RetrogeneDB ID:

retro_hsap_3022

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:4:10480325..10480556(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000248419
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:HRSP12
Ensembl ID:ENSG00000132541
Aliases:HRSP12, P14.5, PSP, UK114
Description:heat-responsive protein 12 [Source:HGNC Symbol;Acc:16897]


Retrocopy-Parental alignment summary:






>retro_hsap_3022
ATGTCATCCTTGATTAAAAAGGTGATCAGGACTGCAAAAGCCCCCAGGGTCCTTGGGCCATATGGCCAAGGTGTGTTAGT
CAACAGGACCATTTACATTTCAGGACAGCTAGTCATGGACTCTTCAAATGCACAGCTTGTGGCAGGAGAGGTAGCCAAAG
CAGCTAAACAAGCTCTTACAAAAATGGGTGAAGTTCTGAAGACTGCAGGCTGTGACTTCACTAATGTGGTA

ORF - retro_hsap_3022 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 71.43 %
Parental protein coverage: 56.2 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMSSLIRRVISTAKAPGAIGPYSQAVLVDRTIYISGQIGMDPSSGQLVSGGVAEEAKQALKNMGEILKAAG
MSSLI..VI.TAKAP...GPY.Q.VLV.RTIYISGQ..MD.S..QLV.G.VA..AKQAL..MGE.LK.AG
RetrocopyMSSLIKKVIRTAKAPRVLGPYGQGVLVNRTIYISGQLVMDSSNAQLVAGEVAKAAKQALTKMGEVLKTAG
ParentalCDFTNVV
CDFTNVV
RetrocopyCDFTNVV

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 24 .03 RPM
bodymap2_adrenal 0 .00 RPM 5 .44 RPM
bodymap2_brain 0 .00 RPM 42 .97 RPM
bodymap2_breast 0 .00 RPM 24 .40 RPM
bodymap2_colon 0 .00 RPM 16 .22 RPM
bodymap2_heart 0 .00 RPM 15 .05 RPM
bodymap2_kidney 0 .00 RPM 104 .35 RPM
bodymap2_liver 0 .00 RPM 332 .63 RPM
bodymap2_lung 0 .00 RPM 6 .08 RPM
bodymap2_lymph_node 0 .00 RPM 11 .55 RPM
bodymap2_ovary 0 .00 RPM 9 .87 RPM
bodymap2_prostate 0 .00 RPM 13 .79 RPM
bodymap2_skeletal_muscle 0 .00 RPM 8 .04 RPM
bodymap2_testis 0 .08 RPM 21 .59 RPM
bodymap2_thyroid 0 .00 RPM 9 .11 RPM
bodymap2_white_blood_cells 0 .00 RPM 4 .59 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_3022 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_3022 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_3022 retrocopy 5' end.

Lab - click to see more details

retro_hsap_3022 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_3022 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_2040
Pongo abelii retro_pabe_2504
Parental genes homology:
Parental genes homology involve 23 parental genes, and 69 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000005751 retrocopy
retro_amel_1033,
Bos taurus ENSBTAG000000125955 retrocopies
retro_btau_1068, retro_btau_1145, retro_btau_1328, retro_btau_771, retro_btau_912,
Canis familiaris ENSCAFG000000302501 retrocopy
retro_cfam_668,
Choloepus hoffmanni ENSCHOG000000012788 retrocopies
retro_chof_133, retro_chof_1972, retro_chof_2434, retro_chof_2503, retro_chof_2676, retro_chof_380, retro_chof_515, retro_chof_757,
Callithrix jacchus ENSCJAG000000155602 retrocopies
retro_cjac_1702, retro_cjac_465,
Dasypus novemcinctus ENSDNOG000000251383 retrocopies
retro_dnov_1155, retro_dnov_224, retro_dnov_793,
Felis catus ENSFCAG000000021671 retrocopy
retro_fcat_624,
Homo sapiens ENSG00000132541 3 retrocopies
retro_hsap_1502, retro_hsap_284, retro_hsap_3022 ,
Gorilla gorilla ENSGGOG000000011851 retrocopy
retro_ggor_1153,
Loxodonta africana ENSLAFG000000020781 retrocopy
retro_lafr_437,
Microcebus murinus ENSMICG0000000435613 retrocopies
retro_mmur_1096, retro_mmur_1206, retro_mmur_1323, retro_mmur_209, retro_mmur_222, retro_mmur_364, retro_mmur_533, retro_mmur_589, retro_mmur_597, retro_mmur_603, retro_mmur_79, retro_mmur_870, retro_mmur_97,
Macaca mulatta ENSMMUG000000118252 retrocopies
retro_mmul_558, retro_mmul_88,
Monodelphis domestica ENSMODG000000065751 retrocopy
retro_mdom_319,
Mustela putorius furoENSMPUG000000152531 retrocopy
retro_mputfur_1449,
Nomascus leucogenys ENSNLEG000000024853 retrocopies
retro_nleu_1721, retro_nleu_3065, retro_nleu_837,
Ornithorhynchus anatinus ENSOANG000000215321 retrocopy
retro_oana_33,
Otolemur garnettii ENSOGAG000000014653 retrocopies
retro_ogar_2308, retro_ogar_2951, retro_ogar_552,
Pongo abelii ENSPPYG000000187763 retrocopies
retro_pabe_1253, retro_pabe_2504, retro_pabe_387,
Pan troglodytes ENSPTRG000000204573 retrocopies
retro_ptro_1019, retro_ptro_2040, retro_ptro_234,
Sus scrofa ENSSSCG000000060791 retrocopy
retro_sscr_834,
Ictidomys tridecemlineatus ENSSTOG000000114524 retrocopies
retro_itri_1591, retro_itri_192, retro_itri_605, retro_itri_894,
Tursiops truncatus ENSTTRG000000160665 retrocopies
retro_ttru_1282, retro_ttru_1589, retro_ttru_1626, retro_ttru_369, retro_ttru_909,
Vicugna pacos ENSVPAG000000082773 retrocopies
retro_vpac_30, retro_vpac_358, retro_vpac_89,

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 .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 .03 RPM
GBR_HG00142 0 .00 RPM
GBR_HG00143 0 .03 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 .02 RPM

Indel association:

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





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