RetrogeneDB ID:

retro_hsap_2964

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:4:99661892..99662379(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000227118
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:BTF3
Ensembl ID:ENSG00000145741
Aliases:BTF3, BETA-NAC, BTF3a, BTF3b, NACB
Description:basic transcription factor 3 [Source:HGNC Symbol;Acc:1125]


Retrocopy-Parental alignment summary:






>retro_hsap_2964
AAGATGAAAGAAATGATCATGAACCAGGAAAACTCGCCAAACTGCAGGCACAAGTGCGCATTGGTGGGAAAGGAACTGCT
CACAGAAAGAAGAAGGTCTTCCATAGAACAGCCACAGCCGATGATAAAAAGCTTCAATTCTCCTTAAAGAAGTTACAGGT
AAACAATATCTCTGGTATTGAAAAGGTGAATATGTTTACAAACCAAGGAACAGTGATCCACTTTAACAACCCTAAATTTC
AGGCATCGCTGGCAGTGAACACTTTCACCATAACAGGTCATGCTGAGGCAAAGCAGGTGACAGAAATGCTACCCAGTGTC
TTAAGCCAGCTTGGTGCAGACAGTCTGACTAGTTTAAGGAGACTGGCTGAAGTTCTGCCCAAACAACCTGTGGATGGAAA
AGCACCACTTGCTACTGGAGGGGATGATGATGATGGAGTTCCAGAATTGTGGAGAATTTTGATGAGGCTTCCAGGAATGA
GGCAAGC

ORF - retro_hsap_2964 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 87.27 %
Parental protein coverage: 79.13 %
Number of stop codons detected: 0
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalQMKETIMNQE-KLAKLQAQVRIGGKGTARRKKKVVHRTATADDKKLQFSLKKLGVNNISGIEEVNMFTNQ
.MKE.IMNQE.KLAKLQAQVRIGGKGTA.RKKKV.HRTATADDKKLQFSLKKL.VNNISGIE.VNMFTNQ
RetrocopyKMKEMIMNQE<KLAKLQAQVRIGGKGTAHRKKKVFHRTATADDKKLQFSLKKLQVNNISGIEKVNMFTNQ
ParentalGTVIHFNNPKVQASLAANTFTITGHAETKQLTEMLPSILNQLGADSLTSLRRLAEALPKQSVDGKAPLAT
GTVIHFNNPK.QASLA.NTFTITGHAE.KQ.TEMLPS.L.QLGADSLTSLRRLAE.LPKQ.VDGKAPLAT
RetrocopyGTVIHFNNPKFQASLAVNTFTITGHAEAKQVTEMLPSVLSQLGADSLTSLRRLAEVLPKQPVDGKAPLAT
ParentalGEDDDDEVPDL-VENFDEASKNEAN
G.DDDD.VP.L.VENFDEAS.NEA.
RetrocopyGGDDDDGVPEL<VENFDEASRNEAS

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 386 .23 RPM
bodymap2_adrenal 0 .00 RPM 350 .97 RPM
bodymap2_brain 0 .00 RPM 194 .62 RPM
bodymap2_breast 0 .00 RPM 299 .26 RPM
bodymap2_colon 0 .00 RPM 505 .75 RPM
bodymap2_heart 0 .00 RPM 164 .84 RPM
bodymap2_kidney 0 .04 RPM 199 .22 RPM
bodymap2_liver 0 .00 RPM 134 .26 RPM
bodymap2_lung 0 .00 RPM 366 .81 RPM
bodymap2_lymph_node 0 .00 RPM 341 .83 RPM
bodymap2_ovary 0 .00 RPM 628 .33 RPM
bodymap2_prostate 0 .00 RPM 552 .15 RPM
bodymap2_skeletal_muscle 0 .02 RPM 371 .32 RPM
bodymap2_testis 0 .00 RPM 329 .97 RPM
bodymap2_thyroid 0 .00 RPM 333 .90 RPM
bodymap2_white_blood_cells 0 .00 RPM 418 .09 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_2964 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_2964 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_1471401570 libraries233 libraries21 libraries3 libraries2 libraries

The graphical summary, for retro_hsap_2964 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_2964 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_2964 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_2006
Gorilla gorilla retro_ggor_2054
Pongo abelii retro_pabe_2458
Parental genes homology:
Parental genes homology involve 20 parental genes, and 155 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG0000001156314 retrocopies
retro_amel_1257, retro_amel_1279, retro_amel_1324, retro_amel_1334, retro_amel_1433, retro_amel_166, retro_amel_1769, retro_amel_182, retro_amel_1841, retro_amel_480, retro_amel_513, retro_amel_784, retro_amel_908, retro_amel_986,
Choloepus hoffmanni ENSCHOG0000000186113 retrocopies
retro_chof_1027, retro_chof_1166, retro_chof_117, retro_chof_1397, retro_chof_1406, retro_chof_1884, retro_chof_1960, retro_chof_2194, retro_chof_2682, retro_chof_2703, retro_chof_344, retro_chof_364, retro_chof_700,
Callithrix jacchus ENSCJAG000000166004 retrocopies
retro_cjac_1454, retro_cjac_1673, retro_cjac_2640, retro_cjac_281,
Cavia porcellus ENSCPOG000000128321 retrocopy
retro_cpor_81,
Ciona savignyi ENSCSAVG000000096531 retrocopy
retro_csav_25,
Dasypus novemcinctus ENSDNOG000000186824 retrocopies
retro_dnov_1958, retro_dnov_2107, retro_dnov_497, retro_dnov_817,
Felis catus ENSFCAG0000002397310 retrocopies
retro_fcat_1044, retro_fcat_1378, retro_fcat_1438, retro_fcat_187, retro_fcat_188, retro_fcat_225, retro_fcat_28, retro_fcat_419, retro_fcat_593, retro_fcat_919,
Homo sapiens ENSG000001347173 retrocopies
retro_hsap_2173, retro_hsap_2514, retro_hsap_3669,
Homo sapiens ENSG00000145741 11 retrocopies
retro_hsap_1215, retro_hsap_1396, retro_hsap_2259, retro_hsap_2525, retro_hsap_2819, retro_hsap_2964 , retro_hsap_3533, retro_hsap_3551, retro_hsap_3972, retro_hsap_4270, retro_hsap_625,
Myotis lucifugus ENSMLUG0000001291211 retrocopies
retro_mluc_1024, retro_mluc_1349, retro_mluc_1459, retro_mluc_1748, retro_mluc_1820, retro_mluc_1823, retro_mluc_2560, retro_mluc_2602, retro_mluc_482, retro_mluc_682, retro_mluc_694,
Macaca mulatta ENSMMUG000000222912 retrocopies
retro_mmul_105, retro_mmul_2424,
Monodelphis domestica ENSMODG000000017623 retrocopies
retro_mdom_189, retro_mdom_454, retro_mdom_931,
Mustela putorius furoENSMPUG0000000586428 retrocopies
retro_mputfur_1125, retro_mputfur_1149, retro_mputfur_1267, retro_mputfur_1289, retro_mputfur_1319, retro_mputfur_1321, retro_mputfur_1386, retro_mputfur_1414, retro_mputfur_1472, retro_mputfur_1525, retro_mputfur_1548, retro_mputfur_1576, retro_mputfur_1599, retro_mputfur_246, retro_mputfur_324, retro_mputfur_392, retro_mputfur_403, retro_mputfur_431, retro_mputfur_618, retro_mputfur_661, retro_mputfur_724, retro_mputfur_728, retro_mputfur_753, retro_mputfur_760, retro_mputfur_795, retro_mputfur_901, retro_mputfur_926, retro_mputfur_972,
Mus musculus ENSMUSG0000002166011 retrocopies
retro_mmus_1904, retro_mmus_2445, retro_mmus_2769, retro_mmus_3054, retro_mmus_3272, retro_mmus_3344, retro_mmus_3525, retro_mmus_443, retro_mmus_451, retro_mmus_470, retro_mmus_707,
Pan troglodytes ENSPTRG0000001697912 retrocopies
retro_ptro_1470, retro_ptro_1599, retro_ptro_1675, retro_ptro_1912, retro_ptro_2006, retro_ptro_2413, retro_ptro_2494, retro_ptro_2697, retro_ptro_2896, retro_ptro_455, retro_ptro_832, retro_ptro_959,
Pteropus vampyrus ENSPVAG0000000716011 retrocopies
retro_pvam_1011, retro_pvam_241, retro_pvam_301, retro_pvam_440, retro_pvam_456, retro_pvam_515, retro_pvam_602, retro_pvam_647, retro_pvam_70, retro_pvam_882, retro_pvam_919,
Sorex araneus ENSSARG000000077365 retrocopies
retro_sara_195, retro_sara_279, retro_sara_354, retro_sara_427, retro_sara_74,
Tarsius syrichta ENSTSYG000000012957 retrocopies
retro_tsyr_1360, retro_tsyr_1388, retro_tsyr_212, retro_tsyr_707, retro_tsyr_878, retro_tsyr_90, retro_tsyr_954,
Tursiops truncatus ENSTTRG000000072902 retrocopies
retro_ttru_1883, retro_ttru_391,
Vicugna pacos ENSVPAG000000096072 retrocopies
retro_vpac_185, retro_vpac_467,

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 = 0.06 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .02 RPM
CEU_NA11843 0 .00 RPM
CEU_NA11930 0 .00 RPM
CEU_NA12004 0 .00 RPM
CEU_NA12400 0 .04 RPM
CEU_NA12751 0 .00 RPM
CEU_NA12760 0 .00 RPM
CEU_NA12827 0 .05 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 .03 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 .06 RPM
TSI_NA20532 0 .03 RPM
TSI_NA20538 0 .00 RPM
TSI_NA20756 0 .03 RPM
TSI_NA20765 0 .00 RPM
TSI_NA20771 0 .00 RPM
TSI_NA20786 0 .03 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 .02 RPM

Indel association:

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





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