RetrogeneDB ID:

retro_hsap_4821

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:X:46506031..46506453(-)
Located in intron of:ENSG00000065923
Retrocopy
information
Ensembl ID:ENSG00000213997
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:PGAM1
Ensembl ID:ENSG00000171314
Aliases:PGAM1, HEL-S-35, PGAM-B, PGAMA
Description:phosphoglycerate mutase 1 (brain) [Source:HGNC Symbol;Acc:8888]


Retrocopy-Parental alignment summary:






>retro_hsap_4821
AGCATGGTAAAGATCTGGAGGCGCTCCTGTGATGTCCCACCACCTCTCATAGAGCCCGATCATCCCTTCTACAGCAGCAT
CAGTAAAGATCGCAGGTATGTACCCCTCACTGAAGATCAGCTACCCTCTTGTGAGGGTCTGAAGGACACTTCTGCCAGAG
CTCTGCCCTTTGGAATGAAGAAATAGTTCCCCAGATTAAGGAGGGGAAATGGGTACTGATTACAGCCCATGGCAACAGCT
TCCCCGGCATTGTCAAGCATCTGGAGGGTCTCTCTGCAGAGCAGAACCTGCTGACTGCTATTCTCGTTGTCTATGAATTG
GACAAGAACTTGAAGCACATCAGGCGCATGCAGTTCCTGGGGGATGAAGAGACCGTGCATAAAGCCATGGAAGCTGTGGC
TGCCCAGGATAAAGAAAAGAGG

ORF - retro_hsap_4821 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 78.08 %
Parental protein coverage: 57.09 %
Number of stop codons detected: 0
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalAQVKIWRRSYDVPPPPMEPDHPFYSNISKDRRYADLTEDQLPSCESLKDTIARALPF-WNEEIVPQIKEG
..VKIWRRS.DVPPP..EPDHPFYS.ISKDRRY..LTEDQLPSCE.LKDT.ARALPF.WNEEIVPQIKEG
RetrocopySMVKIWRRSCDVPPPLIEPDHPFYSSISKDRRYVPLTEDQLPSCEGLKDTSARALPF<WNEEIVPQIKEG
ParentalKRVLIAAHGNSLRGIVKHLEGLSEEAIMELNLPTGIPIVYELDKNLKPIKPMQFLGDEETVRKAMEAVAA
K.VLI.AHGNS..GIVKHLEGLS.E.....NL.T.I..VYELDKNLK.I..MQFLGDEETV.KAMEAVAA
RetrocopyKWVLITAHGNSFPGIVKHLEGLSAEQ----NLLTAILVVYELDKNLKHIRRMQFLGDEETVHKAMEAVAA
ParentalQGKAKK
Q.K.K.
RetrocopyQDKEKR

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 19 .84 RPM
bodymap2_adrenal 0 .25 RPM 25 .01 RPM
bodymap2_brain 0 .05 RPM 35 .75 RPM
bodymap2_breast 0 .06 RPM 22 .74 RPM
bodymap2_colon 0 .00 RPM 22 .08 RPM
bodymap2_heart 0 .00 RPM 24 .70 RPM
bodymap2_kidney 0 .00 RPM 27 .55 RPM
bodymap2_liver 0 .06 RPM 17 .30 RPM
bodymap2_lung 0 .00 RPM 24 .98 RPM
bodymap2_lymph_node 0 .20 RPM 22 .86 RPM
bodymap2_ovary 0 .13 RPM 26 .16 RPM
bodymap2_prostate 0 .00 RPM 27 .40 RPM
bodymap2_skeletal_muscle 0 .00 RPM 3 .98 RPM
bodymap2_testis 0 .04 RPM 23 .06 RPM
bodymap2_thyroid 0 .02 RPM 16 .06 RPM
bodymap2_white_blood_cells 0 .00 RPM 37 .03 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_4821 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_4821 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_4821 retrocopy 5' end.

Lab - click to see more details

retro_hsap_4821 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_4821 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Gorilla gorilla retro_ggor_3005
Pongo abelii retro_pabe_3749
Parental genes homology:
Parental genes homology involve 22 parental genes, and 90 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000126972 retrocopies
retro_btau_1611, retro_btau_472,
Canis familiaris ENSCAFG000000090621 retrocopy
retro_cfam_1297,
Callithrix jacchus ENSCJAG000000165751 retrocopy
retro_cjac_370,
Erinaceus europaeus ENSEEUG000000056301 retrocopy
retro_eeur_680,
Echinops telfairi ENSETEG000000024671 retrocopy
retro_etel_1595,
Homo sapiens ENSG00000171314 12 retrocopies
retro_hsap_1048, retro_hsap_1052, retro_hsap_1142, retro_hsap_2235, retro_hsap_2604, retro_hsap_3083, retro_hsap_3488, retro_hsap_4249, retro_hsap_4686, retro_hsap_4821 , retro_hsap_885, retro_hsap_913,
Gorilla gorilla ENSGGOG0000002860213 retrocopies
retro_ggor_1220, retro_ggor_1500, retro_ggor_1667, retro_ggor_1824, retro_ggor_2061, retro_ggor_2118, retro_ggor_2353, retro_ggor_2849, retro_ggor_3005, retro_ggor_3034, retro_ggor_716, retro_ggor_738, retro_ggor_827,
Loxodonta africana ENSLAFG000000159791 retrocopy
retro_lafr_886,
Microcebus murinus ENSMICG000000076571 retrocopy
retro_mmur_135,
Myotis lucifugus ENSMLUG000000091176 retrocopies
retro_mluc_1280, retro_mluc_1595, retro_mluc_1741, retro_mluc_2246, retro_mluc_632, retro_mluc_745,
Macaca mulatta ENSMMUG000000200271 retrocopy
retro_mmul_119,
Monodelphis domestica ENSMODG000000042424 retrocopies
retro_mdom_1342, retro_mdom_1893, retro_mdom_610, retro_mdom_668,
Mustela putorius furoENSMPUG000000170451 retrocopy
retro_mputfur_1409,
Mus musculus ENSMUSG000000117526 retrocopies
retro_mmus_1741, retro_mmus_2221, retro_mmus_3012, retro_mmus_411, retro_mmus_729, retro_mmus_769,
Nomascus leucogenys ENSNLEG0000001380410 retrocopies
retro_nleu_1367, retro_nleu_1535, retro_nleu_1658, retro_nleu_2012, retro_nleu_2139, retro_nleu_2196, retro_nleu_2205, retro_nleu_2488, retro_nleu_2667, retro_nleu_280,
Oryctolagus cuniculus ENSOCUG000000056795 retrocopies
retro_ocun_1016, retro_ocun_1081, retro_ocun_350, retro_ocun_706, retro_ocun_976,
Pongo abelii ENSPPYG000000025309 retrocopies
retro_pabe_1325, retro_pabe_2309, retro_pabe_2554, retro_pabe_2639, retro_pabe_2881, retro_pabe_3389, retro_pabe_3639, retro_pabe_3749, retro_pabe_671,
Rattus norvegicus ENSRNOG000000505857 retrocopies
retro_rnor_1669, retro_rnor_2241, retro_rnor_2275, retro_rnor_2361, retro_rnor_2568, retro_rnor_691, retro_rnor_703,
Sarcophilus harrisii ENSSHAG000000182301 retrocopy
retro_shar_323,
Sus scrofa ENSSSCG000000105171 retrocopy
retro_sscr_373,
Tupaia belangeri ENSTBEG000000059135 retrocopies
retro_tbel_1677, retro_tbel_1708, retro_tbel_2756, retro_tbel_3667, retro_tbel_563,
Drosophila melanogaster FBgn00148691 retrocopy
retro_dmel_57,

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 = 1.01 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .30 RPM
CEU_NA11843 0 .31 RPM
CEU_NA11930 0 .78 RPM
CEU_NA12004 0 .23 RPM
CEU_NA12400 0 .21 RPM
CEU_NA12751 0 .53 RPM
CEU_NA12760 0 .27 RPM
CEU_NA12827 0 .33 RPM
CEU_NA12872 0 .60 RPM
CEU_NA12873 0 .41 RPM
FIN_HG00183 0 .27 RPM
FIN_HG00277 0 .52 RPM
FIN_HG00315 0 .22 RPM
FIN_HG00321 0 .24 RPM
FIN_HG00328 0 .36 RPM
FIN_HG00338 0 .19 RPM
FIN_HG00349 0 .26 RPM
FIN_HG00375 0 .24 RPM
FIN_HG00377 0 .40 RPM
FIN_HG00378 0 .40 RPM
GBR_HG00099 0 .55 RPM
GBR_HG00111 0 .37 RPM
GBR_HG00114 0 .34 RPM
GBR_HG00119 0 .55 RPM
GBR_HG00131 0 .57 RPM
GBR_HG00133 0 .80 RPM
GBR_HG00134 0 .48 RPM
GBR_HG00137 0 .27 RPM
GBR_HG00142 0 .50 RPM
GBR_HG00143 0 .35 RPM
TSI_NA20512 0 .17 RPM
TSI_NA20513 0 .60 RPM
TSI_NA20518 0 .22 RPM
TSI_NA20532 0 .65 RPM
TSI_NA20538 0 .51 RPM
TSI_NA20756 0 .23 RPM
TSI_NA20765 0 .64 RPM
TSI_NA20771 0 .31 RPM
TSI_NA20786 0 .29 RPM
TSI_NA20798 0 .72 RPM
YRI_NA18870 0 .88 RPM
YRI_NA18907 0 .62 RPM
YRI_NA18916 0 .65 RPM
YRI_NA19093 0 .29 RPM
YRI_NA19099 0 .53 RPM
YRI_NA19114 0 .39 RPM
YRI_NA19118 0 .44 RPM
YRI_NA19213 0 .33 RPM
YRI_NA19214 0 .74 RPM
YRI_NA19223 1 .01 RPM

Indel association:

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





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