RetrogeneDB ID:

retro_hsap_2896

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:3:183744159..183745544(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000223529
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:EEF1A1
Ensembl ID:ENSG00000156508
Aliases:EEF1A1, CCS-3, CCS3, EE1A1, EEF-1, EEF1A, EF-Tu, EF1A, GRAF-1EF, HNGC:16303, LENG7, PTI1, eEF1A-1
Description:eukaryotic translation elongation factor 1 alpha 1 [Source:HGNC Symbol;Acc:3189]


Retrocopy-Parental alignment summary:






>retro_hsap_2896
ATGGGAAAGGAAAAGACGCATATCAACATTATTGTCACTGGACATGTAGATTCAGGCAAGTCCACCACTACTGGCCATCT
GATCTACAAATGCGGCGTCATTGACAAAAGAACCATTGAAAAATTTAAGAATGAGGCTGCTGAGATGGGAAAGGCCTCCT
TCAAGTATGCCTCGGTCTTGGATAAACTGAAAGCTGAGCATGAACGTGGTATCATCATTGGTATCTCTTTTGTGGAAATT
TGAGACTAGCAAGTACTACGTGACTATCATTGATGCCCCAGGACACAGAGACGTCATCAAAAACATGATTACAGGGACAT
CTCAGGCTGACCGTGCTGTCCTGATTGTTGCTGCTGGTGTTGGCGAATTTGAAGCTGGTATCTCCAAGAATGGGCAGACC
CGAGAGCATGCCCTTCTGGCTTACACACTGGGTGTGAAACAACCAATTGTTGGTGTTAACAAAATGGTTACACTGAGCCA
CCCTATAGCCAGAAGAGATACAAGGAAATCGTTAAGGAAGTCAGCACTACATTAAGAAAATTGGCTACAACCCCGACACA
GTAGCATTTGTGCCAATTTCTGGTTGGAATGATGACAACATGCTGGAGCCAAGTGCTAACACGCCTTGGTTCAAGGGATG
GAAAGTCACCGGTAACAATGGCAATGCCAGTGGAACCACACTGCTTGAGGCTCTGGACTGCGTCCTACCACCAACTGGTC
CAACTGACAAGCCCTTGTGCCTGTTCCTCCAGGATGTCTACAAAATTGGTGGTATTGGTACTGTTCCTATTGGCTGAGTG
GAGACTGGCATTCTCAAACCTGGTATGGTGGTCACCTTTGCTCCAGTCAACGTTACAACTGAAGTAAAGTCTGTCAAAAC
GCACCATGAAGCTTTGAGTGAAGCTCTTCCTGGGGACAATGTGGGCTTCAGTGTCAAGAATGTGTTTGTCAAGGATGTTC
GTCATGACAATGTTGCTGGTGACAGCAAAAACGAACCACCAATGGAAGCAGCTGGCTTGACTGCTCAGGTGACTATCCGG
AACCATTCAGGCCAAATCAGCGCTGGCTATGCCCCTGTACTGAATTGCCACATGGCTCACATTGCATGCAAGTTTCCTGT
GCAGAAGGAAAAAATTGATCGCTGTTCTGGTAAGAAACTGGAAGATGGCCCTAAATTCTTGAAGTCTGGTGATGCTGCCA
TTGTTGATACGGTTCCTGGCAAGCCCTTGTGTGTTGAGAGCTTCTCAGACTATCCACCTGTGGGTCGCTTTGCTGTTCAT
GATCTGAGACAGACAGTTGTCGTGGGTGTCATCAAAGCAGTGGACAAAAAGGCTGCGGAAGCTGGCAAGGTCACCAAGCC
TGCCCAGAAAGCTCAGAAGGCTAAA

ORF - retro_hsap_2896 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 87.96 %
Parental protein coverage: 100. %
Number of stop codons detected: 1
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalMGKEKTHINIVVIGHVDSGKSTTTGHLIYKCGGIDKRTIEKFEKEAAEMGKGSFKYAWVLDKLKAERERG
MGKEKTHINI.V.GHVDSGKSTTTGHLIYKCG.IDKRTIEKF..EAAEMGK.SFKYA.VLDKLKAE.ERG
RetrocopyMGKEKTHINIIVTGHVDSGKSTTTGHLIYKCGVIDKRTIEKFKNEAAEMGKASFKYASVLDKLKAEHERG
ParentalITIDIS-LWKFETSKYYVTIIDAPGHRDFIKNMITGTSQADCAVLIVAAGVGEFEAGISKNGQTREHALL
I.I.IS.LWKFETSKYYVTIIDAPGHRD.IKNMITGTSQAD.AVLIVAAGVGEFEAGISKNGQTREHALL
RetrocopyIIIGIS>LWKFETSKYYVTIIDAPGHRDVIKNMITGTSQADRAVLIVAAGVGEFEAGISKNGQTREHALL
ParentalAYTLGVKQLIVGVNKMDS-TEPPYSQKRYEEIVKEVST-YIKKIGYNPDTVAFVPISGWNGDNMLEPSAN
AYTLGVKQ.IVGVNKM...TEPPYSQKRY.EIVKEVST.YIKKIGYNPDTVAFVPISGWN.DNMLEPSAN
RetrocopyAYTLGVKQPIVGVNKMVT<TEPPYSQKRYKEIVKEVST<YIKKIGYNPDTVAFVPISGWNDDNMLEPSAN
ParentalMPWFKGWKVTRKDGNASGTTLLEALDCILPPTRPTDKPLRLPLQDVYKIGGIGTVPVGRVETGVLKPGMV
.PWFKGWKVT...GNASGTTLLEALDC.LPPT.PTDKPL.L.LQDVYKIGGIGTVP.G.VETG.LKPGMV
RetrocopyTPWFKGWKVTGNNGNASGTTLLEALDCVLPPTGPTDKPLCLFLQDVYKIGGIGTVPIG*VETGILKPGMV
ParentalVTFAPVNVTTEVKSVEMHHEALSEALPGDNVGFNVKNVSVKDVRRGNVAGDSKNDPPMEAAGFTAQVIIL
VTFAPVNVTTEVKSV..HHEALSEALPGDNVGF.VKNV.VKDVR..NVAGDSKN.PPMEAAG.TAQV.I.
RetrocopyVTFAPVNVTTEVKSVKTHHEALSEALPGDNVGFSVKNVFVKDVRHDNVAGDSKNEPPMEAAGLTAQVTIR
ParentalNHPGQISAGYAPVLDCHTAHIACKFAELKEKIDRRSGKKLEDGPKFLKSGDAAIVDMVPGKPMCVESFSD
NH.GQISAGYAPVL.CH.AHIACKF...KEKIDR.SGKKLEDGPKFLKSGDAAIVD.VPGKP.CVESFSD
RetrocopyNHSGQISAGYAPVLNCHMAHIACKFPVQKEKIDRCSGKKLEDGPKFLKSGDAAIVDTVPGKPLCVESFSD
ParentalYPPLGRFAVRDMRQTVAVGVIKAVDKKAAGAGKVTKSAQKAQKAK
YPP.GRFAV.D.RQTV.VGVIKAVDKKAA.AGKVTK.AQKAQKAK
RetrocopyYPPVGRFAVHDLRQTVVVGVIKAVDKKAAEAGKVTKPAQKAQKAK

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 .06 RPM 5264 .08 RPM
bodymap2_adrenal 0 .08 RPM 4408 .93 RPM
bodymap2_brain 0 .07 RPM 1165 .02 RPM
bodymap2_breast 0 .08 RPM 3630 .18 RPM
bodymap2_colon 0 .06 RPM 6218 .58 RPM
bodymap2_heart 0 .04 RPM 698 .42 RPM
bodymap2_kidney 0 .04 RPM 2811 .08 RPM
bodymap2_liver 0 .00 RPM 1314 .04 RPM
bodymap2_lung 0 .07 RPM 6336 .68 RPM
bodymap2_lymph_node 0 .04 RPM 5735 .42 RPM
bodymap2_ovary 0 .19 RPM 7786 .50 RPM
bodymap2_prostate 0 .17 RPM 8544 .31 RPM
bodymap2_skeletal_muscle 0 .00 RPM 972 .29 RPM
bodymap2_testis 0 .13 RPM 3096 .81 RPM
bodymap2_thyroid 0 .00 RPM 4724 .61 RPM
bodymap2_white_blood_cells 0 .00 RPM 9598 .56 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_2896 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_2896 retrocopy.

TSS - click to see more details



TSS No. TSS Name TSS expression level (Expr) in TPM range:
no expression 0 < Expr ≤ 1 1 < Expr ≤ 5 5 < Expr ≤ 10 Expr > 10
TSS #1 TSS_13232659 libraries13 libraries263 libraries501 libraries993 libraries

The graphical summary, for retro_hsap_2896 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1829 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)

Display detail expression values in each library
... or ...
Directly download all expression values

Lab - click to see more details

retro_hsap_2896 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_2896 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Gorilla gorilla retro_ggor_2006
Parental genes homology:
Parental genes homology involve 16 parental genes, and 126 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000145343 retrocopies
retro_btau_114, retro_btau_115, retro_btau_192,
Canis familiaris ENSCAFG000000132491 retrocopy
retro_cfam_1007,
Equus caballus ENSECAG000000203632 retrocopies
retro_ecab_66, retro_ecab_93,
Equus caballus ENSECAG000000222601 retrocopy
retro_ecab_802,
Felis catus ENSFCAG0000003097714 retrocopies
retro_fcat_1021, retro_fcat_1388, retro_fcat_1569, retro_fcat_1683, retro_fcat_1825, retro_fcat_184, retro_fcat_1915, retro_fcat_220, retro_fcat_221, retro_fcat_334, retro_fcat_515, retro_fcat_566, retro_fcat_688, retro_fcat_737,
Homo sapiens ENSG00000156508 27 retrocopies
retro_hsap_1093, retro_hsap_1181, retro_hsap_1567, retro_hsap_1671, retro_hsap_190, retro_hsap_2302, retro_hsap_2455, retro_hsap_2637, retro_hsap_2712, retro_hsap_278, retro_hsap_283, retro_hsap_2896 , retro_hsap_2920, retro_hsap_2967, retro_hsap_2983, retro_hsap_3239, retro_hsap_3291, retro_hsap_3314, retro_hsap_363, retro_hsap_3701, retro_hsap_3706, retro_hsap_3758, retro_hsap_3825, retro_hsap_3917, retro_hsap_4220, retro_hsap_4730, retro_hsap_989,
Loxodonta africana ENSLAFG000000280811 retrocopy
retro_lafr_651,
Myotis lucifugus ENSMLUG0000001353724 retrocopies
retro_mluc_110, retro_mluc_1252, retro_mluc_1392, retro_mluc_1430, retro_mluc_1558, retro_mluc_1628, retro_mluc_1644, retro_mluc_1853, retro_mluc_1901, retro_mluc_1910, retro_mluc_2071, retro_mluc_2148, retro_mluc_2154, retro_mluc_2277, retro_mluc_2355, retro_mluc_2358, retro_mluc_2359, retro_mluc_2391, retro_mluc_441, retro_mluc_470, retro_mluc_677, retro_mluc_950, retro_mluc_956, retro_mluc_966,
Monodelphis domestica ENSMODG000000185334 retrocopies
retro_mdom_1053, retro_mdom_1146, retro_mdom_311, retro_mdom_792,
Mustela putorius furoENSMPUG000000038166 retrocopies
retro_mputfur_1514, retro_mputfur_1643, retro_mputfur_220, retro_mputfur_502, retro_mputfur_844, retro_mputfur_862,
Mustela putorius furoENSMPUG0000000427110 retrocopies
retro_mputfur_1179, retro_mputfur_1276, retro_mputfur_1351, retro_mputfur_1394, retro_mputfur_284, retro_mputfur_355, retro_mputfur_474, retro_mputfur_678, retro_mputfur_920, retro_mputfur_973,
Oryctolagus cuniculus ENSOCUG000000084813 retrocopies
retro_ocun_1102, retro_ocun_187, retro_ocun_71,
Ochotona princeps ENSOPRG000000166856 retrocopies
retro_opri_1049, retro_opri_1076, retro_opri_1197, retro_opri_298, retro_opri_325, retro_opri_383,
Sus scrofa ENSSSCG000000044894 retrocopies
retro_sscr_169, retro_sscr_492, retro_sscr_612, retro_sscr_758,
Tursiops truncatus ENSTTRG0000000011419 retrocopies
retro_ttru_1020, retro_ttru_1150, retro_ttru_1196, retro_ttru_1349, retro_ttru_1351, retro_ttru_1368, retro_ttru_1384, retro_ttru_1810, retro_ttru_1861, retro_ttru_1876, retro_ttru_384, retro_ttru_390, retro_ttru_401, retro_ttru_523, retro_ttru_664, retro_ttru_698, retro_ttru_844, retro_ttru_941, retro_ttru_998,
Drosophila melanogaster FBgn00005571 retrocopy
retro_dmel_9,

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 = 0.19 RPM Legend:


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

Indel association:

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





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