RetrogeneDB ID:

retro_hsap_4182

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:9:80793178..80793922(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000233947
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:ASS1
Ensembl ID:ENSG00000130707
Aliases:ASS1, ASS, CTLN1
Description:argininosuccinate synthase 1 [Source:HGNC Symbol;Acc:758]


Retrocopy-Parental alignment summary:






>retro_hsap_4182
ATGTCCAGCAAAGACTCCATGGTTCTGGCCTACAGTGGGGCCTGGACACCTCCTGCATCCTCATGTGGCCGAAGGAACAA
GGCTATGACATAATTGCCTACCTAGCCAACATTGGCCAGAAGGAAGACTTCGAGGAAGCCAGGAAGAAGGCACTGAAGCT
TGGGGCCAAAAAGGTGTTCATTGAGGATGCCAGCAGGGAGTTTGTGGAGGAGTTCATCTGGCCGGCCATCCAGTCCAGGG
CACTGTATGAAGACCACTGCCTCCTGGGCACCTCTCTTGCCAGGCCCTGCATTGCCTGCAAACAAATGGAAATTGTCCAG
CAGGAGGGGGCCAAGTATGTGTCCCACGGTGCCACGGGAAAGGGGACCGATCAGTTCTGATTTGAACTCACCTGCTACTC
ACTGGCCCCCCCCCAGATAAAGGTCATTGCTCCCTGGAGGATGCCCGAGTTCTACAACTGGTTCAAGGCCTTCAATGACC
TGATGGAAGAATACACAAAAGCAACACGGGATTCCCATCCTGGTCACTTCCAAGAAGCCATGGAGCATGGAACAGAACCT
CATGCACATCAGCTGTGAGGCTGGAATCCTGGAGAACCCCAAGAACTAAGTGCCTCCAGGTCTCTACACGAAGACCCAGG
ACCTGGCCAAAGCCCCCAACACCCCTGATATTCTCGAGTTCCAAAACGGGGTCCCTGTGAAGGTGACCAACGTCAAGGAT
GGCACCACCCACCAGACCTCCTTG

ORF - retro_hsap_4182 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 83.73 %
Parental protein coverage: 60.19 %
Number of stop codons detected: 2
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalMSSKGSVVLAYSG-GLDTSCILVWLKEQGYDVIAYLANIGQKEDFEEARKKALKLGAKKVFIEDVSREFV
MSSK.S.VLAYSG.GLDTSCIL.W.KEQGYD.IAYLANIGQKEDFEEARKKALKLGAKKVFIED.SREFV
RetrocopyMSSKDSMVLAYSG<GLDTSCILMWPKEQGYDIIAYLANIGQKEDFEEARKKALKLGAKKVFIEDASREFV
ParentalEEFIWPAIQSSALYEDRYLLGTSLARPCIARKQVEIAQREGAKYVSHGATGKGNDQVRFELSCYSL-APQ
EEFIWPAIQS.ALYED..LLGTSLARPCIA.KQ.EI.Q.EGAKYVSHGATGKG.DQ..FEL.CYSL....
RetrocopyEEFIWPAIQSRALYEDHCLLGTSLARPCIACKQMEIVQQEGAKYVSHGATGKGTDQF*FELTCYSLXXXX
ParentalIKVIAPWRMPEFYNRFKGRNDLM-EYAK-QHGIPIPVTPKNPWSMDENLMHISYEAGILENPKNQAPPGL
IKVIAPWRMPEFYN.FK..NDLM.EY.K.QHGIPI.VT.K.PWSM..NLMHIS.EAGILENPKN..PPGL
RetrocopyIKVIAPWRMPEFYNWFKAFNDLMEEYTK>QHGIPILVTSKKPWSMEQNLMHISCEAGILENPKN*VPPGL
ParentalYTKTQDPAKAPNTPDILEIEFKKGVPVKVTNVKDGTTHQTSL
YTKTQD.AKAPNTPDIL..EF..GVPVKVTNVKDGTTHQTSL
RetrocopyYTKTQDLAKAPNTPDIL--EFQNGVPVKVTNVKDGTTHQTSL

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 238 .28 RPM
bodymap2_adrenal 0 .00 RPM 46 .81 RPM
bodymap2_brain 0 .00 RPM 23 .44 RPM
bodymap2_breast 0 .00 RPM 183 .45 RPM
bodymap2_colon 0 .00 RPM 77 .38 RPM
bodymap2_heart 0 .00 RPM 33 .05 RPM
bodymap2_kidney 0 .00 RPM 245 .71 RPM
bodymap2_liver 0 .00 RPM 432 .27 RPM
bodymap2_lung 0 .00 RPM 79 .76 RPM
bodymap2_lymph_node 0 .00 RPM 41 .15 RPM
bodymap2_ovary 0 .00 RPM 93 .22 RPM
bodymap2_prostate 0 .00 RPM 119 .92 RPM
bodymap2_skeletal_muscle 0 .00 RPM 31 .65 RPM
bodymap2_testis 0 .06 RPM 118 .38 RPM
bodymap2_thyroid 0 .00 RPM 69 .49 RPM
bodymap2_white_blood_cells 0 .00 RPM 0 .18 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_4182 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_4182 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_4182 retrocopy 5' end.

Lab - click to see more details

retro_hsap_4182 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_4182 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_2836
Parental genes homology:
Parental genes homology involve 8 parental genes, and 68 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG000000205543 retrocopies
retro_cjac_1219, retro_cjac_4038, retro_cjac_4209,
Homo sapiens ENSG00000130707 14 retrocopies
retro_hsap_2247, retro_hsap_2885, retro_hsap_3109, retro_hsap_3175, retro_hsap_3252, retro_hsap_3564, retro_hsap_3824, retro_hsap_4149, retro_hsap_4182 , retro_hsap_4648, retro_hsap_4743, retro_hsap_4934, retro_hsap_820, retro_hsap_985,
Gorilla gorilla ENSGGOG000000102288 retrocopies
retro_ggor_1346, retro_ggor_1675, retro_ggor_2134, retro_ggor_2403, retro_ggor_2574, retro_ggor_2787, retro_ggor_671, retro_ggor_787,
Myotis lucifugus ENSMLUG000000060662 retrocopies
retro_mluc_1058, retro_mluc_1304,
Mus musculus ENSMUSG000000764411 retrocopy
retro_mmus_135,
Nomascus leucogenys ENSNLEG0000001250013 retrocopies
retro_nleu_1088, retro_nleu_1245, retro_nleu_1317, retro_nleu_1381, retro_nleu_1390, retro_nleu_1424, retro_nleu_1701, retro_nleu_1792, retro_nleu_220, retro_nleu_253, retro_nleu_2680, retro_nleu_2764, retro_nleu_625,
Pongo abelii ENSPPYG0000001969213 retrocopies
retro_pabe_1963, retro_pabe_2390, retro_pabe_2637, retro_pabe_2696, retro_pabe_2937, retro_pabe_3069, retro_pabe_3197, retro_pabe_3422, retro_pabe_3460, retro_pabe_3521, retro_pabe_3522, retro_pabe_731, retro_pabe_834,
Pan troglodytes ENSPTRG0000002147314 retrocopies
retro_ptro_1590, retro_ptro_1951, retro_ptro_2101, retro_ptro_2199, retro_ptro_2268, retro_ptro_2421, retro_ptro_2602, retro_ptro_2821, retro_ptro_2836, retro_ptro_3064, retro_ptro_3158, retro_ptro_3298, retro_ptro_571, retro_ptro_762,

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 .03 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 .02 RPM
FIN_HG00338 0 .06 RPM
FIN_HG00349 0 .06 RPM
FIN_HG00375 0 .02 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 .03 RPM
GBR_HG00143 0 .00 RPM
TSI_NA20512 0 .00 RPM
TSI_NA20513 0 .02 RPM
TSI_NA20518 0 .00 RPM
TSI_NA20532 0 .00 RPM
TSI_NA20538 0 .00 RPM
TSI_NA20756 0 .03 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 .04 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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