RetrogeneDB ID:

retro_hsap_3192

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:5:75206380..75207693(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000248684
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:BIN2
Ensembl ID:ENSG00000110934
Aliases:BIN2, BRAP-1
Description:bridging integrator 2 [Source:HGNC Symbol;Acc:1053]


Retrocopy-Parental alignment summary:






>retro_hsap_3192
TACTTCACCCAGTTCAGTGAGATTGAGGAGAGAATTGCCAAGTGGGGTTGAAAACTTGTGGATTATGATGGTGCCCAACA
TCACCTGGATGCAGTGCAGAATGCCAAGAAGAAAGACGAGGCCAAGACTGCCAAGGCAGAGGAAGAGTTCAACAAAGCCC
AGACTATGTTTGAAGATCTGAACCAAAAACTACTAGAGGAGCTGCCTATTCTTTATAACAGTCATGTTGGCTGCTATGTG
ACCATCTTCCAAAACATTTCCAATTTGAGGGATGTCTTCTACAGGGAAATGAGCAAGCTGAACTGCAATCTCTATGAGAT
GATGAGCAAACTGCAGAAGCAACATTCCAACAAAGTCTTTGTGGTGAAGGGACTATCAAGCAGCAGCAGGCTCTCTTTAG
TCATTTATCCCCCAGTTCGAACATCTATGGCCTCCAGTCCTCTTACCTCACCTACTAGTCCCTCTACACTTTCCTTGAAG
AGTGAGAGTGAATCTGTCGCAACAACTGAAGATCTGGAACCTGATGCAGCCCGGGGGAAGATAATTCTGAGATCAAGGAG
CACTTAGAAGATGAGGAAATAGAGAAGGAAGGATCTGAAGCAAGCTCCTCTGAGGAAGAAGAGCCTCTACCAGCCTGCAA
TGGCCCTGCCCAGGCCCAGCCCTCTCCTACCATTGGGAGTGGCAAGTCCCAGGAGGAAGTTCTCCCTAGCTCCCCAGCTC
CATCACCAGGCAGAACCCTGAGCCCTTCAGGGCAGCCTTCATCATCTGCCACAGAAGTAGTCCTCCAAACCCGCACAGAA
AATGAAGGATCTGAACAACCAAAGAAGAGAACCTATATCCAGAGGACGTCAGCACCCCCTAGTAGGCCTCCTCCACCCAG
AGCCACTCCAAACCCCAGGCCCTCCTCAGGGAACATACCCTCCAGTCCTCCAGCCTCTGGAGGGGGTTCAACCACTGGCC
CTAGGGTCTCCTTGGGGACTGAGACTCCAAGTCCTAGTACCTCCCTAGAGTTCTCCCCTAATCCAGAACTACAAAAGAAG
CCAGTAAGAACTCCTGAGGTCAAAGAAAATGAAAACATCCACAATCAGAACCCCGAAGAACTTTGCACTTTTCCCACCTT
AATGACATCTCAGATTGCTTCAGAGCCTGGAGAGGCAAAGAAGATGGAAGACAAGAAAGAGGATAATAAGCTTGTCTTAG
CTGACTCCTCGGAGGGCCAAGACCAGCTTTAAGTCTCCACAGTACCAGACAAGAGCAACCTCACAGCACCTGAACCTCAA
GAATAGGTATCTACAAGTGAAAATGCACAACTC

ORF - retro_hsap_3192 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 84.28 %
Parental protein coverage: 77.52 %
Number of stop codons detected: 3
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalYVAQFSEIKERIAKRGRKLVDYDSARHHLEAVQNAKKKDEAKTAKAEEEFNKAQTVFEDLNQELLEELPI
Y..QFSEI.ERIAK.G.KLVDYD.A.HHL.AVQNAKKKDEAKTAKAEEEFNKAQT.FEDLNQ.LLEELPI
RetrocopyYFTQFSEIEERIAKWG*KLVDYDGAQHHLDAVQNAKKKDEAKTAKAEEEFNKAQTMFEDLNQKLLEELPI
ParentalLYNSRIGCYVTIFQNISNLRDVFYREMSKLNHNLYEVMSKLEKQHSNKVFVVKGLSSSSRRSLVISPPVR
LYNS..GCYVTIFQNISNLRDVFYREMSKLN.NLYE.MSKL.KQHSNKVFVVKGLSSSSR.SLVI.PPVR
RetrocopyLYNSHVGCYVTIFQNISNLRDVFYREMSKLNCNLYEMMSKLQKQHSNKVFVVKGLSSSSRLSLVIYPPVR
ParentalTATVSSPLTSPTSPSTLSLKSESESVSATEDLAPDAAQG-EDNSEIKELLEEEEIEKEGSEASSSEEDEP
T...SSPLTSPTSPSTLSLKSESESV..TEDL.PDAA.G.EDNSEIKE.LE.EEIEKEGSEASSSEE.EP
RetrocopyTSMASSPLTSPTSPSTLSLKSESESVATTEDLEPDAARG<EDNSEIKEHLEDEEIEKEGSEASSSEEEEP
ParentalLPACNGPAQAQPSPTTERAKSQEEVLPSSTTPSPGGALSPSGQPSSSATEVVLRTRTASEGSEQPKKRAS
LPACNGPAQAQPSPT....KSQEEVLPSS..PSPG..LSPSGQPSSSATEVVL.TRT..EGSEQPKKR..
RetrocopyLPACNGPAQAQPSPTIGSGKSQEEVLPSSPAPSPGRTLSPSGQPSSSATEVVLQTRTENEGSEQPKKRTY
ParentalIQRTSAPPSRPPPPRATASPRPSSGNIPSSPTASGGGSPTSPRASLGTGTASPRTSLEVSPNPEPPEKPV
IQRTSAPPSRPPPPRAT..PRPSSGNIPSSP.ASGGGS.T.PR.SLGT.T.SP.TSLE.SPNPE...KPV
RetrocopyIQRTSAPPSRPPPPRATPNPRPSSGNIPSSPPASGGGSTTGPRVSLGTETPSPSTSLEFSPNPELQKKPV
ParentalRTPEAKENENIHNQNPEELCTSPTLMTSQVASEPGEAKKMEDKEKDNKLISANSSEGQDQLQVSMVPENN
RTPE.KENENIHNQNPEELCT.PTLMTSQ.ASEPGEAKKMEDK..DNKL..A.SSEGQDQL.VS.VP...
RetrocopyRTPEVKENENIHNQNPEELCTFPTLMTSQIASEPGEAKKMEDKKEDNKLVLADSSEGQDQL*VSTVPDKS
ParentalNLTAPEPQEEVSTSENPQL
NLTAPEPQE.VSTSEN.QL
RetrocopyNLTAPEPQE*VSTSENAQL

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 8 .81 RPM
bodymap2_adrenal 0 .00 RPM 33 .84 RPM
bodymap2_brain 0 .00 RPM 3 .05 RPM
bodymap2_breast 0 .00 RPM 2 .76 RPM
bodymap2_colon 0 .00 RPM 2 .32 RPM
bodymap2_heart 0 .00 RPM 1 .83 RPM
bodymap2_kidney 0 .00 RPM 2 .09 RPM
bodymap2_liver 0 .00 RPM 4 .06 RPM
bodymap2_lung 0 .00 RPM 22 .20 RPM
bodymap2_lymph_node 0 .00 RPM 36 .77 RPM
bodymap2_ovary 0 .00 RPM 3 .62 RPM
bodymap2_prostate 0 .00 RPM 4 .24 RPM
bodymap2_skeletal_muscle 0 .00 RPM 0 .60 RPM
bodymap2_testis 0 .00 RPM 11 .97 RPM
bodymap2_thyroid 0 .00 RPM 1 .75 RPM
bodymap2_white_blood_cells 0 .02 RPM 321 .50 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_3192 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_3192 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_3192 retrocopy 5' end.

Lab - click to see more details

retro_hsap_3192 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_3192 has 4 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_2251
Gorilla gorilla retro_ggor_1336
Pongo abelii retro_pabe_2648
Macaca mulatta retro_mmul_2013
Parental genes homology:
Parental genes homology involve 6 parental genes, and 9 retrocopies.

Species Parental gene accession Retrocopies number
Homo sapiens ENSG00000110934 2 retrocopies
retro_hsap_2952, retro_hsap_3192 ,
Gorilla gorilla ENSGGOG000000094231 retrocopy
retro_ggor_1336,
Loxodonta africana ENSLAFG000000023871 retrocopy
retro_lafr_1163,
Nomascus leucogenys ENSNLEG000000177741 retrocopy
retro_nleu_1636,
Pongo abelii ENSPPYG000000045262 retrocopies
retro_pabe_2448, retro_pabe_2648,
Pan troglodytes ENSPTRG000000049542 retrocopies
retro_ptro_2049, retro_ptro_2251,

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 = 0.04 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 .04 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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