RetrogeneDB ID:

retro_hsap_3288

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:5:13553760..13554108(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000248462
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:NENF
Ensembl ID:ENSG00000117691
Aliases:NENF, CIR2, SCIRP10, SPUF
Description:neudesin neurotrophic factor [Source:HGNC Symbol;Acc:30384]


Retrocopy-Parental alignment summary:






>retro_hsap_3288
GAGCAGAATGATCACCACAGCTGCATTTCAACAAAGGATGTGGTGTTTGCTGTCACTTTGGGAAAGGGGTTTCAAGGAAG
AGGAGCCCCCTTACAATGCCTTGACCTGGAAAACCTCCACCACAGGGATAGCCTAAGAAGTCCTTGGTTCCTGCAAAACT
CACCCATGACTCTATGGGTTACTAGGCTGAGGAGCTGGAGTCCTCAGGATGAGGTCTTCACCAAAATGTACAAAGCAAAA
TATCCCATTGTGAAATACACAGCCCAAAGAATTCTTAATGAGAACAGGAGCTCCAGCATGGACTTGAAACTGAAAGCCCA
GACCCATTTTGACATAAAGGATGAGTTC

ORF - retro_hsap_3288 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 62.71 %
Parental protein coverage: 66.86 %
Number of stop codons detected: 1
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalEEEDQPIYLAVKGVVFDVTSGKEFYGRGAP-YNALTGKDSTRGVA-KMSLDPADLTHDTTGLTAKELEAL
E..D.......K.VVF.VT.GK.F.GRGAP.YNALT.K.ST.G.A.K.SL.PA.LTHD..G..A.ELE..
RetrocopyEQNDHHSCISTKDVVFAVTLGKGFQGRGAP>YNALTWKTSTTGIA>KKSLVPAKLTHDSMGY*AEELESS
Parental-DEVFTKVYKAKYPIVGYTARRILNEDGSPNLDFKPEDQPHFDIKDEF
.DEVFTK.YKAKYPIV.YTA.RILNE..S...D.K...Q.HFDIKDEF
Retrocopy>DEVFTKMYKAKYPIVKYTAQRILNENRSSSMDLKLKAQTHFDIKDEF

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 25 .01 RPM
bodymap2_adrenal 0 .00 RPM 26 .16 RPM
bodymap2_brain 0 .00 RPM 28 .69 RPM
bodymap2_breast 0 .00 RPM 26 .77 RPM
bodymap2_colon 0 .00 RPM 32 .35 RPM
bodymap2_heart 0 .00 RPM 34 .04 RPM
bodymap2_kidney 0 .00 RPM 25 .91 RPM
bodymap2_liver 0 .00 RPM 17 .19 RPM
bodymap2_lung 0 .00 RPM 48 .29 RPM
bodymap2_lymph_node 0 .00 RPM 28 .67 RPM
bodymap2_ovary 0 .00 RPM 35 .43 RPM
bodymap2_prostate 0 .00 RPM 49 .86 RPM
bodymap2_skeletal_muscle 0 .00 RPM 32 .37 RPM
bodymap2_testis 0 .00 RPM 11 .14 RPM
bodymap2_thyroid 0 .00 RPM 23 .86 RPM
bodymap2_white_blood_cells 0 .00 RPM 12 .44 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_3288 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_3288 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_3288 retrocopy 5' end.

Lab - click to see more details

retro_hsap_3288 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_3288 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_2224
Pongo abelii retro_pabe_2717
Macaca mulatta retro_mmul_2064
Parental genes homology:
Parental genes homology involve 15 parental genes, and 23 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000013411 retrocopy
retro_amel_836,
Bos taurus ENSBTAG000000007591 retrocopy
retro_btau_1238,
Dasypus novemcinctus ENSDNOG000000033991 retrocopy
retro_dnov_1256,
Felis catus ENSFCAG000000317961 retrocopy
retro_fcat_1171,
Homo sapiens ENSG00000117691 2 retrocopies
retro_hsap_3288 , retro_hsap_379,
Gorilla gorilla ENSGGOG000000251971 retrocopy
retro_ggor_830,
Macaca mulatta ENSMMUG000000021422 retrocopies
retro_mmul_2064, retro_mmul_490,
Mus musculus ENSMUSG000000374991 retrocopy
retro_mmus_3309,
Nomascus leucogenys ENSNLEG000000028931 retrocopy
retro_nleu_1354,
Ochotona princeps ENSOPRG000000142042 retrocopies
retro_opri_127, retro_opri_775,
Pongo abelii ENSPPYG000000002362 retrocopies
retro_pabe_2717, retro_pabe_328,
Pan troglodytes ENSPTRG000000019612 retrocopies
retro_ptro_2224, retro_ptro_295,
Sus scrofa ENSSSCG000000155971 retrocopy
retro_sscr_393,
Ictidomys tridecemlineatus ENSSTOG000000222932 retrocopies
retro_itri_1876, retro_itri_340,
Tarsius syrichta ENSTSYG000000018803 retrocopies
retro_tsyr_1189, retro_tsyr_411, retro_tsyr_549,

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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