RetrogeneDB ID:

retro_hsap_4174

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:9:65973158..65974601(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000237086
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:RBPJ
Ensembl ID:ENSG00000168214
Aliases:RBPJ, AOS3, CBF1, IGKJRB, IGKJRB1, KBF2, RBP-J, RBPJK, RBPSUH, SUH, csl
Description:recombination signal binding protein for immunoglobulin kappa J region [Source:HGNC Symbol;Acc:5724]


Retrocopy-Parental alignment summary:






>retro_hsap_4174
ATGGCATGGATTAAAAGGAAATTTGGTAAGTGGCCTCCATTTAAACGACTTACTAGGGAAGCTATGTGAAATTATTTAAA
AGGGTAAGGGGATCAAATAGTACTTAGCCTTCATGCAAAAGTTGTACAGAAGTCATATGGAAATGAAAAAAGGTTTTTTT
GCCCTCCCCCTTGTGTATATCTTATGGGCAGTGGATGGAAGAAAATAAAATAACAAATGAAATGCGATGGTTGTTCTGAA
CAAGGGTCTCAACCATGTGCATTTATTGGCATAGGAAATAGTGACCAAGAAATGCAGCAGCTAAACTTGGAAGGAAAGAA
CTATTGCACAGCCAAAACATTGTACATATCTGATTTAGACAAGCAAAAGCACTTCATGTTGTCTGTAAAGGTGTTCTATG
GCAACAGTGATGACATTGGTGTGTTCCTCAGCAAGTCGTCCAAACCTTCCAAAAAGAAGCAGTCATTGAAAAATGCTGAC
TTATGCATTGCCTCAGGAAGAAAGGTGGCTCTGTTTAATCGACTACTATCCCAGACAGTTAGTACCAGATACTTGCACGT
AGAAAGAGGTAATTTTCATGCTAGTTCACAGCAATGGGGAGCATTTTACATTATTCTTGGATGATGATGGATCAGAAGGA
GAAGAATTCACAGTCTGAGATGGCTACATTCATTATGGACAAACAGTCAAACTTGTGTGCTCAGTTACTGGCATGGCACT
CCCAAGATTGATAATTAGGAAAGTTGATAAGCAGACCACATTATTGGATGCAGATGATCCTGTGTCACAACTCCATAAAT
GTGCATTTGACCTTGAGGATACAGAAAGAAAGTACTTATGCCTTTCTCAAGAAAGAATAATTCAATTTCAGGCCACTCCA
TGCCCAAAAGAACCAAATAAAGAGAAGATAAATGATGGTGCTTCCTGGGCAATCATTAGCACACATAAGGCGAAGCATAC
ATTTTACGAGAGAGTGGGCCCTGTCCTTGCCCTGGTCATGCCTCCGCCTGTCGTAGAGAGCCTTAAGTTGAATGGCGGTG
GGGACGAACCAATGCTTGAACTTACAGGACAGAATTTCACTCCAAATTTACAAGTGTGGTTTGGGGATGTAGAAGCTGAA
GCTATGTACAGGTGTGGAGAGAGTATGCTCGTGTTGTCCCAGACGTTTCTGCATTCTGAGAAGGTTGGAGATAGGTCCAG
CAACCAATACAGGTTTCAGTAACTTTGGTCCGAAATGATGGAATCATATATTCCACCAGCCTTACCTTTACCTACACACC
AGAAGCAGGGCCGCGGCCACATTGCAGTGTAGCAGGTGCCATCCTTCAAGCCAGTTCAAGCCACGTGCCCCCTAATGAAT
TAAACACAAACAGCGACGGAAGTTACACAAACGCCAGCACAAATTCAACCAGTGTCACATCATCTACACCAACAGTGGTA
TCC

ORF - retro_hsap_4174 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 85.25 %
Parental protein coverage: 100. %
Number of stop codons detected: 6
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalMAWIKRKFGERPPPKRLTREAMRNYLKERGDQTVLILHAKVAQKSYGNEKRFFCPPPCVYLMGSGWKKKK
MAWIKRKFG..PP.KRLTREAM.NYLK..GDQ.VL.LHAKV.QKSYGNEKRFFCPPPCVYLMGSGWKK.K
RetrocopyMAWIKRKFGKWPPFKRLTREAM*NYLKG*GDQIVLSLHAKVVQKSYGNEKRFFCPPPCVYLMGSGWKKIK
ParentalEQMERDGCSEQESQPCAFIGIGNSDQEMQQLNLEGKNYCTAKTLYISDSDKRKHFMLSVKMFYGNSDDIG
.QM..DGCSEQ.SQPCAFIGIGNSDQEMQQLNLEGKNYCTAKTLYISD.DK.KHFMLSVK.FYGNSDDIG
Retrocopy*QMKCDGCSEQGSQPCAFIGIGNSDQEMQQLNLEGKNYCTAKTLYISDLDKQKHFMLSVKVFYGNSDDIG
ParentalVFLSKRIKVISKPSKKKQSLKNADLCIASGTKVALFNRLRSQTVSTRYLHVEGGNFHASSQQW-GAFFIH
VFLSK.....SKPSKKKQSLKNADLCIASG.KVALFNRL.SQTVSTRYLHVE.GNFH..S.Q..G..F..
RetrocopyVFLSKS----SKPSKKKQSLKNADLCIASGRKVALFNRLLSQTVSTRYLHVERGNFH-ASSQQ>GEHFTL
ParentalLLDDDESEGEEFTVRDGYIHYGQTVKLVCSVTGMALPRLIIRKVDKQTALLDADDPVSQLHKCAFYLKDT
.LDDD.SEGEEFTV.DGYIHYGQTVKLVCSVTGMALPRLIIRKVDKQT.LLDADDPVSQLHKCAF.L.DT
RetrocopyFLDDDGSEGEEFTV*DGYIHYGQTVKLVCSVTGMALPRLIIRKVDKQTTLLDADDPVSQLHKCAFDLEDT
ParentalERMYLCLSQERIIQFQATPCPKEPNKEMINDGASWTIISTDKAEYTFYEGMGPVLAPVTPVPVVESLQLN
ER.YLCLSQERIIQFQATPCPKEPNKE.INDGASW.IIST.KA..TFYE..GPVLA.V.P.PVVESL.LN
RetrocopyERKYLCLSQERIIQFQATPCPKEPNKEKINDGASWAIISTHKAKHTFYERVGPVLALVMPPPVVESLKLN
ParentalGGGDVAMLELTGQNFTPNLRVWFGDVEAETMYRCGESMLC-VVPDISAFREGWRWVRQPVQVPVTLVRND
GGGD..MLELTGQNFTPNL.VWFGDVEAE.MYRCGESML..VVPD.SAF.EGWR.V.QP.QV.VTLVRND
RetrocopyGGGDEPMLELTGQNFTPNLQVWFGDVEAEAMYRCGESMLV<VVPDVSAF*EGWR*VQQPIQVSVTLVRND
ParentalGIIYSTSLTFTYTPEPGPRPHCSAAGAILRANSSQVPPNESNTNSEGSYTNASTNSTSVTSSTATVVS
GIIYSTSLTFTYTPE.GPRPHCS.AGAIL.A.SS.VPPNE.NTNS.GSYTNASTNSTSVTSST.TVVS
RetrocopyGIIYSTSLTFTYTPEAGPRPHCSVAGAILQASSSHVPPNELNTNSDGSYTNASTNSTSVTSSTPTVVS

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 243 .92 RPM
bodymap2_adrenal 0 .00 RPM 167 .50 RPM
bodymap2_brain 0 .00 RPM 162 .25 RPM
bodymap2_breast 0 .00 RPM 202 .51 RPM
bodymap2_colon 0 .00 RPM 252 .87 RPM
bodymap2_heart 0 .00 RPM 79 .27 RPM
bodymap2_kidney 0 .00 RPM 100 .20 RPM
bodymap2_liver 0 .00 RPM 31 .71 RPM
bodymap2_lung 0 .00 RPM 162 .04 RPM
bodymap2_lymph_node 0 .00 RPM 172 .28 RPM
bodymap2_ovary 0 .00 RPM 209 .71 RPM
bodymap2_prostate 0 .00 RPM 214 .93 RPM
bodymap2_skeletal_muscle 0 .00 RPM 91 .59 RPM
bodymap2_testis 0 .00 RPM 219 .11 RPM
bodymap2_thyroid 0 .00 RPM 112 .95 RPM
bodymap2_white_blood_cells 0 .00 RPM 223 .63 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_4174 was not detected

EST - click to see more details

5 EST(s) were mapped to retro_hsap_4174 retrocopy
EST ID Start End Identity Match Mis-match Score
BX119131 65973388 65973902 100 514 0 514
F01398 65973390 65973633 100 243 0 243
R37405 65973388 65973811 96.9 415 4 406
R44578 65973388 65973765 95.7 366 2 355
T23712 65973390 65973914 98.4 299 5 293

TSS - click to see more details

No TSS is located nearby retro_hsap_4174 retrocopy 5' end.

Lab - click to see more details

retro_hsap_4174 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_4174 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 9 parental genes, and 19 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000036021 retrocopy
retro_btau_1507,
Choloepus hoffmanni ENSCHOG000000015824 retrocopies
retro_chof_1172, retro_chof_1278, retro_chof_2449, retro_chof_371,
Homo sapiens ENSG00000168214 6 retrocopies
retro_hsap_4169, retro_hsap_4171, retro_hsap_4173, retro_hsap_4174 , retro_hsap_4256, retro_hsap_4316,
Gorilla gorilla ENSGGOG000000045821 retrocopy
retro_ggor_2853,
Mus musculus ENSMUSG000000391912 retrocopies
retro_mmus_2348, retro_mmus_2819,
Nomascus leucogenys ENSNLEG000000168951 retrocopy
retro_nleu_2305,
Oryctolagus cuniculus ENSOCUG000000134491 retrocopy
retro_ocun_1445,
Pan troglodytes ENSPTRG000000159681 retrocopy
retro_ptro_2829,
Tursiops truncatus ENSTTRG000000090222 retrocopies
retro_ttru_1151, retro_ttru_1593,

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 ) 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 .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 .00 RPM
FIN_HG00377 0 .00 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 .00 RPM
GBR_HG00134 0 .00 RPM
GBR_HG00137 0 .00 RPM
GBR_HG00142 0 .00 RPM
GBR_HG00143 0 .00 RPM
TSI_NA20512 0 .00 RPM
TSI_NA20513 0 .00 RPM
TSI_NA20518 0 .00 RPM
TSI_NA20532 0 .00 RPM
TSI_NA20538 0 .00 RPM
TSI_NA20756 0 .00 RPM
TSI_NA20765 0 .00 RPM
TSI_NA20771 0 .00 RPM
TSI_NA20786 0 .00 RPM
TSI_NA20798 0 .00 RPM
YRI_NA18870 0 .00 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 .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).





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