RetrogeneDB ID:

retro_hsap_3370

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:5:114624729..114625026(-)
Located in intron of:ENSG00000164221
Retrocopy
information
Ensembl ID:ENSG00000250197
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:HMGN1
Ensembl ID:ENSG00000205581
Aliases:HMGN1, HMG14
Description:high mobility group nucleosome binding domain 1 [Source:HGNC Symbol;Acc:4984]


Retrocopy-Parental alignment summary:






>retro_hsap_3370
CCCAAGTGGAAAGTCAGCTCAGCAGAAGGGGAAGTGAAGGAAGAGCCCAAGAGGAGATTCTTGCAATTGTCATCTAAACC
TGCTCCTACAAAAGCAGAAATGAAGCCAAAAAAGGCAGTCATGAAAGGATAAATCTTCAGACACAAAGTGCAAACCGAAG
GGAAAAGGAGAACAAAAGGAAAACTGGCCAAAGTGGCTAACCAATAAACTAAAGAAGACTTATCTGCAGAAAACAAAGAA
ACTAAAACCAAAGAGGGTCCTGCCTTTGATGAAGGCTGAGGGAAAGAAGCCAAGTCT

ORF - retro_hsap_3370 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 70.3 %
Parental protein coverage: 98. %
Number of stop codons detected: 2
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalPKRKVSSAEGAAKEEPKRRSARLSAKP-PAKVEAKPKKAAA-KDKSSD-KKVQTKGKRGAKGKQAEVANQ
PK.KVSSAEG..KEEPKRR...LS.KP.P.K.E.KPKKA...KDKSSD..KVQT.GKR..KGK.A.VANQ
RetrocopyPKWKVSSAEGEVKEEPKRRFLQLSSKPAPTKAEMKPKKAVM>KDKSSD<HKVQTEGKRRTKGKLAKVANQ
ParentalETKEDLPAENGETKTEESPASDEAGEKEAKS
.TKEDL.AEN.ETKT.E.PA.DE...KEAKS
Retrocopy*TKEDLSAENKETKTKEGPAFDEG*GKEAKS

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 62 .20 RPM
bodymap2_adrenal 0 .04 RPM 100 .83 RPM
bodymap2_brain 0 .19 RPM 28 .88 RPM
bodymap2_breast 0 .00 RPM 67 .18 RPM
bodymap2_colon 0 .00 RPM 68 .29 RPM
bodymap2_heart 0 .00 RPM 23 .08 RPM
bodymap2_kidney 0 .00 RPM 94 .80 RPM
bodymap2_liver 0 .00 RPM 31 .52 RPM
bodymap2_lung 0 .00 RPM 105 .05 RPM
bodymap2_lymph_node 0 .00 RPM 69 .48 RPM
bodymap2_ovary 0 .06 RPM 151 .40 RPM
bodymap2_prostate 0 .07 RPM 88 .92 RPM
bodymap2_skeletal_muscle 0 .00 RPM 6 .15 RPM
bodymap2_testis 0 .02 RPM 75 .70 RPM
bodymap2_thyroid 0 .00 RPM 114 .83 RPM
bodymap2_white_blood_cells 0 .14 RPM 99 .29 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_3370 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_3370 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_3370 retrocopy 5' end.

Lab - click to see more details

retro_hsap_3370 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_3370 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_2290
Pongo abelii retro_pabe_2771
Parental genes homology:
Parental genes homology involve 9 parental genes, and 129 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG0000001410011 retrocopies
retro_amel_1103, retro_amel_1157, retro_amel_1307, retro_amel_1378, retro_amel_1580, retro_amel_1839, retro_amel_349, retro_amel_352, retro_amel_408, retro_amel_439, retro_amel_670,
Bos taurus ENSBTAG0000001876812 retrocopies
retro_btau_1178, retro_btau_1475, retro_btau_1560, retro_btau_1746, retro_btau_1801, retro_btau_388, retro_btau_504, retro_btau_572, retro_btau_607, retro_btau_617, retro_btau_897, retro_btau_928,
Cavia porcellus ENSCPOG000000023367 retrocopies
retro_cpor_1129, retro_cpor_1389, retro_cpor_334, retro_cpor_349, retro_cpor_4, retro_cpor_884, retro_cpor_949,
Equus caballus ENSECAG000000190295 retrocopies
retro_ecab_1130, retro_ecab_285, retro_ecab_362, retro_ecab_800, retro_ecab_848,
Homo sapiens ENSG00000205581 7 retrocopies
retro_hsap_1097, retro_hsap_1418, retro_hsap_1581, retro_hsap_1758, retro_hsap_1874, retro_hsap_3370 , retro_hsap_762,
Monodelphis domestica ENSMODG000000209725 retrocopies
retro_mdom_1085, retro_mdom_109, retro_mdom_284, retro_mdom_755, retro_mdom_88,
Otolemur garnettii ENSOGAG0000001032935 retrocopies
retro_ogar_1062, retro_ogar_1186, retro_ogar_1245, retro_ogar_1304, retro_ogar_1355, retro_ogar_1437, retro_ogar_1527, retro_ogar_1529, retro_ogar_175, retro_ogar_1812, retro_ogar_1901, retro_ogar_1932, retro_ogar_2057, retro_ogar_2311, retro_ogar_2325, retro_ogar_2522, retro_ogar_2523, retro_ogar_266, retro_ogar_2712, retro_ogar_2729, retro_ogar_278, retro_ogar_2913, retro_ogar_2964, retro_ogar_3095, retro_ogar_3133, retro_ogar_3138, retro_ogar_3155, retro_ogar_333, retro_ogar_3354, retro_ogar_370, retro_ogar_393, retro_ogar_657, retro_ogar_699, retro_ogar_723, retro_ogar_958,
Pongo abelii ENSPPYG0000001142625 retrocopies
retro_pabe_1066, retro_pabe_1149, retro_pabe_1172, retro_pabe_1190, retro_pabe_123, retro_pabe_1264, retro_pabe_1302, retro_pabe_1504, retro_pabe_1604, retro_pabe_1842, retro_pabe_2152, retro_pabe_2211, retro_pabe_2284, retro_pabe_2380, retro_pabe_251, retro_pabe_2518, retro_pabe_2771, retro_pabe_3086, retro_pabe_3648, retro_pabe_3825, retro_pabe_504, retro_pabe_698, retro_pabe_699, retro_pabe_702, retro_pabe_760,
Pan troglodytes ENSPTRG0000003142622 retrocopies
retro_ptro_1256, retro_ptro_1299, retro_ptro_1301, retro_ptro_1454, retro_ptro_1556, retro_ptro_1740, retro_ptro_1821, retro_ptro_1830, retro_ptro_2058, retro_ptro_2290, retro_ptro_2559, retro_ptro_2716, retro_ptro_3119, retro_ptro_3278, retro_ptro_363, retro_ptro_463, retro_ptro_586, retro_ptro_61, retro_ptro_637, retro_ptro_696, retro_ptro_970, retro_ptro_980,

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 = 0.1 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .00 RPM
CEU_NA11843 0 .00 RPM
CEU_NA11930 0 .07 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 .03 RPM
FIN_HG00183 0 .00 RPM
FIN_HG00277 0 .04 RPM
FIN_HG00315 0 .03 RPM
FIN_HG00321 0 .03 RPM
FIN_HG00328 0 .00 RPM
FIN_HG00338 0 .00 RPM
FIN_HG00349 0 .00 RPM
FIN_HG00375 0 .02 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 .05 RPM
GBR_HG00131 0 .06 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 .10 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 .03 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 .04 RPM

Indel association:

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





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