RetrogeneDB ID:

retro_hsap_2439

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:20:3276363..3276798(-)
Located in intron of:ENSG00000088854
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:UBE2F
Ensembl ID:ENSG00000184182
Aliases:UBE2F, NCE2
Description:ubiquitin-conjugating enzyme E2F (putative) [Source:HGNC Symbol;Acc:12480]


Retrocopy-Parental alignment summary:






>retro_hsap_2439
GTTGCAGAACTTGAAGCTAATTTACCTTGTACATGTAAAGTGCATTTTCCTGATCCAAACAAGCTTCACTGTTCTCAGCT
AACAGTAACTCCAGATGAGGGTTACTACCAGGGTGGAAAATTTCAGCTTGAAACCGAAAGTTCCCGATGTGTACAACATG
GTGCCTCCCAAAGTGAAATGCCTGACCAAGATCTGGCACCCCAACATCACAGAGACAGGGGAAATATGTCTGAGTTTACT
GAGAGAACATTCAATTGACGGCACTGGCTGGGCTCCCATGAGAACATTAAAGGATGTCGTTTGGGGATTAAACTCTTTGT
TTACTGATTTTTGAATTTTGATGATCCACTGAATATTGAAGCTGCAGAACATCATTTGCAGGACAAGGAGGACTTCCAGA
ATAAAGTGGACAACTACATCACGCGTTATGCCAGA

ORF - retro_hsap_2439 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 92.52 %
Parental protein coverage: 90.06 %
Number of stop codons detected: 0
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalVAELEANLPCTCKVHFPDPNKLHCFQLTVTPDEGYYQGGKFQFETE-VPDAYNMVPPKVKCLTKIWHPNI
VAELEANLPCTCKVHFPDPNKLHC.QLTVTPDEGYYQGGKFQ.ETE.VPD.YNMVPPKVKCLTKIWHPNI
RetrocopyVAELEANLPCTCKVHFPDPNKLHCSQLTVTPDEGYYQGGKFQLETE>VPDVYNMVPPKVKCLTKIWHPNI
ParentalTETGEICLSLLREHSIDGTGWAPTRTLKDVVWGLNSLFTD-LLNFDDPLNIEAAEHHLRDKEDFRNKVDD
TETGEICLSLLREHSIDGTGWAP.RTLKDVVWGLNSLFTD..LNFDDPLNIEAAEHHL.DKEDF.NKVD.
RetrocopyTETGEICLSLLREHSIDGTGWAPMRTLKDVVWGLNSLFTD<FLNFDDPLNIEAAEHHLQDKEDFQNKVDN
ParentalYIKRYAR
YI.RYAR
RetrocopyYITRYAR

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 .14 RPM 16 .30 RPM
bodymap2_adrenal 0 .08 RPM 18 .36 RPM
bodymap2_brain 0 .14 RPM 20 .49 RPM
bodymap2_breast 0 .00 RPM 22 .53 RPM
bodymap2_colon 0 .08 RPM 20 .50 RPM
bodymap2_heart 0 .04 RPM 17 .30 RPM
bodymap2_kidney 0 .02 RPM 19 .54 RPM
bodymap2_liver 0 .02 RPM 14 .81 RPM
bodymap2_lung 0 .21 RPM 17 .49 RPM
bodymap2_lymph_node 0 .04 RPM 20 .83 RPM
bodymap2_ovary 0 .15 RPM 18 .87 RPM
bodymap2_prostate 0 .10 RPM 21 .81 RPM
bodymap2_skeletal_muscle 0 .27 RPM 19 .73 RPM
bodymap2_testis 0 .02 RPM 33 .69 RPM
bodymap2_thyroid 0 .06 RPM 31 .77 RPM
bodymap2_white_blood_cells 0 .04 RPM 34 .49 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_2439 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_2439 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_2439 retrocopy 5' end.

Lab - click to see more details

retro_hsap_2439 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_2439 has 4 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_1410
Gorilla gorilla retro_ggor_1519
Pongo abelii retro_pabe_1785
Macaca mulatta retro_mmul_628
Parental genes homology:
Parental genes homology involve 25 parental genes, and 60 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000085511 retrocopy
retro_amel_572,
Bos taurus ENSBTAG000000261142 retrocopies
retro_btau_1698, retro_btau_948,
Canis familiaris ENSCAFG000000123631 retrocopy
retro_cfam_1275,
Callithrix jacchus ENSCJAG000000004763 retrocopies
retro_cjac_2378, retro_cjac_2980, retro_cjac_3219,
Cavia porcellus ENSCPOG000000063681 retrocopy
retro_cpor_1122,
Dasypus novemcinctus ENSDNOG000000005062 retrocopies
retro_dnov_1301, retro_dnov_132,
Equus caballus ENSECAG000000116871 retrocopy
retro_ecab_158,
Echinops telfairi ENSETEG000000092301 retrocopy
retro_etel_1534,
Homo sapiens ENSG000001307251 retrocopy
retro_hsap_1677,
Homo sapiens ENSG00000184182 2 retrocopies
retro_hsap_2439 , retro_hsap_2773,
Gorilla gorilla ENSGGOG000000107093 retrocopies
retro_ggor_1518, retro_ggor_1519, retro_ggor_1930,
Microcebus murinus ENSMICG000000120755 retrocopies
retro_mmur_1014, retro_mmur_114, retro_mmur_1365, retro_mmur_584, retro_mmur_815,
Myotis lucifugus ENSMLUG000000012865 retrocopies
retro_mluc_1237, retro_mluc_1674, retro_mluc_1747, retro_mluc_1789, retro_mluc_2627,
Macaca mulatta ENSMMUG000000184824 retrocopies
retro_mmul_1450, retro_mmul_1585, retro_mmul_254, retro_mmul_628,
Mustela putorius furoENSMPUG000000001011 retrocopy
retro_mputfur_782,
Mus musculus ENSMUSG000000343433 retrocopies
retro_mmus_2161, retro_mmus_255, retro_mmus_845,
Nomascus leucogenys ENSNLEG000000111522 retrocopies
retro_nleu_1340, retro_nleu_677,
Otolemur garnettii ENSOGAG000000053087 retrocopies
retro_ogar_1109, retro_ogar_1995, retro_ogar_2491, retro_ogar_2551, retro_ogar_2715, retro_ogar_639, retro_ogar_761,
Pongo abelii ENSPPYG000000133153 retrocopies
retro_pabe_1395, retro_pabe_1785, retro_pabe_2242,
Pan troglodytes ENSPTRG000000130812 retrocopies
retro_ptro_1410, retro_ptro_1876,
Rattus norvegicus ENSRNOG000000199531 retrocopy
retro_rnor_2696,
Sus scrofa ENSSSCG000000277233 retrocopies
retro_sscr_291, retro_sscr_423, retro_sscr_542,
Tarsius syrichta ENSTSYG000000115103 retrocopies
retro_tsyr_1718, retro_tsyr_1944, retro_tsyr_2133,
Tursiops truncatus ENSTTRG000000115282 retrocopies
retro_ttru_1297, retro_ttru_1455,
Vicugna pacos ENSVPAG000000104851 retrocopy
retro_vpac_361,

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 = 0.09 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 .02 RPM
CEU_NA12760 0 .09 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 .06 RPM
FIN_HG00328 0 .00 RPM
FIN_HG00338 0 .02 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 .03 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