RetrogeneDB ID:

retro_hsap_1867

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:18:3415127..3415567(+)
Located in intron of:ENSG00000177426
Retrocopy
information
Ensembl ID:ENSG00000263460
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:BOD1
Ensembl ID:ENSG00000145919
Aliases:BOD1, FAM44B
Description:biorientation of chromosomes in cell division 1 [Source:HGNC Symbol;Acc:25114]


Retrocopy-Parental alignment summary:






>retro_hsap_1867
GGCAACGCAGGCACCATGATCCCGGCTCTGCCTTCCGGCGACCCGGAGCTCATTGCTCTCATCCTGGAGTGGCTCAAGAG
CCAGGCCCGTTTGGCAGCTTCTGTCGATGCTGCCTGGCCCCTGTGGACACCAAGCCAGCTTACCAAAACCAGAGGCAGAA
AGCTGAGGGTTCGGTGTCCACACACCTGGATGAGCAGAACTGGAATCTTATGATGCGCAAAAGCCTATTGCGAAATGGTC
AGAGGCAGAGTGAGATTCAGTCAGGGACATTGGAAGCTGGAGTAGACAGGGTTATTTCTCAGGCAGAGGATCCAAAATTA
AACCACATCCTCAGGCCACCAACGGAAGGAGCAAGTCATGAGTTCCTGGGTGCCCAGAAGACAGCAATGGTGCCAGCACC
CCCTTTAGAGCCCGCAGACCAGGACCCTCCAGCTCCAGCC

ORF - retro_hsap_1867 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 67.79 %
Parental protein coverage: 80. %
Number of stop codons detected: 0
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalGGGGPINPASLPPGDPQLIALIVEQLKSR-GLFDSFRRDCLADVDTKPAYQNLRQKVDNFVSTHLDKQEW
G..G...PA.LP.GDP.LIALI.E.LKS..G.F.SF.R.CLA.VDTKPAYQN.RQK....VSTHLD.Q.W
RetrocopyGNAGTMIPA-LPSGDPELIALILEWLKSQ<GPFGSFCRCCLAPVDTKPAYQNQRQKAEGSVSTHLDEQNW
ParentalNPTMNKNQLRNGLRQSVVQSGMLEAGVDRIISQVVDPKLNHIFRPQIERAIHEFLAAQKKAAVPAPPPEP
N..M.K..LRNG.RQS..QSG.LEAGVDR.ISQ..DPKLNHI.RP..E.A.HEFL.AQK.A.VPAPP.EP
RetrocopyNLMMRKSLLRNGQRQSEIQSGTLEAGVDRVISQAEDPKLNHILRPPTEGASHEFLGAQKTAMVPAPPLEP
ParentalEGQDPPAPS
..QDPPAP.
RetrocopyADQDPPAPA

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 35 .18 RPM
bodymap2_adrenal 0 .06 RPM 25 .55 RPM
bodymap2_brain 0 .00 RPM 22 .13 RPM
bodymap2_breast 0 .00 RPM 32 .35 RPM
bodymap2_colon 0 .00 RPM 37 .14 RPM
bodymap2_heart 0 .00 RPM 26 .03 RPM
bodymap2_kidney 0 .00 RPM 27 .92 RPM
bodymap2_liver 0 .00 RPM 9 .70 RPM
bodymap2_lung 0 .00 RPM 27 .97 RPM
bodymap2_lymph_node 0 .00 RPM 29 .04 RPM
bodymap2_ovary 0 .00 RPM 45 .47 RPM
bodymap2_prostate 0 .00 RPM 46 .52 RPM
bodymap2_skeletal_muscle 0 .00 RPM 41 .18 RPM
bodymap2_testis 0 .00 RPM 51 .39 RPM
bodymap2_thyroid 0 .00 RPM 61 .33 RPM
bodymap2_white_blood_cells 0 .00 RPM 15 .83 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_1867 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_1867 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_1867 retrocopy 5' end.

Lab - click to see more details

retro_hsap_1867 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_1867 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_1282
Gorilla gorilla retro_ggor_1365
Parental genes homology:
Parental genes homology involve 18 parental genes, and 30 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000345981 retrocopy
retro_btau_663,
Canis familiaris ENSCAFG000000167761 retrocopy
retro_cfam_1374,
Callithrix jacchus ENSCJAG000000319714 retrocopies
retro_cjac_1154, retro_cjac_1515, retro_cjac_1536, retro_cjac_953,
Homo sapiens ENSG00000145919 3 retrocopies
retro_hsap_102, retro_hsap_1867 , retro_hsap_993,
Gorilla gorilla ENSGGOG000000109252 retrocopies
retro_ggor_1365, retro_ggor_794,
Microcebus murinus ENSMICG000000026261 retrocopy
retro_mmur_1126,
Macaca mulatta ENSMMUG000000137932 retrocopies
retro_mmul_803, retro_mmul_869,
Mus musculus ENSMUSG000000445021 retrocopy
retro_mmus_3661,
Nomascus leucogenys ENSNLEG000000004761 retrocopy
retro_nleu_1224,
Oryctolagus cuniculus ENSOCUG000000142831 retrocopy
retro_ocun_1071,
Otolemur garnettii ENSOGAG000000011073 retrocopies
retro_ogar_1477, retro_ogar_2663, retro_ogar_3112,
Pongo abelii ENSPPYG000000160572 retrocopies
retro_pabe_1567, retro_pabe_1587,
Pan troglodytes ENSPTRG000000175442 retrocopies
retro_ptro_1282, retro_ptro_757,
Ictidomys tridecemlineatus ENSSTOG000000135051 retrocopy
retro_itri_1164,
Tupaia belangeri ENSTBEG000000140461 retrocopy
retro_tbel_3451,
Tarsius syrichta ENSTSYG000000076171 retrocopy
retro_tsyr_818,
Tursiops truncatus ENSTTRG000000003842 retrocopies
retro_ttru_1004, retro_ttru_457,
Vicugna pacos ENSVPAG000000042601 retrocopy
retro_vpac_452,

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 ) Legend:


Library Retrogene expression
CEU_NA11831 0 .00 RPM
CEU_NA11843 0 .00 RPM
CEU_NA11930 0 .00 RPM
CEU_NA12004 0 .00 RPM
CEU_NA12400 0 .00 RPM
CEU_NA12751 0 .00 RPM
CEU_NA12760 0 .00 RPM
CEU_NA12827 0 .00 RPM
CEU_NA12872 0 .00 RPM
CEU_NA12873 0 .00 RPM
FIN_HG00183 0 .00 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 .00 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 .00 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 .00 RPM
YRI_NA19093 0 .00 RPM
YRI_NA19099 0 .00 RPM
YRI_NA19114 0 .00 RPM
YRI_NA19118 0 .00 RPM
YRI_NA19213 0 .00 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