RetrogeneDB ID:

retro_hsap_3059

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:4:83322730..83323609(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000250325
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:IGBP1
Ensembl ID:ENSG00000089289
Aliases:IGBP1, ALPHA-4, IBP1
Description:immunoglobulin (CD79A) binding protein 1 [Source:HGNC Symbol;Acc:5461]


Retrocopy-Parental alignment summary:






>retro_hsap_3059
ATGGATCTCCTTGAGAAGGCTGCCGAAATGTTATCGCAGCTCGAGTTGTTCAGCCGAAATGAAGATTTGGAAGAGATTGC
TTCCACCGACCTGAAGTACCTGGTGGTGCCAGTGTTTCAAGGAGCCCTCACCATGAAACAAGTCAACTCCAGCAAGCGTC
TAGATCATTTGCAGCGGGCTCGAGAACACTTTATAAACCACTTAACTCAGTGTCATTGCTATCATGTGGCAGAGTTTGAG
CTGCCCAAAGCCAAGAACAACTCAGCCGAAAATCACACTGCTAATTCCTCCATGGCTTATTCTAGCCTCGTTGCTATGGC
ATCTCGAAGACAGGGTAAAATAGAGAGATACAAGCAGAAGAAGGAGTTGGAGCATAGGTTGTCTGAAATGAAACCTGCTG
TGGAAAGTGGTCAAGCAGATGATGAGCGTGTTTGTGAATATTATCTTCTTCACCTTCAGCGGTGGATTGATATTAGCTTA
GAAGAGATTGAGAACATTGACCAGGAAATAAAGATCCCGAGAGAAAGAGACTCTTCAGGAGGCATCAACTTCTAACTCAT
CTCACCAGGAGAGGCCTCCAGTGAAACCCTTCATTCTCACTCAGAACACGGCCCAAGCCAAAGTATTTGGAGCAGGTTAT
CCAAGTCTGGCAACTATGACGGTGAGTGACTGGTTGAGCAACATCGGAAATATGGAGCATTACGAGATCAGGAAATAGCC
AAGGCAACACCAGAGGAATTCAGAAAAGCGGCTCAGCAATAGGAACATCAAGAAGAAAAGGAGGAAGAGGATGATGAACA
AACACTCTACAGAGCTCTGGAGTGGGATGACTGGAAGGACACCCATCCTTGGGGCTATGGCAACCGATAGAACATGGGC

ORF - retro_hsap_3059 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 86.15 %
Parental protein coverage: 86.73 %
Number of stop codons detected: 2
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalLDLLEKAAEMLSQLDLFSRNEDLEEIASTDLKYLLVPAFQGALTMKQVNPSKRLDHLQRAREHFINYLTQ
.DLLEKAAEMLSQL.LFSRNEDLEEIASTDLKYL.VP.FQGALTMKQVN.SKRLDHLQRAREHFIN.LTQ
RetrocopyMDLLEKAAEMLSQLELFSRNEDLEEIASTDLKYLVVPVFQGALTMKQVNSSKRLDHLQRAREHFINHLTQ
ParentalCHCYHVAEFELPKTMNNSAENHTANSSMAYPSLVAMASQRQAKIQRYKQKKELEHRLSAMKSAVESGQAD
CHCYHVAEFELPK..NNSAENHTANSSMAY.SLVAMAS.RQ.KI.RYKQKKELEHRLS.MK.AVESGQAD
RetrocopyCHCYHVAEFELPKAKNNSAENHTANSSMAYSSLVAMASRRQGKIERYKQKKELEHRLSEMKPAVESGQAD
ParentalDERVREYYLLHLQRWIDISLEEIESIDQEIKILRERDSS-REASTSNSSRQERPPVKPFILTRNMAQAKV
DERV.EYYLLHLQRWIDISLEEIE.IDQEIKI.RERDSS........S..QERPPVKPFILT.N.AQAKV
RetrocopyDERVCEYYLLHLQRWIDISLEEIENIDQEIKIPRERDSS>EASTSNSS-HQERPPVKPFILTQNTAQAKV
ParentalFGAGYPSLPTMTVSDW-YEQHRKYGALPDQGIAKAAPEEFRKAAQQQEEQEEKEEEDDEQTLHRAREWDD
FGAGYPSL.TMTVSDW..EQHRKYGAL.DQ.IAKA.PEEFRKAAQQ.E.QEEKEEEDDEQTL.RA.EWDD
RetrocopyFGAGYPSLATMTVSDW<VEQHRKYGALRDQEIAKATPEEFRKAAQQ*EHQEEKEEEDDEQTLYRALEWDD
ParentalWKDTHPRGYGNRQNMG
WKDTHP.GYGNR.NMG
RetrocopyWKDTHPWGYGNR*NMG

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 60 .19 RPM
bodymap2_adrenal 0 .06 RPM 43 .27 RPM
bodymap2_brain 0 .05 RPM 34 .57 RPM
bodymap2_breast 0 .00 RPM 37 .45 RPM
bodymap2_colon 0 .00 RPM 87 .51 RPM
bodymap2_heart 0 .00 RPM 33 .73 RPM
bodymap2_kidney 0 .00 RPM 34 .37 RPM
bodymap2_liver 0 .00 RPM 9 .97 RPM
bodymap2_lung 0 .00 RPM 38 .50 RPM
bodymap2_lymph_node 0 .00 RPM 75 .49 RPM
bodymap2_ovary 0 .02 RPM 98 .47 RPM
bodymap2_prostate 0 .00 RPM 103 .61 RPM
bodymap2_skeletal_muscle 0 .00 RPM 80 .54 RPM
bodymap2_testis 0 .17 RPM 44 .32 RPM
bodymap2_thyroid 0 .15 RPM 59 .04 RPM
bodymap2_white_blood_cells 0 .00 RPM 86 .31 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_3059 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_3059 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_3059 retrocopy 5' end.

Lab - click to see more details

retro_hsap_3059 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_3059 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_1982
Pongo abelii retro_pabe_2533
Parental genes homology:
Parental genes homology involve 19 parental genes, and 48 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000077971 retrocopy
retro_btau_215,
Choloepus hoffmanni ENSCHOG000000136543 retrocopies
retro_chof_1523, retro_chof_2206, retro_chof_438,
Callithrix jacchus ENSCJAG000000125256 retrocopies
retro_cjac_111, retro_cjac_1225, retro_cjac_2278, retro_cjac_2968, retro_cjac_3417, retro_cjac_47,
Cavia porcellus ENSCPOG000000107971 retrocopy
retro_cpor_44,
Dasypus novemcinctus ENSDNOG000000147315 retrocopies
retro_dnov_1160, retro_dnov_2029, retro_dnov_2340, retro_dnov_2380, retro_dnov_678,
Echinops telfairi ENSETEG000000033971 retrocopy
retro_etel_1637,
Felis catus ENSFCAG000000296881 retrocopy
retro_fcat_23,
Homo sapiens ENSG00000089289 5 retrocopies
retro_hsap_1317, retro_hsap_1848, retro_hsap_2766, retro_hsap_2919, retro_hsap_3059 ,
Gorilla gorilla ENSGGOG000000277952 retrocopies
retro_ggor_112, retro_ggor_2020,
Myotis lucifugus ENSMLUG000000041791 retrocopy
retro_mluc_316,
Macaca mulatta ENSMMUG000000139292 retrocopies
retro_mmul_1545, retro_mmul_31,
Mus musculus ENSMUSG000000312211 retrocopy
retro_mmus_169,
Nomascus leucogenys ENSNLEG000000007475 retrocopies
retro_nleu_1399, retro_nleu_1653, retro_nleu_2334, retro_nleu_671, retro_nleu_828,
Otolemur garnettii ENSOGAG000000117971 retrocopy
retro_ogar_110,
Pongo abelii ENSPPYG000000204354 retrocopies
retro_pabe_1099, retro_pabe_1451, retro_pabe_2245, retro_pabe_2533,
Pan troglodytes ENSPTRG000000219905 retrocopies
retro_ptro_1233, retro_ptro_1873, retro_ptro_1973, retro_ptro_1982, retro_ptro_901,
Pteropus vampyrus ENSPVAG000000054831 retrocopy
retro_pvam_1462,
Rattus norvegicus ENSRNOG000000262671 retrocopy
retro_rnor_311,
Tarsius syrichta ENSTSYG000000062142 retrocopies
retro_tsyr_1537, retro_tsyr_2131,

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 = 0.09 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .02 RPM
CEU_NA11843 0 .06 RPM
CEU_NA11930 0 .07 RPM
CEU_NA12004 0 .04 RPM
CEU_NA12400 0 .07 RPM
CEU_NA12751 0 .00 RPM
CEU_NA12760 0 .04 RPM
CEU_NA12827 0 .09 RPM
CEU_NA12872 0 .03 RPM
CEU_NA12873 0 .03 RPM
FIN_HG00183 0 .00 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 .03 RPM
FIN_HG00375 0 .00 RPM
FIN_HG00377 0 .05 RPM
FIN_HG00378 0 .04 RPM
GBR_HG00099 0 .03 RPM
GBR_HG00111 0 .00 RPM
GBR_HG00114 0 .03 RPM
GBR_HG00119 0 .00 RPM
GBR_HG00131 0 .00 RPM
GBR_HG00133 0 .02 RPM
GBR_HG00134 0 .00 RPM
GBR_HG00137 0 .08 RPM
GBR_HG00142 0 .06 RPM
GBR_HG00143 0 .00 RPM
TSI_NA20512 0 .00 RPM
TSI_NA20513 0 .05 RPM
TSI_NA20518 0 .06 RPM
TSI_NA20532 0 .00 RPM
TSI_NA20538 0 .00 RPM
TSI_NA20756 0 .03 RPM
TSI_NA20765 0 .02 RPM
TSI_NA20771 0 .00 RPM
TSI_NA20786 0 .00 RPM
TSI_NA20798 0 .00 RPM
YRI_NA18870 0 .00 RPM
YRI_NA18907 0 .07 RPM
YRI_NA18916 0 .04 RPM
YRI_NA19093 0 .00 RPM
YRI_NA19099 0 .00 RPM
YRI_NA19114 0 .00 RPM
YRI_NA19118 0 .04 RPM
YRI_NA19213 0 .00 RPM
YRI_NA19214 0 .00 RPM
YRI_NA19223 0 .04 RPM

Indel association:

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





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