RetrogeneDB ID:

retro_hsap_1004

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:12:53547055..53548024(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000257790
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:EIF4A1
Ensembl ID:ENSG00000161960
Aliases:EIF4A1, DDX2A, EIF-4A, EIF4A, eIF-4A-I, eIF4A-I
Description:eukaryotic translation initiation factor 4A1 [Source:HGNC Symbol;Acc:3282]


Retrocopy-Parental alignment summary:






>retro_hsap_1004
ATGTCTGCGAGCCAGGATTCCTGATCCAGAGACAACGGCCCCAATGGGATGGAGCCCAAAGGTGTCATTGAGAGTAACTG
GAATGAGATTGTTGACAGCTTTGATGACATGAACCTCTCAGAGTCCCTTCTCCGTGGCATCTACGCCTATGGTTTAGAGA
AGCCGTCTGCCATCCAGCAGCGAGCCATTCTACCTTGTATCAAGGGTTATCACGTGATTGCTCAAGCCCAATCTGGGGCT
GGGAAAATGGCCACATTTGCCATATTGATTCTGCAGCAGATTGAATTAGATCTAAAAGCCACCCAGGCCTTGCTCCTAGC
ACCCACTCAAGAATTGGCTCAGCAGATACAGAAGGTGGTCATGGCACTAGGAGACTACATGGGTGCCTCCTGTCATGCCT
GTATCAGGGGCACCAACATGCGTGCTGAGGTGCAGAAACTGCAGACGAAGCTCCTCACATCATTGTGGGTACCCCTGGCC
ATGTGTTTGATATGCTTAACGGGAGATACCTGTCTCCCAAATACATCAAGATGTTTGTACTGGACGAAGCTGACGAAATG
TTAAGCCGTGGATTCAAGGACCAGATCTATGACATATTCCAAAAGCTCAACAGCAACACCCAGGTAGTTTTGCTGTCAGC
TGCGATGCCTTCTGATGTGCTTGAGGTGACCAAGAAGTTCATGAGGGACCTCATTCGGATTCTTGTCACGAAGGAAGTGT
TGACCTTGGAGGGTATCCGCCAATTCTACATCAATTTGGAACGAGAGGAGTGGAAGCTGGACACACTATGTGACTTGTAT
GAAACCCTGACCATCACCCCAGGCAGTCATCTTCATCAACACCCGGAGGAAGGTGGACTGGCTCACCGAGAAGATGCATG
CTCGAGATTTCACTGTCTTCACCATTCGTGGAGATATGGACCAAAACGAACAAGACGTGATCTTGAGGGAGTTTCGTTAT
GGCTCTAGC

ORF - retro_hsap_1004 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 90.77 %
Parental protein coverage: 79.56 %
Number of stop codons detected: 1
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalMSASQDSRSRDNGPDGMEPEGVIESNWNEIVDSFDDMNLSESLLRGIYAYGFEKPSAIQQRAILPCIKGY
MSASQDS.SRDNGP.GMEP.GVIESNWNEIVDSFDDMNLSESLLRGIYAYG.EKPSAIQQRAILPCIKGY
RetrocopyMSASQDS*SRDNGPNGMEPKGVIESNWNEIVDSFDDMNLSESLLRGIYAYGLEKPSAIQQRAILPCIKGY
ParentalDVIAQAQSGTGKTATFAISILQQIELDLKATQALVLAPTRELAQQIQKVVMALGDYMGASCHACIGGTNV
.VIAQAQSG.GK.ATFAI.ILQQIELDLKATQAL.LAPT.ELAQQIQKVVMALGDYMGASCHACI.GTN.
RetrocopyHVIAQAQSGAGKMATFAILILQQIELDLKATQALLLAPTQELAQQIQKVVMALGDYMGASCHACIRGTNM
ParentalRAEVQKLQM-EAPHIIVGTPGRVFDMLNRRYLSPKYIKMFVLDEADEMLSRGFKDQIYDIFQKLNSNTQV
RAEVQKLQ..EAPHIIVGTPG.VFDMLN.RYLSPKYIKMFVLDEADEMLSRGFKDQIYDIFQKLNSNTQV
RetrocopyRAEVQKLQT<EAPHIIVGTPGHVFDMLNGRYLSPKYIKMFVLDEADEMLSRGFKDQIYDIFQKLNSNTQV
ParentalVLLSATMPSDVLEVTKKFMRDPIRILVKKEELTLEGIRQFYINVEREEWKLDTLCDLYETLTIT-QAVIF
VLLSA.MPSDVLEVTKKFMRD.IRILV.KE.LTLEGIRQFYIN.EREEWKLDTLCDLYETLTIT.QAVIF
RetrocopyVLLSAAMPSDVLEVTKKFMRDLIRILVTKEVLTLEGIRQFYINLEREEWKLDTLCDLYETLTIT>QAVIF
ParentalINTRRKVDWLTEKMHARDFTVSAMHGDMDQKERDVIMREFRSGSS
INTRRKVDWLTEKMHARDFTV....GDMDQ.E.DVI.REFR.GSS
RetrocopyINTRRKVDWLTEKMHARDFTVFTIRGDMDQNEQDVILREFRYGSS

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 .12 RPM 4 .06 RPM
bodymap2_adrenal 0 .10 RPM 24 .05 RPM
bodymap2_brain 0 .00 RPM 3 .59 RPM
bodymap2_breast 0 .02 RPM 7 .61 RPM
bodymap2_colon 0 .02 RPM 3 .27 RPM
bodymap2_heart 0 .00 RPM 1 .90 RPM
bodymap2_kidney 0 .06 RPM 4 .74 RPM
bodymap2_liver 0 .00 RPM 1 .94 RPM
bodymap2_lung 0 .02 RPM 11 .81 RPM
bodymap2_lymph_node 0 .00 RPM 10 .49 RPM
bodymap2_ovary 0 .08 RPM 12 .09 RPM
bodymap2_prostate 0 .00 RPM 5 .92 RPM
bodymap2_skeletal_muscle 0 .00 RPM 1 .07 RPM
bodymap2_testis 0 .04 RPM 1 .85 RPM
bodymap2_thyroid 0 .04 RPM 6 .67 RPM
bodymap2_white_blood_cells 0 .02 RPM 3 .11 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_1004 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_1004 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_2642431 libraries8 libraries67 libraries69 libraries1654 libraries

The graphical summary, for retro_hsap_1004 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_1004 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_1004 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_750
Gorilla gorilla retro_ggor_798
Parental genes homology:
Parental genes homology involve 16 parental genes, and 67 retrocopies.

Species Parental gene accession Retrocopies number
Cavia porcellus ENSCPOG000000049001 retrocopy
retro_cpor_1088,
Erinaceus europaeus ENSEEUG000000035811 retrocopy
retro_eeur_610,
Felis catus ENSFCAG000000248971 retrocopy
retro_fcat_370,
Homo sapiens ENSG000001569762 retrocopies
retro_hsap_593, retro_hsap_878,
Homo sapiens ENSG00000161960 10 retrocopies
retro_hsap_1004 , retro_hsap_1182, retro_hsap_1252, retro_hsap_1270, retro_hsap_1796, retro_hsap_2520, retro_hsap_4836, retro_hsap_4873, retro_hsap_4931, retro_hsap_610,
Gorilla gorilla ENSGGOG000000247028 retrocopies
retro_ggor_1321, retro_ggor_1572, retro_ggor_3015, retro_ggor_537, retro_ggor_798, retro_ggor_920, retro_ggor_983, retro_ggor_998,
Macropus eugenii ENSMEUG000000107802 retrocopies
retro_meug_158, retro_meug_179,
Myotis lucifugus ENSMLUG000000034153 retrocopies
retro_mluc_1047, retro_mluc_1229, retro_mluc_1805,
Macaca mulatta ENSMMUG000000134991 retrocopy
retro_mmul_1280,
Monodelphis domestica ENSMODG000000070903 retrocopies
retro_mdom_1282, retro_mdom_326, retro_mdom_711,
Mus musculus ENSMUSG000000597967 retrocopies
retro_mmus_1810, retro_mmus_1853, retro_mmus_2320, retro_mmus_2473, retro_mmus_3122, retro_mmus_325, retro_mmus_527,
Nomascus leucogenys ENSNLEG000000095477 retrocopies
retro_nleu_2109, retro_nleu_2117, retro_nleu_230, retro_nleu_2470, retro_nleu_2769, retro_nleu_440, retro_nleu_701,
Pan troglodytes ENSPTRG0000000869410 retrocopies
retro_ptro_1201, retro_ptro_1465, retro_ptro_2954, retro_ptro_3112, retro_ptro_3247, retro_ptro_450, retro_ptro_750, retro_ptro_810, retro_ptro_862, retro_ptro_870,
Rattus norvegicus ENSRNOG000000306283 retrocopies
retro_rnor_1059, retro_rnor_2213, retro_rnor_2306,
Sorex araneus ENSSARG000000060177 retrocopies
retro_sara_224, retro_sara_383, retro_sara_461, retro_sara_567, retro_sara_6, retro_sara_605, retro_sara_89,
Ictidomys tridecemlineatus ENSSTOG000000248141 retrocopy
retro_itri_610,

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