RetrogeneDB ID:

retro_hsap_3663

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:6:133189473..133189955(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000220557
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:HMGB2
Ensembl ID:ENSG00000164104
Aliases:None
Description:high mobility group box 2 [Source:HGNC Symbol;Acc:5000]


Retrocopy-Parental alignment summary:






>retro_hsap_3663
CACAGCATTCTTGTGCAAACTTGTCGGGAGGAGCACAAGAAGCAGCACAAAGATGCTTCGGTCAATTTCTCAGAATTTTC
TAAGACGTGCTCAGAGAGGTGGAAGACCATGTCTGCTAAAGAGAAAAGAAAAATGTGAAGATATGGCAGAGGCGGACAAG
GCCTGTTATGAAAGAGAAATGAGAACCTGTATCCCTTCTAAAGGGGAGATAAAAAAGAAGTTCAAGGATCCCAATGCACA
CAAGAGGCCTCCTTTGGCCTTTTTCTTGTTGTGTTCTAAGTATCACTAAAAAATCAAAGGAGAACATCCATCCTGGCCTA
TCCATTGGTGGTGTTGTGAAGAAGGTGGGAAATCTGTGGAACGACACAGCTGCAGATGACAAGCATCCTTAGGAAAAGAA
GGCTGTGAACCTGAAGAAAAAATATGAAAAGGATATTGCTCCACAACAAGCTAAAGGAAAACCTGAGGCAGTTAAAGAGG
GA

ORF - retro_hsap_3663 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 60.49 %
Parental protein coverage: 76.08 %
Number of stop codons detected: 1
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalYAFFVQTCREEHKKKHPDSSVNFAEFSKKCSERWKTMSAKEKSKF-EDMAKSDKARYDREMKNYVPPKGD
....VQTCREEHKK.H.D.SVNF.EFSK.CSERWKTMSAKEK.K..EDMA..DKA.Y.REM....P.KG.
RetrocopyHSILVQTCREEHKKQHKDASVNFSEFSKTCSERWKTMSAKEKRKM>EDMAEADKACYEREMRTCIPSKGE
ParentalKKGKKKDPNAPKRPPSA-FFLFCSEH-RPKIKSEHPGLSIGDTAKKLGEMWSEQSAKDKQPYEQKAAKLK
.K.K.KDPNA.KRPP.A.F.L....H........HPGLSIG...KK.G..W....A.DK.P.E.KA..LK
RetrocopyIKKKFKDPNAHKRPPLAFFLLCSKYH>KKSKENIHPGLSIGGVVKKVGNLWNDTAADDKHP*EKKAVNLK
ParentalEKYEKDIAAYRAKGKSEAGKKG
.KYEKDIA...AKGK.EA.K.G
RetrocopyKKYEKDIAPQQAKGKPEAVKEG

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 100 .50 RPM
bodymap2_adrenal 0 .00 RPM 44 .52 RPM
bodymap2_brain 0 .00 RPM 34 .97 RPM
bodymap2_breast 0 .00 RPM 34 .90 RPM
bodymap2_colon 0 .00 RPM 110 .08 RPM
bodymap2_heart 0 .00 RPM 23 .35 RPM
bodymap2_kidney 0 .00 RPM 35 .30 RPM
bodymap2_liver 0 .00 RPM 7 .10 RPM
bodymap2_lung 0 .00 RPM 70 .96 RPM
bodymap2_lymph_node 0 .00 RPM 78 .98 RPM
bodymap2_ovary 0 .00 RPM 66 .83 RPM
bodymap2_prostate 0 .00 RPM 80 .52 RPM
bodymap2_skeletal_muscle 0 .04 RPM 22 .17 RPM
bodymap2_testis 0 .00 RPM 114 .85 RPM
bodymap2_thyroid 0 .00 RPM 76 .85 RPM
bodymap2_white_blood_cells 0 .00 RPM 137 .44 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_3663 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_3663 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_3663 retrocopy 5' end.

Lab - click to see more details

retro_hsap_3663 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_3663 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_2484
Gorilla gorilla retro_ggor_2474
Pongo abelii retro_pabe_3005
Parental genes homology:
Parental genes homology involve 26 parental genes, and 135 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000151011 retrocopy
retro_btau_58,
Callithrix jacchus ENSCJAG000000051122 retrocopies
retro_cjac_2555, retro_cjac_832,
Cavia porcellus ENSCPOG000000035524 retrocopies
retro_cpor_1100, retro_cpor_604, retro_cpor_890, retro_cpor_980,
Dasypus novemcinctus ENSDNOG000000194404 retrocopies
retro_dnov_1142, retro_dnov_1457, retro_dnov_454, retro_dnov_532,
Erinaceus europaeus ENSEEUG000000122388 retrocopies
retro_eeur_118, retro_eeur_223, retro_eeur_345, retro_eeur_49, retro_eeur_54, retro_eeur_661, retro_eeur_702, retro_eeur_86,
Echinops telfairi ENSETEG000000103793 retrocopies
retro_etel_1474, retro_etel_1841, retro_etel_2023,
Echinops telfairi ENSETEG000000163791 retrocopy
retro_etel_414,
Felis catus ENSFCAG000000042182 retrocopies
retro_fcat_279, retro_fcat_52,
Homo sapiens ENSG000000299938 retrocopies
retro_hsap_1461, retro_hsap_1873, retro_hsap_2621, retro_hsap_3064, retro_hsap_3683, retro_hsap_4251, retro_hsap_4904, retro_hsap_627,
Homo sapiens ENSG00000164104 1 retrocopy
retro_hsap_3663 ,
Homo sapiens ENSG0000018940337 retrocopies
retro_hsap_1230, retro_hsap_1357, retro_hsap_1504, retro_hsap_1589, retro_hsap_1608, retro_hsap_176, retro_hsap_1832, retro_hsap_1954, retro_hsap_2103, retro_hsap_2192, retro_hsap_2219, retro_hsap_2228, retro_hsap_2340, retro_hsap_2490, retro_hsap_2552, retro_hsap_2613, retro_hsap_2660, retro_hsap_2858, retro_hsap_2947, retro_hsap_3317, retro_hsap_3340, retro_hsap_3592, retro_hsap_3615, retro_hsap_3666, retro_hsap_382, retro_hsap_3942, retro_hsap_4003, retro_hsap_4109, retro_hsap_4309, retro_hsap_4669, retro_hsap_470, retro_hsap_4738, retro_hsap_4832, retro_hsap_525, retro_hsap_554, retro_hsap_758, retro_hsap_933,
Gorilla gorilla ENSGGOG000000158821 retrocopy
retro_ggor_2474,
Loxodonta africana ENSLAFG000000104173 retrocopies
retro_lafr_1096, retro_lafr_1142, retro_lafr_595,
Macropus eugenii ENSMEUG000000022563 retrocopies
retro_meug_1920, retro_meug_1989, retro_meug_550,
Myotis lucifugus ENSMLUG000000263034 retrocopies
retro_mluc_1113, retro_mluc_1381, retro_mluc_1726, retro_mluc_2011,
Monodelphis domestica ENSMODG000000035273 retrocopies
retro_mdom_1160, retro_mdom_1919, retro_mdom_69,
Mustela putorius furoENSMPUG000000019199 retrocopies
retro_mputfur_1134, retro_mputfur_1167, retro_mputfur_1379, retro_mputfur_1475, retro_mputfur_1631, retro_mputfur_1633, retro_mputfur_1644, retro_mputfur_940, retro_mputfur_989,
Mus musculus ENSMUSG0000005471723 retrocopies
retro_mmus_1477, retro_mmus_1745, retro_mmus_1974, retro_mmus_1975, retro_mmus_2269, retro_mmus_2527, retro_mmus_2528, retro_mmus_2529, retro_mmus_2530, retro_mmus_2531, retro_mmus_2843, retro_mmus_2884, retro_mmus_3248, retro_mmus_3426, retro_mmus_461, retro_mmus_626, retro_mmus_642, retro_mmus_796, retro_mmus_861, retro_mmus_901, retro_mmus_902, retro_mmus_904, retro_mmus_905,
Nomascus leucogenys ENSNLEG000000066623 retrocopies
retro_nleu_113, retro_nleu_517, retro_nleu_550,
Oryctolagus cuniculus ENSOCUG000000000741 retrocopy
retro_ocun_1829,
Otolemur garnettii ENSOGAG000000171493 retrocopies
retro_ogar_3117, retro_ogar_3323, retro_ogar_3336,
Pongo abelii ENSPPYG000000152043 retrocopies
retro_pabe_297, retro_pabe_3005, retro_pabe_3380,
Pan troglodytes ENSPTRG000000165973 retrocopies
retro_ptro_19, retro_ptro_2484, retro_ptro_2789,
Rattus norvegicus ENSRNOG000000131672 retrocopies
retro_rnor_173, retro_rnor_54,
Ictidomys tridecemlineatus ENSSTOG000000239802 retrocopies
retro_itri_1720, retro_itri_880,
Tursiops truncatus ENSTTRG000000156501 retrocopy
retro_ttru_1640,

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 = 0.02 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 .00 RPM
CEU_NA12751 0 .00 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 .00 RPM
FIN_HG00321 0 .00 RPM
FIN_HG00328 0 .00 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 .02 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 .00 RPM
TSI_NA20756 0 .00 RPM
TSI_NA20765 0 .00 RPM
TSI_NA20771 0 .00 RPM
TSI_NA20786 0 .00 RPM
TSI_NA20798 0 .00 RPM
YRI_NA18870 0 .00 RPM
YRI_NA18907 0 .00 RPM
YRI_NA18916 0 .00 RPM
YRI_NA19093 0 .00 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 .00 RPM

Indel association:

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



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