RetrogeneDB ID:

retro_hsap_1051

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:12:101462035..101463010(+)
Located in intron of:ENSG00000151572
Retrocopy
information
Ensembl ID:ENSG00000258033
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:SNX5
Ensembl ID:ENSG00000089006
Aliases:None
Description:sorting nexin 5 [Source:HGNC Symbol;Acc:14969]


Retrocopy-Parental alignment summary:






>retro_hsap_1051
GAGACTCATGAGTTCCTGCCTCTGCTGCAGATTCCGCCTGCTCCTACGAAGGCTGACTTCAATGGTCCTTGAGAGAAGAT
GCAGAAACTGGGAGAAGGTAAAGGGTCTTTGACCAAAGAAGAATTTGCCAAGATGAAATAAGAACTGGAAGCTGAGTATC
TCGCTGTTTTTAAGAAGACTGTGTCCTCCCATGAAGCCTTTCTTTAGTGGCTTTCTTCTCACCCTGTTCTCAGTAAAGAT
CGCAACTTTCATATTTTCCTGGAATATGATCAGGATCTAAGTGTTAGGTGGAAAAATACTAAAGAGATGTTTGGTGGCTT
CTTCAAAAGTGTGGTGAAAGTGCTGATGCAGTCCTTTTTACTGGAGTTAAGGAGGTAGATGACTTCTTTGAGCAAGAGAA
TGACTTCCTTATTAACTATTAGAGTAGGATCAAAGATTCTTGTGTGAAAGCTGACAAAATGACCAGATCTCATAAAAATG
TTGCCGATGACTATATTCACACTGCAGCCTGCTTACATAGCCTGGCTTTAGAAGAGCCCACAGTCATCAAAAAGTATCTA
TTGAAGGTTGCTGAGCTATTTGAAAAACTTAGGAAAGTAGAGGGTTGAATCTCATCAGATGAAGATTTAAAGCTAACAGA
GCTCCTCCGATACTACATGCTCAACATCGAAGCTGCTAAGGATCTCTTACACAGATGCACCAAAGCCCTCATTGACTATG
AAAAATCAAACAAAGCTCTGGATAAGGCCCAGTTTAAAGAGCAAAGATGTCAAGTTGGCTAAGGTACACTAGGAGGAGTG
CTGCCAGAAATTTGAATAGCTTTCCAAATCTGCAAAGGAAGAACTGATAAATTTCAAACGGAAGAAAGTGGCAGCATTTA
GAAAGAATCTAATTGAAATGTCTGAACTGGAAATAAAACATGCGAGGAACAGTGTCTCCCTTTTGCAGAGCTGTATTGAC
TTGTTCAAGAATAAC

ORF - retro_hsap_1051 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 88.07 %
Parental protein coverage: 80.2 %
Number of stop codons detected: 7
Number of frameshifts detected: 2


Retrocopy - Parental Gene Alignment:

ParentalETTDYAGLI-IPPAPTKPDFDGPREKMQKLGEGEGSMTKEEFAKMKQELEAEYLAVFKKTVSSHEVFLQR
ET.....L..IPPAPTK.DF.GP.EKMQKLGEG.GS.TKEEFAKMK.ELEAEYLAVFKKTVSSHE.FL..
RetrocopyETHEFLPLLQIPPAPTKADFNGP*EKMQKLGEGKGSLTKEEFAKMK*ELEAEYLAVFKKTVSSHEAFL*W
ParentalLSSHPVLSKDRNFHVFLEYDQDLSVRRKNTKEMFGGFFKSVVK-SADEVLFTGVKEVDDFFEQEKNFLIN
LSSHPVLSKDRNFH.FLEYDQDLSVR.KNTKEMFGGFFKSVVK.SAD.VLFTGVKEVDDFFEQE..FLIN
RetrocopyLSSHPVLSKDRNFHIFLEYDQDLSVRWKNTKEMFGGFFKSVVK<SADAVLFTGVKEVDDFFEQENDFLIN
ParentalYYNRIKDSCVKADKMTRSHKNVADDYIHTAACLHSLALEEPTVIKKYLLKVAELFEKLRKVEGRVSSDED
Y..RIKDSCVKADKMTRSHKNVADDYIHTAACLHSLALEEPTVIKKYLLKVAELFEKLRKVEG..SSDED
RetrocopyY*SRIKDSCVKADKMTRSHKNVADDYIHTAACLHSLALEEPTVIKKYLLKVAELFEKLRKVEG*ISSDED
ParentalLKLTELLRYYMLNIEAAKDLLYRRTKALIDYENSNKALDKAR-LKSKDVKLAEAHQQECCQKFEQLSESA
LKLTELLRYYMLNIEAAKDLL.R.TKALIDYE.SNKALDKA..LKSKDVKLA..H..ECCQKFE.LS.SA
RetrocopyLKLTELLRYYMLNIEAAKDLLHRCTKALIDYEKSNKALDKAQ>LKSKDVKLAKVH*EECCQKFE*LSKSA
ParentalKEELINFKRKRVAAFRKNLIEMSELEIKHARNNVSLLQSCIDLFKNN
KEELINFKRK.VAAFRKNLIEMSELEIKHARN.VSLLQSCIDLFKNN
RetrocopyKEELINFKRKKVAAFRKNLIEMSELEIKHARNSVSLLQSCIDLFKNN

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 70 .67 RPM
bodymap2_adrenal 0 .00 RPM 123 .27 RPM
bodymap2_brain 0 .45 RPM 65 .02 RPM
bodymap2_breast 0 .00 RPM 98 .99 RPM
bodymap2_colon 0 .00 RPM 68 .76 RPM
bodymap2_heart 0 .02 RPM 33 .16 RPM
bodymap2_kidney 0 .02 RPM 118 .52 RPM
bodymap2_liver 0 .00 RPM 51 .92 RPM
bodymap2_lung 0 .00 RPM 69 .97 RPM
bodymap2_lymph_node 0 .00 RPM 94 .84 RPM
bodymap2_ovary 0 .02 RPM 138 .18 RPM
bodymap2_prostate 0 .00 RPM 81 .21 RPM
bodymap2_skeletal_muscle 0 .04 RPM 57 .29 RPM
bodymap2_testis 0 .02 RPM 88 .89 RPM
bodymap2_thyroid 0 .00 RPM 257 .80 RPM
bodymap2_white_blood_cells 0 .00 RPM 87 .37 RPM

ChIP-Seq - click to see more details

RNA Polymerase II activity near the 5' end of retro_hsap_1051 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_1051 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_1051 retrocopy 5' end.

Lab - click to see more details

retro_hsap_1051 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_1051 has 5 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_717
Gorilla gorilla retro_ggor_829
Pongo abelii retro_pabe_877
Macaca mulatta retro_mmul_832
Callithrix jacchus retro_cjac_3243
Parental genes homology:
Parental genes homology involve 15 parental genes, and 21 retrocopies.

Species Parental gene accession Retrocopies number
Choloepus hoffmanni ENSCHOG000000101282 retrocopies
retro_chof_1478, retro_chof_2166,
Callithrix jacchus ENSCJAG000000049472 retrocopies
retro_cjac_2192, retro_cjac_3243,
Homo sapiens ENSG00000089006 2 retrocopies
retro_hsap_1051 , retro_hsap_2945,
Homo sapiens ENSG000001728031 retrocopy
retro_hsap_2045,
Gorilla gorilla ENSGGOG000000089531 retrocopy
retro_ggor_829,
Macropus eugenii ENSMEUG000000091101 retrocopy
retro_meug_475,
Macaca mulatta ENSMMUG000000114762 retrocopies
retro_mmul_1746, retro_mmul_832,
Nomascus leucogenys ENSNLEG000000097141 retrocopy
retro_nleu_2071,
Oryctolagus cuniculus ENSOCUG000000170721 retrocopy
retro_ocun_1323,
Otolemur garnettii ENSOGAG000000061571 retrocopy
retro_ogar_1203,
Pongo abelii ENSPPYG000000107302 retrocopies
retro_pabe_2442, retro_pabe_877,
Pan troglodytes ENSPTRG000000132782 retrocopies
retro_ptro_2052, retro_ptro_717,
Sus scrofa ENSSSCG000000070881 retrocopy
retro_sscr_593,
Ictidomys tridecemlineatus ENSSTOG000000154161 retrocopy
retro_itri_1176,
Tursiops truncatus ENSTTRG000000164321 retrocopy
retro_ttru_410,

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 = 0.1 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .02 RPM
CEU_NA11843 0 .03 RPM
CEU_NA11930 0 .10 RPM
CEU_NA12004 0 .00 RPM
CEU_NA12400 0 .04 RPM
CEU_NA12751 0 .00 RPM
CEU_NA12760 0 .04 RPM
CEU_NA12827 0 .00 RPM
CEU_NA12872 0 .00 RPM
CEU_NA12873 0 .03 RPM
FIN_HG00183 0 .03 RPM
FIN_HG00277 0 .04 RPM
FIN_HG00315 0 .00 RPM
FIN_HG00321 0 .00 RPM
FIN_HG00328 0 .02 RPM
FIN_HG00338 0 .00 RPM
FIN_HG00349 0 .03 RPM
FIN_HG00375 0 .00 RPM
FIN_HG00377 0 .03 RPM
FIN_HG00378 0 .04 RPM
GBR_HG00099 0 .00 RPM
GBR_HG00111 0 .06 RPM
GBR_HG00114 0 .03 RPM
GBR_HG00119 0 .02 RPM
GBR_HG00131 0 .03 RPM
GBR_HG00133 0 .00 RPM
GBR_HG00134 0 .00 RPM
GBR_HG00137 0 .00 RPM
GBR_HG00142 0 .03 RPM
GBR_HG00143 0 .00 RPM
TSI_NA20512 0 .00 RPM
TSI_NA20513 0 .00 RPM
TSI_NA20518 0 .03 RPM
TSI_NA20532 0 .00 RPM
TSI_NA20538 0 .00 RPM
TSI_NA20756 0 .00 RPM
TSI_NA20765 0 .10 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 .02 RPM
YRI_NA19093 0 .03 RPM
YRI_NA19099 0 .05 RPM
YRI_NA19114 0 .03 RPM
YRI_NA19118 0 .02 RPM
YRI_NA19213 0 .02 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).



Copyright © RetrogeneDB 2014-2017