RetrogeneDB ID:

retro_hsap_3255

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:5:151229417..151230352(+)
Located in intron of:ENSG00000145888
Retrocopy
information
Ensembl ID:ENSG00000270978
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:GLUL
Ensembl ID:ENSG00000135821
Aliases:GLUL, GLNS, GS, PIG43, PIG59
Description:glutamate-ammonia ligase [Source:HGNC Symbol;Acc:4341]


Retrocopy-Parental alignment summary:






>retro_hsap_3255
AATTTTGATGGCTCTAGTATTTTACAGTCTGAAGGCTCCAACAGTGACATGCATTTCATGCCTCCTGCCATGTTTTGGGA
TACCTTCAGTAAGGACCCTACAAGCTGGTGTTCTGTGAAGTTTTCGAGTACAACCGAAAGCCTGCAGTGACCAATTTGAG
GCACACTTGTAAGTGGATAATGGACATGGTGAGCAACCAGCACCCTGGTTTGGCATGGAGCAGGAATATACCCTCATGGG
GACAGATGGGTACCACTTTGGTTGGCCTTCCAATGGCTTCCCAGGACCCCAGGGTCCATATTACTGCAGTGTGGGAGCAG
GCAAAGCCCATGGCAGGGACATCGTGGAGGCCCATTACCAGGCCTGCTTGTATGCTGGAGCCAAGATGGTGGGTACTAAT
GCTGAGGTCATGCCTGCCCAGTGGGAATTTCAAACCGGACCCTGTGAAAGAATCAGCATGGGAGATCATTTCTGGGTGGG
CTGTTTCATTTTGCATCATGTATGTGAAGACTTTGGAGTGATAGCAACCTTTGATCCCAAGCCCATTCCTGGGAACAGGA
AGTGTTCAGGCTGCCATACCAACTTCAGCACCAAGGCCATGTGGGAGGAGAATGGTCTGAAGTACACTGAGGAGGCCATC
GAGAAACTAAGCAGTGGCACCAGTACCACATCCACGCTTATGATCCCAAGGGAGGCCTGGACAAAGCCCAACACCTAGCT
GGATTCCATGAAACCTCCAACATCAACGACTTTTCTGCTGGTGTAGCCAATCGTAGTGCCAACATACACATTCCCTGGAC
TGTTGGCCAGGAGAAGAAGGGTTACTTTGAAGACTGTTGCCCCTCTGCCACTGCGAACCCTTTTCGGTGACAGAAGCCCT
CATCAACACGTGTCTTCTCAATGAAACCGGCAATGAGCCCTTCCAGTACAAAAAC

ORF - retro_hsap_3255 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 82.33 %
Parental protein coverage: 83.91 %
Number of stop codons detected: 0
Number of frameshifts detected 4


Retrocopy - Parental Gene Alignment:

ParentalNFDGSSTLQSEGSNSDMYLVPAAMFRDPFRKDPN-KLVLCEVFKYNRRPAETNLRHTCKRIMDMVSNQHP
NFDGSS.LQSEGSNSDM...P.AMF.D.F.KDP..KLV.CEVF.YNR.PA.TNLRHTCK.IMDMVSNQHP
RetrocopyNFDGSSILQSEGSNSDMHFMPPAMFWDTFSKDPT<KLVFCEVFEYNRKPAVTNLRHTCKWIMDMVSNQHP
Parental-WFGMEQEYTLMGTDGHPFGWPSNGFPGPQGPYYCGVGADRAYGRDIVEAHYRACLYAGVKIAGTNAEVM
.WFGMEQEYTLMGTDG..FGWPSNGFPGPQGPYYC.VGA..A.GRDIVEAHY.ACLYAG.K..GTNAEVM
Retrocopy<WFGMEQEYTLMGTDGYHFGWPSNGFPGPQGPYYCSVGAGKAHGRDIVEAHYQACLYAGAKMVGTNAEVM
ParentalPAQWEFQIGPCEGISMGDHLWVARFILHRVCEDFGVIATFDPKPIPGNWNGAGCHTNFSTKAMREENGLK
PAQWEFQ.GPCE.ISMGDH.WV..FILH.VCEDFGVIATFDPKPIPGN....GCHTNFSTKAM.EENGLK
RetrocopyPAQWEFQTGPCERISMGDHFWVGCFILHHVCEDFGVIATFDPKPIPGNRKCSGCHTNFSTKAMWEENGLK
ParentalYIEEAIEKLS-KRHQYHIRAYDPKGGLDNARRLTGFHETSNINDFSAGVANRSASIRIPRTVGQEKKGYF
Y.EEAIEKLS...HQYHI.AYDPKGGLD.A..L.GFHETSNINDFSAGVANRSA.I.IP.TVGQEKKGYF
RetrocopyYTEEAIEKLS<QWHQYHIHAYDPKGGLDKAQHLAGFHETSNINDFSAGVANRSANIHIPWTVGQEKKGYF
ParentalEDRRPSA-NCDPFSVTEALIRTCLLNETGDEPFQYKN
ED..PSA..C.PFSVTEALI.TCLLNETG.EPFQYKN
RetrocopyEDCCPSA<HCEPFSVTEALINTCLLNETGNEPFQYKN

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 .02 RPM 4613 .03 RPM
bodymap2_adrenal 0 .00 RPM 611 .01 RPM
bodymap2_brain 0 .02 RPM 4847 .97 RPM
bodymap2_breast 0 .00 RPM 736 .04 RPM
bodymap2_colon 0 .00 RPM 1297 .32 RPM
bodymap2_heart 0 .06 RPM 484 .75 RPM
bodymap2_kidney 0 .00 RPM 414 .13 RPM
bodymap2_liver 0 .00 RPM 491 .59 RPM
bodymap2_lung 0 .00 RPM 858 .19 RPM
bodymap2_lymph_node 0 .00 RPM 968 .07 RPM
bodymap2_ovary 0 .00 RPM 613 .31 RPM
bodymap2_prostate 0 .00 RPM 641 .57 RPM
bodymap2_skeletal_muscle 0 .00 RPM 3895 .84 RPM
bodymap2_testis 0 .00 RPM 710 .52 RPM
bodymap2_thyroid 0 .00 RPM 2233 .35 RPM
bodymap2_white_blood_cells 0 .00 RPM 506 .51 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_3255 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_3255 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_3255 retrocopy 5' end.

Lab - click to see more details

retro_hsap_3255 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_3255 has 4 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_2201
Gorilla gorilla retro_ggor_2216
Pongo abelii retro_pabe_2698
Macaca mulatta retro_mmul_2047
Parental genes homology:
Parental genes homology involve 24 parental genes, and 57 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000136314 retrocopies
retro_btau_1050, retro_btau_1474, retro_btau_336, retro_btau_824,
Canis familiaris ENSCAFG000000131022 retrocopies
retro_cfam_1691, retro_cfam_2143,
Callithrix jacchus ENSCJAG000000046541 retrocopy
retro_cjac_2837,
Dasypus novemcinctus ENSDNOG000000139484 retrocopies
retro_dnov_1386, retro_dnov_1870, retro_dnov_2393, retro_dnov_842,
Equus caballus ENSECAG000000158651 retrocopy
retro_ecab_979,
Echinops telfairi ENSETEG000000083293 retrocopies
retro_etel_143, retro_etel_189, retro_etel_1968,
Felis catus ENSFCAG000000105511 retrocopy
retro_fcat_1811,
Homo sapiens ENSG00000135821 4 retrocopies
retro_hsap_2364, retro_hsap_3255 , retro_hsap_848, retro_hsap_935,
Gorilla gorilla ENSGGOG000000247123 retrocopies
retro_ggor_1794, retro_ggor_2216, retro_ggor_754,
Loxodonta africana ENSLAFG000000007001 retrocopy
retro_lafr_196,
Macropus eugenii ENSMEUG000000017746 retrocopies
retro_meug_1013, retro_meug_1394, retro_meug_1561, retro_meug_409, retro_meug_433, retro_meug_746,
Macaca mulatta ENSMMUG000000228842 retrocopies
retro_mmul_2047, retro_mmul_954,
Monodelphis domestica ENSMODG000000067874 retrocopies
retro_mdom_1268, retro_mdom_488, retro_mdom_823, retro_mdom_892,
Mus musculus ENSMUSG000000264733 retrocopies
retro_mmus_1730, retro_mmus_1767, retro_mmus_696,
Nomascus leucogenys ENSNLEG000000180073 retrocopies
retro_nleu_1388, retro_nleu_293, retro_nleu_416,
Pongo abelii ENSPPYG000000004401 retrocopy
retro_pabe_2698,
Pan troglodytes ENSPTRG000000017514 retrocopies
retro_ptro_2201, retro_ptro_2823, retro_ptro_589, retro_ptro_647,
Sarcophilus harrisii ENSSHAG000000001161 retrocopy
retro_shar_553,
Sus scrofa ENSSSCG000000155451 retrocopy
retro_sscr_726,
Ictidomys tridecemlineatus ENSSTOG000000145292 retrocopies
retro_itri_1083, retro_itri_743,
Tupaia belangeri ENSTBEG000000035223 retrocopies
retro_tbel_2230, retro_tbel_3079, retro_tbel_3992,
Tarsius syrichta ENSTSYG000000020661 retrocopy
retro_tsyr_385,
Tursiops truncatus ENSTTRG000000107811 retrocopy
retro_ttru_543,
Drosophila melanogaster FBgn00011451 retrocopy
retro_dmel_44,

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 = 0.06 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 .04 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 .03 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 .04 RPM
TSI_NA20771 0 .06 RPM
TSI_NA20786 0 .00 RPM
TSI_NA20798 0 .03 RPM
YRI_NA18870 0 .00 RPM
YRI_NA18907 0 .00 RPM
YRI_NA18916 0 .02 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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