RetrogeneDB ID:

retro_hsap_422

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:1:93112646..93113199(-)
Located in intron of:ENSG00000067208
Retrocopy
information
Ensembl ID:ENSG00000229992
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:HMGB3
Ensembl ID:ENSG00000269411
Aliases:None
Description:high mobility group box 3 [Source:HGNC Symbol;Acc:5004]


Retrocopy-Parental alignment summary:






>retro_hsap_422
ATGGCTAAAGGTGATCCCAAGAAACCAGAGGGAAAGGTGTCTGCTTATTCCTTCTTTGTGCAGACATGCAGAGAAGAACA
TAAGAGAAACCCAGAGGTCTCTGTCAATTTTGCAGAATTTTCCAAGAAGTGCTCTGAGAGGTGGAAGACAGTGTCTGGCA
AAGAGAATCCTAAATGTGGTGAAATGACAAAGGCAGATAAAGTATGCTATGCTTGGAAGGTGCAGGATTGTGAACCAGTT
AAGTGAGGCAAGAAGAAGGACCTTCATGTCTCCAAAAGAGACATGTCTGTATTCTTCCTGCACCGTTCAGAATTTCACCC
CAAGATCAAATCCACAAACCCTGGCATCTTTATTAGAGATGTAGCAAAAAAGCTGTGTGAGGTGTGGGATAACTTAAATG
TCAGTGAAAAGCAGCCTTGCATCACTAAGGCAGTGAAGCTGAGGGAGAAATACGAGAAGGATGTTGCTGACTTTAAGTCT
AACGGCAAGTCTGGTGCAAAGGGTCCTGCTTAAAGTTCCTTGGAAAAAGGTGGAAGAAGTAGTCAAAGAAGAT

ORF - retro_hsap_422 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 71.81 %
Parental protein coverage: 93.5 %
Number of stop codons detected: 1
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMAKGDPKKPKGKMSAYAFFVQTCREEHKKKNPEVPVNFAEFSKKCSERWKTMSGKEKSKFDEMAKADKVR
MAKGDPKKP.GK.SAY.FFVQTCREEHK..NPEV.VNFAEFSKKCSERWKT.SGKE..K..EM.KADKV.
RetrocopyMAKGDPKKPEGKVSAYSFFVQTCREEHKR-NPEVSVNFAEFSKKCSERWKTVSGKENPKCGEMTKADKVC
ParentalYDREMKDYGPAKGGKKKKDPNAPKRPPSGFFLFCSEFRPKIKSTNPGISIGDVAKKLGEMWNNLNDSEKQ
Y.....D..P.K.GKKK.D....KR..S.FFL..SEF.PKIKSTNPGI.I.DVAKKL.E.W.NLN.SEKQ
RetrocopyYAWKVQDCEPVK*GKKK-DLHVSKRDMSVFFLHRSEFHPKIKSTNPGIFIRDVAKKLCEVWDNLNVSEKQ
ParentalPYITKAAKLKEKYEKDVADYKSKGKFDGAKGPA-KVARKKVEEEDEEE
P.ITKA.KL.EKYEKDVAD.KS.GK..GAKGPA.KV..KKVEE...E.
RetrocopyPCITKAVKLREKYEKDVADFKSNGK-SGAKGPA>KVPWKKVEEVVKED

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 .06 RPM 0 .00 RPM
bodymap2_adrenal 0 .06 RPM 0 .00 RPM
bodymap2_brain 0 .09 RPM 0 .00 RPM
bodymap2_breast 0 .16 RPM 0 .00 RPM
bodymap2_colon 0 .00 RPM 0 .00 RPM
bodymap2_heart 0 .11 RPM 0 .00 RPM
bodymap2_kidney 0 .00 RPM 0 .00 RPM
bodymap2_liver 0 .00 RPM 0 .00 RPM
bodymap2_lung 0 .16 RPM 0 .00 RPM
bodymap2_lymph_node 0 .00 RPM 0 .00 RPM
bodymap2_ovary 0 .23 RPM 0 .00 RPM
bodymap2_prostate 0 .00 RPM 0 .00 RPM
bodymap2_skeletal_muscle 0 .00 RPM 0 .00 RPM
bodymap2_testis 0 .15 RPM 0 .00 RPM
bodymap2_thyroid 0 .00 RPM 0 .00 RPM
bodymap2_white_blood_cells 0 .00 RPM 0 .00 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_422 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_422 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_422 retrocopy 5' end.

Lab - click to see more details

retro_hsap_422 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_422 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Gorilla gorilla retro_ggor_414
Pongo abelii retro_pabe_297
Macaca mulatta retro_mmul_514
Parental genes homology:
Parental genes homology involve 1 parental gene, and 14 retrocopies.

Species Parental gene accession Retrocopies number
Homo sapiens ENSG00000269411 14 retrocopies
retro_hsap_1643, retro_hsap_1755, retro_hsap_193, retro_hsap_2135, retro_hsap_2473, retro_hsap_2475, retro_hsap_248, retro_hsap_3279, retro_hsap_3653, retro_hsap_3831, retro_hsap_422 , retro_hsap_4739, retro_hsap_734, retro_hsap_909,

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 = 0.06 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .00 RPM
CEU_NA11843 0 .00 RPM
CEU_NA11930 0 .03 RPM
CEU_NA12004 0 .04 RPM
CEU_NA12400 0 .00 RPM
CEU_NA12751 0 .05 RPM
CEU_NA12760 0 .00 RPM
CEU_NA12827 0 .05 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 .03 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 .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 .05 RPM
TSI_NA20756 0 .00 RPM
TSI_NA20765 0 .02 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 .00 RPM
YRI_NA19093 0 .03 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 .06 RPM

Indel association:

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



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