPPLQNSGENRGGDSSDDVSNGDSIIDWLNSVRQTGNTTRSGQRGNQSWRAVSRTNPNSGNFRFSL
ParentalEINVNRNNGSQNSENENEPSARRSSGENVENNSQRQVENPRSESTSARPSRSERNSTEALTEVPPTRGQR
EINVN.NNGSQNSENENEPSARRSSGENVENNSQRQVENPRSESTSARPSRSERNSTEALTEVPPTRG..
RetrocopyEINVNSNNGSQNSENENEPSARRSSGENVENNSQRQVENPRSESTSARPSRSERNSTEALTEVPPTRGRG
Parental-RARSRSPDHRRTRARAERSRSPLHPMSEIPRRSHHSISSQTFEHPLVNETEGSSRTRHHVTLRQQISGP
.RARSRSPD..R.RARAERSRSPLHPMSEIPRRSHHSISSQTFEHPLVNE.EGSSRTR..VTLRQQISGP
Retrocopy<RARSRSPDRGRARARAERSRSPLHPMSEIPRRSHHSISSQTFEHPLVNEMEGSSRTRPCVTLRQQISGP
ParentalELLSRGLFAASGTRNASQGAGSSDTAASGESTGSGQRPPTIVLDLQVRRVRPGEYRQRDSIASRTRSRSQ
ELLSRGLFAASG.RNASQ.AGSSDTAA.GESTGS.QRP.TIVLDLQV.RV.PGEYRQRDSIASRTRSRSQ
RetrocopyELLSRGLFAASGKRNASQAAGSSDTAANGESTGSAQRPLTIVLDLQVKRVSPGEYRQRDSIASRTRSRSQ
ParentalTPNNTVTYESERGGFRRTFSRSERAGVRTYVSTIRIPIRRILNTGLSETTSVAIQTMLRQIMTGFGELSY
.PNNT.TYESERGGFRRTFSRSE.AGVRTYVS..RIPI.RILNTGL.ETTSVAIQTMLRQIMTGFGELSY
RetrocopyRPNNTITYESERGGFRRTFSRSEWAGVRTYVSSTRIPICRILNTGLCETTSVAIQTMLRQIMTGFGELSY
ParentalFMYSDSDSEPTGSVSNRNMERAESRSGRGGSGGGSSSGSSSSSSSSSSSSSSSSSSSSPSSSSGGESSET
FMYSDSDSEPTGSV.N.NMERAES...R.G.GG...SG...SS....................GGESSET
RetrocopyFMYSDSDSEPTGSVPNQNMERAES---RSGRGG---SGGGNSSXXXXXXXXXXXXXXXXXXXXGGESSET
ParentalSSDLFEGSNEGSSSSGSSGARREGRHRAPVTFDESGSLPFL-SLAQF-FLLNEDDDDQPRGLTKEQIDNL
SSDLFEGSNEGS.SSGSSGARREGRH.APV.F..SGSLPFL.SLAQF.FLLNEDDDDQPRGLTKEQIDNL
RetrocopySSDLFEGSNEGSLSSGSSGARREGRHTAPVIFH*SGSLPFL<SLAQF<FLLNEDDDDQPRGLTKEQIDNL
ParentalAMRSFGENDALKTCSVCITEYTEGNKLRKLPCSHEYHVHCIDRWL
AMRSFGEN.ALKTCSVCITEYTE.NKLRKLPCSHEYHVH...R.L
RetrocopyAMRSFGENGALKTCSVCITEYTESNKLRKLPCSHEYHVH*LHRSL

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 96 .47 RPM
bodymap2_adrenal 0 .04 RPM 71 .66 RPM
bodymap2_brain 0 .00 RPM 159 .49 RPM
bodymap2_breast 0 .00 RPM 73 .48 RPM
bodymap2_colon 0 .00 RPM 68 .64 RPM
bodymap2_heart 0 .00 RPM 54 .07 RPM
bodymap2_kidney 0 .00 RPM 75 .22 RPM
bodymap2_liver 0 .00 RPM 30 .78 RPM
bodymap2_lung 0 .00 RPM 100 .30 RPM
bodymap2_lymph_node 0 .00 RPM 67 .27 RPM
bodymap2_ovary 0 .00 RPM 125 .82 RPM
bodymap2_prostate 0 .00 RPM 70 .96 RPM
bodymap2_skeletal_muscle 0 .00 RPM 48 .29 RPM
bodymap2_testis 0 .00 RPM 73 .62 RPM
bodymap2_thyroid 0 .00 RPM 110 .43 RPM
bodymap2_white_blood_cells 0 .00 RPM 99 .44 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_1495 was not detected

EST - click to see more details

1 EST(s) were mapped to retro_hsap_1495 retrocopy
EST ID Start End Identity Match Mis-match Score
AA393966 50087405 50087719 100 312 0 310

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_44241858 libraries220 libraries605 libraries107 libraries39 libraries

The graphical summary, for retro_hsap_1495 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_1495 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_1495 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_1014
Pongo abelii retro_pabe_1245
Macaca mulatta retro_mmul_2139
Parental genes homology:
Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species Parental gene accession Retrocopies number
Homo sapiens ENSG00000131263 1 retrocopy
retro_hsap_1495 ,
Macaca mulatta ENSMMUG000000092491 retrocopy
retro_mmul_2139,
Pongo abelii ENSPPYG000000204811 retrocopy
retro_pabe_1245,
Pan troglodytes ENSPTRG000000220371 retrocopy
retro_ptro_1014,

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 .05 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 .04 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 .02 RPM
FIN_HG00377 0 .00 RPM
FIN_HG00378 0 .02 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 .03 RPM
GBR_HG00143 0 .00 RPM
TSI_NA20512 0 .00 RPM
TSI_NA20513 0 .02 RPM
TSI_NA20518 0 .00 RPM
TSI_NA20532 0 .00 RPM
TSI_NA20538 0 .00 RPM
TSI_NA20756 0 .03 RPM
TSI_NA20765 0 .00 RPM
TSI_NA20771 0 .00 RPM
TSI_NA20786 0 .00 RPM
TSI_NA20798 0 .00 RPM
YRI_NA18870 0 .03 RPM
YRI_NA18907 0 .00 RPM
YRI_NA18916 0 .00 RPM
YRI_NA19093 0 .00 RPM
YRI_NA19099 0 .00 RPM
YRI_NA19114 0 .03 RPM
YRI_NA19118 0 .02 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).



Copyright © RetrogeneDB 2014-2017