RetrogeneDB ID:

retro_hsap_3690

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:6:167114584..167115902(-)
Located in intron of:ENSG00000071242
Retrocopy
information
Ensembl ID:ENSG00000235008
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:IGF2BP3
Ensembl ID:ENSG00000136231
Aliases:IGF2BP3, CT98, IMP-3, IMP3, KOC, KOC1, VICKZ3
Description:insulin-like growth factor 2 mRNA binding protein 3 [Source:HGNC Symbol;Acc:28868]


Retrocopy-Parental alignment summary:






>retro_hsap_3690
CTGAATGGATTTCAGTTAGAGAATTTCACCTTGAAAGTAGCCTATATCCCTGATGAAATGGCCACCCAGCAAAACCCCTT
TCTGCAGCCCCGAGGTCGCCGGGGGCTTGGGCAGAGGGGCTCCTCAAGGCAGGGGTCTCCAGGATCCGTGTCCAAGCAGA
AACCATGTGATTTGCCTCTGTGCCTGCTGGTTCCCACCCAATTTGTTGGAGCCATTATAGGAAAAGAAGGTGCCACCATT
CGGAACATCACCAAACAGACCCAGTCTAAAATCGATGTCCACCGTAAAGAAAATGCAGGGGCTGCTGAGAAGTCGATTAC
TATCCTCTCTACTCCTGAAGGCACCTCTGCGGCTTGTAAGTCTATTCTGGAGATTATGCGTAAGGAAACTCAAGATGTAA
AATTCACAGAAGAGATCCCCTTGAAGATTTTAGCTCAAAATAACTTTGTTGGCCGTCTTATTGGTAAAGAAGGAAGAAAT
CTTAAAAAAATTGAGCAAGACACAGACACTAAAATCACGATATCTCCATTGCAGGAACTGATGCAGTATAATCCAGAACA
CACCATTACAGCTAAAGGCAATGTTGAGACATGTGCCAAAGCTGAGGAAGAGATCATGAAGAAAATCAGGGAGCGTTAGG
AAAATGATATCACTTCTATGATTTCAAGCACATTTAATTCCTGGATTAAATCTGAACGCCTTGGGTCTGTTCCCACCCAC
TTCAGGGATGCCACCTCCCACCTCAGGGCCCCCTTCAGCCATGACTCCTCCCTCCCCGCAGTCTGAGCAATCAGAATCCG
AGACTGTTCATCTGTTTATCCCGGCTCTATCAGTCAGAGCCCTCATCAGCAAGCAGGGCCAGCACATCAAGCAGCTTTCT
CGCTTTGCTGGAGCTTCAAGTAAGATTGCTCCAGTGGAAGCACCAGATGCTAAGGTGAGGATGGTGATGATCGCTGGATC
ACCAGAGGCTCGGTTCAAGGCTCAGGGAAGAATTATGGAAAAATGAAAGAAGAAAACTTCGTTAGTCCTAAAGAAGAGGT
GAAACTTGAAGCTCATATCAGAGTGCCATCCTTTGCTGCTGGCAGTTACTGGAAAAGGAGGCAAAACGGTGAATGAACTT
CAGAATTTGTCAAGTGCAGAAGTTGTTGTCCCTTGTGACCAGACACCTGATGAGAATGACCAAGTGGTTGTCAAAATAAC
TGGTCACTTCTATGCTTGCCAGGTTGCCCAGAGAAAAATTCAGGAAATTCTGACTCAGGTAAAGCAGCAGCAACAACAGA
AGGCTCTGCAAAGTGGACCACCTCAGTCAAGACGGAAG

ORF - retro_hsap_3690 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 87.42 %
Parental protein coverage: 76.17 %
Number of stop codons detected: 1
Number of frameshifts detected 4


Retrocopy - Parental Gene Alignment:

ParentalLNGFQLENFTLKVAYIPDEMAAQQNPLQQPRGRRGLGQRGSSRQGSPGSVSKQKPCDLPLRLLVPTQFVG
LNGFQLENFTLKVAYIPDEMA.QQNP..QPRGRRGLGQRGSSRQGSPGSVSKQKPCDLPL.LLVPTQFVG
RetrocopyLNGFQLENFTLKVAYIPDEMATQQNPFLQPRGRRGLGQRGSSRQGSPGSVSKQKPCDLPLCLLVPTQFVG
ParentalAIIGKEGATIRNITKQTQSKIDVHRKENAGAAEKSITILSTPEGTSAACKSILEIMHKEAQDIKFTEEIP
AIIGKEGATIRNITKQTQSKIDVHRKENAGAAEKSITILSTPEGTSAACKSILEIM.KE.QD.KFTEEIP
RetrocopyAIIGKEGATIRNITKQTQSKIDVHRKENAGAAEKSITILSTPEGTSAACKSILEIMRKETQDVKFTEEIP
ParentalLKILAHNNFVGRLIGKEGRNLKKIEQDTDTKITISPLQELTLYNPERTITVKGNVETCAKAEEEIMKKIR
LKILA.NNFVGRLIGKEGRNLKKIEQDTDTKITISPLQEL..YNPE.TIT.KGNVETCAKAEEEIMKKIR
RetrocopyLKILAQNNFVGRLIGKEGRNLKKIEQDTDTKITISPLQELMQYNPEHTITAKGNVETCAKAEEEIMKKIR
ParentalESYENDIASMNLQAHLIPGLNLNALGLFP-PTSGMPPPTSGPPSAMTPPYPQFEQSETETVHLFIPALSV
E..ENDI.SM..............LG..P.PTSGMPPPTSGPPSAMTPP.PQ.EQSE.ETVHLFIPALSV
RetrocopyER*ENDITSM-ISSTFNSWIKSERLGSVP>PTSGMPPPTSGPPSAMTPPSPQSEQSESETVHLFIPALSV
ParentalGAIIGKQGQHIKQLSRFAGASIKIAPAEAPDAKVRMVIITGPPEAQFKAQGRI-YGKIKEENFVSPKEEV
.A.I.KQGQHIKQLSRFAGAS.KIAP.EAPDAKVRMV.I.G.PEA.FKAQGRI.YGK.KEENFVSPKEEV
RetrocopyRALISKQGQHIKQLSRFAGASSKIAPVEAPDAKVRMVMIAGSPEARFKAQGRI<YGKMKEENFVSPKEEV
ParentalKLEAHIRVPSFAAG-RVIGKGGK-TVNELQNLSSAEVVVPRDQTPDENDQVVVKITGHFYACQVAQRKIQ
KLEAHIRVPSFAAG.....K..K.TVNELQNLSSAEVVVP.DQTPDENDQVVVKITGHFYACQVAQRKIQ
RetrocopyKLEAHIRVPSFAAG<QLLEKEAK<TVNELQNLSSAEVVVPCDQTPDENDQVVVKITGHFYACQVAQRKIQ
ParentalEILTQVKQHQQQKALQSGPPQSRRK
EILTQVKQ.QQQKALQSGPPQSRRK
RetrocopyEILTQVKQQQQQKALQSGPPQSRRK

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 .76 RPM
bodymap2_adrenal 0 .00 RPM 0 .29 RPM
bodymap2_brain 0 .00 RPM 0 .23 RPM
bodymap2_breast 0 .00 RPM 0 .16 RPM
bodymap2_colon 0 .00 RPM 0 .17 RPM
bodymap2_heart 0 .02 RPM 0 .07 RPM
bodymap2_kidney 0 .00 RPM 0 .04 RPM
bodymap2_liver 0 .00 RPM 0 .00 RPM
bodymap2_lung 0 .00 RPM 1 .23 RPM
bodymap2_lymph_node 0 .00 RPM 0 .24 RPM
bodymap2_ovary 0 .00 RPM 0 .44 RPM
bodymap2_prostate 0 .00 RPM 0 .31 RPM
bodymap2_skeletal_muscle 0 .00 RPM 0 .00 RPM
bodymap2_testis 0 .00 RPM 7 .96 RPM
bodymap2_thyroid 0 .00 RPM 0 .89 RPM
bodymap2_white_blood_cells 0 .00 RPM 3 .25 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_3690 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_3690 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_3690 retrocopy 5' end.

Lab - click to see more details

retro_hsap_3690 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_3690 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Gorilla gorilla retro_ggor_2495
Pongo abelii retro_pabe_3023
Parental genes homology:
Parental genes homology involve 6 parental genes, and 7 retrocopies.

Species Parental gene accession Retrocopies number
Choloepus hoffmanni ENSCHOG000000023411 retrocopy
retro_chof_828,
Homo sapiens ENSG000000737922 retrocopies
retro_hsap_216, retro_hsap_4096,
Homo sapiens ENSG00000136231 1 retrocopy
retro_hsap_3690 ,
Gorilla gorilla ENSGGOG000000102861 retrocopy
retro_ggor_2520,
Nomascus leucogenys ENSNLEG000000147801 retrocopy
retro_nleu_2277,
Pongo abelii ENSPPYG000000177301 retrocopy
retro_pabe_3023,

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 = 0.47 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .06 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 .04 RPM
CEU_NA12827 0 .05 RPM
CEU_NA12872 0 .00 RPM
CEU_NA12873 0 .06 RPM
FIN_HG00183 0 .11 RPM
FIN_HG00277 0 .04 RPM
FIN_HG00315 0 .00 RPM
FIN_HG00321 0 .06 RPM
FIN_HG00328 0 .00 RPM
FIN_HG00338 0 .00 RPM
FIN_HG00349 0 .03 RPM
FIN_HG00375 0 .00 RPM
FIN_HG00377 0 .00 RPM
FIN_HG00378 0 .02 RPM
GBR_HG00099 0 .06 RPM
GBR_HG00111 0 .00 RPM
GBR_HG00114 0 .00 RPM
GBR_HG00119 0 .07 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 .17 RPM
TSI_NA20518 0 .03 RPM
TSI_NA20532 0 .00 RPM
TSI_NA20538 0 .05 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 .07 RPM
YRI_NA18907 0 .00 RPM
YRI_NA18916 0 .00 RPM
YRI_NA19093 0 .00 RPM
YRI_NA19099 0 .05 RPM
YRI_NA19114 0 .03 RPM
YRI_NA19118 0 .02 RPM
YRI_NA19213 0 .05 RPM
YRI_NA19214 0 .47 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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