RetrogeneDB ID:

retro_hsap_216

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:1:146522378..146524040(+)
Located in intron of:ENSG00000227242
Retrocopy
information
Ensembl ID:ENSG00000225603
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:IGF2BP2
Ensembl ID:ENSG00000073792
Aliases:IGF2BP2, IMP-2, IMP2, VICKZ2, p62
Description:insulin-like growth factor 2 mRNA binding protein 2 [Source:HGNC Symbol;Acc:28867]


Retrocopy-Parental alignment summary:






>retro_hsap_216
GTGATGAACAATCTTTACATCGGGAACCTTAGCCCTGCGGTCACCGCCGACGACCTCTGGCAGCTCTTTGGGGACAGGAA
GCTGCCCCCCACCGGACAGGTCCTGCTCAAGTCCGGCTATGCCTTCGTGGACTACCCCTACAAGAACTGGGCCATCCGCG
CCATCGAGACCCTCTCGGGTAAAGTGGAATTGCATGGGAAAATCATGGAAGTTGATTACTCAGTCTCTAAAAAGCTAAGG
AGGAGAAAAATTCAGATTCGAAACATCCCTCCTCACCTCCAGTGGGAGGTGTTGGATGGACTTTTGGCTCAATATGGAAC
AGTGGAGAATGTGGAACAACAAGTCAACACAGACACAGAAACCACTGTTGTCAACGTCACATATGCAACAAGAGAAGAAA
ATAGACATGGAGAGGCTAAGCGGGCATCAGTTTGAGAACTAGTCCTTCAAGATTTCCTACATCCCGGATGAAGAGGTGAG
CTCCCCTTCGCCCCCTCAGCGAGCCCAGCGTGGGGACCACTCTTCCCGGGGAGCAAGGCCACGACCCTGGGGGCGCTTCT
TAGGCCAGACAGATTGATTTCCTGCTGCAGGTCCTGGTCCCCTACAGTTTGCAGTTTGTTGGTGCCATCATCAGAAAGGA
GGGCTTGACCATAAAGAACATCACTAAGTAGACCCAGTCCCGGATAGATATCCATAGAAAAGAGAACTCTGGAGCTGCAG
AGAAGCCTGTCACCATCCATGCCACCCCAGGGGGGACTTCTGAAGCATGCCTCATGATTCTTGAAATCATGCAGAAAGAG
GCAGATGAGAACAAACTAGCCGAAGAGATTCCTCTGAAAATCTTGGCCCACAATGGCTTGGTTGGAAAAGAAGGCAGAAA
TTTGAAGAAAATTGAACATGAAACAGGGACCAAGATAGCAATCTCATCTTTGCAGGATTTGAGCATAAATAACCAGGAAA
GAATCATCACTGTGAAGGGCACAGTTTGAGGCCTGTGCCAGTGCTGAGATAGAGATTATGAAGAAGCTGCGTGAGACCTT
TGAAAATGATATGTTGGCTGTTAATACGCACTCCGGATACTTCTCCAGCTTGTACCCCCATCACCAGGTTGGCCCGTTCC
CGCATCATCACTCTTATCCAGAGCAGGAGGTTGTGAATCTCTTCATCCCAACCCAGGCTGTGGGCGCCATTATCAGGAAG
AGGGGAGCACACATCAAACAGCTGGCGAGATTCGCCACAGCCTCCATCAAGATCGCCCTTGCGGAAGGCCCAGACGTCAA
CGAAAGGATGGTCATCATCACCCGGCCACCGGAAGCCCAGTTCAAGGCCCAGGGACGGATCTTTGGGAAACTGAAAGAAG
AAAACTTCTTTAACCCCAAAGAAGAAGTGAAGCTGGAAGCCCGTATCAGAGTGCCCTCTTCCACAGCTGGCCGGGTGATT
GGCAAAGGTGTCAATACCTTGAATGAACTGCAGAACTTAACCAGTGCAGAAGTCATCGTGCCTCGTGACCAAAGGCCAGA
TGAAAATGAGGAAGTGATCGTCAGAATTATTGGACACTTCTTTGCTACCCCAACTGCATAGCACAAGATCAGGGAAACTG
TACAACAGGTGAAGCAGCAAGAGCAGAAATACCCTCAGGGAGTCGCCTCACAGCACAGCAAG

ORF - retro_hsap_216 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 86.63 %
Parental protein coverage: 100. %
Number of stop codons detected: 4
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalMMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLLKSGYAFVDYPDQNWAIRAIETLSGKVELHGKIME
.MN.LYIGNLSPAVTADDL.QLFGDRKLP..GQVLLKSGYAFVDYP..NWAIRAIETLSGKVELHGKIME
RetrocopyVMNNLYIGNLSPAVTADDLWQLFGDRKLPPTGQVLLKSGYAFVDYPYKNWAIRAIETLSGKVELHGKIME
ParentalVDYSVSKKLRSRKIQIRNIPPHLQWEVLDGLLAQYGTVENVEQV-NTDTETAVVNVTYATREEAKIAMEK
VDYSVSKKLR.RKIQIRNIPPHLQWEVLDGLLAQYGTVENVEQ...T.T.............E.KI.ME.
RetrocopyVDYSVSKKLRRRKIQIRNIPPHLQWEVLDGLLAQYGTVENVEQQ>STQTQKPLLSTSHM-QQEKKIDMER
ParentalLSGHQFENYSFKISYIPDEEVSSPSPPQRAQRGDHSSR-EQGHAPGGTSQARQIDFPLRILVP--TQFVG
LSGHQFEN.SFKISYIPDEEVSSPSPPQRAQRGDHSSR.EQGH.PGG.S.ARQIDF.L..LVP...QFVG
RetrocopyLSGHQFEN*SFKISYIPDEEVSSPSPPQRAQRGDHSSR>EQGHDPGGAS*ARQIDFLLQVLVPYSLQFVG
ParentalAIIGKEGLTIKNITKQTQSRVDIHRKENSGAAEKPVTIHATPEGTSEACRMILEIMQKEADETKLAEEIP
AII.KEGLTIKNITK.TQSR.DIHRKENSGAAEKPVTIHATP.GTSEAC.MILEIMQKEADE.KLAEEIP
RetrocopyAIIRKEGLTIKNITK*TQSRIDIHRKENSGAAEKPVTIHATPGGTSEACLMILEIMQKEADENKLAEEIP
ParentalLKILAHNGLVGRLIGKEGRNLKKIEHETGTKITISSLQDLSIYNPERTITVKGTV-EACASAEIEIMKKL
LKILAHNG....L.GKEGRNLKKIEHETGTKI.ISSLQDLSI.N.ER.ITVKGTV.EACASAEIEIMKKL
RetrocopyLKILAHNG----LVGKEGRNLKKIEHETGTKIAISSLQDLSINNQERIITVKGTV>EACASAEIEIMKKL
ParentalREAFENDMLAVNTHSGYFSSLYPHHQFGPFPHHHSYPEQEIVNLFIPTQAVGAIIGKKGAHIKQLARFAG
RE.FENDMLAVNTHSGYFSSLYPHHQ.GPFPHHHSYPEQE.VNLFIPTQAVGAII.K.GAHIKQLARFA.
RetrocopyRETFENDMLAVNTHSGYFSSLYPHHQVGPFPHHHSYPEQEVVNLFIPTQAVGAIIRKRGAHIKQLARFAT
ParentalASIKIAPAEGPDVSERMVIITGPPEAQFKAQGRIFGKLKEENFFNPKEEVKLEAHIRVPSSTAGRVIGKG
ASIKIA.AEGPDV.ERMVIIT.PPEAQFKAQGRIFGKLKEENFFNPKEEVKLEA.IRVPSSTAGRVIGKG
RetrocopyASIKIALAEGPDVNERMVIITRPPEAQFKAQGRIFGKLKEENFFNPKEEVKLEARIRVPSSTAGRVIGKG
ParentalGKTVNELQNLTSAEVIVPRDQTPDENEEVIVRIIGHFFASQTAQRKIREIVQQVKQQEQKYPQGVASQRS
..T.NELQNLTSAEVIVPRDQ.PDENEEVIVRIIGHFFA..TA..KIRE.VQQVKQQEQKYPQGVASQ.S
RetrocopyVNTLNELQNLTSAEVIVPRDQRPDENEEVIVRIIGHFFATPTA*HKIRETVQQVKQQEQKYPQGVASQHS
ParentalK
K
RetrocopyK

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 28 .41 RPM
bodymap2_adrenal 0 .00 RPM 4 .30 RPM
bodymap2_brain 0 .02 RPM 0 .38 RPM
bodymap2_breast 0 .08 RPM 5 .84 RPM
bodymap2_colon 0 .00 RPM 17 .25 RPM
bodymap2_heart 0 .00 RPM 19 .86 RPM
bodymap2_kidney 0 .00 RPM 17 .16 RPM
bodymap2_liver 0 .06 RPM 1 .86 RPM
bodymap2_lung 0 .42 RPM 56 .10 RPM
bodymap2_lymph_node 0 .00 RPM 10 .84 RPM
bodymap2_ovary 0 .00 RPM 8 .67 RPM
bodymap2_prostate 0 .00 RPM 7 .62 RPM
bodymap2_skeletal_muscle 0 .00 RPM 2 .46 RPM
bodymap2_testis 0 .09 RPM 18 .99 RPM
bodymap2_thyroid 0 .00 RPM 12 .30 RPM
bodymap2_white_blood_cells 0 .00 RPM 7 .80 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_216 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_216 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_216 retrocopy 5' end.

Lab - click to see more details

retro_hsap_216 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_216 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 6 parental genes, and 12 retrocopies.

Species Parental gene accession Retrocopies number
Homo sapiens ENSG00000073792 2 retrocopies
retro_hsap_216 , retro_hsap_4096,
Homo sapiens ENSG000001362311 retrocopy
retro_hsap_3690,
Gorilla gorilla ENSGGOG000000150352 retrocopies
retro_ggor_2679, retro_ggor_2748,
Myotis lucifugus ENSMLUG000000026311 retrocopy
retro_mluc_599,
Macaca mulatta ENSMMUG000000234163 retrocopies
retro_mmul_2361, retro_mmul_409, retro_mmul_530,
Pongo abelii ENSPPYG000000143733 retrocopies
retro_pabe_1723, retro_pabe_281, retro_pabe_837,

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 = 1.33 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .02 RPM
CEU_NA11843 0 .00 RPM
CEU_NA11930 0 .00 RPM
CEU_NA12004 0 .00 RPM
CEU_NA12400 0 .04 RPM
CEU_NA12751 0 .05 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 .03 RPM
FIN_HG00321 0 .06 RPM
FIN_HG00328 0 .02 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 .02 RPM
GBR_HG00114 0 .00 RPM
GBR_HG00119 0 .05 RPM
GBR_HG00131 0 .03 RPM
GBR_HG00133 0 .05 RPM
GBR_HG00134 0 .02 RPM
GBR_HG00137 0 .00 RPM
GBR_HG00142 0 .00 RPM
GBR_HG00143 0 .00 RPM
TSI_NA20512 0 .03 RPM
TSI_NA20513 1 .33 RPM
TSI_NA20518 0 .19 RPM
TSI_NA20532 0 .00 RPM
TSI_NA20538 0 .00 RPM
TSI_NA20756 0 .00 RPM
TSI_NA20765 0 .04 RPM
TSI_NA20771 0 .06 RPM
TSI_NA20786 0 .26 RPM
TSI_NA20798 0 .09 RPM
YRI_NA18870 0 .00 RPM
YRI_NA18907 0 .00 RPM
YRI_NA18916 0 .02 RPM
YRI_NA19093 0 .03 RPM
YRI_NA19099 0 .00 RPM
YRI_NA19114 0 .03 RPM
YRI_NA19118 0 .00 RPM
YRI_NA19213 0 .00 RPM
YRI_NA19214 0 .00 RPM
YRI_NA19223 0 .06 RPM

Indel association:

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



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