RetrogeneDB ID:

retro_hsap_3750

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:7:74619884..74620426(+)
Located in intron of:ENSG00000232561
Retrocopy
information
Ensembl ID:ENSG00000223981
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:PHB
Ensembl ID:ENSG00000167085
Aliases:PHB, HEL-215, HEL-S-54e, PHB1
Description:prohibitin [Source:HGNC Symbol;Acc:8912]


Retrocopy-Parental alignment summary:






>retro_hsap_3750
GTCACCATCACACTGGGCGTCCTCTTCCCGCCTTGTTGCTGGCCAGGTCCTTGCATCTTCCAATTACTGGAGAAGCCAAT
GAAGAATGTGCTGCCATCCATCACTGCGGAGCTCCTCAAGCTGGGGGCGGCTCAGGCTGACGCTGGAGAACTGATCACGC
AGGGAGAGCTGGGCTCCAGACAGGTGAGCAATTAACTTCGGAGCAAGCAGCAACCTTTGGGTTCCTCCTGGATGCTGTGA
CCTTGGATCTGACCTTCGGGAAGGAATTTGCAGAAGCAGTGGAACCAAAGAGGTGGCTCAGCAGGAAGAAGAGAGGGCCA
GATCTGTGGTGGCAAGGGCTGAGCAGCAGAAGACGGCGGCCATCATCTCTGCCGAGGGCGACTCCAAGGCCACGGAGTTC
ATCGCCAGCTCAGTGGCCACCGCAGGTGACGGCCTGATCAAGCCCACAAGCTGGAACCATGGAGGACACTGTACCGGCCC
TCCAGCTCTCAGAACTCATCCACCTGCCCGTGGGGACATCTGTGCTCCTCCAGCTGCCCCAG

ORF - retro_hsap_3750 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 61.9 %
Parental protein coverage: 68.01 %
Number of stop codons detected: 1
Number of frameshifts detected 4


Retrocopy - Parental Gene Alignment:

ParentalVNITLRILFRPVASQLPRIFTSIGEDYDERVLPSITTEILKSVVARFDAGELITQRELVSRQVSDDL-TE
V.ITL..LF.P.....P.IF....E.....VLPSIT.E.LK...A..DAGELITQ.EL.SRQVS..L..E
RetrocopyVTITLGVLFPPCCWPGPCIFQLL-EKPMKNVLPSITAELLKLGAAQADAGELITQGELGSRQVSN*L<SE
ParentalRAATFGLILDDVSLTHLTFGKEFTEAVE-AKQVAQQEAERARFVVEKAEQQKKAAIISAEGDSKAAELIA
.AATFG..LD.V.L..LTFGKEF.EAVE..K.VAQQE.ERAR.VV..AEQQK.AAIISAEGDSKA.E.IA
RetrocopyQAATFGFLLDAVTLD-LTFGKEFAEAVE<TKEVAQQEEERARSVVARAEQQKTAAIISAEGDSKATEFIA
ParentalNSLATAGDGLI-ELRKLEAAEDIAYQLSRSRN-ITYLPAGQSVLLQLPQ
.S.ATAGDGLI....KLE......Y..S.S.N....LP.G.SVLLQLPQ
RetrocopySSVATAGDGLI<QAHKLEPWRTL-YRPSSSQN<LIHLPVGTSVLLQLPQ

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 39 .46 RPM
bodymap2_adrenal 0 .00 RPM 52 .03 RPM
bodymap2_brain 0 .00 RPM 22 .36 RPM
bodymap2_breast 0 .00 RPM 45 .64 RPM
bodymap2_colon 0 .00 RPM 47 .41 RPM
bodymap2_heart 0 .00 RPM 35 .91 RPM
bodymap2_kidney 0 .00 RPM 68 .45 RPM
bodymap2_liver 0 .00 RPM 35 .78 RPM
bodymap2_lung 0 .00 RPM 25 .91 RPM
bodymap2_lymph_node 0 .00 RPM 30 .64 RPM
bodymap2_ovary 0 .00 RPM 45 .03 RPM
bodymap2_prostate 0 .00 RPM 46 .63 RPM
bodymap2_skeletal_muscle 0 .00 RPM 28 .39 RPM
bodymap2_testis 0 .00 RPM 34 .60 RPM
bodymap2_thyroid 0 .00 RPM 65 .33 RPM
bodymap2_white_blood_cells 0 .00 RPM 25 .44 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_3750 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_3750 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_3750 retrocopy 5' end.

Lab - click to see more details

retro_hsap_3750 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_3750 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 23 parental genes, and 152 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000047971 retrocopy
retro_acar_49,
Ailuropoda melanoleuca ENSAMEG000000123641 retrocopy
retro_amel_258,
Bos taurus ENSBTAG000000171201 retrocopy
retro_btau_481,
Canis familiaris ENSCAFG000000169261 retrocopy
retro_cfam_202,
Choloepus hoffmanni ENSCHOG000000075882 retrocopies
retro_chof_1159, retro_chof_2193,
Callithrix jacchus ENSCJAG0000000717422 retrocopies
retro_cjac_1048, retro_cjac_1403, retro_cjac_1683, retro_cjac_1761, retro_cjac_1820, retro_cjac_2261, retro_cjac_2389, retro_cjac_2390, retro_cjac_2391, retro_cjac_2445, retro_cjac_2523, retro_cjac_2659, retro_cjac_2663, retro_cjac_2909, retro_cjac_4205, retro_cjac_570, retro_cjac_635, retro_cjac_662, retro_cjac_872, retro_cjac_937, retro_cjac_966, retro_cjac_980,
Erinaceus europaeus ENSEEUG000000064813 retrocopies
retro_eeur_219, retro_eeur_285, retro_eeur_369,
Homo sapiens ENSG00000167085 15 retrocopies
retro_hsap_1113, retro_hsap_1514, retro_hsap_161, retro_hsap_1640, retro_hsap_2170, retro_hsap_2692, retro_hsap_3534, retro_hsap_3750 , retro_hsap_3868, retro_hsap_3869, retro_hsap_4186, retro_hsap_4888, retro_hsap_517, retro_hsap_617, retro_hsap_776,
Gorilla gorilla ENSGGOG0000002800212 retrocopies
retro_ggor_124, retro_ggor_1722, retro_ggor_1876, retro_ggor_238, retro_ggor_2387, retro_ggor_246, retro_ggor_2607, retro_ggor_3053, retro_ggor_476, retro_ggor_643, retro_ggor_741, retro_ggor_870,
Macropus eugenii ENSMEUG000000051221 retrocopy
retro_meug_708,
Microcebus murinus ENSMICG000000069669 retrocopies
retro_mmur_1097, retro_mmur_1297, retro_mmur_1374, retro_mmur_1426, retro_mmur_1483, retro_mmur_1537, retro_mmur_1626, retro_mmur_62, retro_mmur_881,
Myotis lucifugus ENSMLUG000000082032 retrocopies
retro_mluc_116, retro_mluc_2190,
Macaca mulatta ENSMMUG0000000015613 retrocopies
retro_mmul_1096, retro_mmul_1119, retro_mmul_1165, retro_mmul_1425, retro_mmul_151, retro_mmul_1565, retro_mmul_2148, retro_mmul_2420, retro_mmul_426, retro_mmul_521, retro_mmul_834, retro_mmul_866, retro_mmul_933,
Monodelphis domestica ENSMODG000000122101 retrocopy
retro_mdom_812,
Nomascus leucogenys ENSNLEG0000000297813 retrocopies
retro_nleu_1190, retro_nleu_1254, retro_nleu_1326, retro_nleu_1557, retro_nleu_1755, retro_nleu_1796, retro_nleu_1874, retro_nleu_191, retro_nleu_195, retro_nleu_2547, retro_nleu_2573, retro_nleu_402, retro_nleu_444,
Oryctolagus cuniculus ENSOCUG000000072091 retrocopy
retro_ocun_579,
Otolemur garnettii ENSOGAG000000270151 retrocopy
retro_ogar_968,
Ochotona princeps ENSOPRG000000008682 retrocopies
retro_opri_180, retro_opri_734,
Procavia capensis ENSPCAG000000088511 retrocopy
retro_pcap_74,
Pongo abelii ENSPPYG0000000892016 retrocopies
retro_pabe_1262, retro_pabe_1357, retro_pabe_1409, retro_pabe_1770, retro_pabe_2291, retro_pabe_289, retro_pabe_3030, retro_pabe_3034, retro_pabe_3426, retro_pabe_3427, retro_pabe_3800, retro_pabe_552, retro_pabe_753, retro_pabe_922, retro_pabe_925, retro_pabe_977,
Pan troglodytes ENSPTRG0000000937614 retrocopies
retro_ptro_1025, retro_ptro_1110, retro_ptro_154, retro_ptro_1656, retro_ptro_1817, retro_ptro_2401, retro_ptro_2545, retro_ptro_2841, retro_ptro_2964, retro_ptro_3256, retro_ptro_386, retro_ptro_451, retro_ptro_542, retro_ptro_686,
Rattus norvegicus ENSRNOG0000004679918 retrocopies
retro_rnor_1058, retro_rnor_1416, retro_rnor_1540, retro_rnor_1542, retro_rnor_2398, retro_rnor_2399, retro_rnor_2610, retro_rnor_2653, retro_rnor_2815, retro_rnor_2826, retro_rnor_2848, retro_rnor_2855, retro_rnor_2909, retro_rnor_292, retro_rnor_2948, retro_rnor_2949, retro_rnor_543, retro_rnor_898,
Ictidomys tridecemlineatus ENSSTOG000000199292 retrocopies
retro_itri_337, retro_itri_945,

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 .03 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 .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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