RetrogeneDB ID:

retro_hsap_3732

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:7:55312296..55313374(+)
Located in intron of:ENSG00000146648
Retrocopy
information
Ensembl ID:ENSG00000237210
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:SLC19A3
Ensembl ID:ENSG00000135917
Aliases:SLC19A3, BBGD, THMD2, THTR2
Description:solute carrier family 19, member 3 [Source:HGNC Symbol;Acc:16266]


Retrocopy-Parental alignment summary:






>retro_hsap_3732
AGCATGGTCAGCCCTGAGACACTGTCAGGAAGTGAGAGGCCACTGTAGGAGTGTCACGCTAACAGCTAACCCAGCGGCCC
CCATGAAGGCTGACGCTTGGCATCCCTGGAGAATGGGTCACACTTTTACCTCATCGCATAGCCATAGTCTCTGCCTCCAC
AGCCTTCATTTTCTCACTTTTTCTATCAATGCCCAAGAAAAGAATGTTTTTCCATGCAAAACCCAGCAAAGAAATAAAGT
CCCCAAGCCTGTGTGCAGGGTTAAAGGAACCTCATGAGAGTGAAGCACTAGGCTGCGAAGGGGAGAAACCCACTTGGGAA
AAGCCCACCACTTCGGGGAACCTGGATGACGGCCCATAGAGCATAGTGCCACAAACAGTGACTCTGAAAGTTCGTGTTCC
ATGGTTCCAAGATTTGAAGTAGTGTTACTCCTCAGAGGCCTTTGTTACTAATCCCCACGGTGGGCTTTTTCCACCACAGG
TTTTAACCTAGCTTTGAACTATGTTCAAGTCCTATGAGGTTGCAAAGCACCACCCCAATATTCTTATACCTATAACGGGG
CACAGAAGCTACTGAAGCATTTGGTAGGGCTGTGGCTGCCTGTGCAGTGGGCTATGTGAAAATCAACTGGAGTCTCCTGG
AGAGTGGGCTCTGGAAGTCTCCTCAGTCATCAACGCAGGCTCTTGACCTCTCGTGCACTATATGACCAAAGTCTACGCAG
GCTATGTGGGCTATTTGCGATTCAAGTCCAGCTATGTGCTGCTTCTAACCCAGGCAGTATTCCAGACTGCAGTCCAGCTG
AGCGTGGAATGTGTATCCTGGTGCCCGGATTCCACACTTCACTGCCTTGGTGATTCAGCCGACCCTCATCACTGTGACTG
CAATTCATCAGAAAGGGCTCAGCCTGTGATCAGCATTCAGTTTGTAGTTTATAGGAGTTATTTTGCAGTCACTTCTAGAA
TTTTCCTAATAAGAAGAATATCTAATGCCTATCAGCCAAATGCCAAGAGGAAGGAGTTCAGAGCCCCGCTATGAGTCAGA
ACCCAGATGGGCCGCACCCAAAGGAGCTGAGCAGTATC

ORF - retro_hsap_3732 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 57.75 %
Parental protein coverage: 73.58 %
Number of stop codons detected: 5
Number of frameshifts detected 10


Retrocopy - Parental Gene Alignment:

ParentalSVVSPE-HYQRVSGYCRSVTLAAYTAGSVLAQL-LVSLANMSYFYL-NVISLASVSVAFLFSLFLPMPKK
S.VSPE.H.Q.V.G.CRSVTL.A..A....A...L.SL.N.S.FYL...I...S.S.AF.FSLFL.MPKK
RetrocopySMVSPE>HCQEVRGHCRSVTLTANPAAPMKADA<LASLENGSHFYL<HRIAIVSASTAFIFSLFLSMPKK
ParentalSMFFHAKPSREIKKSSSVNPVLEETHEGEAPGCEEQKPTSEILSTSGKLNKGQLNSLKPSNVTVDVFVQW
.MFFHAKPS.EI.KS.S....L.E.HE.EA.GCE..KPT.E...TSG.L..G...S..P..VT..V.V.W
RetrocopyRMFFHAKPSKEI-KSPSLCAGLKEPHESEALGCEGEKPTWEKPTTSGNLDDGP-*SIVPQTVTLKVRVPW
ParentalFQDLKECYSS-KRLFYWSLWWAFATAGFNQVLNYVQILWDYKAPSQDSSIYNGA-VEAIATFGGAVAAFA
FQDLK.CYSS...L.Y.S..WAF.T.GFN..LNYVQ.L...KAP.Q.S..YNGA..EA...FG.AVAA.A
RetrocopyFQDLK*CYSS<RGLCY*SPRWAFSTTGFNLALNYVQVL*GCKAPPQYSYTYNGA<TEATEAFGRAVAACA
ParentalVGYVKVNWDLL-GELALVVFSVVNAGSLFLMHYTANIWACYAGYLIFKSSYMLLITIAVFQIAVNLNVER
VGYVK.NW.LL.GE.AL.V.SV.NAGS..L.HY.....A.Y.GYL.FKSSY.LL.T.AVFQ.AV.L.VE.
RetrocopyVGYVKINWSLL<GEWALEVSSVINAGS*PLVHYMTKVYAGYVGYLRFKSSYVLLLTQAVFQTAVQLSVEC
ParentalYA-LVFGINT-FIALVIQ-TIMTVIVVDQRGLNL-PVSIQFLVYGSYFAVIAGIFLMRSMYITY-STKSQ
...LV.G..T.F.ALVIQ.T..TV....Q.GL.L...SIQF.VY.SYFAV...IFL.R.....Y.S.K.Q
RetrocopyVS<LVPGFHT<FTALVIQPTLITVTAIHQKGLSL<VISIQFVVYRSYFAVTSRIFLIRRISNAY<SAKCQ
ParentalKD-VQSPAPSENPDVSHPEEESNI
...VQSPA.S.NPD..HP.E.S.I
RetrocopyEEGVQSPAMSQNPDGPHPKELSSI

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 318 .76 RPM
bodymap2_adrenal 0 .06 RPM 15 .17 RPM
bodymap2_brain 0 .00 RPM 3 .33 RPM
bodymap2_breast 0 .00 RPM 252 .30 RPM
bodymap2_colon 0 .00 RPM 9 .47 RPM
bodymap2_heart 0 .00 RPM 3 .06 RPM
bodymap2_kidney 0 .00 RPM 11 .25 RPM
bodymap2_liver 0 .00 RPM 9 .61 RPM
bodymap2_lung 0 .00 RPM 18 .27 RPM
bodymap2_lymph_node 0 .00 RPM 22 .55 RPM
bodymap2_ovary 0 .00 RPM 2 .93 RPM
bodymap2_prostate 0 .00 RPM 5 .13 RPM
bodymap2_skeletal_muscle 0 .00 RPM 0 .85 RPM
bodymap2_testis 0 .02 RPM 1 .81 RPM
bodymap2_thyroid 0 .09 RPM 1 .96 RPM
bodymap2_white_blood_cells 0 .00 RPM 0 .00 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_3732 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_3732 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_3732 retrocopy 5' end.

Lab - click to see more details

retro_hsap_3732 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_3732 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_2526
Parental genes homology:
Parental genes homology involve 7 parental genes, and 7 retrocopies.

Species Parental gene accession Retrocopies number
Homo sapiens ENSG00000135917 1 retrocopy
retro_hsap_3732 ,
Gorilla gorilla ENSGGOG000000043441 retrocopy
retro_ggor_2518,
Monodelphis domestica ENSMODG000000212201 retrocopy
retro_mdom_955,
Mustela putorius furoENSMPUG000000013741 retrocopy
retro_mputfur_1211,
Nomascus leucogenys ENSNLEG000000135011 retrocopy
retro_nleu_2561,
Pongo abelii ENSPPYG000000132421 retrocopy
retro_pabe_3209,
Pan troglodytes ENSPTRG000000289981 retrocopy
retro_ptro_2526,

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 ) 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 .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 .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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