RetrogeneDB ID:

retro_hsap_1990

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:19:23563118..23563675(+)
Located in intron of:ENSG00000167232
Retrocopy
information
Ensembl ID:ENSG00000269431
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:BNIP3
Ensembl ID:ENSG00000176171
Aliases:None
Description:BCL2/adenovirus E1B 19kDa interacting protein 3 [Source:HGNC Symbol;Acc:1084]


Retrocopy-Parental alignment summary:






>retro_hsap_1990
CTGCAGAAGGAGAGCTTGCAGGCCTCCCGGGTAGAATCGCACCTTCACAATAATGGGAATGCGAGCATTATCTAAGCCAC
AGTTTCTATTTATAATGGTGACATGGAAAATATACTGCTGGGTTTCCAGCATGCATCCAGATAGAGATAGCTCTAAGAGT
TCTCACTGTGACAGCCCATGTCTTTCACAGACATTATGGGATACTAATAGGGTTTCTAAAACAGATACACAAAGCATTAG
AAAGAAAAACAGCTCTCATTCCGAGAAAGATTATATTGAGAGAAAAAAACAAGTTAAAAGCGTCTTAAGAAAAAACTGAG
ATTACATATAAGATTGATCAAGTCAGCCAGAAAATATTCCTCTAAAAATAATTTCTCTCTAAATATCCAAAGTGCATAGC
TACTCACAGCATGAGAAACATGAGTGTTATGAAGAAAGGGCACATTATCAGCAGAATTTTAGAAGATTTTTTTCTATCTC
TGCTGCTCTCTAATCTGCTGCCCATTAAATGTGGAATCTATATAGAAATATATCTGACAACTACCACCAGCACTTTT

ORF - retro_hsap_1990 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 63.83 %
Parental protein coverage: 95.88 %
Number of stop codons detected: 4
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalMQEESLQGSWVELHFSNNGNGGSVPASVSIYNGDMEKILLDAQHES-GRSSSKSSHCDSPPRSQTPQDTN
.Q.ESLQ.S.VE.H..NNGN.....A.VSIYNGDME.ILL..QH.S..R.SSKSSHCDSP..SQT..DTN
RetrocopyLQKESLQASRVESHLHNNGNASII*ATVSIYNGDMENILLGFQHAS>DRDSSKSSHCDSPCLSQTLWDTN
ParentalRASETDTHSIGEKNSSQSEEDDIERRKEVESILKKNSDWIWDWSSRPENIPPKE-FLFKHPKRTATLSMR
R.S.TDT.SI..KNSS.SE.D.IER.K.V.S.L.KN.D.I.D.SS.PENIP.K..FL.K.PK..AT.SMR
RetrocopyRVSKTDTQSIRKKNSSHSEKDYIERKKQVKSVLRKN*DYI*D*SSQPENIPLKI>FLSKYPKCIATHSMR
ParentalNTSVMKKGGIFSAEFLKVFLPSLLLSHLLAIGLGIYIGRRLTTSTSTF
N.SVMKKG.I.S...L..F..SLLLS.LL.I..GIYI...LTT.TSTF
RetrocopyNMSVMKKGHIIS-RILEDFFLSLLLSNLLPIKCGIYIEIYLTTTTSTF

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 44 .33 RPM
bodymap2_adrenal 0 .12 RPM 10 .87 RPM
bodymap2_brain 0 .00 RPM 89 .99 RPM
bodymap2_breast 0 .02 RPM 50 .86 RPM
bodymap2_colon 0 .00 RPM 54 .80 RPM
bodymap2_heart 0 .07 RPM 96 .75 RPM
bodymap2_kidney 0 .00 RPM 59 .73 RPM
bodymap2_liver 0 .00 RPM 85 .68 RPM
bodymap2_lung 0 .00 RPM 21 .48 RPM
bodymap2_lymph_node 0 .00 RPM 28 .96 RPM
bodymap2_ovary 0 .00 RPM 28 .72 RPM
bodymap2_prostate 0 .00 RPM 40 .91 RPM
bodymap2_skeletal_muscle 0 .00 RPM 162 .78 RPM
bodymap2_testis 0 .00 RPM 41 .48 RPM
bodymap2_thyroid 0 .06 RPM 42 .54 RPM
bodymap2_white_blood_cells 0 .00 RPM 10 .81 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_1990 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_1990 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_1990 retrocopy 5' end.

Lab - click to see more details

retro_hsap_1990 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_1990 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_1327
Gorilla gorilla retro_ggor_1440
Parental genes homology:
Parental genes homology involve 19 parental genes, and 146 retrocopies.

Species Parental gene accession Retrocopies number
Choloepus hoffmanni ENSCHOG000000021502 retrocopies
retro_chof_1555, retro_chof_559,
Callithrix jacchus ENSCJAG000000002288 retrocopies
retro_cjac_1882, retro_cjac_2068, retro_cjac_2105, retro_cjac_2106, retro_cjac_2107, retro_cjac_2108, retro_cjac_3953, retro_cjac_4031,
Cavia porcellus ENSCPOG000000058827 retrocopies
retro_cpor_1138, retro_cpor_1283, retro_cpor_344, retro_cpor_376, retro_cpor_496, retro_cpor_600, retro_cpor_647,
Dipodomys ordii ENSDORG000000125111 retrocopy
retro_dord_431,
Equus caballus ENSECAG000000174583 retrocopies
retro_ecab_652, retro_ecab_921, retro_ecab_969,
Echinops telfairi ENSETEG000000117041 retrocopy
retro_etel_1779,
Homo sapiens ENSG00000176171 21 retrocopies
retro_hsap_1308, retro_hsap_1486, retro_hsap_1976, retro_hsap_1979, retro_hsap_1980, retro_hsap_1983, retro_hsap_1985, retro_hsap_1986, retro_hsap_1988, retro_hsap_1990 , retro_hsap_2035, retro_hsap_2036, retro_hsap_2039, retro_hsap_2040, retro_hsap_2042, retro_hsap_2043, retro_hsap_2044, retro_hsap_2046, retro_hsap_3741, retro_hsap_3743, retro_hsap_3858,
Gorilla gorilla ENSGGOG0000001452017 retrocopies
retro_ggor_1138, retro_ggor_1433, retro_ggor_1434, retro_ggor_1436, retro_ggor_1437, retro_ggor_1438, retro_ggor_1439, retro_ggor_1440, retro_ggor_1466, retro_ggor_1467, retro_ggor_1468, retro_ggor_1469, retro_ggor_1472, retro_ggor_1474, retro_ggor_1475, retro_ggor_2521, retro_ggor_2599,
Microcebus murinus ENSMICG000000119851 retrocopy
retro_mmur_563,
Macaca mulatta ENSMMUG0000002244513 retrocopies
retro_mmul_1367, retro_mmul_1369, retro_mmul_1371, retro_mmul_1392, retro_mmul_1393, retro_mmul_1394, retro_mmul_1681, retro_mmul_355, retro_mmul_421, retro_mmul_739, retro_mmul_754, retro_mmul_772, retro_mmul_819,
Mus musculus ENSMUSG000000785664 retrocopies
retro_mmus_1194, retro_mmus_1195, retro_mmus_2207, retro_mmus_3577,
Nomascus leucogenys ENSNLEG0000000161326 retrocopies
retro_nleu_140, retro_nleu_1708, retro_nleu_2220, retro_nleu_2306, retro_nleu_2617, retro_nleu_2619, retro_nleu_2620, retro_nleu_2621, retro_nleu_2870, retro_nleu_2872, retro_nleu_2903, retro_nleu_2904, retro_nleu_2905, retro_nleu_2907, retro_nleu_2910, retro_nleu_2917, retro_nleu_2918, retro_nleu_2919, retro_nleu_2920, retro_nleu_2921, retro_nleu_2923, retro_nleu_2924, retro_nleu_2942, retro_nleu_3064, retro_nleu_3103, retro_nleu_3104,
Pongo abelii ENSPPYG0000000277118 retrocopies
retro_pabe_1629, retro_pabe_1631, retro_pabe_1632, retro_pabe_1633, retro_pabe_1665, retro_pabe_1666, retro_pabe_1667, retro_pabe_1670, retro_pabe_1688, retro_pabe_1694, retro_pabe_1703, retro_pabe_2499, retro_pabe_3049, retro_pabe_3050, retro_pabe_3120, retro_pabe_3122, retro_pabe_3533, retro_pabe_3569,
Pan troglodytes ENSPTRG0000000306717 retrocopies
retro_ptro_1005, retro_ptro_1317, retro_ptro_1319, retro_ptro_1323, retro_ptro_1324, retro_ptro_1325, retro_ptro_1327, retro_ptro_1353, retro_ptro_1354, retro_ptro_1356, retro_ptro_1357, retro_ptro_1359, retro_ptro_1360, retro_ptro_1361, retro_ptro_1363, retro_ptro_2629, retro_ptro_3062,
Rattus norvegicus ENSRNOG000000172433 retrocopies
retro_rnor_1070, retro_rnor_2645, retro_rnor_2732,
Sus scrofa ENSSSCG000000243881 retrocopy
retro_sscr_827,
Ictidomys tridecemlineatus ENSSTOG000000124561 retrocopy
retro_itri_299,
Tupaia belangeri ENSTBEG000000004871 retrocopy
retro_tbel_2600,
Tursiops truncatus ENSTTRG000000080381 retrocopy
retro_ttru_1538,

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 = 0.09 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .02 RPM
CEU_NA11843 0 .00 RPM
CEU_NA11930 0 .00 RPM
CEU_NA12004 0 .04 RPM
CEU_NA12400 0 .00 RPM
CEU_NA12751 0 .00 RPM
CEU_NA12760 0 .00 RPM
CEU_NA12827 0 .09 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 .03 RPM
GBR_HG00119 0 .00 RPM
GBR_HG00131 0 .00 RPM
GBR_HG00133 0 .02 RPM
GBR_HG00134 0 .04 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 .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 .03 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 .05 RPM
YRI_NA19114 0 .00 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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