RetrogeneDB ID: retro_hsap_3533

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 6:150299057..150299546(+)
• Located in intron of: ENSG00000219298

Retrocopy information

• Ensembl ID: ENSG00000231120
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: BTF3
• Ensembl ID: ENSG00000145741
• Aliases: BTF3, BETA-NAC, BTF3a, BTF3b, NACB
• Description: basic transcription factor 3 [Source:HGNC Symbol;Acc:1125]

Sequence

>retro_hsap_3533
AAGATGAAAGAAACAATCACGAACCAGGAAAAACTTGCCAAACTGCAGGCACAAGTGTGCATTGGTGGGAAAGGACCTGC
TTGCAGAAAGAAGAAGGTGGTTCATAGAACAGCCACAGCAGAAGATAAAAACTTTCAGTTCTCCTTAAAGAAGTTAGGGG
TAAACAATATCTCTGGTATTGAAGAGGTGAATATGTTTACAAACCAAGGAACAGTGATCCACTTTAACAACCCTGAAGTT
CAGACATCTCTGGCAGGGAACACTTTCACCATTACAGGCCATGCTAAGACAAAGCAGCTGACAGAAATGCTACCCAGCAT
CTTAATCCAGCTTGGTGTAGACAGTCTGGCTAGTTTAAGGAGACTGGCTGAAGCTCTGCCCAAACAATCTGTGGATGGAA
CAGCACCATTTGCAACTGGAGAGGATGATGATGATGAAGTTCCAGATCTTGTGGAGAATTTTTATGAGGCTTTCAAGGAT
GAGGCAAAC

Alignment

ORF - retro_hsap_3533 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.73 %
• Parental protein coverage: 79.13 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QMKETIMNQEKLAKLQAQVRIGGKGTARRKKKVVHRTATADDKKLQFSLKKLGVNNISGIEEVNMFTNQG
          .MKETI.NQEKLAKLQAQV.IGGKG.A.RKKKVVHRTATA.DK..QFSLKKLGVNNISGIEEVNMFTNQG
Retrocopy KMKETITNQEKLAKLQAQVCIGGKGPACRKKKVVHRTATAEDKNFQFSLKKLGVNNISGIEEVNMFTNQG

Parental  TVIHFNNPKVQASLAANTFTITGHAETKQLTEMLPSILNQLGADSLTSLRRLAEALPKQSVDGKAPLATG
          TVIHFNNP.VQ.SLA.NTFTITGHA.TKQLTEMLPSIL.QLG.DSL.SLRRLAEALPKQSVDG.AP.ATG
Retrocopy TVIHFNNPEVQTSLAGNTFTITGHAKTKQLTEMLPSILIQLGVDSLASLRRLAEALPKQSVDGTAPFATG

Parental  EDDDDEVPDLVENFDEASKNEAN
          EDDDDEVPDLVENF.EA.K.EAN
Retrocopy EDDDDEVPDLVENFYEAFKDEAN

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

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	0.02 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	0.00 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	0.04 RPM	371.32 RPM
bodymap2_testis	0.11 RPM	329.97 RPM
bodymap2_thyroid	0.00 RPM	333.90 RPM
bodymap2_white_blood_cells	0.00 RPM	418.09 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_3533 was not detected

EST

No EST(s) were mapped for retro_hsap_3533 retrocopy.

TSS

No TSS is located nearby retro_hsap_3533 retrocopy 5' end.

Lab

retro_hsap_3533 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_3533 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pongo abelii	retro_pabe_2918

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Parental genes homology:

Parental genes homology involve 20 parental genes, and 155 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011563	14 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	ENSCHOG00000001861	13 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	ENSCJAG00000016600	4 retrocopies	retro_cjac_1454, retro_cjac_1673, retro_cjac_2640, retro_cjac_281,
Cavia porcellus	ENSCPOG00000012832	1 retrocopy	retro_cpor_81,
Ciona savignyi	ENSCSAVG00000009653	1 retrocopy	retro_csav_25,
Dasypus novemcinctus	ENSDNOG00000018682	4 retrocopies	retro_dnov_1958, retro_dnov_2107, retro_dnov_497, retro_dnov_817,
Felis catus	ENSFCAG00000023973	10 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	ENSG00000134717	3 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	ENSMLUG00000012912	11 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	ENSMMUG00000022291	2 retrocopies	retro_mmul_105, retro_mmul_2424,
Monodelphis domestica	ENSMODG00000001762	3 retrocopies	retro_mdom_189, retro_mdom_454, retro_mdom_931,
Mustela putorius furo	ENSMPUG00000005864	28 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	ENSMUSG00000021660	11 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	ENSPTRG00000016979	12 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	ENSPVAG00000007160	11 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	ENSSARG00000007736	5 retrocopies	retro_sara_195, retro_sara_279, retro_sara_354, retro_sara_427, retro_sara_74,
Tarsius syrichta	ENSTSYG00000001295	7 retrocopies	retro_tsyr_1360, retro_tsyr_1388, retro_tsyr_212, retro_tsyr_707, retro_tsyr_878, retro_tsyr_90, retro_tsyr_954,
Tursiops truncatus	ENSTTRG00000007290	2 retrocopies	retro_ttru_1883, retro_ttru_391,
Vicugna pacos	ENSVPAG00000009607	2 retrocopies	retro_vpac_185, retro_vpac_467,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.02 RPM
CEU_NA11843	0.03 RPM
CEU_NA11930	0.00 RPM
CEU_NA12004	0.04 RPM
CEU_NA12400	0.11 RPM
CEU_NA12751	0.05 RPM
CEU_NA12760	0.09 RPM
CEU_NA12827	0.28 RPM
CEU_NA12872	0.03 RPM
CEU_NA12873	0.00 RPM
FIN_HG00183	0.08 RPM
FIN_HG00277	0.11 RPM
FIN_HG00315	0.03 RPM
FIN_HG00321	0.06 RPM
FIN_HG00328	0.07 RPM
FIN_HG00338	0.11 RPM
FIN_HG00349	0.11 RPM
FIN_HG00375	0.02 RPM
FIN_HG00377	0.05 RPM
FIN_HG00378	0.02 RPM
GBR_HG00099	0.09 RPM
GBR_HG00111	0.02 RPM
GBR_HG00114	0.03 RPM
GBR_HG00119	0.05 RPM
GBR_HG00131	0.03 RPM
GBR_HG00133	0.02 RPM
GBR_HG00134	0.04 RPM
GBR_HG00137	0.03 RPM
GBR_HG00142	0.06 RPM
GBR_HG00143	0.10 RPM
TSI_NA20512	0.08 RPM
TSI_NA20513	0.02 RPM
TSI_NA20518	0.06 RPM
TSI_NA20532	0.10 RPM
TSI_NA20538	0.05 RPM
TSI_NA20756	0.06 RPM
TSI_NA20765	0.04 RPM
TSI_NA20771	0.06 RPM
TSI_NA20786	0.10 RPM
TSI_NA20798	0.03 RPM
YRI_NA18870	0.00 RPM
YRI_NA18907	0.03 RPM
YRI_NA18916	0.13 RPM
YRI_NA19093	0.00 RPM
YRI_NA19099	0.11 RPM
YRI_NA19114	0.05 RPM
YRI_NA19118	0.00 RPM
YRI_NA19213	0.05 RPM
YRI_NA19214	0.05 RPM
YRI_NA19223	0.16 RPM

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Indel association:

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