RetrogeneDB ID:

retro_hsap_808

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:11:90015825..90016944(+)
Located in intron of:ENSG00000261645
Retrocopy
information
Ensembl ID:ENSG00000214391
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:TUBA1B
Ensembl ID:ENSG00000123416
Aliases:TUBA1B, K-ALPHA-1
Description:tubulin, alpha 1b [Source:HGNC Symbol;Acc:18809]


Retrocopy-Parental alignment summary:






>retro_hsap_808
ATGCGTGAATGCGTCTCCATCCACGTTGGCCAGGCTGGTGTCCAGATTGGCAATGTCTGCTGGGAGCTCTACTGCCTGGA
ACATGGCATCCAGCCCGATGGCCAGATGCCAAGTGACAAGACCATTGGGGGAGGAGATGACTCCTTCAACACCTTCAGTG
AGACGGGTGCTGGCAAGCATGTGCCCCGGGCTGTGTTTGTAGACTTGGAACCCATGGTCATTGATGAAGTTTGCACTGGC
ACCTACCGCCAGCTCTTCCACCCTGAGCAGCTCATCACAGGCAAGGAAGATGCTGCCAATAACTATGCCCGAGGGCACTA
CACCATTGGCAAGGAGATCATTGACCTTGTGTTGGACCGAATTCGCAAGCTGGCTAACCAGTGCACTGGTTTTCAGGGCT
TCTTGGTTTTCCACAGCTTTGGTGGGGGAACTGGTTCTGGGTTCACCTCCCTGCTCATAGAACGTCTCTTAGTTGATTAT
GGCAAGAAGTCCAAGCTGGAGTTCTCCAATTACCCAGCGCCCCAGGTTTCCACAGCTGTAGTTGAGCCCTACAACTCCAT
CCTCACCACCCACACCACCCTGGAGCACTCTGATTGTGCCTTCATGGTAGACAATGAGGCCATCTGTGACATCTGTTGTA
GAAACCTCAATATCGAGCGCCCAACCTACACTAACCTTAACCACCTTATTAGCCAGATTGTGTCCTCTATCACTGCTTCC
CTGAGATTTGATGGAGCCCTGAATGTTGACCTGACAGAATTCCAGACCAACCTGGTACCCTACTCCCACATCCACTTCCC
TCTGGCGACATATGCCCCTGTCATTTCTGCTGAGAAAGCCTACCATGAACAGCTTTCTGTAGCAGAGATCACCAATGCTT
CCTTTGAGCCAGCCAACCAGATGGTGAAATGTGACCCTCGCCATGGTAAATACATGGCTTGCTGCCTATTGTGCCATGGT
GATGTGGTTCCCAAAGATGCCAATGCTGCCATTGCCACCATCAAGACCAAGCGTAGCATCCAGTTTGTAGATTGGTGCCC
CACTGGCTTCAAGGTTGGCATCAACTACCAGTCTCCCACTGTGGTGCCTGGTGGAGACCTGGCCATGGTACAGAGTGCA

ORF - retro_hsap_808 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 93.85 %
Parental protein coverage: 82.93 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGKHVPRAVFVDL
MREC.SIHVGQAGVQIGN.CWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTF.SETGAGKHVPRAVFVDL
RetrocopyMRECVSIHVGQAGVQIGNVCWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTF-SETGAGKHVPRAVFVDL
ParentalEPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLDRIRKLADQCTGLQGFLVFHS
EP.VIDEV.TGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLDRIRKLA.QCTG.QGFLVFHS
RetrocopyEPMVIDEVCTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLDRIRKLANQCTGFQGFLVFHS
ParentalFGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTAVVEPYNSILTTHTTLEHSDCAFMVDNEAIY
FGGGTGSGFTSLL.ERL.VDYGKKSKLEFS.YPAPQVSTAVVEPYNSILTTHTTLEHSDCAFMVDNEAI.
RetrocopyFGGGTGSGFTSLLIERLLVDYGKKSKLEFSNYPAPQVSTAVVEPYNSILTTHTTLEHSDCAFMVDNEAIC
ParentalDICRRNLDIERPTYTNLNRLISQIVSSITASLRFDGALNVDLTEFQTNLVPYPRIHFPLATYAPVISAEK
DIC.RNL.IERPTYTNLN.LISQIVSSITASLRFDGALNVDLTEFQTNLVPY..IHFPLATYAPVISAEK
RetrocopyDICCRNLNIERPTYTNLNHLISQIVSSITASLRFDGALNVDLTEFQTNLVPYSHIHFPLATYAPVISAEK
ParentalAYHEQLSVAEITNACFEPANQMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRSIQFVDWCPTG
AYHEQLSVAEITNA.FEPANQMVKCDPRHGKYMACCLL..GDVVPKD.NAAIATIKTKRSIQFVDWCPTG
RetrocopyAYHEQLSVAEITNASFEPANQMVKCDPRHGKYMACCLLCHGDVVPKDANAAIATIKTKRSIQFVDWCPTG
ParentalFKVGINYQPPTVVPGGDLAKVQRA
FKVGINYQ.PTVVPGGDLA.VQ.A
RetrocopyFKVGINYQSPTVVPGGDLAMVQSA

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 .04 RPM 62 .73 RPM
bodymap2_adrenal 0 .08 RPM 120 .36 RPM
bodymap2_brain 0 .14 RPM 173 .86 RPM
bodymap2_breast 0 .06 RPM 61 .48 RPM
bodymap2_colon 0 .00 RPM 69 .07 RPM
bodymap2_heart 0 .09 RPM 40 .74 RPM
bodymap2_kidney 0 .12 RPM 84 .00 RPM
bodymap2_liver 0 .04 RPM 21 .65 RPM
bodymap2_lung 0 .00 RPM 135 .72 RPM
bodymap2_lymph_node 0 .13 RPM 68 .25 RPM
bodymap2_ovary 0 .13 RPM 75 .35 RPM
bodymap2_prostate 0 .02 RPM 62 .84 RPM
bodymap2_skeletal_muscle 0 .04 RPM 42 .67 RPM
bodymap2_testis 0 .06 RPM 79 .16 RPM
bodymap2_thyroid 0 .00 RPM 45 .52 RPM
bodymap2_white_blood_cells 0 .02 RPM 60 .23 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_808 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_808 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_19473155 libraries94 libraries597 libraries532 libraries451 libraries
TSS #2 TSS_19474518 libraries722 libraries525 libraries34 libraries30 libraries
TSS #3 TSS_19475370 libraries527 libraries858 libraries65 libraries9 libraries

The graphical summary, for retro_hsap_808 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_808 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_808 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 13 parental genes, and 28 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000122441 retrocopy
retro_btau_402,
Choloepus hoffmanni ENSCHOG000000084442 retrocopies
retro_chof_179, retro_chof_360,
Callithrix jacchus ENSCJAG000000208742 retrocopies
retro_cjac_1603, retro_cjac_1861,
Felis catus ENSFCAG000000286893 retrocopies
retro_fcat_1802, retro_fcat_254, retro_fcat_798,
Homo sapiens ENSG00000123416 1 retrocopy
retro_hsap_808 ,
Homo sapiens ENSG000001675521 retrocopy
retro_hsap_3313,
Macropus eugenii ENSMEUG000000107792 retrocopies
retro_meug_1648, retro_meug_2174,
Macropus eugenii ENSMEUG000000111674 retrocopies
retro_meug_1121, retro_meug_157, retro_meug_1616, retro_meug_1964,
Monodelphis domestica ENSMODG000000152062 retrocopies
retro_mdom_1632, retro_mdom_348,
Mus musculus ENSMUSG000000230046 retrocopies
retro_mmus_1562, retro_mmus_1607, retro_mmus_1742, retro_mmus_1987, retro_mmus_3297, retro_mmus_3327,
Otolemur garnettii ENSOGAG000000094351 retrocopy
retro_ogar_240,
Pan troglodytes ENSPTRG000000129501 retrocopy
retro_ptro_2158,
Sus scrofa ENSSSCG000000001902 retrocopies
retro_sscr_380, retro_sscr_702,

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 = 0.78 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .17 RPM
CEU_NA11843 0 .14 RPM
CEU_NA11930 0 .78 RPM
CEU_NA12004 0 .15 RPM
CEU_NA12400 0 .14 RPM
CEU_NA12751 0 .15 RPM
CEU_NA12760 0 .31 RPM
CEU_NA12827 0 .33 RPM
CEU_NA12872 0 .14 RPM
CEU_NA12873 0 .16 RPM
FIN_HG00183 0 .27 RPM
FIN_HG00277 0 .18 RPM
FIN_HG00315 0 .17 RPM
FIN_HG00321 0 .15 RPM
FIN_HG00328 0 .26 RPM
FIN_HG00338 0 .17 RPM
FIN_HG00349 0 .71 RPM
FIN_HG00375 0 .20 RPM
FIN_HG00377 0 .33 RPM
FIN_HG00378 0 .17 RPM
GBR_HG00099 0 .26 RPM
GBR_HG00111 0 .15 RPM
GBR_HG00114 0 .13 RPM
GBR_HG00119 0 .02 RPM
GBR_HG00131 0 .09 RPM
GBR_HG00133 0 .10 RPM
GBR_HG00134 0 .26 RPM
GBR_HG00137 0 .14 RPM
GBR_HG00142 0 .14 RPM
GBR_HG00143 0 .26 RPM
TSI_NA20512 0 .20 RPM
TSI_NA20513 0 .24 RPM
TSI_NA20518 0 .25 RPM
TSI_NA20532 0 .20 RPM
TSI_NA20538 0 .00 RPM
TSI_NA20756 0 .44 RPM
TSI_NA20765 0 .21 RPM
TSI_NA20771 0 .23 RPM
TSI_NA20786 0 .08 RPM
TSI_NA20798 0 .25 RPM
YRI_NA18870 0 .37 RPM
YRI_NA18907 0 .07 RPM
YRI_NA18916 0 .13 RPM
YRI_NA19093 0 .13 RPM
YRI_NA19099 0 .48 RPM
YRI_NA19114 0 .08 RPM
YRI_NA19118 0 .25 RPM
YRI_NA19213 0 .10 RPM
YRI_NA19214 0 .07 RPM
YRI_NA19223 0 .28 RPM

Indel association:

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



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