RetrogeneDB ID:

retro_hsap_2713

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:3:142168947..142170160(+)
Located in intron of:ENSG00000175054
Retrocopy
information
Ensembl ID:ENSG00000242479
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:EIF2AK1
Ensembl ID:ENSG00000086232
Aliases:EIF2AK1, HCR, HRI
Description:eukaryotic translation initiation factor 2-alpha kinase 1 [Source:HGNC Symbol;Acc:24921]


Retrocopy-Parental alignment summary:






>retro_hsap_2713
GGCTGCGCTGCAGCCCACGAGCACAAAGAGGAGGGCCACGGGGTGGAGACTGTTGCTGTGCCATCTGCCATCGACTTTTC
CGCCAAGAGCCTGGACTCCAAATATGACTTATGTTCCAGCAGAACTCCAGGTATTAAAATAACCCCTACAACAGCCAACT
TTCCCTTTTGCAGTTGCAAACCAGCTGCCGCTTATTTCTTTGGTGAAGCACTTGAGCCATGTGCGTGAACCAAACCCAGT
TCATTCAAGACAGTGTTTAAGTTACTTTGCCAGACCTTTATCAAAATGGGGCTGCTGTCTTCTTTCACTTGTGACAAGTT
TAGCTCATTGAGACTACATCACCACAGAGCTATTACTCACTTAATGAGGTCCACTAAAGAGAGAGTTCATCAGGATCCTT
GTGAGGCTATTTCTCATATCCAGAAAATCAGATCAAGGGAAGTACCCTTTGAAGCACAAACTTCACGTTACTTAAATGAA
TTTGAAGAACTTGCCATCTTAGGAAAAGGTGGATATGGAAGAGTATACAAGGTCAGGAATAAATTAGATGGTCAGTATTA
TGCAATTTAAAAAATCCTGATTAAGGGTGCAACAAAAACACATTACATGAAAGAACTACGGGGAATGAAGGTGCTGGCAG
GTCTTCAGCACCCTAATATCATTCGTTATCACACTGCGTGGACAGAACATGTTCAAGTGGTCCAACCACAAGCAGACAGA
GCTTCCGTTCAGTTGCCATTTCTGGAAGTGTTCTCCGACCAAGCAGACAGATACCAATACGGTGTTAAAAATGGTGAAAA
TAGCAGCTCACCCATTATCTTCGCGGAGCTCACCTCAGAAAAGAAAAACCCTTTGCAGAATCTGACACTCAAAATCAGAA
CAACAAGCTGTGAACTACACCATCAATTCCGTCTTAAGAGACACCAGTGAATATGAATCATCCCTGGAGCTCCAGGAAAA
TGGCCTGGCTGGTTTGTCTACCTGGTCAATTGTGAAACAGCCCCTGCTGCTCAGGTGTAATTCCCTCCTAGAGGAGAATT
TCACATCCACTGAGGAATCTTCCAAAGAAAACTTCAACTTGTTGGGGATCGAGGTGCAGTACCACCTGATGCTGCACATC
CAGATGCAGGTGTGCAAGCTCCAGCTGTGGGACTGGCTAGCTGAGAGAAACAAACAGGGCCAAGAGTGTGTGGGCAAGTT
TGCCTGTCCTTAT

ORF - retro_hsap_2713 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 73.19 %
Parental protein coverage: 65.08 %
Number of stop codons detected: 2
Number of frameshifts detected 4


Retrocopy - Parental Gene Alignment:

ParentalGNSGVRKREEEGDGAGAVAAPPAID-FPAEGPDPEYDESDVPAEIQVLKEPLQQPTFPFAVANQLLLVSL
G........EEG.G...VA.P.AID.FP.....P......VPAE.QVLK.PLQQPTFPFAVANQL.L.SL
RetrocopyGCAAAHEHKEEGHGVETVAVPSAID>FPPRAWTPNM--TYVPAELQVLK*PLQQPTFPFAVANQLPLISL
ParentalLEHLSHVHEPNPLRSRQ-VFKLLCQTFIKMGLLSSFTCSDEFSSLRLHHNRAITHLMRSAKERVRQDPCE
..HLSHV.EPNP..SRQ.VFKLLCQTFIKMGLLSSFTC.D.FSSLRLHH.RAITHLMRS.KERV.QDPCE
RetrocopyVKHLSHVREPNPVHSRQ<VFKLLCQTFIKMGLLSSFTC-DKFSSLRLHHHRAITHLMRSTKERVHQDPCE
ParentalDISRIQKIRSREVALEAQTSRYLNEFEELAILGKGGYGRVYKVRNKLDGQYYAIKKILIKGATKTVCMKV
.IS.IQKIRSREV..EAQTSRYLNEFEELAILGKGGYGRVYKVRNKLDGQYYAI.KILIKGATKT..MK.
RetrocopyAISHIQKIRSREVPFEAQTSRYLNEFEELAILGKGGYGRVYKVRNKLDGQYYAI*KILIKGATKTHYMKE
ParentalLREVKVLAGLQHPNIVGYHTAWIEHVHVIQPRADRAAIELPSLEVLSDQEEDREQCGVKNDESSSSSIIF
LR..KVLAGLQHPNI..YHTAW.EHV.V.QP.ADRA...LP.LEV.SDQ..DR.Q.GVKN.E.SSS.IIF
RetrocopyLRGMKVLAGLQHPNIIRYHTAWTEHVQVVQPQADRASVQLPFLEVFSDQ-ADRYQYGVKNGENSSSPIIF
ParentalAEPTPE-KEKRFGESDTENQNNK-SVKYTTNLVIRESGELESTLELQENGLAGLSASSIVEQQLPLRRNS
AE.T.E.KEK.F.ESDT.NQNNK..V.YT.N.V.R...E.ES.LELQENGLAGLS..SIV.Q.L.LR.NS
RetrocopyAELTSE<KEKPFAESDTQNQNNK<AVNYTINSVLRDTSEYESSLELQENGLAGLSTWSIVKQPLLLRCNS
ParentalHLEESFTSTEESSEENVNFLGQTEAQYHLMLHIQMQLCELSLWDWIVERNKRGREYVDESACPY
.LEE.FTSTEESS.EN.N.LG..E.QYHLMLHIQMQ.C.L.LWDW..ERNK.G.E.V...ACPY
RetrocopyLLEENFTSTEESSKENFNLLG-IEVQYHLMLHIQMQVCKLQLWDWLAERNKQGQECVGKFACPY

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 .42 RPM 79 .57 RPM
bodymap2_adrenal 6 .24 RPM 82 .72 RPM
bodymap2_brain 1 .50 RPM 128 .76 RPM
bodymap2_breast 1 .52 RPM 83 .76 RPM
bodymap2_colon 0 .39 RPM 67 .23 RPM
bodymap2_heart 0 .50 RPM 63 .88 RPM
bodymap2_kidney 0 .85 RPM 97 .16 RPM
bodymap2_liver 0 .85 RPM 111 .19 RPM
bodymap2_lung 0 .76 RPM 80 .43 RPM
bodymap2_lymph_node 0 .29 RPM 82 .94 RPM
bodymap2_ovary 3 .14 RPM 105 .87 RPM
bodymap2_prostate 1 .21 RPM 91 .29 RPM
bodymap2_skeletal_muscle 0 .55 RPM 91 .70 RPM
bodymap2_testis 0 .47 RPM 84 .20 RPM
bodymap2_thyroid 2 .28 RPM 122 .57 RPM
bodymap2_white_blood_cells 1 .12 RPM 160 .67 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_2713 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_2713 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_2713 retrocopy 5' end.

Lab - click to see more details

retro_hsap_2713 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_2713 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_1833
Parental genes homology:
Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species Parental gene accession Retrocopies number
Homo sapiens ENSG00000086232 1 retrocopy
retro_hsap_2713 ,
Nomascus leucogenys ENSNLEG000000009921 retrocopy
retro_nleu_1586,
Pan troglodytes ENSPTRG000000189041 retrocopy
retro_ptro_1833,

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 = 3.08 RPM Legend:


Library Retrogene expression
CEU_NA11831 1 .28 RPM
CEU_NA11843 1 .73 RPM
CEU_NA11930 1 .79 RPM
CEU_NA12004 1 .06 RPM
CEU_NA12400 1 .47 RPM
CEU_NA12751 2 .04 RPM
CEU_NA12760 0 .94 RPM
CEU_NA12827 2 .17 RPM
CEU_NA12872 1 .25 RPM
CEU_NA12873 1 .24 RPM
FIN_HG00183 2 .83 RPM
FIN_HG00277 2 .00 RPM
FIN_HG00315 2 .04 RPM
FIN_HG00321 1 .99 RPM
FIN_HG00328 1 .35 RPM
FIN_HG00338 1 .53 RPM
FIN_HG00349 1 .54 RPM
FIN_HG00375 1 .30 RPM
FIN_HG00377 1 .31 RPM
FIN_HG00378 1 .36 RPM
GBR_HG00099 0 .96 RPM
GBR_HG00111 2 .49 RPM
GBR_HG00114 1 .58 RPM
GBR_HG00119 1 .68 RPM
GBR_HG00131 2 .50 RPM
GBR_HG00133 2 .36 RPM
GBR_HG00134 1 .66 RPM
GBR_HG00137 2 .28 RPM
GBR_HG00142 3 .08 RPM
GBR_HG00143 1 .60 RPM
TSI_NA20512 1 .30 RPM
TSI_NA20513 2 .68 RPM
TSI_NA20518 1 .47 RPM
TSI_NA20532 2 .01 RPM
TSI_NA20538 1 .20 RPM
TSI_NA20756 1 .22 RPM
TSI_NA20765 1 .47 RPM
TSI_NA20771 1 .08 RPM
TSI_NA20786 0 .89 RPM
TSI_NA20798 1 .28 RPM
YRI_NA18870 1 .39 RPM
YRI_NA18907 0 .83 RPM
YRI_NA18916 2 .13 RPM
YRI_NA19093 0 .62 RPM
YRI_NA19099 0 .83 RPM
YRI_NA19114 0 .76 RPM
YRI_NA19118 1 .08 RPM
YRI_NA19213 1 .03 RPM
YRI_NA19214 0 .84 RPM
YRI_NA19223 1 .53 RPM

Indel association:

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





Copyright © RetrogeneDB 2014-2017