RetrogeneDB ID:

retro_hsap_2638

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:3:39685536..39686193(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000230757
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:NFU1
Ensembl ID:ENSG00000169599
Aliases:NFU1, HIRIP, HIRIP5, MMDS1, NIFUC, Nfu, NifU
Description:NFU1 iron-sulfur cluster scaffold homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:16287]


Retrocopy-Parental alignment summary:






>retro_hsap_2638
CAGCCTCTGCATCAATTTGTAGAAAGACTACTCTTCCCACTACCTGCAGCCTTTTGTAACCCAGTGAGATACATGTTTAT
TCAAACACAAGATATCTCAAATCCTAACAGTTTAAAGTTTATACCATGAAAACCAGTTTTTGAGACAAGGCCCATGGATT
TTCCCACCCCAGCTGCAGCATTTTGCTCCCCTTTGGCTAGGCAGTTATTTAGGATTGAAGGAGTAAAAAGTGTTTTCTTT
GGGCCAGATTTCATCACTGCCACAAAGGAAAATGAAAAATTAGACTGGAATTTACTGAAACCAGATATTTACGCAACAAC
CACGGACTTCTTTGCATCTGGTTTACCCCTAGTTACTGAGGAAACATCTTCAAGGAGAAGCAGGATGTGAAGATGATGAA
GTTGTGGCATTGATTAAGGAAGTGTTAGATACTAGAATGTGGCCAACTGTGCAAGAAGATGGAGGAGACGTAATCTACAA
AGGTTTTGAAGATGGTATCGTATGACTGAAACTCCAGGGTTCTTGTACCAGCTGCCCTAGTTCAATCATTACTCTGAAAA
ATGGAATTCAGAACATGCTGCAGTTTATATTCCAGAGGTAGAAGGTGTAGAACAGGGTATGGATGATGAATCAGATGAAA
AGGAAGCAAACTCACCT

ORF - retro_hsap_2638 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 88.74 %
Parental protein coverage: 95.65 %
Number of stop codons detected: 2
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalQPLHQFVQRPLFPLPAAFYHPVRYMFIQTQDTPNPNSLKFIPGKPVLETRTMDFPTPAAAFRSPLARQLF
QPLHQFV.R.LFPLPAAF..PVRYMFIQTQD..NPNSLKFIP.KPV.ETR.MDFPTPAAAF.SPLARQLF
RetrocopyQPLHQFVERLLFPLPAAFCNPVRYMFIQTQDISNPNSLKFIP*KPVFETRPMDFPTPAAAFCSPLARQLF
ParentalRIEGVKSVFFGPDFITVTKENEELDWNLLKPDIYATIMDFFASGLPLVTEETPS-GEAGSEEDDEVVAMI
RIEGVKSVFFGPDFIT.TKENE.LDWNLLKPDIYAT..DFFASGLPLVTEET.S.GEAG..EDDEVVA.I
RetrocopyRIEGVKSVFFGPDFITATKENEKLDWNLLKPDIYATTTDFFASGLPLVTEETSS>GEAGC-EDDEVVALI
ParentalKELLDTRIRPTVQEDGGDVIYKGFEDGIVQLKLQGSCTSCPSSIITLKNGIQNMLQF-YIPEVEGVEQVM
KE.LDTR..PTVQEDGGDVIYKGFEDGIV.LKLQGSCTSCPSSIITLKNGIQNMLQF.YIPEVEGVEQ.M
RetrocopyKEVLDTRMWPTVQEDGGDVIYKGFEDGIV*LKLQGSCTSCPSSIITLKNGIQNMLQF<YIPEVEGVEQGM
ParentalDDESDEKEANSP
DDESDEKEANSP
RetrocopyDDESDEKEANSP

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 33 .57 RPM
bodymap2_adrenal 0 .00 RPM 26 .84 RPM
bodymap2_brain 0 .00 RPM 24 .61 RPM
bodymap2_breast 0 .00 RPM 43 .13 RPM
bodymap2_colon 0 .00 RPM 35 .13 RPM
bodymap2_heart 0 .00 RPM 44 .49 RPM
bodymap2_kidney 0 .00 RPM 33 .98 RPM
bodymap2_liver 0 .00 RPM 11 .70 RPM
bodymap2_lung 0 .00 RPM 20 .75 RPM
bodymap2_lymph_node 0 .00 RPM 22 .88 RPM
bodymap2_ovary 0 .00 RPM 29 .59 RPM
bodymap2_prostate 0 .00 RPM 35 .68 RPM
bodymap2_skeletal_muscle 0 .00 RPM 35 .72 RPM
bodymap2_testis 0 .00 RPM 40 .14 RPM
bodymap2_thyroid 0 .00 RPM 33 .88 RPM
bodymap2_white_blood_cells 0 .00 RPM 13 .90 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_2638 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_2638 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_2638 retrocopy 5' end.

Lab - click to see more details

retro_hsap_2638 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_2638 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_1778
Pongo abelii retro_pabe_2329
Macaca mulatta retro_mmul_1524
Parental genes homology:
Parental genes homology involve 14 parental genes, and 15 retrocopies.

Species Parental gene accession Retrocopies number
Choloepus hoffmanni ENSCHOG000000059781 retrocopy
retro_chof_456,
Callithrix jacchus ENSCJAG000000191561 retrocopy
retro_cjac_1573,
Echinops telfairi ENSETEG000000190021 retrocopy
retro_etel_1371,
Homo sapiens ENSG00000169599 1 retrocopy
retro_hsap_2638 ,
Macaca mulatta ENSMMUG000000004351 retrocopy
retro_mmul_1524,
Monodelphis domestica ENSMODG000000118051 retrocopy
retro_mdom_1395,
Mustela putorius furoENSMPUG000000066631 retrocopy
retro_mputfur_67,
Mus musculus ENSMUSG000000299931 retrocopy
retro_mmus_1401,
Nomascus leucogenys ENSNLEG000000101011 retrocopy
retro_nleu_646,
Ochotona princeps ENSOPRG000000167602 retrocopies
retro_opri_380, retro_opri_48,
Pongo abelii ENSPPYG000000123391 retrocopy
retro_pabe_2329,
Pan troglodytes ENSPTRG000000120161 retrocopy
retro_ptro_1778,
Tupaia belangeri ENSTBEG000000086161 retrocopy
retro_tbel_525,
Tarsius syrichta ENSTSYG000000137651 retrocopy
retro_tsyr_108,

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).





Copyright © RetrogeneDB 2014-2017