RetrogeneDB ID:

retro_hsap_3617

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:6:80146624..80146884(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000218748
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:DBI
Ensembl ID:ENSG00000155368
Aliases:DBI, ACBD1, ACBP, CCK-RP, EP
Description:diazepam binding inhibitor (GABA receptor modulator, acyl-CoA binding protein) [Source:HGNC Symbol;Acc:2690]


Retrocopy-Parental alignment summary:






>retro_hsap_3617
ATGTCTCAGGCTGAGTTTGAGAGAGCTGTGGAAGACGTTAAACACCTTAAGACCAAGCCAGGGGATGATGAGATGTGTTC
CTCTATGGCCACTACAAACAAGCAACTGTGGGCGACATAAATACAGAATGGCCTGGGATGTTGGATTTCAAAGGCAAGAC
CAAGTGGGATGCCTGGAATGAGCTGAAAGGGACTACCAAGGAAGATGCCATGAAAGCTTACGTCAACAATGTAGAAGAGC
TAAGGAAAAAACATGGAATG

ORF - retro_hsap_3617 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 79.55 %
Parental protein coverage: 100.0 %
Number of stop codons detected: 0
Number of frameshifts detected: 1


Retrocopy - Parental Gene Alignment:

ParentalMSQAEFEKAAEEVRHLKTKPSDEEM-LFIYGHYKQATVGDINTERPGMLDFTGKAKWDAWNELKGTSKED
MSQAEFE.A.E.V.HLKTKP.D.EM..F.YGHYKQATVGDINTE.PGMLDF.GK.KWDAWNELKGT.KED
RetrocopyMSQAEFERAVEDVKHLKTKPGDDEM<VFLYGHYKQATVGDINTEWPGMLDFKGKTKWDAWNELKGTTKED
ParentalAMKAYINKVEELKKKYGI
AMKAY.N.VEEL.KK.G.
RetrocopyAMKAYVNNVEELRKKHGM

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 53 .91 RPM
bodymap2_adrenal 0 .00 RPM 54 .10 RPM
bodymap2_brain 0 .00 RPM 78 .08 RPM
bodymap2_breast 0 .02 RPM 123 .29 RPM
bodymap2_colon 0 .00 RPM 52 .26 RPM
bodymap2_heart 0 .00 RPM 105 .23 RPM
bodymap2_kidney 0 .00 RPM 121 .85 RPM
bodymap2_liver 0 .00 RPM 160 .96 RPM
bodymap2_lung 0 .00 RPM 55 .91 RPM
bodymap2_lymph_node 0 .00 RPM 57 .82 RPM
bodymap2_ovary 0 .00 RPM 30 .40 RPM
bodymap2_prostate 0 .00 RPM 62 .02 RPM
bodymap2_skeletal_muscle 0 .00 RPM 11 .26 RPM
bodymap2_testis 0 .00 RPM 64 .80 RPM
bodymap2_thyroid 0 .00 RPM 47 .00 RPM
bodymap2_white_blood_cells 0 .00 RPM 57 .04 RPM

ChIP-Seq - click to see more details

RNA Polymerase II activity near the 5' end of retro_hsap_3617 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_3617 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_167946406 libraries 558 libraries 779 libraries 72 libraries 14 libraries

The graphical summary, for retro_hsap_3617 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_3617 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_3617 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_2446
Pongo abelii retro_pabe_2968
Parental genes homology:
Parental genes homology involve 28 parental genes, and 79 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000085093 retrocopies
retro_amel_1587, retro_amel_69, retro_amel_993,
Bos taurus ENSBTAG000000095172 retrocopies
retro_btau_154, retro_btau_1718,
Canis familiaris ENSCAFG000000048956 retrocopies
retro_cfam_1228, retro_cfam_134, retro_cfam_1452, retro_cfam_1599, retro_cfam_570, retro_cfam_857,
Callithrix jacchus ENSCJAG000000214361 retrocopy
retro_cjac_954,
Cavia porcellus ENSCPOG000000004152 retrocopies
retro_cpor_576, retro_cpor_59,
Equus caballus ENSECAG000000189491 retrocopy
retro_ecab_14,
Erinaceus europaeus ENSEEUG000000121152 retrocopies
retro_eeur_101, retro_eeur_33,
Echinops telfairi ENSETEG000000002205 retrocopies
retro_etel_1131, retro_etel_1403, retro_etel_1761, retro_etel_754, retro_etel_849,
Homo sapiens ENSG00000155368 3 retrocopies
retro_hsap_1619, retro_hsap_3345, retro_hsap_3617 ,
Homo sapiens ENSG000001762442 retrocopies
retro_hsap_1501, retro_hsap_1669,
Gorilla gorilla ENSGGOG000000103723 retrocopies
retro_ggor_1224, retro_ggor_1289, retro_ggor_2442,
Loxodonta africana ENSLAFG000000050022 retrocopies
retro_lafr_280, retro_lafr_42,
Microcebus murinus ENSMICG000000002942 retrocopies
retro_mmur_1233, retro_mmur_291,
Macaca mulatta ENSMMUG000000111263 retrocopies
retro_mmul_168, retro_mmul_651, retro_mmul_757,
Monodelphis domestica ENSMODG000000003931 retrocopy
retro_mdom_61,
Mustela putorius furoENSMPUG000000009452 retrocopies
retro_mputfur_170, retro_mputfur_438,
Mus musculus ENSMUSG000000263852 retrocopies
retro_mmus_2307, retro_mmus_712,
Nomascus leucogenys ENSNLEG000000102902 retrocopies
retro_nleu_1170, retro_nleu_807,
Oryctolagus cuniculus ENSOCUG000000045661 retrocopy
retro_ocun_234,
Ochotona princeps ENSOPRG000000083633 retrocopies
retro_opri_125, retro_opri_594, retro_opri_794,
Pongo abelii ENSPPYG000000127882 retrocopies
retro_pabe_2755, retro_pabe_2968,
Pan troglodytes ENSPTRG000000124012 retrocopies
retro_ptro_2140, retro_ptro_2446,
Pteropus vampyrus ENSPVAG000000143495 retrocopies
retro_pvam_1120, retro_pvam_1121, retro_pvam_168, retro_pvam_529, retro_pvam_85,
Rattus norvegicus ENSRNOG000000468893 retrocopies
retro_rnor_1801, retro_rnor_2737, retro_rnor_879,
Sus scrofa ENSSSCG000000234353 retrocopies
retro_sscr_167, retro_sscr_375, retro_sscr_41,
Ictidomys tridecemlineatus ENSSTOG000000067591 retrocopy
retro_itri_1,
Tupaia belangeri ENSTBEG0000000206713 retrocopies
retro_tbel_1617, retro_tbel_2338, retro_tbel_2726, retro_tbel_273, retro_tbel_3096, retro_tbel_3097, retro_tbel_3305, retro_tbel_3392, retro_tbel_3454, retro_tbel_3602, retro_tbel_4015, retro_tbel_556, retro_tbel_579,
Tarsius syrichta ENSTSYG000000021082 retrocopies
retro_tsyr_142, retro_tsyr_1654,

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 = 0.03 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 .03 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 .02 RPM
YRI_NA19093 0 .00 RPM
YRI_NA19099 0 .00 RPM
YRI_NA19114 0 .00 RPM
YRI_NA19118 0 .00 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).



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