RetrogeneDB ID:

retro_hsap_3501

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:6:100625087..100626022(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000216378
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:ARG2
Ensembl ID:ENSG00000081181
Aliases:None
Description:arginase 2 [Source:HGNC Symbol;Acc:664]


Retrocopy-Parental alignment summary:






>retro_hsap_3501
AGTCTGGTTGTGATAGGAGCCCCGTTCTTGTAGGGACAGAAAAGAAAAGGAGTGGAACATGGTCCAGCTGCCAGAAGAAA
AATTGGATTGATGAAAAGGGTCTCCAATTTGGGCTGCTGCCTGAAAGACTTTGAAAAGTTTAGTTTTACTCCAGTCCCCA
CAGATGAGCTCTTCAACAACCCTACAGTGAATCTGTGCTCAGTGGCCCAGCCAACCAGCAACTGGCTGAGTTGGTTAGCA
GAGCAGTGTTGTCTGGCTACAGCTGCGTCACGGTGAGAGGAGACCCCAGCCTGGCAATTAGTACCATTAGTGGTCATGCC
TGGAACTGCCCAGACCTTTGTGTCACTTGGGTTGATGCCCAGAAGACATCAGTACACCCCTTACCACTTCATCAGGAAAT
CTCCATGGACTATCAGTTTCATTTCTCCTCACAGAACTACAGGGAAAGGTACCAGAACTTCCAGGATTTCCCTGGACAAA
CCTTGTATCTCCTCCCCAAGTATAGCGTATTCTGATCTAGGAGACATGGACCCTCTGGAACATTTTTTTAAAAGAACAAT
GATATCTAGTATTTTTCCGTGAGAGACATCAATCCATTTGGCACCCAGGAGGTCATGCAACAGAAATTTGATCTGCTGAT
TGGCAAAAGACAAAGGTCTGTCCATCTGAGTTTTGATATTGATGTATTTGACTGTACACTGGCTCCAGCTGCAGGAATCC
CTATTGTAGGGGGACTGACCTTTCAAGAAGGCATCTATATTACTGGGGAAATACATAGTACAGGGTTGCTGTCAGCACTG
GATCTTGTTGAAGTCAATCCTCAACTGGGCACTTTAGAGGAAAGGGCAAAGGCCACAGCTAGCCTGCCAGTAGATGTAAC
TGCTTTATGTTTGGGTCAGACAAGGGAAGGAGGGCACATTGCCCATGGCCAGATT

ORF - retro_hsap_3501 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 70.66 %
Parental protein coverage: 88.42 %
Number of stop codons detected: 2
Number of frameshifts detected 4


Retrocopy - Parental Gene Alignment:

ParentalSVAVIGAPFSQGQKRKGVEHGPAAIREAGLMKRLSSLGCHLKDFGDLSFTPVPKDDLYNNLIVNPRSV-G
S..VIGAPF..GQKRKGVEHGPAA.R..GLMKR.S.LGC.LKDF...SFTPVP.D.L.NN..VN..SV.G
RetrocopySLVVIGAPFL*GQKRKGVEHGPAARRKIGLMKRVSNLGCCLKDFEKFSFTPVPTDELFNNPTVNLCSV<G
ParentalLANQELAEVVSRAVSDGYSCVTLGGDHSLAIGTISGHARHCPDLCVVWVDAHA-DINTPLTTSSGNLHGQ
.ANQ.LAE.VSRAV..GYSCVT..GD.SLAI.TISGHA..CPDLCV.WVDA...DI.TPLTTSSGNLHG.
RetrocopyPANQQLAELVSRAVLSGYSCVTVRGDPSLAISTISGHAWNCPDLCVTWVDAQK<DISTPLTTSSGNLHGL
ParentalPVSFLLRELQDKVPQLPGFSWI-KPCISSASIVYIGLRDVDPPEHFIL-KNYDIQYFSMRDIDRLGIQKV
.VSFLL.ELQ.KVP.LPGF.W..KPCISS.SI.Y..L.D.DP.EHF...KN.DI.YFS.RDI...G.Q.V
RetrocopySVSFLLTELQGKVPELPGFPWT<KPCISSPSIAYSDLGDMDPLEHFFK<KNNDI*YFSVRDINPFGTQEV
ParentalMERTFDLLIGKRQRPIHLSFDIDAFDPTLAPATGTPVVGGLTYREGMYIAEEIHNTGLLSALDLVEVNPQ
M...FDLLIGKRQR..HLSFDID.FD.TLAPA.G.P.VGGLT..EG.YI..EIH.TGLLSALDLVEVNPQ
RetrocopyMQQKFDLLIGKRQRSVHLSFDIDVFDCTLAPAAGIPIVGGLTFQEGIYITGEIHSTGLLSALDLVEVNPQ
ParentalLATSEEEAKTTANLAVDVIASSFGQTREGGHIVYDQL
L.T.EE.AK.TA.L.VDV.A...GQTREGGHI...Q.
RetrocopyLGTLEERAKATASLPVDVTALCLGQTREGGHIAHGQI

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 2 .84 RPM
bodymap2_adrenal 0 .00 RPM 1 .70 RPM
bodymap2_brain 0 .00 RPM 2 .84 RPM
bodymap2_breast 0 .00 RPM 1 .09 RPM
bodymap2_colon 0 .00 RPM 0 .97 RPM
bodymap2_heart 0 .00 RPM 0 .74 RPM
bodymap2_kidney 0 .00 RPM 37 .76 RPM
bodymap2_liver 0 .00 RPM 0 .42 RPM
bodymap2_lung 0 .00 RPM 3 .74 RPM
bodymap2_lymph_node 0 .00 RPM 3 .36 RPM
bodymap2_ovary 0 .00 RPM 2 .87 RPM
bodymap2_prostate 0 .00 RPM 4 .38 RPM
bodymap2_skeletal_muscle 0 .00 RPM 10 .48 RPM
bodymap2_testis 0 .00 RPM 1 .72 RPM
bodymap2_thyroid 0 .00 RPM 28 .44 RPM
bodymap2_white_blood_cells 0 .00 RPM 1 .02 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_3501 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_3501 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_3501 retrocopy 5' end.

Lab - click to see more details

retro_hsap_3501 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_3501 has 4 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_2373
Gorilla gorilla retro_ggor_2367
Pongo abelii retro_pabe_2893
Callithrix jacchus retro_cjac_2357
Parental genes homology:
Parental genes homology involve 11 parental genes, and 15 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000057221 retrocopy
retro_acar_91,
Choloepus hoffmanni ENSCHOG000000071591 retrocopy
retro_chof_1179,
Callithrix jacchus ENSCJAG000000152774 retrocopies
retro_cjac_1933, retro_cjac_2357, retro_cjac_2561, retro_cjac_902,
Dasypus novemcinctus ENSDNOG000000048081 retrocopy
retro_dnov_251,
Homo sapiens ENSG00000081181 1 retrocopy
retro_hsap_3501 ,
Gorilla gorilla ENSGGOG000000056151 retrocopy
retro_ggor_2367,
Monodelphis domestica ENSMODG000000099781 retrocopy
retro_mdom_257,
Nomascus leucogenys ENSNLEG000000007412 retrocopies
retro_nleu_2875, retro_nleu_792,
Oryctolagus cuniculus ENSOCUG000000005841 retrocopy
retro_ocun_277,
Pongo abelii ENSPPYG000000059261 retrocopy
retro_pabe_2893,
Pan troglodytes ENSPTRG000000064671 retrocopy
retro_ptro_2373,

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).





Copyright © RetrogeneDB 2014-2017