RetrogeneDB ID:

retro_hsap_855

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:11:18511785..18512195(-)
Located in intron of:ENSG00000074319
Retrocopy
information
Ensembl ID:ENSG00000256464
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:YWHAB
Ensembl ID:ENSG00000166913
Aliases:YWHAB, GW128, HEL-S-1, HS1, KCIP-1, YWHAA
Description:tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, beta polypeptide [Source:HGNC Symbol;Acc:12849]


Retrocopy-Parental alignment summary:






>retro_hsap_855
TCTTGTTCTCAATTCTATACAACCATTTTCTATTTGAAAATGAAAGGAGATTATTTTAGGTATTTTTCTGAAGTGGCATC
TGGAGACAACAAACAAACCACTGTGTGGAATTCCCAGCAGGCTTACCAGGAAGCATTTGAAATTAGTAAGAAAGAAGAAA
TGCAGCCTACACATCCAGTTTGACTTGGTCTGGCACTTAATTTCTCAGTCTTTTACTATGAGATTCTAAACTCTACTGAA
AAGGCCTGCAGCCTGGCAAAAACAGTATTTGATGAAGCAATTACTGAATTGGATACACTGAATGAAGAGTCTTATAAAGA
CAGCACTCTGATCATGCAATTACTTGGGACAGTGTTACTCTGTGGACATCGGAAAACCAGGAAGATGAAGGAGATGCTGG
GGAGGGAGAG

ORF - retro_hsap_855 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 84.78 %
Parental protein coverage: 55.28 %
Number of stop codons detected: 1
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalNATQPESKVFYLKMKGDYFRYLSEVASGDNKQTTVSNSQQAYQEAFEISKKE-MQPTHPIRLGLALNFSV
...Q.....FYLKMKGDYFRY.SEVASGDNKQTTV.NSQQAYQEAFEISKKE.MQPTHP..LGLALNFSV
RetrocopySCSQFYTTIFYLKMKGDYFRYFSEVASGDNKQTTVWNSQQAYQEAFEISKKEEMQPTHPV*LGLALNFSV
ParentalFYYEILNSPEKACSLAKTAFDEAIAELDTLNEESYKDSTLIMQLLR-DNLTLWTSENQGDEGDAGEGE
FYYEILNS.EKACSLAKT.FDEAI.ELDTLNEESYKDSTLIMQLL..D..TLWTSENQ.DEGDAGEGE
RetrocopyFYYEILNSTEKACSLAKTVFDEAITELDTLNEESYKDSTLIMQLLG<DSVTLWTSENQEDEGDAGEGE

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 .14 RPM 427 .87 RPM
bodymap2_adrenal 0 .57 RPM 314 .12 RPM
bodymap2_brain 0 .16 RPM 574 .14 RPM
bodymap2_breast 0 .23 RPM 310 .10 RPM
bodymap2_colon 0 .12 RPM 324 .15 RPM
bodymap2_heart 0 .09 RPM 169 .92 RPM
bodymap2_kidney 0 .08 RPM 403 .45 RPM
bodymap2_liver 0 .00 RPM 106 .06 RPM
bodymap2_lung 0 .00 RPM 277 .99 RPM
bodymap2_lymph_node 0 .22 RPM 363 .77 RPM
bodymap2_ovary 0 .17 RPM 335 .92 RPM
bodymap2_prostate 0 .19 RPM 323 .54 RPM
bodymap2_skeletal_muscle 0 .00 RPM 139 .66 RPM
bodymap2_testis 0 .13 RPM 284 .76 RPM
bodymap2_thyroid 0 .26 RPM 265 .90 RPM
bodymap2_white_blood_cells 0 .14 RPM 895 .11 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity may be related with retro_hsap_855 in 1 libraries
ENCODE library ID Target ChIP-Seq Peak coordinates
ENCFF002CXQ POLR2A 11:18512601..18513251

EST - click to see more details

No EST(s) were mapped for retro_hsap_855 retrocopy.

TSS - click to see more details



TSS No. TSS Name TSS expression level (Expr) in TPM range:
no expression 0 < Expr ≤ 1 1 < Expr ≤ 5 5 < Expr ≤ 10 Expr > 10
TSS #1 TSS_12490885 libraries804 libraries132 libraries7 libraries1 library
TSS #2 TSS_124911806 libraries20 libraries2 libraries0 libraries1 library

The graphical summary, for retro_hsap_855 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1829 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)

Display detail expression values in each library
... or ...
Directly download all expression values

Lab - click to see more details

retro_hsap_855 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_855 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 28 parental genes, and 146 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000117961 retrocopy
retro_acar_8,
Choloepus hoffmanni ENSCHOG0000000578215 retrocopies
retro_chof_1049, retro_chof_1325, retro_chof_1630, retro_chof_1670, retro_chof_1975, retro_chof_22, retro_chof_2221, retro_chof_2350, retro_chof_2423, retro_chof_2619, retro_chof_326, retro_chof_352, retro_chof_487, retro_chof_707, retro_chof_971,
Callithrix jacchus ENSCJAG000000176642 retrocopies
retro_cjac_1002, retro_cjac_2214,
Dipodomys ordii ENSDORG0000000106414 retrocopies
retro_dord_235, retro_dord_236, retro_dord_255, retro_dord_256, retro_dord_258, retro_dord_259, retro_dord_262, retro_dord_263, retro_dord_332, retro_dord_442, retro_dord_545, retro_dord_681, retro_dord_725, retro_dord_9,
Echinops telfairi ENSETEG000000099674 retrocopies
retro_etel_1221, retro_etel_1380, retro_etel_1536, retro_etel_1705,
Homo sapiens ENSG000001089534 retrocopies
retro_hsap_2324, retro_hsap_3739, retro_hsap_3851, retro_hsap_4703,
Homo sapiens ENSG000001343082 retrocopies
retro_hsap_3004, retro_hsap_8,
Homo sapiens ENSG000001649241 retrocopy
retro_hsap_549,
Homo sapiens ENSG00000166913 4 retrocopies
retro_hsap_4160, retro_hsap_4841, retro_hsap_622, retro_hsap_855 ,
Gorilla gorilla ENSGGOG000000045802 retrocopies
retro_ggor_2795, retro_ggor_699,
Microcebus murinus ENSMICG000000009737 retrocopies
retro_mmur_1044, retro_mmur_1100, retro_mmur_1288, retro_mmur_1576, retro_mmur_27, retro_mmur_305, retro_mmur_979,
Myotis lucifugus ENSMLUG000000063191 retrocopy
retro_mluc_871,
Macaca mulatta ENSMMUG000000132063 retrocopies
retro_mmul_1061, retro_mmul_236, retro_mmul_673,
Monodelphis domestica ENSMODG000000162002 retrocopies
retro_mdom_1557, retro_mdom_212,
Nomascus leucogenys ENSNLEG000000066432 retrocopies
retro_nleu_42, retro_nleu_422,
Oryctolagus cuniculus ENSOCUG000000030021 retrocopy
retro_ocun_273,
Otolemur garnettii ENSOGAG000000089093 retrocopies
retro_ogar_122, retro_ogar_1243, retro_ogar_2934,
Ochotona princeps ENSOPRG000000118362 retrocopies
retro_opri_56, retro_opri_924,
Pongo abelii ENSPPYG000000110415 retrocopies
retro_pabe_3453, retro_pabe_3454, retro_pabe_3519, retro_pabe_3520, retro_pabe_692,
Pan troglodytes ENSPTRG0000001352912 retrocopies
retro_ptro_1010, retro_ptro_1686, retro_ptro_2390, retro_ptro_2828, retro_ptro_2887, retro_ptro_3125, retro_ptro_3201, retro_ptro_3225, retro_ptro_412, retro_ptro_453, retro_ptro_594, retro_ptro_965,
Pteropus vampyrus ENSPVAG000000126621 retrocopy
retro_pvam_157,
Sarcophilus harrisii ENSSHAG000000112411 retrocopy
retro_shar_483,
Sus scrofa ENSSSCG000000073811 retrocopy
retro_sscr_506,
Ictidomys tridecemlineatus ENSSTOG000000037331 retrocopy
retro_itri_1214,
Tupaia belangeri ENSTBEG0000000280647 retrocopies
retro_tbel_1038, retro_tbel_1272, retro_tbel_1460, retro_tbel_1472, retro_tbel_1572, retro_tbel_1653, retro_tbel_1664, retro_tbel_2127, retro_tbel_2128, retro_tbel_2229, retro_tbel_2246, retro_tbel_228, retro_tbel_2371, retro_tbel_2373, retro_tbel_2379, retro_tbel_2397, retro_tbel_2512, retro_tbel_2536, retro_tbel_2540, retro_tbel_2542, retro_tbel_2583, retro_tbel_2584, retro_tbel_2615, retro_tbel_2617, retro_tbel_3502, retro_tbel_3554, retro_tbel_3604, retro_tbel_3642, retro_tbel_3743, retro_tbel_390, retro_tbel_3989, retro_tbel_3993, retro_tbel_40, retro_tbel_4101, retro_tbel_4121, retro_tbel_4338, retro_tbel_4447, retro_tbel_4456, retro_tbel_4459, retro_tbel_4510, retro_tbel_4514, retro_tbel_4604, retro_tbel_4664, retro_tbel_4690, retro_tbel_5, retro_tbel_705, retro_tbel_854,
Tarsius syrichta ENSTSYG000000065374 retrocopies
retro_tsyr_1065, retro_tsyr_1473, retro_tsyr_1637, retro_tsyr_2084,
Tursiops truncatus ENSTTRG000000076151 retrocopy
retro_ttru_762,
Vicugna pacos ENSVPAG000000050233 retrocopies
retro_vpac_396, retro_vpac_516, retro_vpac_9,

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 = 0.17 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .02 RPM
CEU_NA11843 0 .03 RPM
CEU_NA11930 0 .03 RPM
CEU_NA12004 0 .04 RPM
CEU_NA12400 0 .00 RPM
CEU_NA12751 0 .12 RPM
CEU_NA12760 0 .04 RPM
CEU_NA12827 0 .00 RPM
CEU_NA12872 0 .03 RPM
CEU_NA12873 0 .03 RPM
FIN_HG00183 0 .08 RPM
FIN_HG00277 0 .00 RPM
FIN_HG00315 0 .06 RPM
FIN_HG00321 0 .03 RPM
FIN_HG00328 0 .02 RPM
FIN_HG00338 0 .02 RPM
FIN_HG00349 0 .03 RPM
FIN_HG00375 0 .02 RPM
FIN_HG00377 0 .03 RPM
FIN_HG00378 0 .04 RPM
GBR_HG00099 0 .12 RPM
GBR_HG00111 0 .06 RPM
GBR_HG00114 0 .11 RPM
GBR_HG00119 0 .07 RPM
GBR_HG00131 0 .03 RPM
GBR_HG00133 0 .00 RPM
GBR_HG00134 0 .04 RPM
GBR_HG00137 0 .03 RPM
GBR_HG00142 0 .11 RPM
GBR_HG00143 0 .06 RPM
TSI_NA20512 0 .08 RPM
TSI_NA20513 0 .15 RPM
TSI_NA20518 0 .03 RPM
TSI_NA20532 0 .14 RPM
TSI_NA20538 0 .14 RPM
TSI_NA20756 0 .03 RPM
TSI_NA20765 0 .17 RPM
TSI_NA20771 0 .06 RPM
TSI_NA20786 0 .16 RPM
TSI_NA20798 0 .06 RPM
YRI_NA18870 0 .14 RPM
YRI_NA18907 0 .07 RPM
YRI_NA18916 0 .06 RPM
YRI_NA19093 0 .10 RPM
YRI_NA19099 0 .11 RPM
YRI_NA19114 0 .08 RPM
YRI_NA19118 0 .06 RPM
YRI_NA19213 0 .05 RPM
YRI_NA19214 0 .02 RPM
YRI_NA19223 0 .12 RPM

Indel association:

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



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