RetrogeneDB ID:

retro_hsap_4867

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:X:85339718..85341344(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000225536
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:STIP1
Ensembl ID:ENSG00000168439
Aliases:STIP1, HEL-S-94n, HOP, IEF-SSP-3521, P60, STI1, STI1L
Description:stress-induced-phosphoprotein 1 [Source:HGNC Symbol;Acc:11387]


Retrocopy-Parental alignment summary:






>retro_hsap_4867
ATGAAGCAGGTCAATGAGCTGAAAGAGAAGGGCAACAAGGCCCTGGGCGTGGAAAACATCGACAATGCCTTACAGTGCTA
CTCTGAAGCCATTAAGCTGGATCCCCACAACCACGTGCTCTACAGCAACTGTTCTGCCACCTATGCCAAGAAAGGAGACT
ACCAGAAGGCTTACAAGGACGGCTGCAAGACCGTCGACCTAAAAGTTTGACTGGGGCAAGGGATATTCACGAAAAGCAGC
AGCTCTAGAGTTCTTAAACCGATTTGAAGAAGCCAAGTGAACCTACGAGGAGAGCTTAAAACACGAGGCAGATAACCCTC
AACTGAAAGAGGGTTTACAGAATATGGAGGCCAGGTTGGCAGAGAGAAAATGTATGAATGCTTTCAACATGCCCAATCTG
TAACAGAAGTTGGAGAGTGATCCCAGGACAAGGACACTGCTCAGTGATCCTACCTACCGGGAGCTGATAGAGCAACTATA
AAACAAGCCTTCTGATCTGGGCACAAAACTACGAGATCCCCGGATCCTGACCACTCTCAGTGTCCTCCTTGAGGTCGATC
GGGGCAGTATGGATGAGGAGGAACAGGTTGCAACACCTTCACCACCACCCCTTCCCAAAAAGGAGACCAAGCCAGAGCCA
GTGGAAGAAGATCTTCCAGAGAATAAGAAGCAGGCACTGAAAGAAAAAGAGCTGAGGAACGATGCCTACAAGAAGAAAGA
CTGACAGCCTTGAAGCATTACGACAAAGCCAAGGAGCTGGACCCCAGCAACATGACTTACATTACCAATCAAGCAGCGGT
ATACTTTGAAAAGGGCGACTACAATAAGTGTTGGGAGCTTTGTGAGAAGTCCATTGAAGTGGGGAGAGAAAACAGAGAAG
ACTATCTACAGATTGCCAAAGTGTGTGCTCGAATTGGCAACTCCTACTTCAAAGAAGAAAAGTACAAGGATGCCATCCAT
TTCTATAACAAGTCTCTGGCAGAGCACCGAACTCCAGATGTGCTCAAGAAATGCCAGCAGGCAGAGAAAATCCTGAAGGA
GCAAGAACGGCTGGCCTACATAAACCCCGACCTGGCTTTAGAAGAGAAGAACAAAGGCAACGAGTGTTTTCAGAAAGGGG
ACTATCCCCACGCCATGAAGCATTATACGGAAGCCATCAAAAGGAACCCGAAAGATGCCAAATTATACAGCAATCGAGCT
GCCTGTTACACCAAACTCCTGGATTCCAGCTGGCACTCAAGGACTGTGAAGAATGTATCCAGCTAGAACCGACCTTCATC
AAGGGTTATACACGGAAAGCCGTTGCCCTGGAAGCGATGAAGGACTACACCAAAGTCATGGATGTGTACCGGAAGGCGCT
AGACCCGGACTCCAGCTGTAAGGAGGCGGCAGACGGCTACCAGCGCTGTATGATGGCGCAGTACAACCGGCACCACAGCC
CCGAAGATGTGAAGCGACGAGCCATGGCCGACCCCGAGGTGCAGCAGATCATGAGTGACATAGCCATGCACCTTATCCTG
GAGCAGATGCAGAAGGACCCCCCAGGCACTCAGCGAACACTTAAAGAATCCTGTAATCGCAAAGAAGATCCAGAAGCTGA
TGGATGTGGGTCTGATTGCAATTCGA

ORF - retro_hsap_4867 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 86.11 %
Parental protein coverage: 100. %
Number of stop codons detected: 3
Number of frameshifts detected 4


Retrocopy - Parental Gene Alignment:

ParentalMEQVNELKEKGNKALSVGNIDDALQCYSEAIKLDPHNHVLYSNRSAAYAKKGDYQKAYEDGCKTVDLKP-
M.QVNELKEKGNKAL.V.NID.ALQCYSEAIKLDPHNHVLYSN.SA.YAKKGDYQKAY.DGCKTVDLK..
RetrocopyMKQVNELKEKGNKALGVENIDNALQCYSEAIKLDPHNHVLYSNCSATYAKKGDYQKAYKDGCKTVDLKV>
ParentalDWGKGYSRKAAALEFLNRFEEAKRTYEEGLKHEANNPQLKEGLQNMEARLAERKFMNPFNMPNLYQKLES
DWGKGYSRKAAALEFLNRFEEAK.TYEE.LKHEA.NPQLKEGLQNMEARLAERK.MN.FNMPNL.QKLES
RetrocopyDWGKGYSRKAAALEFLNRFEEAK*TYEESLKHEADNPQLKEGLQNMEARLAERKCMNAFNMPNL*QKLES
ParentalDPRTRTLLSDPTYRELIEQLRNKPSDLGTKLQDPRIMTTLSVLLGVDLGSMDEEEEIATPPPPPPPKKET
DPRTRTLLSDPTYRELIEQL.NKPSDLGTKL.DPRI.TTLSVLL.VD.GSMDEEE..ATP.P.PP..K..
RetrocopyDPRTRTLLSDPTYRELIEQL*NKPSDLGTKLRDPRILTTLSVLLEVDRGSMDEEEQVATPSP-PPLPKKE
ParentalKPEPMEEDLPENKK-QALKEKELGNDAYKKKDFDTALKHYDKAKELDPTNMTYITNQAAVYFEKGDYNKC
......E......K..A..E..............TALKHYDKAKELDP.NMTYITNQAAVYFEKGDYNKC
RetrocopyTKPEPVEEDLPENK<EAGTERKRAEERCLQEERLTALKHYDKAKELDPSNMTYITNQAAVYFEKGDYNKC
ParentalRELCEKAIEVGRENREDYRQIAKAYARIGNSYFKEEKYKDAIHFYNKSLAEHRTPDVLKKCQQAEKILKE
.ELCEK.IEVGRENREDY.QIAK..ARIGNSYFKEEKYKDAIHFYNKSLAEHRTPDVLKKCQQAEKILKE
RetrocopyWELCEKSIEVGRENREDYLQIAKVCARIGNSYFKEEKYKDAIHFYNKSLAEHRTPDVLKKCQQAEKILKE
ParentalQERLAYINPDLALEEKNKGNECFQKGDYPQAMKHYTEAIKRNPKDAKLYSNRAACYTKLLE-FQLALKDC
QERLAYINPDLALEEKNKGNECFQKGDYP.AMKHYTEAIKRNPKDAKLYSNRAACYTKLL..FQLALKDC
RetrocopyQERLAYINPDLALEEKNKGNECFQKGDYPHAMKHYTEAIKRNPKDAKLYSNRAACYTKLLD<FQLALKDC
ParentalEECIQLEPTFIKGYTRKAAALEAMKDYTKAMDVYQKALDLDSSCKEAADGYQRCMMAQYNRHDSPEDVKR
EECIQLEPTFIKGYTRKA.ALEAMKDYTK.MDVY.KALD.DSSCKEAADGYQRCMMAQYNRH.SPEDVKR
RetrocopyEECIQLEPTFIKGYTRKAVALEAMKDYTKVMDVYRKALDPDSSCKEAADGYQRCMMAQYNRHHSPEDVKR
ParentalRAMADPEVQQIMSDPAMRLILEQMQKD-PQALSEHLKNPVIAQKIQKLMDVGLIAIR
RAMADPEVQQIMSD.AM.LILEQMQKD.PQALSEHLKNPVIA.KIQKLMDVGLIAIR
RetrocopyRAMADPEVQQIMSDIAMHLILEQMQKD>PQALSEHLKNPVIAKKIQKLMDVGLIAIR

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 .02 RPM 80 .98 RPM
bodymap2_adrenal 0 .00 RPM 64 .25 RPM
bodymap2_brain 0 .00 RPM 77 .96 RPM
bodymap2_breast 0 .00 RPM 64 .81 RPM
bodymap2_colon 0 .00 RPM 225 .98 RPM
bodymap2_heart 0 .00 RPM 52 .26 RPM
bodymap2_kidney 0 .00 RPM 124 .74 RPM
bodymap2_liver 0 .00 RPM 36 .35 RPM
bodymap2_lung 0 .00 RPM 121 .92 RPM
bodymap2_lymph_node 0 .00 RPM 216 .43 RPM
bodymap2_ovary 0 .02 RPM 177 .44 RPM
bodymap2_prostate 0 .02 RPM 116 .46 RPM
bodymap2_skeletal_muscle 0 .02 RPM 152 .38 RPM
bodymap2_testis 0 .00 RPM 255 .70 RPM
bodymap2_thyroid 0 .00 RPM 194 .02 RPM
bodymap2_white_blood_cells 0 .08 RPM 88 .52 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_4867 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_4867 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_4867 retrocopy 5' end.

Lab - click to see more details

retro_hsap_4867 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_4867 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_3242
Gorilla gorilla retro_ggor_3040
Parental genes homology:
Parental genes homology involve 14 parental genes, and 22 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000156632 retrocopies
retro_btau_836, retro_btau_913,
Canis familiaris ENSCAFG000000146726 retrocopies
retro_cfam_1077, retro_cfam_1172, retro_cfam_1722, retro_cfam_1982, retro_cfam_474, retro_cfam_497,
Callithrix jacchus ENSCJAG000000182092 retrocopies
retro_cjac_1043, retro_cjac_2222,
Cavia porcellus ENSCPOG000000029141 retrocopy
retro_cpor_1443,
Felis catus ENSFCAG000000059371 retrocopy
retro_fcat_1510,
Homo sapiens ENSG00000168439 1 retrocopy
retro_hsap_4867 ,
Gorilla gorilla ENSGGOG000000121321 retrocopy
retro_ggor_3040,
Microcebus murinus ENSMICG000000169331 retrocopy
retro_mmur_1045,
Macaca mulatta ENSMMUG000000129531 retrocopy
retro_mmul_2607,
Nomascus leucogenys ENSNLEG000000047771 retrocopy
retro_nleu_2000,
Pan troglodytes ENSPTRG000000038201 retrocopy
retro_ptro_3242,
Rattus norvegicus ENSRNOG000000211642 retrocopies
retro_rnor_2862, retro_rnor_468,
Ictidomys tridecemlineatus ENSSTOG000000142621 retrocopy
retro_itri_1578,
Tursiops truncatus ENSTTRG000000102351 retrocopy
retro_ttru_1900,

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 = 0.15 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .02 RPM
CEU_NA11843 0 .00 RPM
CEU_NA11930 0 .07 RPM
CEU_NA12004 0 .00 RPM
CEU_NA12400 0 .00 RPM
CEU_NA12751 0 .00 RPM
CEU_NA12760 0 .09 RPM
CEU_NA12827 0 .09 RPM
CEU_NA12872 0 .03 RPM
CEU_NA12873 0 .03 RPM
FIN_HG00183 0 .03 RPM
FIN_HG00277 0 .07 RPM
FIN_HG00315 0 .08 RPM
FIN_HG00321 0 .00 RPM
FIN_HG00328 0 .07 RPM
FIN_HG00338 0 .04 RPM
FIN_HG00349 0 .06 RPM
FIN_HG00375 0 .02 RPM
FIN_HG00377 0 .03 RPM
FIN_HG00378 0 .02 RPM
GBR_HG00099 0 .00 RPM
GBR_HG00111 0 .00 RPM
GBR_HG00114 0 .00 RPM
GBR_HG00119 0 .02 RPM
GBR_HG00131 0 .06 RPM
GBR_HG00133 0 .05 RPM
GBR_HG00134 0 .00 RPM
GBR_HG00137 0 .00 RPM
GBR_HG00142 0 .06 RPM
GBR_HG00143 0 .03 RPM
TSI_NA20512 0 .11 RPM
TSI_NA20513 0 .15 RPM
TSI_NA20518 0 .06 RPM
TSI_NA20532 0 .10 RPM
TSI_NA20538 0 .09 RPM
TSI_NA20756 0 .00 RPM
TSI_NA20765 0 .06 RPM
TSI_NA20771 0 .00 RPM
TSI_NA20786 0 .00 RPM
TSI_NA20798 0 .00 RPM
YRI_NA18870 0 .07 RPM
YRI_NA18907 0 .00 RPM
YRI_NA18916 0 .02 RPM
YRI_NA19093 0 .03 RPM
YRI_NA19099 0 .05 RPM
YRI_NA19114 0 .00 RPM
YRI_NA19118 0 .02 RPM
YRI_NA19213 0 .00 RPM
YRI_NA19214 0 .00 RPM
YRI_NA19223 0 .04 RPM

Indel association:

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





Copyright © RetrogeneDB 2014-2017