RetrogeneDB ID:

retro_hsap_4908

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:X:135889589..135890036(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000225125
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:RAN
Ensembl ID:ENSG00000132341
Aliases:None
Description:RAN, member RAS oncogene family [Source:HGNC Symbol;Acc:9846]


Retrocopy-Parental alignment summary:






>retro_hsap_4908
GTGGCTGCCCAAGGAGAGCCCCAAGTCCAGTTCAAATTGGTATTGGTTGGTGATGGTGGTACTGGAAAAACTGCATTCAT
GAAATGTCATCTGACCAGTGAATTTGAGAAGTGTGTAGCCACCTTAGGTGTTGAGGTTTATCACCTTGTGTTCCACACCA
ACAGAGGATCTATTAAGTTCACTATATGAGATACAGCTGGCCAGGAGAAATTTGGTATACTGAGAAATGGCTATTATATT
CAAGCCCAGTGTGCCGTTATAATGTTTGATGTAACATCTTGAGTTATTTACAAGAATGTGCCTAACTGGCATAGAGATCT
GGTATGAATATGTGAAAACATCCTCATGTTGTATGGCAACAAAATGGATATTAAGTATGGGAAAGTGAAGGAAAAATCTA
CTGTCTTCTACTGAAAGAAGAATCTTCAGTATTATGACATTTCTGCC

ORF - retro_hsap_4908 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 79.47 %
Parental protein coverage: 69.91 %
Number of stop codons detected: 4
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMAAQGEPQVQFKLVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGPIKFNVWDTAGQE
.AAQGEPQVQFKLVLVGDGGTGKT.F.K.HLT.EFEK..VATLGVEV..LVFHTNRG.IKF...DTAGQE
RetrocopyVAAQGEPQVQFKLVLVGDGGTGKTAFMKCHLTSEFEK-CVATLGVEVYHLVFHTNRGSIKFTI*DTAGQE
ParentalKFGGLRDGYYIQAQCAIIMFDVTSRVTYKNVPNWHRDLVRVCENIPIVLCGNKVDIKDRKVKAKSIVFHR
KFG.LR.GYYIQAQCA.IMFDVTS.V.YKNVPNWHRDLV..CENI...L.GNK.DIK..KVK.KS.VF..
RetrocopyKFGILRNGYYIQAQCAVIMFDVTS*VIYKNVPNWHRDLV*ICENI-LMLYGNKMDIKYGKVKEKSTVFY*
ParentalKKNLQYYDISA
KKNLQYYDISA
RetrocopyKKNLQYYDISA

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 .20 RPM 140 .54 RPM
bodymap2_adrenal 0 .10 RPM 205 .14 RPM
bodymap2_brain 0 .66 RPM 207 .80 RPM
bodymap2_breast 0 .62 RPM 122 .16 RPM
bodymap2_colon 0 .91 RPM 178 .68 RPM
bodymap2_heart 0 .33 RPM 81 .39 RPM
bodymap2_kidney 0 .31 RPM 163 .05 RPM
bodymap2_liver 0 .00 RPM 87 .28 RPM
bodymap2_lung 0 .12 RPM 151 .18 RPM
bodymap2_lymph_node 0 .26 RPM 193 .85 RPM
bodymap2_ovary 1 .68 RPM 226 .77 RPM
bodymap2_prostate 0 .55 RPM 154 .22 RPM
bodymap2_skeletal_muscle 0 .40 RPM 109 .29 RPM
bodymap2_testis 0 .09 RPM 304 .50 RPM
bodymap2_thyroid 0 .49 RPM 198 .73 RPM
bodymap2_white_blood_cells 0 .00 RPM 162 .39 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_4908 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_4908 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_4908 retrocopy 5' end.

Lab - click to see more details

retro_hsap_4908 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_4908 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_3273
Callithrix jacchus retro_cjac_4222
Parental genes homology:
Parental genes homology involve 20 parental genes, and 90 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000042224 retrocopies
retro_amel_1119, retro_amel_1625, retro_amel_1631, retro_amel_700,
Callithrix jacchus ENSCJAG000000039278 retrocopies
retro_cjac_1558, retro_cjac_1844, retro_cjac_2509, retro_cjac_2952, retro_cjac_3071, retro_cjac_3107, retro_cjac_4222, retro_cjac_492,
Echinops telfairi ENSETEG0000001187518 retrocopies
retro_etel_1051, retro_etel_1161, retro_etel_1351, retro_etel_1365, retro_etel_1584, retro_etel_1673, retro_etel_1878, retro_etel_1896, retro_etel_1915, retro_etel_2141, retro_etel_2150, retro_etel_2189, retro_etel_294, retro_etel_383, retro_etel_409, retro_etel_412, retro_etel_514, retro_etel_813,
Homo sapiens ENSG00000132341 3 retrocopies
retro_hsap_3126, retro_hsap_3446, retro_hsap_4908 ,
Gorilla gorilla ENSGGOG000000153404 retrocopies
retro_ggor_2142, retro_ggor_2328, retro_ggor_2556, retro_ggor_3066,
Loxodonta africana ENSLAFG000000176731 retrocopy
retro_lafr_1253,
Macaca mulatta ENSMMUG000000209272 retrocopies
retro_mmul_1990, retro_mmul_2641,
Monodelphis domestica ENSMODG000000156018 retrocopies
retro_mdom_100, retro_mdom_1718, retro_mdom_1990, retro_mdom_543, retro_mdom_580, retro_mdom_806, retro_mdom_814, retro_mdom_969,
Mus musculus ENSMUSG000000294304 retrocopies
retro_mmus_1653, retro_mmus_182, retro_mmus_2029, retro_mmus_265,
Nomascus leucogenys ENSNLEG000000082824 retrocopies
retro_nleu_1565, retro_nleu_2303, retro_nleu_2353, retro_nleu_775,
Ornithorhynchus anatinus ENSOANG000000064471 retrocopy
retro_oana_62,
Oryctolagus cuniculus ENSOCUG000000265062 retrocopies
retro_ocun_1139, retro_ocun_958,
Otolemur garnettii ENSOGAG000000250468 retrocopies
retro_ogar_1482, retro_ogar_1611, retro_ogar_2058, retro_ogar_2560, retro_ogar_2692, retro_ogar_2810, retro_ogar_377, retro_ogar_497,
Pongo abelii ENSPPYG000000051243 retrocopies
retro_pabe_2582, retro_pabe_2853, retro_pabe_3815,
Pan troglodytes ENSPTRG000000056364 retrocopies
retro_ptro_1762, retro_ptro_2115, retro_ptro_2338, retro_ptro_3273,
Rattus norvegicus ENSRNOG000000009383 retrocopies
retro_rnor_138, retro_rnor_410, retro_rnor_917,
Sarcophilus harrisii ENSSHAG000000180181 retrocopy
retro_shar_538,
Sus scrofa ENSSSCG000000097463 retrocopies
retro_sscr_1136, retro_sscr_194, retro_sscr_771,
Tursiops truncatus ENSTTRG000000127326 retrocopies
retro_ttru_1481, retro_ttru_204, retro_ttru_387, retro_ttru_439, retro_ttru_792, retro_ttru_892,
Vicugna pacos ENSVPAG000000088803 retrocopies
retro_vpac_436, retro_vpac_589, retro_vpac_85,

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 = 0.42 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .06 RPM
CEU_NA11843 0 .09 RPM
CEU_NA11930 0 .20 RPM
CEU_NA12004 0 .08 RPM
CEU_NA12400 0 .14 RPM
CEU_NA12751 0 .15 RPM
CEU_NA12760 0 .00 RPM
CEU_NA12827 0 .14 RPM
CEU_NA12872 0 .11 RPM
CEU_NA12873 0 .10 RPM
FIN_HG00183 0 .27 RPM
FIN_HG00277 0 .07 RPM
FIN_HG00315 0 .30 RPM
FIN_HG00321 0 .24 RPM
FIN_HG00328 0 .07 RPM
FIN_HG00338 0 .02 RPM
FIN_HG00349 0 .09 RPM
FIN_HG00375 0 .17 RPM
FIN_HG00377 0 .13 RPM
FIN_HG00378 0 .11 RPM
GBR_HG00099 0 .00 RPM
GBR_HG00111 0 .04 RPM
GBR_HG00114 0 .13 RPM
GBR_HG00119 0 .17 RPM
GBR_HG00131 0 .14 RPM
GBR_HG00133 0 .19 RPM
GBR_HG00134 0 .20 RPM
GBR_HG00137 0 .11 RPM
GBR_HG00142 0 .42 RPM
GBR_HG00143 0 .00 RPM
TSI_NA20512 0 .00 RPM
TSI_NA20513 0 .07 RPM
TSI_NA20518 0 .22 RPM
TSI_NA20532 0 .17 RPM
TSI_NA20538 0 .32 RPM
TSI_NA20756 0 .09 RPM
TSI_NA20765 0 .23 RPM
TSI_NA20771 0 .06 RPM
TSI_NA20786 0 .08 RPM
TSI_NA20798 0 .06 RPM
YRI_NA18870 0 .14 RPM
YRI_NA18907 0 .03 RPM
YRI_NA18916 0 .06 RPM
YRI_NA19093 0 .08 RPM
YRI_NA19099 0 .03 RPM
YRI_NA19114 0 .08 RPM
YRI_NA19118 0 .04 RPM
YRI_NA19213 0 .05 RPM
YRI_NA19214 0 .00 RPM
YRI_NA19223 0 .12 RPM

Indel association:

No indels were associated with its genomic coordinates. Based on Kabza et al. 2015 (PubMed).



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