RetrogeneDB ID:

retro_hsap_3733

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:7:55713312..55714638(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000235207
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:RP11-683L23.1
Ensembl ID:ENSG00000173213
Aliases:None
Description:Tubulin beta-8 chain-like protein LOC260334 [Source:UniProtKB/Swiss-Prot;Acc:A6NNZ2]


Retrocopy-Parental alignment summary:






>retro_hsap_3733
ATGAAGGAAATTGTGCACATCCAAGCCAGTCACTGTGGCAACCAGATCAGTGCCAAGTTCTGGGAGGTGATCAGTGATGA
ACATGGCATCAACCCACCGGCACCTACCACAGGGACAGCGCCCTGCAGCTGGACCGCATCTCCGTGTACTACTATGAAGC
CACAGGTGGCAAATATGTTCCTCATGCGATCCTGGTGGATCTAGAACCTGGGACCATGGACTCTGTTCACTCAGGTCCTT
TTGGCCAGATCTTTAGACCAGACAACTTTGCTTCTGATCAGTCTGGGGCAGGCAACAACTGGGCCAAATGCCACTACACA
GAGGGGGCTGAGCTGGTTTATTCGGTCCTGGATTTGGTATGGAAGGAGGCGGAGAGCTGTGACTGCCTTCAGGGCTTCCA
GCTGACCCACTCACTTGACTGGGACACAGGCTCTGGAATCGGCACTCTCCTTATGAGCAAGATCCAAGAAGAGTACCCTG
ATTGCTTCATGAATACCTTCAGTGTGGTACCTTCACACAAGGTATCTGACACCGTGGTTGAGCCCTACAATGCCACCCTC
TCCGTCCATCAGTTGGTAGAGAACACTGATGAGACCTATTGTATTGACAATGAGGCCCTCTAGGATATCTGCTTCCGCAA
TCTGAAGCTGACCACACCAACCTACTGGGATCTGAACTACCTCGTCTTAGCCACCATGAGTGGTGTCACCACCTGCCTCC
ACTTCCTGGCCAGCTCAGTGCTGACCTCTGCAAGTTGGCAGTCAACATGGTTCCCTTCCCATATCTCCATTTCTTTATGC
CTGGCTTTGCCCCTTTCACCAGCCGTGGAAGCCAGTAGTATCAAGCTCTCACCGTGCCCCAACTTACCCAGCAGGTCTTC
GATGCCAAAAACCTGATGGCTGCTTGTGACCCCCGCCACGGCCAATACCTCACCATGGCTGCTGTCTCCAGTGGTCGAAT
GTCCATGAAAGCGGTCAATGAGCAGATGCTCAAAGTGCAGAACAAGAACAGCAGCTACTTTGTGGAATGGATCCCCAACA
ACATCAAGACAGCTGTCTGTGACATCCACCTCATGGCCTCAAGATGGCTGTCACCTTCATCGGAAACAGCACTGGCATCC
AGTAGCTCTTCAAGCGCATCTCGGAGCAGTTCACTGCCATGTTCTACCAGAAGGCCTTCCTCCACTGCTACACAGGCGAG
GGCATGGACGAGATGGAGTTCACTGAGGCTGAGAGCAACATGAACAACTTCATCTCTGAGGATCAGCAGTACCAGGATGC
TACCACAGAAGAGGAAGAGGATTTCAGTAAGGAGGCTGAAGAGGAG

ORF - retro_hsap_3733 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 75.56 %
Parental protein coverage: 99.55 %
Number of stop codons detected: 3
Number of frameshifts detected: 3


Retrocopy - Parental Gene Alignment:

ParentalMREIVLTQTGQCGNQIGAKFWEVISDEHAIDS-AGTYHGDSHLQLERINVHHHEASGGRYVPRAVLVDLE
M.EIV..Q...CGNQI.AKFWEVISDEH.I....GTYH.DS.LQL.RI.V...EA.GG.YVP.A.LVDLE
RetrocopyMKEIVHIQASHCGNQISAKFWEVISDEHGINP<TGTYHRDSALQLDRISVYYYEATGGKYVPHAILVDLE
ParentalPGTMDSVHSGPFGQVFRPDNFISGQCGAGNNWAKGRYTEGAELTESVMDVVRKEAESCDCLQGFQLTHSL
PGTMDSVHSGPFGQ.FRPDNF.S.Q.GAGNNWAK..YTEGAEL..SV.D.V.KEAESCDCLQGFQLTHSL
RetrocopyPGTMDSVHSGPFGQIFRPDNFASDQSGAGNNWAKCHYTEGAELVYSVLDLVWKEAESCDCLQGFQLTHSL
ParentalGGGTGSGMGTLLISKIREEYPDRIINTFSILPSPKVSDTVVEPYNATLSVHQLIENADETFCIDNEALYD
...TGSG.GTLL.SKI.EEYPD...NTFS..PS.KVSDTVVEPYNATLSVHQL.EN.DET.CIDNEAL.D
RetrocopyDWDTGSGIGTLLMSKIQEEYPDCFMNTFSVVPSHKVSDTVVEPYNATLSVHQLVENTDETYCIDNEAL*D
ParentalICSRTLKLPTPTYGDLNHLVSATMSGVTTCLRF-PGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSRGS
IC.R.LKL.TPTY.DLN.LV.ATMSGVTTCL.F.PGQL.ADL.KLAVNMVPFP.LHFFMPGFAP.TSRGS
RetrocopyICFRNLKLTTPTYWDLNYLVLATMSGVTTCLHF<PGQLSADLCKLAVNMVPFPYLHFFMPGFAPFTSRGS
ParentalQQYRALTVAELTQQMFDAKNMMAACDPRHGCYLTVAAIFRGRMPMREVDEQMFNIQDKNSSYFADWFPDN
Q.Y.ALTV..LTQQ.FDAKN.MAACDPRHG.YLT.AA...GRM.M..V.EQM...Q.KNSSYF..W.P.N
RetrocopyQ*YQALTVPQLTQQVFDAKNLMAACDPRHGQYLTMAAVSSGRMSMKAVNEQMLKVQNKNSSYFVEWIPNN
ParentalVKTAVCDI-PPRGLKMSATFIGNNAAIQELFTCVSEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMND
.KTAVCDI.PP.GLKM..TFIGN...IQ.LF...SEQFTAMF..KAFLH.YTGEGMDEMEFTEAESNMN.
RetrocopyIKTAVCDI<PPHGLKMAVTFIGNSTGIQ*LFKRISEQFTAMFYQKAFLHCYTGEGMDEMEFTEAESNMNN
ParentalLVSEYQQYQDATAEEEED-EEYAEEE
..SE.QQYQDAT.EEEED....AEEE
RetrocopyFISEDQQYQDATTEEEEDFSKEAEEE

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 0 .14 RPM
bodymap2_adrenal 0 .00 RPM 0 .00 RPM
bodymap2_brain 0 .00 RPM 0 .00 RPM
bodymap2_breast 0 .00 RPM 0 .19 RPM
bodymap2_colon 0 .00 RPM 0 .00 RPM
bodymap2_heart 0 .00 RPM 0 .00 RPM
bodymap2_kidney 0 .00 RPM 0 .00 RPM
bodymap2_liver 0 .00 RPM 0 .00 RPM
bodymap2_lung 0 .00 RPM 0 .00 RPM
bodymap2_lymph_node 0 .00 RPM 0 .22 RPM
bodymap2_ovary 0 .00 RPM 0 .13 RPM
bodymap2_prostate 0 .00 RPM 0 .02 RPM
bodymap2_skeletal_muscle 0 .00 RPM 0 .00 RPM
bodymap2_testis 0 .06 RPM 2 .32 RPM
bodymap2_thyroid 0 .00 RPM 0 .00 RPM
bodymap2_white_blood_cells 0 .00 RPM 0 .06 RPM

ChIP-Seq - click to see more details

RNA Polymerase II activity near the 5' end of retro_hsap_3733 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_3733 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_3733 retrocopy 5' end.

Lab - click to see more details

retro_hsap_3733 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_3733 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_2527
Gorilla gorilla retro_ggor_2519
Parental genes homology:
Parental genes homology involve 9 parental genes, and 9 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG000000101011 retrocopy
retro_cjac_800,
Callithrix jacchus ENSCJAG000000116971 retrocopy
retro_cjac_3284,
Dipodomys ordii ENSDORG000000158891 retrocopy
retro_dord_254,
Homo sapiens ENSG000001048331 retrocopy
retro_hsap_4751,
Homo sapiens ENSG00000173213 1 retrocopy
retro_hsap_3733 ,
Homo sapiens ENSG000001738761 retrocopy
retro_hsap_3944,
Homo sapiens ENSG000002589471 retrocopy
retro_hsap_155,
Mus musculus ENSMUSG000000162551 retrocopy
retro_mmus_1109,
Pongo abelii ENSPPYG000000111801 retrocopy
retro_pabe_3250,

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 = 0.14 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .00 RPM
CEU_NA11843 0 .00 RPM
CEU_NA11930 0 .03 RPM
CEU_NA12004 0 .00 RPM
CEU_NA12400 0 .04 RPM
CEU_NA12751 0 .02 RPM
CEU_NA12760 0 .04 RPM
CEU_NA12827 0 .05 RPM
CEU_NA12872 0 .00 RPM
CEU_NA12873 0 .00 RPM
FIN_HG00183 0 .11 RPM
FIN_HG00277 0 .04 RPM
FIN_HG00315 0 .00 RPM
FIN_HG00321 0 .03 RPM
FIN_HG00328 0 .02 RPM
FIN_HG00338 0 .00 RPM
FIN_HG00349 0 .00 RPM
FIN_HG00375 0 .00 RPM
FIN_HG00377 0 .05 RPM
FIN_HG00378 0 .04 RPM
GBR_HG00099 0 .03 RPM
GBR_HG00111 0 .04 RPM
GBR_HG00114 0 .00 RPM
GBR_HG00119 0 .02 RPM
GBR_HG00131 0 .09 RPM
GBR_HG00133 0 .07 RPM
GBR_HG00134 0 .00 RPM
GBR_HG00137 0 .05 RPM
GBR_HG00142 0 .00 RPM
GBR_HG00143 0 .03 RPM
TSI_NA20512 0 .00 RPM
TSI_NA20513 0 .00 RPM
TSI_NA20518 0 .00 RPM
TSI_NA20532 0 .00 RPM
TSI_NA20538 0 .05 RPM
TSI_NA20756 0 .00 RPM
TSI_NA20765 0 .04 RPM
TSI_NA20771 0 .00 RPM
TSI_NA20786 0 .05 RPM
TSI_NA20798 0 .00 RPM
YRI_NA18870 0 .14 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 .05 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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