RetrogeneDB ID:

retro_hsap_2883

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:3:174777151..174777819(-)
Located in intron of:ENSG00000177694
Retrocopy
information
Ensembl ID:ENSG00000230497
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_2883
ATGGGTTTCAGAGACCTGAAAAGCCCTGCTGGCCTCCATGTGCTCAATGATTACCTGGCAGACAAGAGCTACATCGAAGG
TTATGTGCCACCACAAGCAGATGTGGCAGTATTTGAAGCAGTCTCTGGCCCATTGCCTGTGAACTCGTGTCTTGCCCTAT
GTTGGTAAAGTCACATCAATTCTCATGAAAAGAAAAGGCCAGCCTTCCAGGAGTGAAGAAACCTTTGGGCAAATACGGTG
CTGCTAATGTAGAAGACACTACAGGAAGCAGAGCTGCAAATAGTAAAGATGATGATGACATTGATCTCCTTGGATCTGAT
AAGGAGGAGGAAGGTGAAGCAGCAAAGAGGTTAATGGAAGAATGGCTTGCCCAGAATGAATCAAAGAAAGCCAAAAAACA
TGCACTTGTTGCCATTTTCCATCATACTGATGTGAAACCGTGGGATGATGTGGCAGATATGGCAAAACTAGAGGAATGTG
TTAGAAGCATTCAAGCAGACGGCTTAGTCTAGGGCTCCTCTAAACTAGTTCTGATGGAATATGTAATTTAAAAACTTCAA
ATCCAGTGTGTAACTGAAGATGATAAAGTTGGAGCAGATACACTGGCGGAGCAGGTCACTGCTTTTGAGGATTCTGTGTA
GTCGATGGATATGGCTGCTTTCCATAAG

ORF - retro_hsap_2883 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 73.78 %
Parental protein coverage: 99.56 %
Number of stop codons detected: 4
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMGFGDLKSPAGLQVLNDYLADKSYIEGYVPSQADVAVFEAVSSPPPADLCHALRWYNHIKSYEK-EKASL
MGF.DLKSPAGL.VLNDYLADKSYIEGYVP.QADVAVFEAVS.P.P...C.AL.W..HI.S.EK.EKASL
RetrocopyMGFRDLKSPAGLHVLNDYLADKSYIEGYVPPQADVAVFEAVSGPLPVNSCLALCW*SHINSHEK<EKASL
ParentalPGVKKALGKYGPADVEDTTGSGATDSKDDDDIDLFGSDDEEESEEAKRLREERLAQYESKKAKKPALVAK
PGVKK.LGKYG.A.VEDTTGS.A..SKDDDDIDL.GSD.EEE.E.AKRL.EE.LAQ.ES.K..K......
RetrocopyPGVKKPLGKYGAANVEDTTGSRAANSKDDDDIDLLGSDKEEEGEAAKRLMEEWLAQNES-KKAKKHALVA
ParentalSSILLDVKPWDDETDMAKLEECVRSIQADGLVWGSSKLVPVGYGIKKLQIQCVVEDDKVGTDMLEEQITA
.....DVKPWDD..DMAKLEECVRSIQADGLV.GSSKLV...Y.I.KLQIQCV.EDDKVG.D.L.EQ.TA
RetrocopyIFHHTDVKPWDDVADMAKLEECVRSIQADGLV*GSSKLVLMEYVI*KLQIQCVTEDDKVGADTLAEQVTA
ParentalFEDYVQSMDVAAFNK
FED.V.SMD.AAF.K
RetrocopyFEDSV*SMDMAAFHK

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






(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 187 .77 RPM
bodymap2_adrenal 0 .00 RPM 282 .83 RPM
bodymap2_brain 0 .02 RPM 104 .64 RPM
bodymap2_breast 0 .00 RPM 143 .58 RPM
bodymap2_colon 0 .00 RPM 319 .29 RPM
bodymap2_heart 0 .00 RPM 61 .66 RPM
bodymap2_kidney 0 .00 RPM 112 .61 RPM
bodymap2_liver 0 .00 RPM 139 .20 RPM
bodymap2_lung 0 .00 RPM 214 .31 RPM
bodymap2_lymph_node 0 .00 RPM 291 .01 RPM
bodymap2_ovary 0 .00 RPM 314 .33 RPM
bodymap2_prostate 0 .00 RPM 279 .88 RPM
bodymap2_skeletal_muscle 0 .00 RPM 175 .31 RPM
bodymap2_testis 0 .00 RPM 184 .38 RPM
bodymap2_thyroid 0 .00 RPM 160 .16 RPM
bodymap2_white_blood_cells 0 .00 RPM 343 .51 RPM
RNA Polymerase II actvity near the 5' end of retro_hsap_2883 was not detected
No EST(s) were mapped for retro_hsap_2883 retrocopy.
No TSS is located nearby retro_hsap_2883 retrocopy 5' end.
retro_hsap_2883 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_2883 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Gorilla gorilla retro_ggor_2000
Pongo abelii retro_pabe_2389
Macaca mulatta retro_mmul_1456

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

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000030151 retrocopy
Bos taurus ENSBTAG000000219798 retrocopies
Canis familiaris ENSCAFG000000296351 retrocopy
Choloepus hoffmanni ENSCHOG000000138351 retrocopy
Callithrix jacchus ENSCJAG000000058052 retrocopies
Dipodomys ordii ENSDORG000000036692 retrocopies
Felis catus ENSFCAG000000102391 retrocopy
Homo sapiens ENSG00000114942 9 retrocopies
Gorilla gorilla ENSGGOG000000070022 retrocopies
Macropus eugenii ENSMEUG000000026548 retrocopies
Microcebus murinus ENSMICG000000106073 retrocopies
Myotis lucifugus ENSMLUG000000166028 retrocopies
Macaca mulatta ENSMMUG000000010546 retrocopies
Nomascus leucogenys ENSNLEG000000070988 retrocopies
Otolemur garnettii ENSOGAG000000112293 retrocopies
Oreochromis niloticus ENSONIG000000176301 retrocopy
Oryzias latipes ENSORLG000000185331 retrocopy
Procavia capensis ENSPCAG000000133481 retrocopy
Pongo abelii ENSPPYG000000131077 retrocopies
Pteropus vampyrus ENSPVAG000000173342 retrocopies
Sorex araneus ENSSARG000000015241 retrocopy
Sarcophilus harrisii ENSSHAG000000178531 retrocopy
Sus scrofa ENSSSCG000000161281 retrocopy
Ictidomys tridecemlineatus ENSSTOG000000054373 retrocopies
Tupaia belangeri ENSTBEG0000000565713 retrocopies
Xiphophorus maculatus ENSXMAG000000060501 retrocopy

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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