RetrogeneDB ID:

retro_hsap_2188

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:2:187229324..187229857(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000227692
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:MED28
Ensembl ID:ENSG00000118579
Aliases:None
Description:mediator complex subunit 28 [Source:HGNC Symbol;Acc:24628]


Retrocopy-Parental alignment summary:






>retro_hsap_2188
ATGGCAGCTCCACCAGGTGTTATGTTCCCTGTGGAGCCACTGGGTCCCCCACCACCCCCACTGGAACTCCCAAGCTAGGC
TTTGCTTCTTCAGGAAGCTCCAGGTTCTCTAAGACCTTATGACAGTACCTTGATGGAAAAGTTGAAGTCATATTTTCAGG
CTTGCTTTGCTTCTCTGGTGAGTCAGAAGTATGTCAATGGCACCAATCAGGAAGAAATTCAAACTGGTGTTGATCAGTGT
ATCCAGGAGTTTCTGGATATTGCAAGACAGATAGGATGTTTTTTTCTTCAAAAAGATTGCAATTATCTGTCCAGAAACCA
GATAATGCTATCAAAGAGGATTTCTTCGAACTAAGGAATGAATTATAGTGGAAAGACATGCTGGTCCAGAAGAACTTGAC
ATAGTTGCGGCATTCATGGCAGGTGCTGGAGGACATCAATGTGCAGCACAGAAAGCTAGCCGACATCCCTCAGGGTTCCT
TGGCCTATCTTGAGTAGGCATCTGCCAATATACTTGCACCTCTGAAGCCAACC

ORF - retro_hsap_2188 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 73.74 %
Parental protein coverage: 100. %
Number of stop codons detected: 4
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMAAPLGGMFSGQPPGPPQAPPGLPGQASLLQAAPGAPRPSSSTLVDELESSFEACFASLVSQDYVNGTDQ
MAAP.G.MF...P.GPP..P..LP..A.LLQ.APG..RP..STL...L.S.F.ACFASLVSQ.YVNGT.Q
RetrocopyMAAPPGVMFPVEPLGPPPPPLELPS*ALLLQEAPGSLRPYDSTLMEKLKSYFQACFASLVSQKYVNGTNQ
ParentalEEIRTGVDQCIQKFLDIARQTECFFLQ-KRLQLSVQKPEQVIKEDVSELRNELQRKDALVQKHLTKLRHW
EEI.TGVDQCIQ.FLDIARQ..CFFLQ.KRLQLSVQKP...IKED..ELRNEL..KD.LVQK.LT.LRH.
RetrocopyEEIQTGVDQCIQEFLDIARQIGCFFLQ<KRLQLSVQKPDNAIKEDFFELRNEL*WKDMLVQKNLT*LRHS
ParentalQQVLEDINVQHKKPADIPQGSLAYLEQASANIPAPLKPT
.QVLEDINVQH.K.ADIPQGSLAYLE.ASANI.APLKPT
RetrocopyWQVLEDINVQHRKLADIPQGSLAYLE*ASANILAPLKPT

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 .04 RPM 37 .73 RPM
bodymap2_adrenal 0 .00 RPM 36 .42 RPM
bodymap2_brain 0 .12 RPM 19 .74 RPM
bodymap2_breast 0 .00 RPM 32 .37 RPM
bodymap2_colon 0 .00 RPM 42 .50 RPM
bodymap2_heart 0 .02 RPM 15 .17 RPM
bodymap2_kidney 0 .15 RPM 28 .93 RPM
bodymap2_liver 0 .04 RPM 13 .67 RPM
bodymap2_lung 0 .00 RPM 59 .76 RPM
bodymap2_lymph_node 0 .00 RPM 52 .23 RPM
bodymap2_ovary 0 .06 RPM 50 .24 RPM
bodymap2_prostate 0 .00 RPM 46 .04 RPM
bodymap2_skeletal_muscle 0 .00 RPM 22 .90 RPM
bodymap2_testis 0 .00 RPM 43 .02 RPM
bodymap2_thyroid 0 .36 RPM 39 .64 RPM
bodymap2_white_blood_cells 0 .24 RPM 76 .43 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_2188 was not detected

EST - click to see more details

1 EST(s) were mapped to retro_hsap_2188 retrocopy
EST ID Start End Identity Match Mis-match Score
FN164827 187229360 187229481 99.2 118 1 115

TSS - click to see more details

No TSS is located nearby retro_hsap_2188 retrocopy 5' end.

Lab - click to see more details

retro_hsap_2188 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_2188 has 5 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_1666
Gorilla gorilla retro_ggor_1733
Pongo abelii retro_pabe_2068
Macaca mulatta retro_mmul_916
Callithrix jacchus retro_cjac_2746
Parental genes homology:
Parental genes homology involve 22 parental genes, and 67 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000017601 retrocopy
retro_amel_1649,
Bos taurus ENSBTAG000000194411 retrocopy
retro_btau_973,
Callithrix jacchus ENSCJAG000000127118 retrocopies
retro_cjac_1545, retro_cjac_1708, retro_cjac_2117, retro_cjac_2603, retro_cjac_2746, retro_cjac_3016, retro_cjac_4156, retro_cjac_848,
Cavia porcellus ENSCPOG000000126162 retrocopies
retro_cpor_1165, retro_cpor_207,
Dasypus novemcinctus ENSDNOG000000085262 retrocopies
retro_dnov_2276, retro_dnov_2595,
Dipodomys ordii ENSDORG000000080421 retrocopy
retro_dord_116,
Homo sapiens ENSG00000118579 5 retrocopies
retro_hsap_2188 , retro_hsap_2465, retro_hsap_2860, retro_hsap_589, retro_hsap_919,
Gorilla gorilla ENSGGOG000000011145 retrocopies
retro_ggor_1534, retro_ggor_1733, retro_ggor_1978, retro_ggor_409, retro_ggor_519,
Loxodonta africana ENSLAFG000000169361 retrocopy
retro_lafr_693,
Microcebus murinus ENSMICG000000067922 retrocopies
retro_mmur_1172, retro_mmur_545,
Myotis lucifugus ENSMLUG000000013511 retrocopy
retro_mluc_1997,
Macaca mulatta ENSMMUG000000057345 retrocopies
retro_mmul_1468, retro_mmul_2453, retro_mmul_507, retro_mmul_639, retro_mmul_916,
Monodelphis domestica ENSMODG000000008131 retrocopy
retro_mdom_1175,
Nomascus leucogenys ENSNLEG000000166203 retrocopies
retro_nleu_2816, retro_nleu_284, retro_nleu_317,
Oryctolagus cuniculus ENSOCUG000000015764 retrocopies
retro_ocun_1473, retro_ocun_1474, retro_ocun_337, retro_ocun_444,
Otolemur garnettii ENSOGAG000000338354 retrocopies
retro_ogar_2031, retro_ogar_3387, retro_ogar_493, retro_ogar_998,
Ochotona princeps ENSOPRG000000039322 retrocopies
retro_opri_134, retro_opri_382,
Pongo abelii ENSPPYG000000146274 retrocopies
retro_pabe_1811, retro_pabe_2068, retro_pabe_2363, retro_pabe_601,
Pan troglodytes ENSPTRG000000159393 retrocopies
retro_ptro_1424, retro_ptro_1666, retro_ptro_431,
Pteropus vampyrus ENSPVAG000000157161 retrocopy
retro_pvam_641,
Ictidomys tridecemlineatus ENSSTOG0000000093010 retrocopies
retro_itri_1064, retro_itri_1201, retro_itri_1437, retro_itri_1622, retro_itri_1660, retro_itri_1671, retro_itri_176, retro_itri_236, retro_itri_462, retro_itri_770,
Tursiops truncatus ENSTTRG000000061771 retrocopy
retro_ttru_484,

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 = 0.27 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .09 RPM
CEU_NA11843 0 .14 RPM
CEU_NA11930 0 .07 RPM
CEU_NA12004 0 .15 RPM
CEU_NA12400 0 .21 RPM
CEU_NA12751 0 .15 RPM
CEU_NA12760 0 .00 RPM
CEU_NA12827 0 .24 RPM
CEU_NA12872 0 .16 RPM
CEU_NA12873 0 .13 RPM
FIN_HG00183 0 .16 RPM
FIN_HG00277 0 .15 RPM
FIN_HG00315 0 .08 RPM
FIN_HG00321 0 .27 RPM
FIN_HG00328 0 .05 RPM
FIN_HG00338 0 .09 RPM
FIN_HG00349 0 .14 RPM
FIN_HG00375 0 .07 RPM
FIN_HG00377 0 .03 RPM
FIN_HG00378 0 .02 RPM
GBR_HG00099 0 .03 RPM
GBR_HG00111 0 .06 RPM
GBR_HG00114 0 .05 RPM
GBR_HG00119 0 .19 RPM
GBR_HG00131 0 .20 RPM
GBR_HG00133 0 .12 RPM
GBR_HG00134 0 .11 RPM
GBR_HG00137 0 .05 RPM
GBR_HG00142 0 .17 RPM
GBR_HG00143 0 .10 RPM
TSI_NA20512 0 .08 RPM
TSI_NA20513 0 .22 RPM
TSI_NA20518 0 .17 RPM
TSI_NA20532 0 .03 RPM
TSI_NA20538 0 .14 RPM
TSI_NA20756 0 .12 RPM
TSI_NA20765 0 .21 RPM
TSI_NA20771 0 .03 RPM
TSI_NA20786 0 .10 RPM
TSI_NA20798 0 .19 RPM
YRI_NA18870 0 .10 RPM
YRI_NA18907 0 .10 RPM
YRI_NA18916 0 .08 RPM
YRI_NA19093 0 .05 RPM
YRI_NA19099 0 .05 RPM
YRI_NA19114 0 .03 RPM
YRI_NA19118 0 .19 RPM
YRI_NA19213 0 .14 RPM
YRI_NA19214 0 .10 RPM
YRI_NA19223 0 .14 RPM

Indel association:

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





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