RetrogeneDB ID:

retro_hsap_4009

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:8:134420248..134421352(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000225259
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:ST13
Ensembl ID:ENSG00000100380
Aliases:ST13, AAG2, FAM10A1, FAM10A4, HIP, HOP, HSPABP, HSPABP1, P48, PRO0786, SNC6
Description:suppression of tumorigenicity 13 (colon carcinoma) (Hsp70 interacting protein) [Source:HGNC Symbol;Acc:11343]


Retrocopy-Parental alignment summary:






>retro_hsap_4009
ATGGACCCCTGCAAAGTGAACGAGCTTCGGGCCTTTGTGAAAATGTGTAAGCAGGATCCGAGCATTCTGCACACCGAGGA
AATGCGCTTCCTGAGGGAGTGGGTGGAGAGCATGGGAGGTAAAGTACCACCTGCTACTCAGAAAGCTAAATCAGAAGAAA
ATACCGAGGAAGAAAAACCTGATAGTAAGAAGGTGGAGGAAGACTTAAAGGCAGACGAACCATCAAGTGAGGAAAGTGAT
CTAGAAATTGATAAAGAAGGTGTGATTGAACCAGACACTGATGCTCCTCAAGAAATGGGAGATGAAAATGCGGAGATAAC
GGAGGAGATGATGGATCAGGCAAATGATAAAAAAGTGGCTGCTATTGAAGCCCTAAATGATGGTGAACTCCAGAAAGCCA
TTGAGTTATTGACAGACGCCATCAAGCTGAATCCTCGCTTGGCCATTTTGTATGCCAAGAGGGCCAGTGTTTTCGTCAAA
TTACAGAAGCCAAATGCTGCCACCCAAGACTGTGACAGAGCCATTGAAATAAATCCTGATTCAGCTCAGCCTCACAAGTG
GCGGGGGAAAGCACACAGACTTCTAGGCCACTGGGGAGAAGCAGACCATGATCTTGCCCTTGCCTGTAAATTGGATTATG
ATGAAGATGCTAGTGCAATGCTGAAAGAAGTTCAACATAGGGCACAGAAAATTGCAGAACATCGGAGAAAGTATGAGCGA
AAACATGAAGAGCGAGAGATCAAAGAAAGAGTAGAACGAGTTAAGAAGGCTCGAAAAGAGCATGAGAGAGCCCAGAGGGA
GGAAGAAGCCAGACGACAGTCAGGAGCTCAGTATGGCTCTTTTCCAGGTGGCTTTCCTGGGGGAATGCCTGGTAATTTTC
CCAGAGGAATGCCTGGAATGGGAGGGGGCATGTCTGGAATGGCTGGAATGCCTGGATTCAATGAAATTCTTAGTGATCCA
GAGGTTCTTGCAGCCATGCAGGATCCAGAAGTTATGGTGGCCTTCCAGGATGTGGCTCAGAACCCAGCAAATGTGTCAAA
ATACCAGAGCAACCCAAAGGTTATGAATCTCATCAGTAAATTGTCAGCCAAATTTGGAGGTCAA

ORF - retro_hsap_4009 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 92.93 %
Parental protein coverage: 99.73 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMDPRKVNELRAFVKMCKQDPSVLHTEEMRFLREWVESMGGKVPPATQKAKSEENTKEEKPDSKKVEEDLK
MDP.KVNELRAFVKMCKQDPS.LHTEEMRFLREWVESMGGKVPPATQKAKSEENT.EEKPDSKKVEEDLK
RetrocopyMDPCKVNELRAFVKMCKQDPSILHTEEMRFLREWVESMGGKVPPATQKAKSEENTEEEKPDSKKVEEDLK
ParentalADEPSSEESDLEIDKEGVIEPDTDAPQEMGDENAEITEEMMDQANDKKVAAIEALNDGELQKAIDLFTDA
ADEPSSEESDLEIDKEGVIEPDTDAPQEMGDENAEITEEMMDQANDKKVAAIEALNDGELQKAI.L.TDA
RetrocopyADEPSSEESDLEIDKEGVIEPDTDAPQEMGDENAEITEEMMDQANDKKVAAIEALNDGELQKAIELLTDA
ParentalIKLNPRLAILYAKRASVFVKLQKPNAAIRDCDRAIEINPDSAQPYKWRGKAHRLLGHWEEAAHDLALACK
IKLNPRLAILYAKRASVFVKLQKPNAA..DCDRAIEINPDSAQP.KWRGKAHRLLGHW.EA.HDLALACK
RetrocopyIKLNPRLAILYAKRASVFVKLQKPNAATQDCDRAIEINPDSAQPHKWRGKAHRLLGHWGEADHDLALACK
ParentalLDYDEDASAMLKEVQPRAQKIAEHRRKYERKREEREIKERIERVKKAREEHERAQREEEARRQSGAQYGS
LDYDEDASAMLKEVQ.RAQKIAEHRRKYERK.EEREIKER.ERVKKAR.EHERAQREEEARRQSGAQYGS
RetrocopyLDYDEDASAMLKEVQHRAQKIAEHRRKYERKHEEREIKERVERVKKARKEHERAQREEEARRQSGAQYGS
ParentalFPGGFPGGMPGNFPGGMPGMGGGMPGMAGMPGLNEILSDPEVLAAMQDPEVMVAFQDVAQNPANMSKYQS
FPGGFPGGMPGNFP.GMPGMGGG..........NEILSDPEVLAAMQDPEVMVAFQDVAQNPAN.SKYQS
RetrocopyFPGGFPGGMPGNFPRGMPGMGGGXXXXXXXXXFNEILSDPEVLAAMQDPEVMVAFQDVAQNPANVSKYQS
ParentalNPKVMNLISKLSAKFGGQ
NPKVMNLISKLSAKFGGQ
RetrocopyNPKVMNLISKLSAKFGGQ

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 .16 RPM 322 .88 RPM
bodymap2_adrenal 0 .08 RPM 198 .92 RPM
bodymap2_brain 0 .07 RPM 280 .81 RPM
bodymap2_breast 0 .10 RPM 341 .58 RPM
bodymap2_colon 0 .08 RPM 497 .30 RPM
bodymap2_heart 0 .15 RPM 152 .58 RPM
bodymap2_kidney 0 .02 RPM 278 .86 RPM
bodymap2_liver 0 .02 RPM 135 .78 RPM
bodymap2_lung 0 .04 RPM 230 .08 RPM
bodymap2_lymph_node 0 .18 RPM 242 .38 RPM
bodymap2_ovary 0 .40 RPM 802 .26 RPM
bodymap2_prostate 0 .21 RPM 455 .26 RPM
bodymap2_skeletal_muscle 0 .33 RPM 303 .76 RPM
bodymap2_testis 0 .11 RPM 342 .45 RPM
bodymap2_thyroid 0 .21 RPM 441 .59 RPM
bodymap2_white_blood_cells 0 .10 RPM 169 .02 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_4009 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_4009 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_181640773 libraries703 libraries324 libraries13 libraries16 libraries

The graphical summary, for retro_hsap_4009 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_4009 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_4009 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Gorilla gorilla retro_ggor_2692
Parental genes homology:
Parental genes homology involve 23 parental genes, and 127 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000052271 retrocopy
retro_acar_2,
Ailuropoda melanoleuca ENSAMEG000000138801 retrocopy
retro_amel_135,
Bos taurus ENSBTAG000000062024 retrocopies
retro_btau_254, retro_btau_427, retro_btau_621, retro_btau_658,
Canis familiaris ENSCAFG0000000113914 retrocopies
retro_cfam_1029, retro_cfam_1101, retro_cfam_1122, retro_cfam_1239, retro_cfam_1467, retro_cfam_1830, retro_cfam_1950, retro_cfam_1958, retro_cfam_247, retro_cfam_262, retro_cfam_582, retro_cfam_808, retro_cfam_901, retro_cfam_969,
Choloepus hoffmanni ENSCHOG000000126761 retrocopy
retro_chof_2222,
Callithrix jacchus ENSCJAG0000000464411 retrocopies
retro_cjac_1843, retro_cjac_1953, retro_cjac_2177, retro_cjac_2275, retro_cjac_2789, retro_cjac_3123, retro_cjac_3570, retro_cjac_4019, retro_cjac_488, retro_cjac_640, retro_cjac_685,
Cavia porcellus ENSCPOG000000022904 retrocopies
retro_cpor_1394, retro_cpor_1477, retro_cpor_166, retro_cpor_961,
Felis catus ENSFCAG000000118472 retrocopies
retro_fcat_920, retro_fcat_987,
Homo sapiens ENSG00000100380 16 retrocopies
retro_hsap_1055, retro_hsap_1203, retro_hsap_178, retro_hsap_201, retro_hsap_2078, retro_hsap_2189, retro_hsap_2853, retro_hsap_3206, retro_hsap_3907, retro_hsap_4009 , retro_hsap_4876, retro_hsap_500, retro_hsap_619, retro_hsap_756, retro_hsap_812, retro_hsap_986,
Gorilla gorilla ENSGGOG0000002674716 retrocopies
retro_ggor_1600, retro_ggor_1734, retro_ggor_1791, retro_ggor_1975, retro_ggor_2177, retro_ggor_2634, retro_ggor_2692, retro_ggor_277, retro_ggor_3045, retro_ggor_629, retro_ggor_666, retro_ggor_749, retro_ggor_788, retro_ggor_832, retro_ggor_833, retro_ggor_938,
Microcebus murinus ENSMICG000000088752 retrocopies
retro_mmur_481, retro_mmur_954,
Myotis lucifugus ENSMLUG000000077642 retrocopies
retro_mluc_1088, retro_mluc_2021,
Macaca mulatta ENSMMUG000000191183 retrocopies
retro_mmul_1842, retro_mmul_402, retro_mmul_438,
Monodelphis domestica ENSMODG000000130422 retrocopies
retro_mdom_1087, retro_mdom_31,
Mus musculus ENSMUSG000000224032 retrocopies
retro_mmus_2997, retro_mmus_651,
Nomascus leucogenys ENSNLEG0000001537817 retrocopies
retro_nleu_1142, retro_nleu_1155, retro_nleu_1606, retro_nleu_1852, retro_nleu_2075, retro_nleu_2088, retro_nleu_2376, retro_nleu_2404, retro_nleu_247, retro_nleu_2555, retro_nleu_2765, retro_nleu_3121, retro_nleu_3122, retro_nleu_319, retro_nleu_447, retro_nleu_552, retro_nleu_988,
Otolemur garnettii ENSOGAG000000169321 retrocopy
retro_ogar_224,
Pongo abelii ENSPPYG0000001185814 retrocopies
retro_pabe_1004, retro_pabe_2181, retro_pabe_2361, retro_pabe_2657, retro_pabe_2885, retro_pabe_3183, retro_pabe_3673, retro_pabe_3794, retro_pabe_437, retro_pabe_554, retro_pabe_727, retro_pabe_763, retro_pabe_798, retro_pabe_880,
Pteropus vampyrus ENSPVAG000000119082 retrocopies
retro_pvam_1104, retro_pvam_393,
Rattus norvegicus ENSRNOG000000190708 retrocopies
retro_rnor_1360, retro_rnor_1725, retro_rnor_1798, retro_rnor_1976, retro_rnor_2204, retro_rnor_2372, retro_rnor_2481, retro_rnor_2543,
Sarcophilus harrisii ENSSHAG000000003192 retrocopies
retro_shar_70, retro_shar_767,
Sus scrofa ENSSSCG000000000711 retrocopy
retro_sscr_428,
Ictidomys tridecemlineatus ENSSTOG000000031651 retrocopy
retro_itri_88,

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 = 0.6 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .39 RPM
CEU_NA11843 0 .31 RPM
CEU_NA11930 0 .39 RPM
CEU_NA12004 0 .19 RPM
CEU_NA12400 0 .18 RPM
CEU_NA12751 0 .27 RPM
CEU_NA12760 0 .49 RPM
CEU_NA12827 0 .14 RPM
CEU_NA12872 0 .16 RPM
CEU_NA12873 0 .16 RPM
FIN_HG00183 0 .30 RPM
FIN_HG00277 0 .30 RPM
FIN_HG00315 0 .30 RPM
FIN_HG00321 0 .36 RPM
FIN_HG00328 0 .21 RPM
FIN_HG00338 0 .23 RPM
FIN_HG00349 0 .60 RPM
FIN_HG00375 0 .22 RPM
FIN_HG00377 0 .18 RPM
FIN_HG00378 0 .30 RPM
GBR_HG00099 0 .23 RPM
GBR_HG00111 0 .17 RPM
GBR_HG00114 0 .13 RPM
GBR_HG00119 0 .24 RPM
GBR_HG00131 0 .14 RPM
GBR_HG00133 0 .07 RPM
GBR_HG00134 0 .11 RPM
GBR_HG00137 0 .03 RPM
GBR_HG00142 0 .22 RPM
GBR_HG00143 0 .29 RPM
TSI_NA20512 0 .17 RPM
TSI_NA20513 0 .17 RPM
TSI_NA20518 0 .33 RPM
TSI_NA20532 0 .24 RPM
TSI_NA20538 0 .28 RPM
TSI_NA20756 0 .35 RPM
TSI_NA20765 0 .21 RPM
TSI_NA20771 0 .28 RPM
TSI_NA20786 0 .21 RPM
TSI_NA20798 0 .12 RPM
YRI_NA18870 0 .30 RPM
YRI_NA18907 0 .14 RPM
YRI_NA18916 0 .23 RPM
YRI_NA19093 0 .13 RPM
YRI_NA19099 0 .16 RPM
YRI_NA19114 0 .16 RPM
YRI_NA19118 0 .12 RPM
YRI_NA19213 0 .38 RPM
YRI_NA19214 0 .20 RPM
YRI_NA19223 0 .20 RPM

Indel association:

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





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