RetrogeneDB ID:

retro_hsap_3669

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:6:137865039..137865509(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000213108
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:BTF3L4
Ensembl ID:ENSG00000134717
Aliases:None
Description:basic transcription factor 3-like 4 [Source:HGNC Symbol;Acc:30547]


Retrocopy-Parental alignment summary:






>retro_hsap_3669
ATGAATCAAGAAAAGTTAGCCAAACTTCAGGCTCAGGTCCGGAAAGGGGGCAAGGGTACACCTCACAGAAAGAAGGTGGT
ACGTAGAACAGCTATAGCTAATGACAAAAAGCTTCAGAATTATCTAAAAAAAACCTGGCTGTGAATAATATAGCTGGTAT
TGAAGAGGTGAACATGATTAAAGATGATAGGACAGTTATTCATTTCAACAATCCCAAAGTCCAAGCTTCCCTTTCTGCTA
ATACCTTTGCAATTACTGGTCATGCAGAAGCCAAACCAATCACAGAAATGCTTCCTGGAATATTAAGTCAGCTTGGTGCT
GACAGCTTAACAATCCTTAAGAAGTTAGCTGAACAGTTCCCATGGCAAGTCTTGGACAGTAAAGCACCAAAACCAGAAGA
CATTGATGAGGAGGAGGAGGATGTTCTAGATCCTGTAGAAAAATCTGATAAGGCATCAAAGAATGAAGCT

ORF - retro_hsap_3669 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 80.38 %
Parental protein coverage: 99.37 %
Number of stop codons detected: 0
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMNQEKLAKLQAQVRIGGKGTARRKKKVVHRTATAD-DKKLQSSLKKLAVNNIAGIEEVNMIKDDGTVIHF
MNQEKLAKLQAQVR.GGKGT..RKK.V.......D..K....S...LAVNNIAGIEEVNMIKDD.TVIHF
RetrocopyMNQEKLAKLQAQVRKGGKGTPHRKKVVRRTAIAND<QKASELSXXXLAVNNIAGIEEVNMIKDDRTVIHF
ParentalNNPKVQASLSANTFAITGHAEAKPITEMLPGILSQLGADSLTSLRKLAEQFPRQVLDSKAPKPEDIDEED
NNPKVQASLSANTFAITGHAEAKPITEMLPGILSQLGADSLT.L.KLAEQFP.QVLDSKAPKPEDIDEE.
RetrocopyNNPKVQASLSANTFAITGHAEAKPITEMLPGILSQLGADSLTILKKLAEQFPWQVLDSKAPKPEDIDEEE
ParentalDDVPDLVENFDEASKNEA
.DV.D.VE..D.ASKNEA
RetrocopyEDVLDPVEKSDKASKNEA

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 56 .29 RPM
bodymap2_adrenal 0 .04 RPM 50 .07 RPM
bodymap2_brain 0 .00 RPM 78 .50 RPM
bodymap2_breast 0 .04 RPM 85 .27 RPM
bodymap2_colon 0 .00 RPM 45 .63 RPM
bodymap2_heart 0 .00 RPM 32 .29 RPM
bodymap2_kidney 0 .00 RPM 47 .79 RPM
bodymap2_liver 0 .00 RPM 19 .03 RPM
bodymap2_lung 0 .00 RPM 37 .71 RPM
bodymap2_lymph_node 0 .00 RPM 34 .37 RPM
bodymap2_ovary 0 .06 RPM 94 .11 RPM
bodymap2_prostate 0 .00 RPM 58 .25 RPM
bodymap2_skeletal_muscle 0 .00 RPM 66 .13 RPM
bodymap2_testis 0 .00 RPM 64 .63 RPM
bodymap2_thyroid 0 .00 RPM 59 .51 RPM
bodymap2_white_blood_cells 0 .00 RPM 68 .00 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_3669 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_3669 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_3669 retrocopy 5' end.

Lab - click to see more details

retro_hsap_3669 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_3669 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_2489
Pongo abelii retro_pabe_3010
Parental genes homology:
Parental genes homology involve 22 parental genes, and 109 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG000000215824 retrocopies
retro_cjac_2000, retro_cjac_2929, retro_cjac_4160, retro_cjac_451,
Cavia porcellus ENSCPOG000000040061 retrocopy
retro_cpor_908,
Ciona savignyi ENSCSAVG000000096531 retrocopy
retro_csav_25,
Dasypus novemcinctus ENSDNOG000000031814 retrocopies
retro_dnov_1690, retro_dnov_1928, retro_dnov_2672, retro_dnov_921,
Erinaceus europaeus ENSEEUG000000045023 retrocopies
retro_eeur_215, retro_eeur_447, retro_eeur_456,
Echinops telfairi ENSETEG0000001192311 retrocopies
retro_etel_1017, retro_etel_1167, retro_etel_1207, retro_etel_1409, retro_etel_1990, retro_etel_2113, retro_etel_2203, retro_etel_291, retro_etel_663, retro_etel_804, retro_etel_953,
Homo sapiens ENSG00000134717 3 retrocopies
retro_hsap_2173, retro_hsap_2514, retro_hsap_3669 ,
Homo sapiens ENSG0000014574111 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,
Loxodonta africana ENSLAFG000000161243 retrocopies
retro_lafr_206, retro_lafr_769, retro_lafr_947,
Macropus eugenii ENSMEUG0000000613510 retrocopies
retro_meug_1114, retro_meug_1164, retro_meug_1333, retro_meug_1395, retro_meug_1512, retro_meug_1663, retro_meug_2008, retro_meug_298, retro_meug_903, retro_meug_966,
Microcebus murinus ENSMICG000000028071 retrocopy
retro_mmur_804,
Myotis lucifugus ENSMLUG000000168841 retrocopy
retro_mluc_912,
Macaca mulatta ENSMMUG000000036361 retrocopy
retro_mmul_59,
Monodelphis domestica ENSMODG000000007702 retrocopies
retro_mdom_33, retro_mdom_992,
Mus musculus ENSMUSG000000285682 retrocopies
retro_mmus_1134, retro_mmus_2743,
Nomascus leucogenys ENSNLEG000000160412 retrocopies
retro_nleu_1439, retro_nleu_521,
Oryctolagus cuniculus ENSOCUG000000015173 retrocopies
retro_ocun_1001, retro_ocun_1412, retro_ocun_1912,
Procavia capensis ENSPCAG000000064283 retrocopies
retro_pcap_129, retro_pcap_307, retro_pcap_373,
Pongo abelii ENSPPYG000000013532 retrocopies
retro_pabe_1850, retro_pabe_3010,
Pan troglodytes ENSPTRG000000007353 retrocopies
retro_ptro_1459, retro_ptro_1658, retro_ptro_2489,
Rattus norvegicus ENSRNOG000000085128 retrocopies
retro_rnor_1113, retro_rnor_1666, retro_rnor_1870, retro_rnor_1871, retro_rnor_1872, retro_rnor_537, retro_rnor_760, retro_rnor_998,
Tupaia belangeri ENSTBEG0000001330730 retrocopies
retro_tbel_1050, retro_tbel_1052, retro_tbel_1178, retro_tbel_1595, retro_tbel_1642, retro_tbel_1785, retro_tbel_1883, retro_tbel_1924, retro_tbel_2245, retro_tbel_2290, retro_tbel_2532, retro_tbel_2979, retro_tbel_3092, retro_tbel_3100, retro_tbel_3340, retro_tbel_3469, retro_tbel_3483, retro_tbel_3520, retro_tbel_3583, retro_tbel_3598, retro_tbel_3986, retro_tbel_4045, retro_tbel_4278, retro_tbel_4283, retro_tbel_4563, retro_tbel_4623, retro_tbel_539, retro_tbel_701, retro_tbel_98, retro_tbel_991,

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 = 0.04 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 .04 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 .03 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).



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