RetrogeneDB ID:

retro_hsap_544

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:10:13912796..13913144(+)
Located in intron of:ENSG00000151474
Retrocopy
information
Ensembl ID:ENSG00000215227
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:NUTF2
Ensembl ID:ENSG00000102898
Aliases:None
Description:nuclear transport factor 2 [Source:HGNC Symbol;Acc:13722]


Retrocopy-Parental alignment summary:






>retro_hsap_544
GGAGGCAAGCCCATGTGGGAGATGACTGGACCCATCTTCATTCAACGTTCAGTTATTGAGTTCTATAACAATAGAACTCA
ACTCAGCACAATTTACATTGACATATCACGCCTTAGGCGGGAAGGAGAGCAGCTCGAGGGGAAAGCTGCCATTGTGAAGA
AGCCATCCAGCCTTCTGTTCCACAAAATCCAGCATAGCATCATGGTGCAGGACCGTCAGCCCACACCAGCTAACTGCATC
CTCAGCATGCTTGTGAGCCAGCCAAATGCCAATGAAGACCCCATTATGGGGCTCCACCAGATGTTCCTATGAAAGGACAT
AATGGATGCTTGGGTTCGCCCTGATGAC

ORF - retro_hsap_544 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 62.07 %
Parental protein coverage: 91.34 %
Number of stop codons detected: 1
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalGDKPIWEQIGSSFIQHYYQLFDNDRTQLGAIYIDASCLTWEGQQFQGKAAIVEKLSSLPFQKIQHSITAQ
G.KP.WE..G..FIQ.....F.N.RTQL..IYID.S.L..EG.Q..GKAAIV.K.SSL.F.KIQHSI..Q
RetrocopyGGKPMWEMTGPIFIQRSVIEFYNNRTQLSTIYIDISRLRREGEQLEGKAAIVKKPSSLLFHKIQHSIMVQ
ParentalDHQPTPDSCIISMVVGQLKADEDPIMGFHQMFLLKNINDAWVCTND
D.QPTP..CI.SM.V.Q..A.EDPIMG.HQMFL.K.I.DAWV...D
RetrocopyDRQPTPANCILSMLVSQPNANEDPIMGLHQMFL*KDIMDAWVRPDD

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 23 .71 RPM
bodymap2_adrenal 0 .00 RPM 29 .72 RPM
bodymap2_brain 0 .00 RPM 16 .95 RPM
bodymap2_breast 0 .02 RPM 18 .66 RPM
bodymap2_colon 0 .00 RPM 17 .17 RPM
bodymap2_heart 0 .00 RPM 18 .15 RPM
bodymap2_kidney 0 .00 RPM 16 .79 RPM
bodymap2_liver 0 .00 RPM 12 .38 RPM
bodymap2_lung 0 .00 RPM 18 .85 RPM
bodymap2_lymph_node 0 .00 RPM 22 .26 RPM
bodymap2_ovary 0 .00 RPM 25 .29 RPM
bodymap2_prostate 0 .00 RPM 25 .55 RPM
bodymap2_skeletal_muscle 0 .00 RPM 31 .41 RPM
bodymap2_testis 0 .00 RPM 32 .35 RPM
bodymap2_thyroid 0 .00 RPM 18 .66 RPM
bodymap2_white_blood_cells 0 .00 RPM 21 .36 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_544 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_544 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_544 retrocopy 5' end.

Lab - click to see more details

retro_hsap_544 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_544 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_409
Parental genes homology:
Parental genes homology involve 24 parental genes, and 103 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000175485 retrocopies
retro_amel_1225, retro_amel_134, retro_amel_1485, retro_amel_415, retro_amel_445,
Choloepus hoffmanni ENSCHOG000000030593 retrocopies
retro_chof_1386, retro_chof_1619, retro_chof_2488,
Callithrix jacchus ENSCJAG0000001601514 retrocopies
retro_cjac_1328, retro_cjac_2247, retro_cjac_2562, retro_cjac_2864, retro_cjac_2913, retro_cjac_2953, retro_cjac_2978, retro_cjac_3126, retro_cjac_3299, retro_cjac_4044, retro_cjac_4173, retro_cjac_587, retro_cjac_777, retro_cjac_924,
Equus caballus ENSECAG000000215301 retrocopy
retro_ecab_151,
Felis catus ENSFCAG000000081673 retrocopies
retro_fcat_154, retro_fcat_743, retro_fcat_845,
Homo sapiens ENSG00000102898 7 retrocopies
retro_hsap_1322, retro_hsap_1480, retro_hsap_1858, retro_hsap_207, retro_hsap_4181, retro_hsap_4854, retro_hsap_544 ,
Gorilla gorilla ENSGGOG000000239255 retrocopies
retro_ggor_1032, retro_ggor_2152, retro_ggor_279, retro_ggor_2806, retro_ggor_3028,
Loxodonta africana ENSLAFG000000310371 retrocopy
retro_lafr_623,
Macropus eugenii ENSMEUG0000000987411 retrocopies
retro_meug_1023, retro_meug_136, retro_meug_1539, retro_meug_1585, retro_meug_1778, retro_meug_2140, retro_meug_253, retro_meug_282, retro_meug_352, retro_meug_676, retro_meug_748,
Myotis lucifugus ENSMLUG000000251753 retrocopies
retro_mluc_1265, retro_mluc_2194, retro_mluc_911,
Macaca mulatta ENSMMUG000000120386 retrocopies
retro_mmul_1160, retro_mmul_1270, retro_mmul_2127, retro_mmul_2169, retro_mmul_2593, retro_mmul_27,
Monodelphis domestica ENSMODG000000055176 retrocopies
retro_mdom_1031, retro_mdom_1291, retro_mdom_1488, retro_mdom_1489, retro_mdom_1903, retro_mdom_37,
Mustela putorius furoENSMPUG000000067374 retrocopies
retro_mputfur_229, retro_mputfur_614, retro_mputfur_714, retro_mputfur_962,
Mus musculus ENSMUSG000000084501 retrocopy
retro_mmus_232,
Nomascus leucogenys ENSNLEG000000048897 retrocopies
retro_nleu_1295, retro_nleu_1791, retro_nleu_1855, retro_nleu_2374, retro_nleu_2384, retro_nleu_2953, retro_nleu_731,
Oryctolagus cuniculus ENSOCUG000000063221 retrocopy
retro_ocun_115,
Ochotona princeps ENSOPRG000000137274 retrocopies
retro_opri_1089, retro_opri_1102, retro_opri_1170, retro_opri_229,
Procavia capensis ENSPCAG000000153441 retrocopy
retro_pcap_56,
Pongo abelii ENSPPYG000000074727 retrocopies
retro_pabe_1101, retro_pabe_1229, retro_pabe_1515, retro_pabe_3421, retro_pabe_3772, retro_pabe_433, retro_pabe_502,
Pan troglodytes ENSPTRG000000082487 retrocopies
retro_ptro_1001, retro_ptro_1239, retro_ptro_2835, retro_ptro_3230, retro_ptro_338, retro_ptro_409, retro_ptro_903,
Pteropus vampyrus ENSPVAG000000166051 retrocopy
retro_pvam_843,
Sarcophilus harrisii ENSSHAG000000061001 retrocopy
retro_shar_274,
Sus scrofa ENSSSCG000000302953 retrocopies
retro_sscr_1223, retro_sscr_710, retro_sscr_740,
Drosophila melanogaster FBgn00311451 retrocopy
retro_dmel_27,

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 = 0.03 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 .03 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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