RetrogeneDB ID:

retro_hsap_3896

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:7:121597117..121597373(-)
Located in intron of:ENSG00000106278
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:HMGN2
Ensembl ID:ENSG00000198830
Aliases:None
Description:high mobility group nucleosomal binding domain 2 [Source:HGNC Symbol;Acc:4986]


Retrocopy-Parental alignment summary:






>retro_hsap_3896
ATGCCCAAGAGAAAGGCTGAAGGGGATGCGAAAGGAGATACAGCCAAAGTGAAGGATGAACCACAGAGAAGATCCGCGAG
ATTGTCTGCTAAACCTGCTCCTCCAAAGCCAGAGCCCAGGCCTAAAAAGGCCCTGCAAAGAAGGGACAGAAGGTACCCAG
AGGGAAAAAGGGAAAAGATGATACTGGCAAGGAGGGGAATAACCCTGCAGAAATGGAGACCAGGCACAGAAAGCTGAAGG
TGCTGGAAATGCCAAG

ORF - retro_hsap_3896 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 85.87 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalMPKRKAEGDAKGDKAKVKDEPQRRSARLSAKPAPPKPEPKPKKA-PAKKGEKVPKGKKGKADAGKEGNNP
MPKRKAEGDAKGD.AKVKDEPQRRSARLSAKPAPPKPEP.PKKA.PAKKG.KVP.GKKGK.D.GKEGNNP
RetrocopyMPKRKAEGDAKGDTAKVKDEPQRRSARLSAKPAPPKPEPRPKKA<PAKKGQKVPRGKKGKDDTGKEGNNP
ParentalAE-NGDAKTDQAQKAEGAGDAK
AE.NGD....QAQKAEGAG.AK
RetrocopyAE<NGD----QAQKAEGAGNAK

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 96 .51 RPM
bodymap2_adrenal 0 .00 RPM 86 .18 RPM
bodymap2_brain 0 .00 RPM 48 .10 RPM
bodymap2_breast 0 .00 RPM 101 .62 RPM
bodymap2_colon 0 .00 RPM 110 .02 RPM
bodymap2_heart 0 .00 RPM 27 .21 RPM
bodymap2_kidney 0 .00 RPM 79 .95 RPM
bodymap2_liver 0 .00 RPM 24 .52 RPM
bodymap2_lung 0 .00 RPM 99 .30 RPM
bodymap2_lymph_node 0 .00 RPM 53 .10 RPM
bodymap2_ovary 0 .00 RPM 163 .04 RPM
bodymap2_prostate 0 .00 RPM 155 .86 RPM
bodymap2_skeletal_muscle 0 .00 RPM 80 .99 RPM
bodymap2_testis 0 .00 RPM 95 .68 RPM
bodymap2_thyroid 0 .00 RPM 157 .77 RPM
bodymap2_white_blood_cells 0 .00 RPM 182 .92 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_3896 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_3896 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_3896 retrocopy 5' end.

Lab - click to see more details

retro_hsap_3896 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_3896 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_2650
Parental genes homology:
Parental genes homology involve 8 parental genes, and 148 retrocopies.

Species Parental gene accession Retrocopies number
Felis catus ENSFCAG000000128123 retrocopies
retro_fcat_1842, retro_fcat_4, retro_fcat_530,
Homo sapiens ENSG00000198830 51 retrocopies
retro_hsap_100, retro_hsap_114, retro_hsap_1208, retro_hsap_1368, retro_hsap_1395, retro_hsap_1427, retro_hsap_1471, retro_hsap_1492, retro_hsap_1512, retro_hsap_1517, retro_hsap_1518, retro_hsap_1586, retro_hsap_1670, retro_hsap_1684, retro_hsap_1787, retro_hsap_1834, retro_hsap_1931, retro_hsap_1934, retro_hsap_2082, retro_hsap_2116, retro_hsap_2296, retro_hsap_2309, retro_hsap_233, retro_hsap_2564, retro_hsap_2592, retro_hsap_2728, retro_hsap_273, retro_hsap_2755, retro_hsap_2779, retro_hsap_2849, retro_hsap_2914, retro_hsap_318, retro_hsap_3189, retro_hsap_3339, retro_hsap_3372, retro_hsap_3412, retro_hsap_3515, retro_hsap_3616, retro_hsap_3755, retro_hsap_3896 , retro_hsap_4124, retro_hsap_4138, retro_hsap_4297, retro_hsap_4791, retro_hsap_4914, retro_hsap_601, retro_hsap_688, retro_hsap_689, retro_hsap_718, retro_hsap_793, retro_hsap_849,
Gorilla gorilla ENSGGOG0000000097111 retrocopies
retro_ggor_114, retro_ggor_146, retro_ggor_162, retro_ggor_166, retro_ggor_182, retro_ggor_186, retro_ggor_197, retro_ggor_23, retro_ggor_38, retro_ggor_40, retro_ggor_54,
Macropus eugenii ENSMEUG000000109668 retrocopies
retro_meug_1178, retro_meug_126, retro_meug_1859, retro_meug_1910, retro_meug_1997, retro_meug_248, retro_meug_369, retro_meug_76,
Mus musculus ENSMUSG000000030382 retrocopies
retro_mmus_202, retro_mmus_2582,
Otolemur garnettii ENSOGAG0000003257114 retrocopies
retro_ogar_1438, retro_ogar_1445, retro_ogar_1603, retro_ogar_1668, retro_ogar_1687, retro_ogar_1998, retro_ogar_2097, retro_ogar_2210, retro_ogar_2231, retro_ogar_2424, retro_ogar_287, retro_ogar_2989, retro_ogar_3411, retro_ogar_52,
Pan troglodytes ENSPTRG0000000038654 retrocopies
retro_ptro_1011, retro_ptro_1024, retro_ptro_1026, retro_ptro_1027, retro_ptro_1040, retro_ptro_1053, retro_ptro_1067, retro_ptro_1094, retro_ptro_1197, retro_ptro_1235, retro_ptro_128, retro_ptro_1291, retro_ptro_1292, retro_ptro_1495, retro_ptro_1516, retro_ptro_1532, retro_ptro_1549, retro_ptro_1625, retro_ptro_1633, retro_ptro_1837, retro_ptro_1844, retro_ptro_1863, retro_ptro_1880, retro_ptro_1929, retro_ptro_1970, retro_ptro_203, retro_ptro_2255, retro_ptro_229, retro_ptro_2292, retro_ptro_2317, retro_ptro_2387, retro_ptro_2445, retro_ptro_2461, retro_ptro_2549, retro_ptro_257, retro_ptro_2650, retro_ptro_2801, retro_ptro_2812, retro_ptro_2840, retro_ptro_2913, retro_ptro_2970, retro_ptro_3187, retro_ptro_3276, retro_ptro_445, retro_ptro_493, retro_ptro_495, retro_ptro_512, retro_ptro_543, retro_ptro_552, retro_ptro_59, retro_ptro_590, retro_ptro_827, retro_ptro_939, retro_ptro_958,
Tursiops truncatus ENSTTRG000000056815 retrocopies
retro_ttru_1392, retro_ttru_1443, retro_ttru_3, retro_ttru_345, retro_ttru_788,

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 = 0.05 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .00 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 .04 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 .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 .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 .05 RPM
TSI_NA20518 0 .00 RPM
TSI_NA20532 0 .00 RPM
TSI_NA20538 0 .05 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 .03 RPM
YRI_NA18916 0 .00 RPM
YRI_NA19093 0 .00 RPM
YRI_NA19099 0 .00 RPM
YRI_NA19114 0 .00 RPM
YRI_NA19118 0 .02 RPM
YRI_NA19213 0 .00 RPM
YRI_NA19214 0 .02 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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