RetrogeneDB ID:

retro_hsap_2478

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:20:37606543..37607065(-)
Located in intron of:ENSG00000101452
Retrocopy
information
Ensembl ID:ENSG00000223864
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:NPM1
Ensembl ID:ENSG00000181163
Aliases:NPM1, B23, NPM
Description:nucleophosmin (nucleolar phosphoprotein B23, numatrin) [Source:HGNC Symbol;Acc:7910]


Retrocopy-Parental alignment summary:






>retro_hsap_2478
ATGAAAGATGTGATGGACACGGACATGAGCCCTGTGAGGCCCCAGAACTATCTTTTTGGTTGTGAACTAAAGGCCATCAA
AGATGATCACTTTAAGGTGGATAATGATGAAGATGAGCACCAGTTATCTTTAAGAACGGTCAGCTCAGGGGCTGGTGCAA
AGGATGAATTGCACATTGTTGAAGCAGAGGCAATGAATTACGAAGGCAGTCCAATTAAAGTAACACTGGCAACTTTGAAA
ATGTCTGTACAGCCAATGATTTCCCTTAGGGGCTTTGAAATAATACCACCGGTGGTCTTACAGTTGAAGTGTGGCTCAGG
GCCAGTGCATATTAGTGGACAGCACTTAGTAGCTGTAGAGGAAGATGCAGAGTCAGAAGATGAAGAGGAAGAAGATGTGA
AATTCTTAAGTATATCTGGAAGGTGATCTGCCCCTGGAGGTGGTAGCAACGTTCCAGAGAAAAAAGTAAAACTTGCTGCT
GCTGCTAATGATGATGATTTTGATGATGAGGAAACTGAAGAA

ORF - retro_hsap_2478 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 77.59 %
Parental protein coverage: 59.18 %
Number of stop codons detected: 1
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMEDSMDMDMSPLRPQNYLFGCELKADKDYHFKVDNDENEHQLSLRTVSLGAGAKDELHIVEAEAMNYEGS
M.D.MD.DMSP.RPQNYLFGCELKA.KD.HFKVDNDE.EHQLSLRTVS.GAGAKDELHIVEAEAMNYEGS
RetrocopyMKDVMDTDMSPVRPQNYLFGCELKAIKDDHFKVDNDEDEHQLSLRTVSSGAGAKDELHIVEAEAMNYEGS
ParentalPIKVTLATLKMSVQPTVSLGGFEITPPVVLRLKCGSGPVHISGQHLVAVEEDAESEDEEEEDVKLLSISG
PIKVTLATLKMSVQP..SL.GFEI.PPVVL.LKCGSGPVHISGQHLVAVE.............K.LSISG
RetrocopyPIKVTLATLKMSVQPMISLRGFEIIPPVVLQLKCGSGPVHISGQHLVAVEXXXXXXXXXXXXXKFLSISG
ParentalKRSAPGGGSKVPQKKVKLAADEDDDDDDEEDDDE
..SAPGGGS.VP.KKVKLAA...DDD.D.E...E
RetrocopyR*SAPGGGSNVPEKKVKLAAAANDDDFDDEETEE

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 332 .62 RPM
bodymap2_adrenal 0 .04 RPM 422 .00 RPM
bodymap2_brain 0 .05 RPM 165 .16 RPM
bodymap2_breast 0 .00 RPM 239 .26 RPM
bodymap2_colon 0 .00 RPM 676 .89 RPM
bodymap2_heart 0 .00 RPM 159 .13 RPM
bodymap2_kidney 0 .00 RPM 255 .78 RPM
bodymap2_liver 0 .00 RPM 151 .05 RPM
bodymap2_lung 0 .00 RPM 383 .42 RPM
bodymap2_lymph_node 0 .00 RPM 324 .63 RPM
bodymap2_ovary 0 .08 RPM 913 .07 RPM
bodymap2_prostate 0 .02 RPM 560 .29 RPM
bodymap2_skeletal_muscle 0 .00 RPM 231 .70 RPM
bodymap2_testis 0 .00 RPM 446 .48 RPM
bodymap2_thyroid 0 .00 RPM 478 .22 RPM
bodymap2_white_blood_cells 0 .00 RPM 368 .83 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_2478 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_2478 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_2478 retrocopy 5' end.

Lab - click to see more details

retro_hsap_2478 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_2478 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Gorilla gorilla retro_ggor_1543
Callithrix jacchus retro_cjac_2605
Parental genes homology:
Parental genes homology involve 13 parental genes, and 93 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000039101 retrocopy
retro_amel_983,
Bos taurus ENSBTAG000000153162 retrocopies
retro_btau_538, retro_btau_56,
Canis familiaris ENSCAFG000000169123 retrocopies
retro_cfam_22, retro_cfam_286, retro_cfam_900,
Callithrix jacchus ENSCJAG0000001933413 retrocopies
retro_cjac_1559, retro_cjac_1682, retro_cjac_1696, retro_cjac_1733, retro_cjac_2075, retro_cjac_2351, retro_cjac_2368, retro_cjac_2533, retro_cjac_2605, retro_cjac_3270, retro_cjac_3416, retro_cjac_4117, retro_cjac_838,
Felis catus ENSFCAG000000302683 retrocopies
retro_fcat_156, retro_fcat_376, retro_fcat_720,
Homo sapiens ENSG000001078331 retrocopy
retro_hsap_792,
Homo sapiens ENSG00000181163 30 retrocopies
retro_hsap_1275, retro_hsap_129, retro_hsap_1526, retro_hsap_1580, retro_hsap_1593, retro_hsap_1621, retro_hsap_2226, retro_hsap_2375, retro_hsap_2478 , retro_hsap_2856, retro_hsap_2862, retro_hsap_3355, retro_hsap_3460, retro_hsap_3609, retro_hsap_3636, retro_hsap_3718, retro_hsap_3776, retro_hsap_3808, retro_hsap_3817, retro_hsap_3822, retro_hsap_3962, retro_hsap_4666, retro_hsap_4753, retro_hsap_4785, retro_hsap_614, retro_hsap_638, retro_hsap_690, retro_hsap_717, retro_hsap_785, retro_hsap_961,
Gorilla gorilla ENSGGOG0000000722012 retrocopies
retro_ggor_1543, retro_ggor_1660, retro_ggor_1976, retro_ggor_2453, retro_ggor_2454, retro_ggor_2539, retro_ggor_2559, retro_ggor_2571, retro_ggor_2681, retro_ggor_2959, retro_ggor_560, retro_ggor_591,
Macaca mulatta ENSMMUG000000157811 retrocopy
retro_mmul_203,
Mus musculus ENSMUSG000000571135 retrocopies
retro_mmus_1301, retro_mmus_1798, retro_mmus_3131, retro_mmus_539, retro_mmus_550,
Otolemur garnettii ENSOGAG0000001361614 retrocopies
retro_ogar_1554, retro_ogar_1623, retro_ogar_1671, retro_ogar_1776, retro_ogar_2015, retro_ogar_2168, retro_ogar_2207, retro_ogar_2461, retro_ogar_2605, retro_ogar_2832, retro_ogar_3037, retro_ogar_536, retro_ogar_595, retro_ogar_614,
Pongo abelii ENSPPYG000000160377 retrocopies
retro_pabe_2405, retro_pabe_3072, retro_pabe_3261, retro_pabe_3627, retro_pabe_3699, retro_pabe_486, retro_pabe_532,
Pteropus vampyrus ENSPVAG000000022111 retrocopy
retro_pvam_851,

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 = 0.13 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .00 RPM
CEU_NA11843 0 .03 RPM
CEU_NA11930 0 .07 RPM
CEU_NA12004 0 .11 RPM
CEU_NA12400 0 .07 RPM
CEU_NA12751 0 .02 RPM
CEU_NA12760 0 .00 RPM
CEU_NA12827 0 .05 RPM
CEU_NA12872 0 .05 RPM
CEU_NA12873 0 .06 RPM
FIN_HG00183 0 .03 RPM
FIN_HG00277 0 .11 RPM
FIN_HG00315 0 .00 RPM
FIN_HG00321 0 .09 RPM
FIN_HG00328 0 .02 RPM
FIN_HG00338 0 .02 RPM
FIN_HG00349 0 .09 RPM
FIN_HG00375 0 .02 RPM
FIN_HG00377 0 .03 RPM
FIN_HG00378 0 .13 RPM
GBR_HG00099 0 .03 RPM
GBR_HG00111 0 .00 RPM
GBR_HG00114 0 .03 RPM
GBR_HG00119 0 .10 RPM
GBR_HG00131 0 .11 RPM
GBR_HG00133 0 .05 RPM
GBR_HG00134 0 .04 RPM
GBR_HG00137 0 .00 RPM
GBR_HG00142 0 .06 RPM
GBR_HG00143 0 .06 RPM
TSI_NA20512 0 .03 RPM
TSI_NA20513 0 .05 RPM
TSI_NA20518 0 .03 RPM
TSI_NA20532 0 .03 RPM
TSI_NA20538 0 .05 RPM
TSI_NA20756 0 .03 RPM
TSI_NA20765 0 .08 RPM
TSI_NA20771 0 .00 RPM
TSI_NA20786 0 .00 RPM
TSI_NA20798 0 .00 RPM
YRI_NA18870 0 .03 RPM
YRI_NA18907 0 .03 RPM
YRI_NA18916 0 .08 RPM
YRI_NA19093 0 .03 RPM
YRI_NA19099 0 .00 RPM
YRI_NA19114 0 .03 RPM
YRI_NA19118 0 .00 RPM
YRI_NA19213 0 .02 RPM
YRI_NA19214 0 .02 RPM
YRI_NA19223 0 .08 RPM

Indel association:

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





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