RetrogeneDB ID:

retro_hsap_2444

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:20:4716314..4716938(-)
Located in intron of:ENSG00000180259
Retrocopy
information
Ensembl ID:ENSG00000231071
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:IDI1
Ensembl ID:ENSG00000067064
Aliases:IDI1, IPP1, IPPI1
Description:isopentenyl-diphosphate delta isomerase 1 [Source:HGNC Symbol;Acc:5387]


Retrocopy-Parental alignment summary:






>retro_hsap_2444
GAGAAGTGTATTCTTATTGATGAAAATGACAGTAATATTGGAACTGAGACCAAGAAGAATTGTCACGAGAATGAAAACAT
TGGGAATGGATTATTGCATCAAGCTCTTAGTGTCTTCTTACTCAACACCAAAATGAGCTACAGTGACAGCAGAGATCAGA
TGCTGAAATTACCTTTCGAGCCAGTTTCACCAATACTTGGTTGTAGTCATCCATTAAGTAATCCAGACAAGCTTGAGAGA
AATGATGTCATTGACATAAGTTGAGTAGCACAGAGGCATCTAAAAGCTGAATTAGGAATTCCCATGGAAGAGGCTCCTCC
AGAAGAAACCTATTATCTAATATCAACTTGCAGCGAAGTCCAATCTGATGGCATCTGGGGAGAACATAAAACTGATTATA
TTTTGTTTGTGAGGAAGAACATAACTTCGAATTCAGATCCCAGTGAGATAAAAAGCTATTTTCTGTGTGTCAAAGGAAGA
GCTAGAACTTCTGAGAAAAGTAGTCATTGGTGAAATTAAAATAACACCATGATTTCAAGTTATTATAGAGACTTTTCTCT
TTAAATGGTGGGATAACTTAAGTCATTTGAATCAGTTTATTGACCATGAAAAATATATAGGATG

ORF - retro_hsap_2444 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 68.54 %
Parental protein coverage: 73.59 %
Number of stop codons detected: 3
Number of frameshifts detected 4


Retrocopy - Parental Gene Alignment:

ParentalEMCILIDENDNKIGAETKKNCHLNENIEKGLLHRAFSVFLFNT-ENKLLLQQRSDAKITFPGCFTNTC-C
E.CILIDEND..IG.ETKKNCH.NENI..GLLH.A.SVFL.NT..N.L..QQRSDA.ITF...FTNT..C
RetrocopyEKCILIDENDSNIGTETKKNCHENENIGNGLLHQALSVFLLNT<QNELQ*QQRSDAEITFRASFTNTW>C
ParentalSHPLSNPAELEESDALGVRRAAQRRLKAELGIPLEEVPPEEINYLTRIHYKAQSDGIWGEHEIDYILLVR
SHPLSNP..LE..D.......AQR.LKAELGIP.EE.PPEE..YL.......QSDGIWGEH..DYIL.VR
RetrocopySHPLSNPDKLERNDVIDIS*VAQRHLKAELGIPMEEAPPEETYYLISTCSEVQSDGIWGEHKTDYILFVR
ParentalKNVTLNPDPNEIKSYCY-VSKEELKELLKKAASGEIKITPWFKIIAATFLFKWWDNLNHLNQFVDHE-KI
KN.T.N.DP.EIKSY...VSKEEL.ELL.K...GEIKITP.F..I..TFLFKWWDNL.HLNQF.DHE.KI
RetrocopyKNITSNSDPSEIKSYFL>VSKEEL-ELLRKVVIGEIKITP*FQVIIETFLFKWWDNLSHLNQFIDHE<KI
ParentalYRM
YRM
RetrocopyYRM

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 .00 RPM 32 .16 RPM
bodymap2_adrenal 0 .00 RPM 65 .58 RPM
bodymap2_brain 0 .00 RPM 137 .24 RPM
bodymap2_breast 0 .00 RPM 48 .74 RPM
bodymap2_colon 0 .00 RPM 33 .01 RPM
bodymap2_heart 0 .00 RPM 24 .74 RPM
bodymap2_kidney 0 .00 RPM 76 .25 RPM
bodymap2_liver 0 .00 RPM 122 .85 RPM
bodymap2_lung 0 .00 RPM 105 .19 RPM
bodymap2_lymph_node 0 .00 RPM 54 .78 RPM
bodymap2_ovary 0 .00 RPM 108 .10 RPM
bodymap2_prostate 0 .00 RPM 35 .37 RPM
bodymap2_skeletal_muscle 0 .00 RPM 42 .85 RPM
bodymap2_testis 0 .00 RPM 59 .46 RPM
bodymap2_thyroid 0 .00 RPM 86 .68 RPM
bodymap2_white_blood_cells 0 .00 RPM 64 .26 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_2444 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_2444 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_2444 retrocopy 5' end.

Lab - click to see more details

retro_hsap_2444 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_2444 has 5 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_1412
Gorilla gorilla retro_ggor_1521
Pongo abelii retro_pabe_1783
Macaca mulatta retro_mmul_632
Callithrix jacchus retro_cjac_2591
Parental genes homology:
Parental genes homology involve 14 parental genes, and 37 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG000000084833 retrocopies
retro_cjac_2083, retro_cjac_2591, retro_cjac_2820,
Erinaceus europaeus ENSEEUG000000125553 retrocopies
retro_eeur_188, retro_eeur_198, retro_eeur_61,
Homo sapiens ENSG00000067064 3 retrocopies
retro_hsap_2161, retro_hsap_2444 , retro_hsap_4053,
Gorilla gorilla ENSGGOG000000009343 retrocopies
retro_ggor_1521, retro_ggor_1717, retro_ggor_2722,
Macaca mulatta ENSMMUG000000171153 retrocopies
retro_mmul_2340, retro_mmul_632, retro_mmul_899,
Monodelphis domestica ENSMODG000000059985 retrocopies
retro_mdom_1107, retro_mdom_1692, retro_mdom_1697, retro_mdom_1724, retro_mdom_547,
Mus musculus ENSMUSG000000582584 retrocopies
retro_mmus_2032, retro_mmus_2660, retro_mmus_417, retro_mmus_552,
Nomascus leucogenys ENSNLEG000000135943 retrocopies
retro_nleu_1810, retro_nleu_2777, retro_nleu_2804,
Oryctolagus cuniculus ENSOCUG000000074931 retrocopy
retro_ocun_267,
Ochotona princeps ENSOPRG000000086922 retrocopies
retro_opri_694, retro_opri_755,
Pongo abelii ENSPPYG000000020392 retrocopies
retro_pabe_1783, retro_pabe_3327,
Pan troglodytes ENSPTRG000000022393 retrocopies
retro_ptro_1412, retro_ptro_1647, retro_ptro_2747,
Ictidomys tridecemlineatus ENSSTOG000000232601 retrocopy
retro_itri_118,
Tursiops truncatus ENSTTRG000000111741 retrocopy
retro_ttru_255,

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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