RetrogeneDB ID:

retro_hsap_4060

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:8:57389388..57390546(-)
Located in intron of:ENSG00000254254
Retrocopy
information
Ensembl ID:ENSG00000253541
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:SEPT10
Ensembl ID:ENSG00000186522
Aliases:None
Description:septin 10 [Source:HGNC Symbol;Acc:14349]


Retrocopy-Parental alignment summary:






>retro_hsap_4060
ATATTCTGTGTGGGGGAAACTGGAATTGGAAAATCAACACTGATTGACACATTGTTTAATACTAATTTGGAAGACTATGA
ATCCTCACATTTTTGCCCAAATGTTAAACTTAAAGTTCAGACATATGAACTCCAGGAAAGTAATGTTCGATTGAAATTGA
TCATTGTGAATACAGTGGGATTTGGTGACCAAATAAATAAAGAAGAGAGCTACCAACCGATAGTTGACTACATAGATGCT
CAGTTTGAGGCCTGTCTCCAAGAATAACTGAAGATTAAACGTTCTCTCTTTACCTACCCTGATTCTCGCATCCGTGTGTG
CCTCTACTTCATTTCACTGACAGGCCACTCTCTGAAGACACTTGATCTCTTAACCATGAAGAACCTTGACAGCAAGGTAA
ACATTATACCAGTGATTGCCAAAGCAGATACGGTTTCTAAAACTGAATTACATAAGTTTAAGATCAAGTTCATGAGTGAA
CTGGTCAGCAATGGCGTCCAGATATACCAGTTTCCAACGGATGATGACACTATTGCTAAGGTCAACGCTGCAATGAATGG
ACAGTTGCCGTTTGCTGTTGTGGGAAGTATGGATGAGATAAAAGTCGGAAACAAGATGGTTAAAGCTCGCCAGTACCCTT
GGGGTGTTGTACAGGTGGAAAATGAAAACCACTGTGACTTTGTAAAGCTGCGGGAAATGTTCATTTGTACAAATATGGAG
GACCTGCGATAGCAGACCCATACCAGGCACTATGAGCTTTACAGGCGCTGCAAACTGGAGGAAATGGGCTTTACAGATGT
GGGCCCAGAAAACAAGCCGGTCAGTCTTCAAGAGACCTATGAAGCCAAAAGACATGAGTTCCATGGTGAACGTCAGAGGA
AGGAAGAAGAAATGAAACAGATGTTTGTGCAGCCAGTGAAGGAGAAAGAAGCCATATTGAAAGAAGCTGAGAGAAAGCTA
CAGGCCAAATTTGAGCACCTTAAGAGACTTCACCAAGAAGAGAGAATGAAGCTTGAAGAACAAAGAAGACTTTTGGAAGA
AGAAATAATTGCTTTCTCTAAAAAGAAAGCTACCTCCGAGATATTTCACAGCCAGTCCTTTCTGGCAACAGGCAGCAACC
TGAGTAAGGACAAGGACCATAAGAACTCCAATTTTTTG

ORF - retro_hsap_4060 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 90.16 %
Parental protein coverage: 89.56 %
Number of stop codons detected: 2
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalILCVGETGIGKSTLIDTLFNTNFEDYESSHFCPNVKLKAQTYELQESNVQLKLTIVNTVGFGDQINKEES
I.CVGETGIGKSTLIDTLFNTN.EDYESSHFCPNVKLK.QTYELQESNV.LKL.IVNTVGFGDQINKEES
RetrocopyIFCVGETGIGKSTLIDTLFNTNLEDYESSHFCPNVKLKVQTYELQESNVRLKLIIVNTVGFGDQINKEES
ParentalYQPIVDYIDAQFEAYLQEELKIKRSLFTYHDSRIHVCLYFISPTGHSLKTLDLLTMKNLDSKVNIIPVIA
YQPIVDYIDAQFEA.LQE.LKIKRSLFTY.DSRI.VCLYFIS.TGHSLKTLDLLTMKNLDSKVNIIPVIA
RetrocopyYQPIVDYIDAQFEACLQE*LKIKRSLFTYPDSRIRVCLYFISLTGHSLKTLDLLTMKNLDSKVNIIPVIA
ParentalKADTVSKTELQKFKIKLMSELVSNGVQIYQFPTDDDTIAKVNAAMNGQLPFAVVGSMDEVKVGNKMVKAR
KADTVSKTEL.KFKIK.MSELVSNGVQIYQFPTDDDTIAKVNAAMNGQLPFAVVGSMDE.KVGNKMVKAR
RetrocopyKADTVSKTELHKFKIKFMSELVSNGVQIYQFPTDDDTIAKVNAAMNGQLPFAVVGSMDEIKVGNKMVKAR
ParentalQYPWGVVQVENENHCDFVKLREMLICTNMEDLREQTHTRHYELYRRCKLEEMGFTDVGPENKPVSVQETY
QYPWGVVQVENENHCDFVKLREM.ICTNMEDLR.QTHTRHYELYRRCKLEEMGFTDVGPENKPVS.QETY
RetrocopyQYPWGVVQVENENHCDFVKLREMFICTNMEDLR*QTHTRHYELYRRCKLEEMGFTDVGPENKPVSLQETY
ParentalEAKRHEFHGERQRKEEEMKQMFVQRVKEKEAILKEAERELQAKFEHLKRLHQEERMKLEEKRRLLEEEII
EAKRHEFHGERQRKEEEMKQMFVQ.VKEKEAILKEAER.LQAKFEHLKRLH..................I
RetrocopyEAKRHEFHGERQRKEEEMKQMFVQPVKEKEAILKEAERKLQAKFEHLKRLHXXXXXXXXXXXXXXXXXXI
ParentalAFSKKKATSEIFHSQSFLATGSNLRKDKDRKNSNFL
AFSKKKATSEIFHSQSFLATGSNL.KDKD.KNSNFL
RetrocopyAFSKKKATSEIFHSQSFLATGSNLSKDKDHKNSNFL

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 .46 RPM 139 .86 RPM
bodymap2_adrenal 0 .10 RPM 73 .03 RPM
bodymap2_brain 0 .05 RPM 38 .28 RPM
bodymap2_breast 0 .43 RPM 96 .60 RPM
bodymap2_colon 0 .08 RPM 144 .96 RPM
bodymap2_heart 0 .00 RPM 55 .81 RPM
bodymap2_kidney 0 .06 RPM 92 .48 RPM
bodymap2_liver 0 .02 RPM 46 .28 RPM
bodymap2_lung 0 .14 RPM 105 .89 RPM
bodymap2_lymph_node 0 .00 RPM 65 .09 RPM
bodymap2_ovary 0 .25 RPM 82 .91 RPM
bodymap2_prostate 0 .03 RPM 159 .74 RPM
bodymap2_skeletal_muscle 0 .02 RPM 58 .06 RPM
bodymap2_testis 5 .54 RPM 152 .31 RPM
bodymap2_thyroid 0 .09 RPM 82 .41 RPM
bodymap2_white_blood_cells 0 .00 RPM 8 .43 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_4060 was not detected

EST - click to see more details

2 EST(s) were mapped to retro_hsap_4060 retrocopy
EST ID Start End Identity Match Mis-match Score
AA861695 57389329 57389829 99.8 499 1 498
HY199689 57389565 57389871 99.4 304 2 302

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_1854421323 libraries434 libraries72 libraries0 libraries0 libraries

The graphical summary, for retro_hsap_4060 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_4060 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_4060 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_2753
Gorilla gorilla retro_ggor_2728
Pongo abelii retro_pabe_3335
Parental genes homology:
Parental genes homology involve 7 parental genes, and 10 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG000000177543 retrocopies
retro_cjac_1736, retro_cjac_2879, retro_cjac_828,
Homo sapiens ENSG000001225452 retrocopies
retro_hsap_3810, retro_hsap_4202,
Homo sapiens ENSG00000186522 1 retrocopy
retro_hsap_4060 ,
Gorilla gorilla ENSGGOG000000136591 retrocopy
retro_ggor_2728,
Myotis lucifugus ENSMLUG000000172731 retrocopy
retro_mluc_2285,
Nomascus leucogenys ENSNLEG000000013281 retrocopy
retro_nleu_2111,
Pongo abelii ENSPPYG000000121441 retrocopy
retro_pabe_3335,

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 = 0.05 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .00 RPM
CEU_NA11843 0 .03 RPM
CEU_NA11930 0 .00 RPM
CEU_NA12004 0 .00 RPM
CEU_NA12400 0 .00 RPM
CEU_NA12751 0 .02 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 .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 .03 RPM
GBR_HG00119 0 .00 RPM
GBR_HG00131 0 .00 RPM
GBR_HG00133 0 .00 RPM
GBR_HG00134 0 .00 RPM
GBR_HG00137 0 .00 RPM
GBR_HG00142 0 .00 RPM
GBR_HG00143 0 .00 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 .02 RPM
TSI_NA20771 0 .00 RPM
TSI_NA20786 0 .00 RPM
TSI_NA20798 0 .00 RPM
YRI_NA18870 0 .03 RPM
YRI_NA18907 0 .00 RPM
YRI_NA18916 0 .00 RPM
YRI_NA19093 0 .00 RPM
YRI_NA19099 0 .00 RPM
YRI_NA19114 0 .05 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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