RetrogeneDB ID:

retro_hsap_3903

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:7:131346707..131347383(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000213261
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:EEF1B2
Ensembl ID:ENSG00000114942
Aliases:EEF1B2, EEF1B, EEF1B1, EF1B
Description:eukaryotic translation elongation factor 1 beta 2 [Source:HGNC Symbol;Acc:3208]


Retrocopy-Parental alignment summary:






>retro_hsap_3903
ATGGGTTTCGGAGACCTGAAAAGCCCCACCGGCCTCCAGGTGCTCAACGATTACCTGGCGGACAAGAGCTACATCAAGGG
GTATGGTGCCATCACAAGCAGATGTGGCAGTATTTGAAGCCGTGTCCGGCCCACCACCTGCCGACTTGTGTCATGCCCTA
CGTTGGTATAATCACATCAAGTCTTACGAAAAGGAAAAGGCCGGCCTGCCAGGAGTGAAGAAAGCTTTGAGCAAGTATGG
TCCTGCCGATGTGGAAGACACTACAGGAAGTGGAGCTACAGACAGTAAAGATGATGATGACATTGATCTCTTTGGATCCG
ATTATGAGGAGGAAAGTGAAGAAGCAAAGAGGCTAAGGGAAGAACATCTTGCACAATATGAATCAAAGAAAGCCAAAAAA
CCTGCACTTGTTGCCAAGTCTTCCATCTTACTAGATGTGAAACCTTGGGATGATGAGACAGATATGGCGAAATTAGAGGA
GTGTGTCAGAAGCATTCAAGCAGACGGCTTAGTCTGGGGCTCATCTAAACTAGTTCCAGTGGGATACGGAATTAAGAAAC
TTCAAATACAGTGTGTAGTTGAAGATGATAAAGTTGGAACAGATATGCTGGAGGAGCAGATCACTGCTTTTGAGGACTAT
GTGCAGTCCATGGATGTGGCTGCTTTCAACAAGATC

ORF - retro_hsap_3903 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 96.46 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMGFGDLKSPAGLQVLNDYLADKSYIEGY-VPSQADVAVFEAVSSPPPADLCHALRWYNHIKSYEKEKASL
MGFGDLKSP.GLQVLNDYLADKSYI.GY.VPSQADVAVFEAVS.PPPADLCHALRWYNHIKSYEKEKA.L
RetrocopyMGFGDLKSPTGLQVLNDYLADKSYIKGY>VPSQADVAVFEAVSGPPPADLCHALRWYNHIKSYEKEKAGL
ParentalPGVKKALGKYGPADVEDTTGSGATDSKDDDDIDLFGSDDEEESEEAKRLREERLAQYESKKAKKPALVAK
PGVKKAL.KYGPADVEDTTGSGATDSKDDDDIDLFGSD.EEESEEAKRLREE.LAQYESKKAKKPALVAK
RetrocopyPGVKKALSKYGPADVEDTTGSGATDSKDDDDIDLFGSDYEEESEEAKRLREEHLAQYESKKAKKPALVAK
ParentalSSILLDVKPWDDETDMAKLEECVRSIQADGLVWGSSKLVPVGYGIKKLQIQCVVEDDKVGTDMLEEQITA
SSILLDVKPWDDETDMAKLEECVRSIQADGLVWGSSKLVPVGYGIKKLQIQCVVEDDKVGTDMLEEQITA
RetrocopySSILLDVKPWDDETDMAKLEECVRSIQADGLVWGSSKLVPVGYGIKKLQIQCVVEDDKVGTDMLEEQITA
ParentalFEDYVQSMDVAAFNKI
FEDYVQSMDVAAFNKI
RetrocopyFEDYVQSMDVAAFNKI

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 .38 RPM 187 .77 RPM
bodymap2_adrenal 0 .57 RPM 282 .83 RPM
bodymap2_brain 0 .33 RPM 104 .64 RPM
bodymap2_breast 0 .60 RPM 143 .58 RPM
bodymap2_colon 1 .12 RPM 319 .29 RPM
bodymap2_heart 0 .15 RPM 61 .66 RPM
bodymap2_kidney 0 .54 RPM 112 .61 RPM
bodymap2_liver 0 .09 RPM 139 .20 RPM
bodymap2_lung 0 .58 RPM 214 .31 RPM
bodymap2_lymph_node 0 .20 RPM 291 .01 RPM
bodymap2_ovary 0 .83 RPM 314 .33 RPM
bodymap2_prostate 0 .17 RPM 279 .88 RPM
bodymap2_skeletal_muscle 0 .16 RPM 175 .31 RPM
bodymap2_testis 0 .40 RPM 184 .38 RPM
bodymap2_thyroid 0 .30 RPM 160 .16 RPM
bodymap2_white_blood_cells 0 .16 RPM 343 .51 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_3903 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_3903 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_3903 retrocopy 5' end.

Lab - click to see more details

retro_hsap_3903 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_3903 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 26 parental genes, and 95 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000030151 retrocopy
retro_amel_427,
Bos taurus ENSBTAG000000219798 retrocopies
retro_btau_1127, retro_btau_1309, retro_btau_1786, retro_btau_366, retro_btau_367, retro_btau_450, retro_btau_512, retro_btau_792,
Canis familiaris ENSCAFG000000296351 retrocopy
retro_cfam_56,
Choloepus hoffmanni ENSCHOG000000138351 retrocopy
retro_chof_725,
Callithrix jacchus ENSCJAG000000058052 retrocopies
retro_cjac_176, retro_cjac_341,
Dipodomys ordii ENSDORG000000036692 retrocopies
retro_dord_510, retro_dord_592,
Felis catus ENSFCAG000000102391 retrocopy
retro_fcat_1735,
Homo sapiens ENSG00000114942 9 retrocopies
retro_hsap_1154, retro_hsap_1500, retro_hsap_2397, retro_hsap_2883, retro_hsap_3332, retro_hsap_3480, retro_hsap_3657, retro_hsap_3903 , retro_hsap_4795,
Gorilla gorilla ENSGGOG000000070022 retrocopies
retro_ggor_134, retro_ggor_2000,
Macropus eugenii ENSMEUG000000026548 retrocopies
retro_meug_1418, retro_meug_1846, retro_meug_1917, retro_meug_240, retro_meug_241, retro_meug_52, retro_meug_775, retro_meug_949,
Microcebus murinus ENSMICG000000106073 retrocopies
retro_mmur_1067, retro_mmur_615, retro_mmur_78,
Myotis lucifugus ENSMLUG000000166028 retrocopies
retro_mluc_1035, retro_mluc_1068, retro_mluc_1104, retro_mluc_1167, retro_mluc_1542, retro_mluc_1578, retro_mluc_1681, retro_mluc_1857,
Macaca mulatta ENSMMUG000000010546 retrocopies
retro_mmul_1456, retro_mmul_1767, retro_mmul_1881, retro_mmul_2140, retro_mmul_894, retro_mmul_969,
Nomascus leucogenys ENSNLEG000000070988 retrocopies
retro_nleu_1220, retro_nleu_1676, retro_nleu_2078, retro_nleu_2107, retro_nleu_2521, retro_nleu_2630, retro_nleu_624, retro_nleu_834,
Otolemur garnettii ENSOGAG000000112293 retrocopies
retro_ogar_2628, retro_ogar_616, retro_ogar_862,
Oreochromis niloticus ENSONIG000000176301 retrocopy
retro_onil_28,
Oryzias latipes ENSORLG000000185331 retrocopy
retro_olat_16,
Procavia capensis ENSPCAG000000133481 retrocopy
retro_pcap_154,
Pongo abelii ENSPPYG000000131077 retrocopies
retro_pabe_1251, retro_pabe_1656, retro_pabe_2163, retro_pabe_2389, retro_pabe_2419, retro_pabe_2746, retro_pabe_2876,
Pteropus vampyrus ENSPVAG000000173342 retrocopies
retro_pvam_1055, retro_pvam_56,
Sorex araneus ENSSARG000000015241 retrocopy
retro_sara_463,
Sarcophilus harrisii ENSSHAG000000178531 retrocopy
retro_shar_208,
Sus scrofa ENSSSCG000000161281 retrocopy
retro_sscr_766,
Ictidomys tridecemlineatus ENSSTOG000000054373 retrocopies
retro_itri_1263, retro_itri_813, retro_itri_873,
Tupaia belangeri ENSTBEG0000000565713 retrocopies
retro_tbel_161, retro_tbel_2046, retro_tbel_2094, retro_tbel_2298, retro_tbel_2700, retro_tbel_2776, retro_tbel_3143, retro_tbel_3541, retro_tbel_3542, retro_tbel_4050, retro_tbel_4073, retro_tbel_4205, retro_tbel_611,
Xiphophorus maculatus ENSXMAG000000060501 retrocopy
retro_xmac_21,

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 = 0.83 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .36 RPM
CEU_NA11843 0 .60 RPM
CEU_NA11930 0 .72 RPM
CEU_NA12004 0 .34 RPM
CEU_NA12400 0 .25 RPM
CEU_NA12751 0 .22 RPM
CEU_NA12760 0 .49 RPM
CEU_NA12827 0 .28 RPM
CEU_NA12872 0 .38 RPM
CEU_NA12873 0 .16 RPM
FIN_HG00183 0 .30 RPM
FIN_HG00277 0 .48 RPM
FIN_HG00315 0 .36 RPM
FIN_HG00321 0 .24 RPM
FIN_HG00328 0 .24 RPM
FIN_HG00338 0 .30 RPM
FIN_HG00349 0 .83 RPM
FIN_HG00375 0 .37 RPM
FIN_HG00377 0 .30 RPM
FIN_HG00378 0 .28 RPM
GBR_HG00099 0 .26 RPM
GBR_HG00111 0 .17 RPM
GBR_HG00114 0 .39 RPM
GBR_HG00119 0 .19 RPM
GBR_HG00131 0 .09 RPM
GBR_HG00133 0 .19 RPM
GBR_HG00134 0 .35 RPM
GBR_HG00137 0 .16 RPM
GBR_HG00142 0 .25 RPM
GBR_HG00143 0 .45 RPM
TSI_NA20512 0 .37 RPM
TSI_NA20513 0 .15 RPM
TSI_NA20518 0 .44 RPM
TSI_NA20532 0 .34 RPM
TSI_NA20538 0 .14 RPM
TSI_NA20756 0 .52 RPM
TSI_NA20765 0 .17 RPM
TSI_NA20771 0 .34 RPM
TSI_NA20786 0 .10 RPM
TSI_NA20798 0 .37 RPM
YRI_NA18870 0 .51 RPM
YRI_NA18907 0 .49 RPM
YRI_NA18916 0 .11 RPM
YRI_NA19093 0 .18 RPM
YRI_NA19099 0 .27 RPM
YRI_NA19114 0 .18 RPM
YRI_NA19118 0 .27 RPM
YRI_NA19213 0 .14 RPM
YRI_NA19214 0 .22 RPM
YRI_NA19223 0 .14 RPM

Indel association:

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



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