RetrogeneDB ID:

retro_hsap_4196

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:9:98908291..98910135(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000224546
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:EIF4B
Ensembl ID:ENSG00000063046
Aliases:EIF4B, EIF-4B, PRO1843
Description:eukaryotic translation initiation factor 4B [Source:HGNC Symbol;Acc:3285]


Retrocopy-Parental alignment summary:






>retro_hsap_4196
GCGGCCTCAGCAAAAAAGAAGAAGAAGAAGGGGAAGACTATCTCCCTAACAGACTTTCTGGCTGAGGATGGGGGTACTGG
TGGAGGAAGGACCTATGTTTCCAAACCAGTCAGCTGAGCTGATGAAACGGATGACCTGGAAGGAGATGTTTCGACAACTT
GGCACAGTAACGATGACGATGTGTATAGGGCGTCTCCAATTGACCGTTCCATCCTTCCCACTGCTCCACGGGCTGCTCGG
GAACCCAATATCGACCGGAGCCATCTTCCCAAATCGCCACCCTACACTGCTTTTCTAGGAAACCTACCCTATGATGTTAC
AGAAGAGTCAATTAAGGAATTCTTTCGAGGATTAAATATCAGTGCAGTGCGTTTACCATGTGAACCCAGCAATCCAGTGA
GGTTGAAAGGTTTTGGTTATGCTGAATTTGAGGACCTGGATTCCCTGCTTAGTGCCCTGAGTCTCAAGGAAGAGTCTCTA
GGTAACAGGAGAATTCGAGTGGACGTTGCTGATCAAGCACAGGATAAAGACAGGGATGATTGTTCTTTTGGCCGTGATAG
AAATCGGGATTCTGACAAAACAGGTACAGACTGGAGGGCTCGTCCTGCTACAGACAGCTTTGATGACTACCCACCTAGAA
GAGGTGATGATAGCTTTGGAGACAAGTATCGAGATCGTTATGATTCAGACCGGTATCGGGATGGGTATCGGGATGGGTAT
CGGGATGGCCAACGCCGGGATATGGATCCATATGGTGGCCGGGATCGCTATGATGACCGAGGCAGCAGAGACTATGATAG
AGGCTATGATTCCCGGATAGGCAGTGGCAGAAGAGCATTTGGCAGTGGGTATCGCAGGGATGATGTCTCAGAGGAGGCGG
GGACCACTATGAAGACCGATATGACAGACGGGATGATCGGTCTTGGAGCTCCAGAGATGATTACTCTCTGGATGATTATA
GGCGTGATGGTAGAGGTCCCCCCCAAAGACCCAAACTGAATCTAAACCCTCGGAGTACTCCTAAGGAAGATGATTCCTCT
GCTAGTACCTCCCAGTCCACTCGAGCTGCTTCTATCTTTGGAGGGGCAAAGCCCGTTGACACAGCTGCTAGAGAAAGAGA
AGTAGAAGAACGGCTACAGAAGGAACAAGAGAAGTTGCAGCATCAGCTGGATGAGCCAAAACTAGAACGACGGCCTCCGG
AGAGACACCCAAGCTGGCGAAGTGAAGAAACTCAGGAACGGGAACGGTCGAGGACAGGAAGTGAGTCATCACAGACTGGG
ACCTCCACCACATCTGGCAGAAGTAAGTCAGCCCAGGATGCACGAAGGAGAGAGAATGAGAAGTCTCTAGAAAATGAAAC
ACTCAATAAGGAGGAAGATTGCCACTCTCCAACTTCTAAACCTCCCAAACCTGATCAGCCCCTAAAGGTAATGCCAGCCC
CTCCACCAAAGGAGAATGCTTGGGTGAAGCGAAGTTCTAACCCTCCTGCTCGATCTCAGAGCTCAGACACAGAGCAGCAA
TCCCCTACAAGTGGTGAGGGAAAAGTAGCTCCAGCTCAACCATCTGAGGAAGGACCAGCAAGGAAAGATGAAAACAAAGT
AGATGGGATGAATGTCCCAAAAGGCCAAACTGGGAACTCTAGCCGTGGTCCAGGAGATGGAGGGAACAAAGACCACTGGA
AGGAGTCAGATAGGAAAGATGGCAAAAAGGATCAAGACTCCAGATCTGCACCTGAGCCAAAGAAACCTGAGGAAAATCCA
GCTTCCAAGTTCAGTTCTGCAAGCAAGTATGCTGCTCTCTCTGTTGATGGTGAAGATGAAAATGAGGGAGAAGATTATGC
CGAA

ORF - retro_hsap_4196 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 93.34 %
Parental protein coverage: 99.84 %
Number of stop codons detected: 1
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalAASAKKKNKKGKTISLTDFLAEDGGTGGGSTYVSKPVSWADETDDLEGDVSTTWHSNDDDVYRAPPIDRS
AASAKKK.KKGKTISLTDFLAEDGGTGGG.TYVSKPVS.ADETDDLEGDVSTTWHSNDDDVYRA.PIDRS
RetrocopyAASAKKKKKKGKTISLTDFLAEDGGTGGGRTYVSKPVS*ADETDDLEGDVSTTWHSNDDDVYRASPIDRS
ParentalILPTAPRAAREPNIDRSRLPKSPPYTAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGY
ILPTAPRAAREPNIDRS.LPKSPPYTAFLGNLPYDVTEESIKEFFRGLNISAVRLP.EPSNP.RLKGFGY
RetrocopyILPTAPRAAREPNIDRSHLPKSPPYTAFLGNLPYDVTEESIKEFFRGLNISAVRLPCEPSNPVRLKGFGY
ParentalAEFEDLDSLLSALSLNEESLGNRRIRVDVADQAQDKDRDDRSFGRDRNRDSDKTDTDWRARPATDSFDDY
AEFEDLDSLLSALSL.EESLGNRRIRVDVADQAQDKDRDD.SFGRDRNRDSDKT.TDWRARPATDSFDDY
RetrocopyAEFEDLDSLLSALSLKEESLGNRRIRVDVADQAQDKDRDDCSFGRDRNRDSDKTGTDWRARPATDSFDDY
ParentalPPRRGDDSFGDKYRDRYDSDRYRDGYRDGYRDGPRRDMDRYGGRDRYDDRGSRDYDRGYDSRIGSGRRAF
PPRRGDDSFGDKYRDRYDSD..............RRDMD.YGGRDRYDDRGSRDYDRGYDSRIGSGRRAF
RetrocopyPPRRGDDSFGDKYRDRYDSDXXXXXXXXXXXXXQRRDMDPYGGRDRYDDRGSRDYDRGYDSRIGSGRRAF
ParentalGSGYRRDDD-YRGGGDRYEDRYDRRDDRSWSSRDDYSRDDYRRDDRGPPQRPKLNLKPRSTPKEDDSSAS
GSGYRRDD...RGGGD.YEDRYDRRDDRSWSSRDDYS.DDYRRD.RGPPQRPKLNL.PRSTPKEDDSSAS
RetrocopyGSGYRRDDV<LRGGGDHYEDRYDRRDDRSWSSRDDYSLDDYRRDGRGPPQRPKLNLNPRSTPKEDDSSAS
ParentalTSQSTRAASIFGGAKPVDTAAREREVEERLQKEQEKLQRQLDEPKLERRPRERHPSWRSEETQERERSRT
TSQSTRAASIFGGAKPVDTAAREREVEERLQKEQEKLQ.QLDEPKLERRP.ERHPSWRSEETQERERSRT
RetrocopyTSQSTRAASIFGGAKPVDTAAREREVEERLQKEQEKLQHQLDEPKLERRPPERHPSWRSEETQERERSRT
ParentalGSESSQTGTSTTSSRSKSDQDARRRESEKSLENETLNKEEDCHSPTSKPPKPDQPLKVMPAPPPKENAWV
GSESSQTGTSTTS.RSKS.QDARRRE.EKSLENETLNKEEDCHSPTSKPPKPDQPLKVMPAPPPKENAWV
RetrocopyGSESSQTGTSTTSGRSKSAQDARRRENEKSLENETLNKEEDCHSPTSKPPKPDQPLKVMPAPPPKENAWV
ParentalKRSSNPPARSQSSDTEQQSPTSGGGKVAPAQPSEEGPGRKDENKVDGMNAPKGQTGNSSRGPGDGGNRDH
KRSSNPPARSQSSDTEQQSPTSG.GKVAPAQPSEEGP.RKDENKVDGMN.PKGQTGNSSRGPGDGGN.DH
RetrocopyKRSSNPPARSQSSDTEQQSPTSGEGKVAPAQPSEEGPARKDENKVDGMNVPKGQTGNSSRGPGDGGNKDH
ParentalWKESDRKDGKKDQDSRSAPEPKKPEENPASKFSSASKYAALSVDGEDENEGEDYAE
WKESDRKDGKKDQDSRSAPEPKKPEENPASKFSSASKYAALSVDGEDENEGEDYAE
RetrocopyWKESDRKDGKKDQDSRSAPEPKKPEENPASKFSSASKYAALSVDGEDENEGEDYAE

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 703 .14 RPM
bodymap2_adrenal 0 .27 RPM 434 .24 RPM
bodymap2_brain 0 .05 RPM 232 .88 RPM
bodymap2_breast 0 .19 RPM 442 .03 RPM
bodymap2_colon 0 .54 RPM 722 .93 RPM
bodymap2_heart 0 .20 RPM 297 .04 RPM
bodymap2_kidney 0 .10 RPM 206 .91 RPM
bodymap2_liver 0 .17 RPM 106 .15 RPM
bodymap2_lung 0 .00 RPM 407 .72 RPM
bodymap2_lymph_node 0 .37 RPM 454 .43 RPM
bodymap2_ovary 0 .54 RPM 1147 .94 RPM
bodymap2_prostate 0 .24 RPM 826 .01 RPM
bodymap2_skeletal_muscle 1 .24 RPM 1007 .06 RPM
bodymap2_testis 0 .23 RPM 372 .14 RPM
bodymap2_thyroid 0 .21 RPM 489 .01 RPM
bodymap2_white_blood_cells 1 .14 RPM 716 .99 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_4196 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_4196 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_195254434 libraries739 libraries643 libraries10 libraries3 libraries

The graphical summary, for retro_hsap_4196 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_4196 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_4196 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 13 parental genes, and 41 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG000000181762 retrocopies
retro_cjac_1717, retro_cjac_2001,
Cavia porcellus ENSCPOG000000055953 retrocopies
retro_cpor_278, retro_cpor_752, retro_cpor_937,
Homo sapiens ENSG00000063046 7 retrocopies
retro_hsap_1686, retro_hsap_2639, retro_hsap_2698, retro_hsap_3767, retro_hsap_4196 , retro_hsap_4848, retro_hsap_4891,
Gorilla gorilla ENSGGOG000000136955 retrocopies
retro_ggor_1233, retro_ggor_1263, retro_ggor_1882, retro_ggor_1883, retro_ggor_3024,
Loxodonta africana ENSLAFG000000095341 retrocopy
retro_lafr_294,
Macropus eugenii ENSMEUG000000123412 retrocopies
retro_meug_1054, retro_meug_585,
Macaca mulatta ENSMMUG000000010625 retrocopies
retro_mmul_1428, retro_mmul_2384, retro_mmul_2589, retro_mmul_731, retro_mmul_783,
Mus musculus ENSMUSG000000586551 retrocopy
retro_mmus_3686,
Nomascus leucogenys ENSNLEG000000177273 retrocopies
retro_nleu_2371, retro_nleu_2601, retro_nleu_721,
Pongo abelii ENSPPYG000000258487 retrocopies
retro_pabe_1388, retro_pabe_1560, retro_pabe_2283, retro_pabe_260, retro_pabe_3532, retro_pabe_3768, retro_pabe_506,
Rattus norvegicus ENSRNOG000000101032 retrocopies
retro_rnor_2467, retro_rnor_2972,
Ictidomys tridecemlineatus ENSSTOG000000068001 retrocopy
retro_itri_604,
Tupaia belangeri ENSTBEG000000054232 retrocopies
retro_tbel_2363, retro_tbel_4167,

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 = 8.14 RPM Legend:


Library Retrogene expression
CEU_NA11831 4 .26 RPM
CEU_NA11843 5 .91 RPM
CEU_NA11930 6 .42 RPM
CEU_NA12004 3 .76 RPM
CEU_NA12400 6 .59 RPM
CEU_NA12751 6 .63 RPM
CEU_NA12760 5 .66 RPM
CEU_NA12827 2 .88 RPM
CEU_NA12872 3 .84 RPM
CEU_NA12873 8 .14 RPM
FIN_HG00183 3 .32 RPM
FIN_HG00277 4 .18 RPM
FIN_HG00315 6 .13 RPM
FIN_HG00321 7 .83 RPM
FIN_HG00328 6 .18 RPM
FIN_HG00338 7 .83 RPM
FIN_HG00349 5 .69 RPM
FIN_HG00375 5 .53 RPM
FIN_HG00377 3 .91 RPM
FIN_HG00378 3 .36 RPM
GBR_HG00099 6 .22 RPM
GBR_HG00111 2 .47 RPM
GBR_HG00114 4 .68 RPM
GBR_HG00119 5 .20 RPM
GBR_HG00131 6 .09 RPM
GBR_HG00133 6 .05 RPM
GBR_HG00134 3 .12 RPM
GBR_HG00137 4 .32 RPM
GBR_HG00142 3 .17 RPM
GBR_HG00143 5 .20 RPM
TSI_NA20512 4 .24 RPM
TSI_NA20513 3 .29 RPM
TSI_NA20518 4 .33 RPM
TSI_NA20532 5 .85 RPM
TSI_NA20538 5 .94 RPM
TSI_NA20756 5 .91 RPM
TSI_NA20765 5 .20 RPM
TSI_NA20771 5 .93 RPM
TSI_NA20786 4 .16 RPM
TSI_NA20798 4 .65 RPM
YRI_NA18870 5 .11 RPM
YRI_NA18907 0 .21 RPM
YRI_NA18916 0 .48 RPM
YRI_NA19093 0 .52 RPM
YRI_NA19099 0 .56 RPM
YRI_NA19114 4 .72 RPM
YRI_NA19118 0 .52 RPM
YRI_NA19213 2 .56 RPM
YRI_NA19214 0 .27 RPM
YRI_NA19223 7 .14 RPM

Indel association:

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



Copyright © RetrogeneDB 2014-2017