RetrogeneDB ID:

retro_hsap_1131

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:12:66627855..66629001(-)
Located in intron of:ENSG00000090376
Retrocopy
information
Ensembl ID:ENSG00000225422
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:RBMS1
Ensembl ID:ENSG00000153250
Aliases:RBMS1, C2orf12, HCC-4, MSSP, MSSP-1, MSSP-2, MSSP-3, SCR2, YC1
Description:RNA binding motif, single stranded interacting protein 1 [Source:HGNC Symbol;Acc:9907]


Retrocopy-Parental alignment summary:






>retro_hsap_1131
CAGCAGTCTCTGGTCCCAGCCCACCCCATGGCCCCTCCCAGTCCCAGCACCACCAGCAGTAATAACAACAGTAGCAGCAG
CAGCAACTCAGGATGGGATCAGCTCAGCAAAACGAACCTCTATATCCGAGGACTGCCTCCCCACACCACCGACCAGGACC
TGGTGAAGCTCTGTCAACCATATGGGAAAATAGTCTCCACAAACGCAATTTTGCATAAGACAACGAACAAATGCAAAGGT
TATGGTTTTGTCGACTTTGACAGCCCTGCAGCAGCTCAAAAAGCTGTGTCTGCCCTGAAGGCCAGTGGGGTTCAAGCTCA
AATGGCAAAGCAACAGGAACAAGATCCTACCAACCTCTACATTTCTAATTTGCCACTCTCCATGGATAAGCAAGAACTAG
AAAATATGCTCAAACCATTTGGACAAGTTATTTCTACAAGGATACTACGTGATGCCAGTGGTACAAGTCGTGGTGTTGGC
TTTGCTAGGACGGAATCAACAGAAAAATGTGAAGCTGTTACTGGTCATTTTAATGGAAAATTTATTAAGACACCACCAGG
AGTTTCTGCCCCCACAGAACCTTTATTGTGTAAGTTTTCTGATGGAGGACAGAAAAAGAGACAGAACCCAAACAAATACA
TCCCTAATGGAAGACCATGGCATAGAGAAGGAGAGGTGAGACTTACTGGAATGACACTTACTTACGACCCAACTACAGCT
GCTATACAAAACGGATTTTATCCTTCACCATACAGTATTGCTACAAACCGAATGATCACTCAAACTTCTATTACACCCTA
TATTGTATCTCCTGTATCTGCCTACCAGGTGCAAAGTCCTTCTTGGACGCAACCTCAACCATATATTCTACAGCACCCCG
GTGCCGTGTTAACTCCCTCAATGGAGCACACCATGTCACTACAGCCCGCATCAATGATCAGCCCTCTGGCCCAGCAGATG
AGTCATCTGTCACTAGGCAGCACCGGAACATACATGCCTGCAACGTCAGCTATGCAAGGAGCCTACTTGCCACAGTATGA
ACATATGCAGACGACAGCGGCTCCTGTTGAGGAGGCAAGTGGTCAACAGCAGGTGGCTGTCGAGACGTCTAATGACCATT
CTCCATATACCTTTCAACCTAATAAG

ORF - retro_hsap_1131 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 96.6 %
Parental protein coverage: 94.09 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalKQSLVPAHPMAPPSPSTTSSNNNSSSSSNSGWDQLSKTNLYIRGLPPHTTDQDLVKLCQPYGKIVSTKAI
.QSLVPAHPMAPPSPSTTSSNNNSSSSSNSGWDQLSKTNLYIRGLPPHTTDQDLVKLCQPYGKIVST.AI
RetrocopyQQSLVPAHPMAPPSPSTTSSNNNSSSSSNSGWDQLSKTNLYIRGLPPHTTDQDLVKLCQPYGKIVSTNAI
ParentalLDKTTNKCKGYGFVDFDSPAAAQKAVSALKASGVQAQMAKQQEQDPTNLYISNLPLSMDEQELENMLKPF
L.KTTNKCKGYGFVDFDSPAAAQKAVSALKASGVQAQMAKQQEQDPTNLYISNLPLSMD.QELENMLKPF
RetrocopyLHKTTNKCKGYGFVDFDSPAAAQKAVSALKASGVQAQMAKQQEQDPTNLYISNLPLSMDKQELENMLKPF
ParentalGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAPTEPLLCKFADGGQKKRQNP
GQVISTRILRD.SGTSRGVGFAR.ESTEKCEAV.GHFNGKFIKTPPGVSAPTEPLLCKF.DGGQKKRQNP
RetrocopyGQVISTRILRDASGTSRGVGFARTESTEKCEAVTGHFNGKFIKTPPGVSAPTEPLLCKFSDGGQKKRQNP
ParentalNKYIPNGRPWHREGEVRLAGMTLTYDPTTAAIQNGFYPSPYSIATNRMITQTSITPYIASPVSAYQVQSP
NKYIPNGRPWHREGEVRL.GMTLTYDPTTAAIQNGFYPSPYSIATNRMITQTSITPYI.SPVSAYQVQSP
RetrocopyNKYIPNGRPWHREGEVRLTGMTLTYDPTTAAIQNGFYPSPYSIATNRMITQTSITPYIVSPVSAYQVQSP
ParentalSWMQPQPYILQHPGAVLTPSMEHTMSLQPASMISPLAQQMSHLSLGSTGTYMPATSAMQGAYLPQYAHMQ
SW.QPQPYILQHPGAVLTPSMEHTMSLQPASMISPLAQQMSHLSLGSTGTYMPATSAMQGAYLPQY.HMQ
RetrocopySWTQPQPYILQHPGAVLTPSMEHTMSLQPASMISPLAQQMSHLSLGSTGTYMPATSAMQGAYLPQYEHMQ
ParentalTTAVPVEEASGQQQVAVETSNDHSPYTFQPNK
TTA.PVEEASGQQQVAVETSNDHSPYTFQPNK
RetrocopyTTAAPVEEASGQQQVAVETSNDHSPYTFQPNK

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 1 .51 RPM 158 .49 RPM
bodymap2_adrenal 1 .70 RPM 142 .63 RPM
bodymap2_brain 0 .07 RPM 20 .16 RPM
bodymap2_breast 0 .31 RPM 135 .84 RPM
bodymap2_colon 0 .77 RPM 126 .40 RPM
bodymap2_heart 0 .78 RPM 85 .09 RPM
bodymap2_kidney 0 .72 RPM 102 .66 RPM
bodymap2_liver 0 .28 RPM 18 .14 RPM
bodymap2_lung 0 .58 RPM 202 .53 RPM
bodymap2_lymph_node 0 .31 RPM 108 .84 RPM
bodymap2_ovary 0 .50 RPM 135 .59 RPM
bodymap2_prostate 0 .35 RPM 111 .78 RPM
bodymap2_skeletal_muscle 0 .00 RPM 26 .37 RPM
bodymap2_testis 0 .09 RPM 81 .50 RPM
bodymap2_thyroid 0 .51 RPM 67 .59 RPM
bodymap2_white_blood_cells 1 .34 RPM 153 .45 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity may be related with retro_hsap_1131 in 2 libraries
ENCODE library ID Target ChIP-Seq Peak coordinates
ENCFF002CQC POLR2A 12:66628850..66629330
ENCFF002CZQ POLR2A 12:66628816..66629266

EST - click to see more details

2 EST(s) were mapped to retro_hsap_1131 retrocopy
EST ID Start End Identity Match Mis-match Score
BF764098 66628235 66628544 100 308 0 307
BF764131 66628179 66628544 99.8 364 0 362

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_28186854 libraries808 libraries161 libraries5 libraries1 library

The graphical summary, for retro_hsap_1131 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_1131 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_1131 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_16
Parental genes homology:
Parental genes homology involve 5 parental genes, and 6 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG000000148611 retrocopy
retro_cjac_1040,
Homo sapiens ENSG000000707561 retrocopy
retro_hsap_88,
Homo sapiens ENSG000000760671 retrocopy
retro_hsap_1143,
Homo sapiens ENSG000000906212 retrocopies
retro_hsap_109, retro_hsap_74,
Homo sapiens ENSG00000153250 1 retrocopy
retro_hsap_1131 ,

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 = 1.21 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .47 RPM
CEU_NA11843 0 .00 RPM
CEU_NA11930 0 .10 RPM
CEU_NA12004 0 .04 RPM
CEU_NA12400 0 .18 RPM
CEU_NA12751 0 .44 RPM
CEU_NA12760 0 .22 RPM
CEU_NA12827 0 .05 RPM
CEU_NA12872 0 .00 RPM
CEU_NA12873 0 .10 RPM
FIN_HG00183 0 .47 RPM
FIN_HG00277 0 .74 RPM
FIN_HG00315 0 .14 RPM
FIN_HG00321 0 .33 RPM
FIN_HG00328 0 .26 RPM
FIN_HG00338 0 .02 RPM
FIN_HG00349 0 .09 RPM
FIN_HG00375 0 .05 RPM
FIN_HG00377 0 .10 RPM
FIN_HG00378 0 .08 RPM
GBR_HG00099 0 .17 RPM
GBR_HG00111 0 .11 RPM
GBR_HG00114 0 .34 RPM
GBR_HG00119 0 .36 RPM
GBR_HG00131 0 .86 RPM
GBR_HG00133 0 .14 RPM
GBR_HG00134 0 .48 RPM
GBR_HG00137 0 .14 RPM
GBR_HG00142 0 .19 RPM
GBR_HG00143 0 .00 RPM
TSI_NA20512 0 .08 RPM
TSI_NA20513 1 .21 RPM
TSI_NA20518 0 .14 RPM
TSI_NA20532 0 .07 RPM
TSI_NA20538 0 .05 RPM
TSI_NA20756 0 .12 RPM
TSI_NA20765 0 .44 RPM
TSI_NA20771 0 .20 RPM
TSI_NA20786 0 .05 RPM
TSI_NA20798 0 .12 RPM
YRI_NA18870 0 .10 RPM
YRI_NA18907 0 .31 RPM
YRI_NA18916 0 .17 RPM
YRI_NA19093 0 .13 RPM
YRI_NA19099 0 .21 RPM
YRI_NA19114 0 .08 RPM
YRI_NA19118 0 .10 RPM
YRI_NA19213 0 .43 RPM
YRI_NA19214 0 .17 RPM
YRI_NA19223 0 .48 RPM

Indel association:

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



Copyright © RetrogeneDB 2014-2017