RetrogeneDB ID:

retro_hsap_3088

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:4:121817272..121817804(-)
Located in intron of:ENSG00000138738
Retrocopy
information
Ensembl ID:ENSG00000251609
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:SET
Ensembl ID:ENSG00000119335
Aliases:SET, 2PP2A, I2PP2A, IGAAD, IPP2A2, PHAPII, TAF-I, TAF-IBETA
Description:SET nuclear oncogene [Source:HGNC Symbol;Acc:10760]


Retrocopy-Parental alignment summary:






>retro_hsap_3088
AAGCACAGGGATGTTGCACAAATTGAAATAGACAGACTTTACAAACAAGCCAGTGAGGAAATTTCCAAAGTAGAACAAAA
ATGTAACAAACTTCAAACTATTTAAAAGAGGTTGTAATTGATCTCCTGAATTTCAAATTTAGAGGTACTGTTAATCAACT
ATGTGCAAGTGACTTCCCTGCTTGAAATGCGAATGAAGAGATGCTGTGCTATCTCTTTAGAATGAAAGTGACAGAATTTA
AAGATATTAAATGATATTATAGAATAGATTTTTATTTTGCTGAAAAACCTTATTTTAAAATAAAGTTCCTCGCAACAAAT
TTCATCTCAAGTAGAGTGGTGGCCCATCTTCAGTGTTGACTAAAGTTAAATGGGAATCTGAGAAGGACTTGATTAAATGA
TCATGTCAGAAGTAAAATAAAGCTGTCTAGAAGAGGAAGCATGAAAAATCTCAGGCCTTCTTCACTTGATTCACCAATGA
TTCTGATGCAGGTGCAGGTGAATTAAGAGAGCTCATCAAAGTTGCTCTTTGG

ORF - retro_hsap_3088 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 55.74 %
Parental protein coverage: 68.05 %
Number of stop codons detected: 9
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalEHIDEVQNEIDRLNEQASEEILKVEQKYNKLRQPFFQKRSELIAKIPNFWVTTFVNHPQVSALLG-EEDE
.H.D..Q.EIDRL..QASEEI.KVEQK.NKL......KR..LI..I.N..V....N..QV..LL.....E
RetrocopyKHRDVAQIEIDRLYKQASEEISKVEQKCNKLQT--I*KRL*LIS*ISNLEVL-LINYVQVTSLLE<NANE
ParentalEALHYLTRVEVTEFEDIKSGYRIDFYFDENPYFE-NKVLSKEFHLNESGDPSSKSTEIKWKSGKDLTKRS
E.L.YL.R..VTEF.DIK..YRIDFYF.E.PYF..NKV....FHL..SG.PSS..T..KW.S.KDL.K.S
RetrocopyEMLCYLFRMKVTEFKDIK*YYRIDFYFAEKPYFK<NKVPRNKFHLK*SGGPSSVLTKVKWESEKDLIK*S
ParentalSQTQNKASRKRQHEEPESFFTWFTDHSDAGADELGEVIKDDIW
.Q..NKA..KR.HE....FFT.FT..SDAGA.EL.E.IK...W
RetrocopyCQK*NKAV*KRKHEKSQAFFT*FTNDSDAGAGELRELIKVALW

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 278 .75 RPM
bodymap2_adrenal 0 .06 RPM 304 .11 RPM
bodymap2_brain 0 .00 RPM 228 .68 RPM
bodymap2_breast 0 .00 RPM 196 .89 RPM
bodymap2_colon 0 .00 RPM 411 .87 RPM
bodymap2_heart 0 .09 RPM 153 .49 RPM
bodymap2_kidney 0 .00 RPM 226 .29 RPM
bodymap2_liver 0 .00 RPM 103 .30 RPM
bodymap2_lung 0 .00 RPM 285 .23 RPM
bodymap2_lymph_node 0 .00 RPM 229 .77 RPM
bodymap2_ovary 0 .19 RPM 454 .22 RPM
bodymap2_prostate 0 .00 RPM 279 .46 RPM
bodymap2_skeletal_muscle 0 .00 RPM 293 .35 RPM
bodymap2_testis 0 .00 RPM 324 .90 RPM
bodymap2_thyroid 0 .13 RPM 345 .95 RPM
bodymap2_white_blood_cells 0 .00 RPM 357 .77 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_3088 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_3088 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_3088 retrocopy 5' end.

Lab - click to see more details

retro_hsap_3088 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_3088 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_2085
Pongo abelii retro_pabe_2557
Equus caballus retro_ecab_505
Parental genes homology:
Parental genes homology involve 13 parental genes, and 117 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000156867 retrocopies
retro_amel_1093, retro_amel_1201, retro_amel_1459, retro_amel_1675, retro_amel_530, retro_amel_631, retro_amel_634,
Bos taurus ENSBTAG000000209598 retrocopies
retro_btau_1179, retro_btau_1490, retro_btau_1519, retro_btau_1556, retro_btau_464, retro_btau_469, retro_btau_749, retro_btau_955,
Canis familiaris ENSCAFG000000327282 retrocopies
retro_cfam_47, retro_cfam_83,
Felis catus ENSFCAG000000058482 retrocopies
retro_fcat_130, retro_fcat_89,
Homo sapiens ENSG00000119335 14 retrocopies
retro_hsap_1336, retro_hsap_1389, retro_hsap_1847, retro_hsap_241, retro_hsap_269, retro_hsap_2719, retro_hsap_2721, retro_hsap_3075, retro_hsap_3088 , retro_hsap_3326, retro_hsap_3358, retro_hsap_420, retro_hsap_4722, retro_hsap_806,
Myotis lucifugus ENSMLUG0000001429113 retrocopies
retro_mluc_1026, retro_mluc_1120, retro_mluc_1673, retro_mluc_1977, retro_mluc_2098, retro_mluc_2188, retro_mluc_2361, retro_mluc_2412, retro_mluc_2584, retro_mluc_419, retro_mluc_524, retro_mluc_855, retro_mluc_881,
Macaca mulatta ENSMMUG0000000853211 retrocopies
retro_mmul_1133, retro_mmul_1261, retro_mmul_1534, retro_mmul_2096, retro_mmul_2175, retro_mmul_2241, retro_mmul_2262, retro_mmul_2614, retro_mmul_362, retro_mmul_419, retro_mmul_569,
Mustela putorius furoENSMPUG0000001306910 retrocopies
retro_mputfur_1330, retro_mputfur_1556, retro_mputfur_1581, retro_mputfur_1605, retro_mputfur_221, retro_mputfur_274, retro_mputfur_286, retro_mputfur_723, retro_mputfur_785, retro_mputfur_799,
Nomascus leucogenys ENSNLEG000000175952 retrocopies
retro_nleu_108, retro_nleu_870,
Oryctolagus cuniculus ENSOCUG0000000750112 retrocopies
retro_ocun_1107, retro_ocun_1110, retro_ocun_1234, retro_ocun_1311, retro_ocun_1563, retro_ocun_276, retro_ocun_407, retro_ocun_421, retro_ocun_423, retro_ocun_476, retro_ocun_859, retro_ocun_923,
Otolemur garnettii ENSOGAG0000000763513 retrocopies
retro_ogar_115, retro_ogar_1370, retro_ogar_3084, retro_ogar_3186, retro_ogar_3195, retro_ogar_3289, retro_ogar_447, retro_ogar_465, retro_ogar_543, retro_ogar_565, retro_ogar_806, retro_ogar_899, retro_ogar_934,
Pongo abelii ENSPPYG0000001965917 retrocopies
retro_pabe_1076, retro_pabe_1110, retro_pabe_1150, retro_pabe_1218, retro_pabe_1452, retro_pabe_1717, retro_pabe_1771, retro_pabe_2549, retro_pabe_2557, retro_pabe_2740, retro_pabe_299, retro_pabe_3667, retro_pabe_400, retro_pabe_414, retro_pabe_470, retro_pabe_720, retro_pabe_838,
Ictidomys tridecemlineatus ENSSTOG000000105466 retrocopies
retro_itri_1204, retro_itri_1588, retro_itri_477, retro_itri_529, retro_itri_603, retro_itri_876,

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 = 0.03 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 .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 .03 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 .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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