RetrogeneDB ID:

retro_hsap_4844

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:X:64770780..64772172(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000227942
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:FRMD8
Ensembl ID:ENSG00000126391
Aliases:None
Description:FERM domain containing 8 [Source:HGNC Symbol;Acc:25462]


Retrocopy-Parental alignment summary:






>retro_hsap_4844
ATGGACGGGACGGAAGGCAGTGTCGGGCAGCCCGGCCCCACTGAGCGGTCCCACCGAAGCAGCGTGTCCTCCGTGGGAGC
CCGAGCGGCTGACGTGCTGGTATACCTGGCAGATGACACGGTGGTGCCCCTGGCTGTGGAGAACCTGCCCTCGCTCCGTG
CCCATGAGCTGCACTGCGCCGTCCGCGAGGTCCTGAAGCTTCCGGACATCGCCCTGGATGTCTTCGCGCTCTGGCTGGTC
TCCCCTCTGCTGGAGGTGCAGCTGAAACCCAAGAACCAGCCCTACAAGCTGGGACGCCAGTGGCCGGAGCTGCTGCTGCG
CTTCACCAGTGCCCCGGACGACGACGTGGCCATGGATGAGCCTTTCCTGCAGTTCCGAAGGAACGTGTTCTTCCCAAAGG
GGCGGGAGCTCCAGATCCCCGACGAGGAGGTCCTGCGGCTGCTCTATGAGGAGGCCAAGGGCAACGTGCTGGCTGCACGG
TACCTGTGCGACGTTGAGGACTGCGAGGCTCTGGGCGCCCTGGTGTGCCGCGTGCAGCTCGTGACCTACCAGCCCGACTG
GCCGGCAGCCTGCGACCTGAGGGAGAAGCTGGACTCCTTCCTCCCTGCCCACCTCTGTAAGCGGGGCCAGGGTCTCTTTG
CTGCCCTCCGGGGCCGTGGGGCCAGGGCCGGGCCGGGTGAGCAGAGCCTGCTGAACGCCTACCGCAAGGTGCAGGAGGTC
AGCAGCGACGGCGGGTGTGAGGCCGCCCTGGGCACCCACTACCGCGCCTACCTCCTCAAGTGCCACAAGCTGCCCTTCTA
TGGGTGTGCCTTCTTCCACGGTGAGGTTGACAAGCCAGCCCAAGGCTTTTTGCACCGGGGTGGGCGCAAATCAGTTTCTG
TGGCCATCAGCCTGGAAGGTGTGCACGTCGTGGACAGCAGAGAGAAGCACGTCCTGCTGGGCCTGTGCTTCCAGGAGCTG
TCGTGGGACCACACCTCCCCTGAGGAGGAGGAGCCCATCCTGTGGCTGGAGTTCGACAGGGACAGCGGGGTCACACCTGT
CAACAAGCTCCTCAAGATCTACTCCAAGCAGGCCGAACTGATGAGCAGCCTCATTGAGTACTGCATCTAACTGAGCCAGG
CGGCGGAGCCCGCAGGCCCCCAGGACAGTGCAACTGGCTCGCCCTCAGACCTCAGCTCCTCGCCAGCTCCTGTTCAGCGC
CCCAAGCTGCGGAGGCAGGGCAGTGTGGTGTCCAGCCGGATCCAGCATCTCTCCACCATCGCCTATGTGGAGGACGGCAA
GGGGATCAGGCGAGTGAAGACGAAGAGCACCACGTCCTTCTTCAGCCAGCAGCTGTCCTTGGGCCAGGGGAGCTACACCG
TGGTGCAGCCCAGCGACAGCCTGGAGCAGGGC

ORF - retro_hsap_4844 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 93.32 %
Parental protein coverage: 100. %
Number of stop codons detected: 1
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMDGTEGSAGQPGPAERSHRSSVSSVGARAADVLVYLADDTVVPLAVENLPSLSAHELHRAVREVLQLPDI
MDGTEGS.GQPGP.ERSHRSSVSSVGARAADVLVYLADDTVVPLAVENLPSL.AHELH.AVREVL.LPDI
RetrocopyMDGTEGSVGQPGPTERSHRSSVSSVGARAADVLVYLADDTVVPLAVENLPSLRAHELHCAVREVLKLPDI
ParentalALDVFALWLVSPLLEVQLKPKHQPYKLGRQWPELLLRFTSAPDDDVAMDEPFLQFRRNVFFPKRRELQIH
ALDVFALWLVSPLLEVQLKPK.QPYKLGRQWPELLLRFTSAPDDDVAMDEPFLQFRRNVFFPK.RELQI.
RetrocopyALDVFALWLVSPLLEVQLKPKNQPYKLGRQWPELLLRFTSAPDDDVAMDEPFLQFRRNVFFPKGRELQIP
ParentalDEEVLRLLYEEAKGNVLAARYPCDVEDCEALGALVCRVQLGPYQPGRPAACDLREKLDSFLPAHLCKRGQ
DEEVLRLLYEEAKGNVLAARY.CDVEDCEALGALVCRVQL..YQP..PAACDLREKLDSFLPAHLCKRGQ
RetrocopyDEEVLRLLYEEAKGNVLAARYLCDVEDCEALGALVCRVQLVTYQPDWPAACDLREKLDSFLPAHLCKRGQ
ParentalSLFAALRGRGARAGPGEQGLLNAYRQVQEVSSDGGCEAALGTHYRAYLLKCHELPFYGCAFFHGEVDKPA
.LFAALRGRGARAGPGEQ.LLNAYR.VQEVSSDGGCEAALGTHYRAYLLKCH.LPFYGCAFFHGEVDKPA
RetrocopyGLFAALRGRGARAGPGEQSLLNAYRKVQEVSSDGGCEAALGTHYRAYLLKCHKLPFYGCAFFHGEVDKPA
ParentalQGFLHRGGRKPVSVAISLEGVHVIDSREKHVLLGLRFQELSWDHTSPEEEEPILWLEFDGDSEGTPVNKL
QGFLHRGGRK.VSVAISLEGVHV.DSREKHVLLGL.FQELSWDHTSPEEEEPILWLEFD.DS..TPVNKL
RetrocopyQGFLHRGGRKSVSVAISLEGVHVVDSREKHVLLGLCFQELSWDHTSPEEEEPILWLEFDRDSGVTPVNKL
ParentalLKIYSKQAELMSSLIEYCIELSQAAEPAGPQDSATGSPSDPSSSLAPVQRPKLRRQGSVVSSRIQHLSTI
LKIYSKQAELMSSLIEYCI.LSQAAEPAGPQDSATGSPSD.SSS.APVQRPKLRRQGSVVSSRIQHLSTI
RetrocopyLKIYSKQAELMSSLIEYCI*LSQAAEPAGPQDSATGSPSDLSSSPAPVQRPKLRRQGSVVSSRIQHLSTI
ParentalDYVEDGKGIRRVKPKRTTSFFSRQLSLGQGSYTVVQPGDSLEQG
.YVEDGKGIRRVK.K.TTSFFS.QLSLGQGSYTVVQP.DSLEQG
RetrocopyAYVEDGKGIRRVKTKSTTSFFSQQLSLGQGSYTVVQPSDSLEQG

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 .00 RPM 51 .86 RPM
bodymap2_adrenal 0 .00 RPM 34 .65 RPM
bodymap2_brain 0 .00 RPM 7 .85 RPM
bodymap2_breast 0 .00 RPM 17 .20 RPM
bodymap2_colon 0 .00 RPM 10 .42 RPM
bodymap2_heart 0 .00 RPM 6 .81 RPM
bodymap2_kidney 0 .00 RPM 16 .92 RPM
bodymap2_liver 0 .00 RPM 7 .94 RPM
bodymap2_lung 0 .00 RPM 40 .35 RPM
bodymap2_lymph_node 0 .00 RPM 31 .10 RPM
bodymap2_ovary 0 .00 RPM 19 .01 RPM
bodymap2_prostate 0 .00 RPM 15 .64 RPM
bodymap2_skeletal_muscle 0 .00 RPM 5 .64 RPM
bodymap2_testis 0 .00 RPM 15 .20 RPM
bodymap2_thyroid 0 .00 RPM 24 .82 RPM
bodymap2_white_blood_cells 0 .00 RPM 37 .74 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_4844 was not detected

EST - click to see more details

1 EST(s) were mapped to retro_hsap_4844 retrocopy
EST ID Start End Identity Match Mis-match Score
BF886527 64771678 64771948 95.6 156 3 140

TSS - click to see more details

No TSS is located nearby retro_hsap_4844 retrocopy 5' end.

Lab - click to see more details

retro_hsap_4844 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_4844 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species Parental gene accession Retrocopies number
Homo sapiens ENSG00000126391 1 retrocopy
retro_hsap_4844 ,
Gorilla gorilla ENSGGOG000000147731 retrocopy
retro_ggor_3022,

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 = 0.03 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 .00 RPM
CEU_NA12872 0 .00 RPM
CEU_NA12873 0 .00 RPM
FIN_HG00183 0 .00 RPM
FIN_HG00277 0 .00 RPM
FIN_HG00315 0 .03 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 .03 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 .02 RPM
GBR_HG00134 0 .00 RPM
GBR_HG00137 0 .03 RPM
GBR_HG00142 0 .00 RPM
GBR_HG00143 0 .00 RPM
TSI_NA20512 0 .00 RPM
TSI_NA20513 0 .00 RPM
TSI_NA20518 0 .03 RPM
TSI_NA20532 0 .03 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 .03 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 .02 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