RetrogeneDB ID:

retro_hsap_4213

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:9:123483358..123484140(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000238181
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:AHCY
Ensembl ID:ENSG00000101444
Aliases:AHCY, SAHH, adoHcyase
Description:adenosylhomocysteinase [Source:HGNC Symbol;Acc:343]


Retrocopy-Parental alignment summary:






>retro_hsap_4213
ACCTCATCCACACCAAGTACGTACCCACAGCTCATGTCGGGCATCTGAGGCATCTCTGAGGAGACCAAAACCGGGGTCCA
CAACCTACACAAGATGATGGCCAGTGCAATCCTGAAGGTGCCTACCATCAACGTCAATGACTCCGTCACCAAGAGCAAAA
TTTGACAACCTCTATGGCTGCCAGGAGTCCCTTATAGATGGCACCAAGTGGACCAAGACGTGATGATTGCCAGCAAGGTA
GCAGTGGTAGCAGGCTATGGTGGTGTGGGCAAGGGCTGTGCCCAGGCCTTGCAGGGTTTTGGGGCCTGCATAATCATCAC
CGAGACTGACCCCATCAGTGCACTGCAGGCTGCCATGGAAGGCTATGAGGTGACCACCATGGACGAGGCCTGTCAGGAGG
GCAACATCTTTGTCACCACCACAACCTGTGTCAATATCATCCTTGGCCGGCACTTTGAGCAGATGAAGGATGATGCCATC
TTATGTAATACTGAACAATTTGACGTGGAGATCGATGTCAGGTGCCTCAACAACAATGCTGTGGAGAAGGCAAACATCAA
GCCCAGGCGGACTGGTACTGGCTGAAGAATGGGTGCCACATCATCGTGCTGGCTGAGGGTTGGCTGGTCAACCTGGGCTG
TGCTATGGGCCGCCCCAGCTTTGTGGGGAGTAACTCCTTCAACCAGGTGATGGTGCAGATTGCGCTGTGGACCCACCCAG
ACAAGTACCCCATTGGGGTTCACTTCCTGCCCAAGAAGCTGGATGAGGCAGTGGCTGAGGCG

ORF - retro_hsap_4213 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 80. %
Parental protein coverage: 64.85 %
Number of stop codons detected: 1
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalTNLIHTKYPQLLPGIRGISEETTTGVHNLYKMMANGILKVPAINVNDSVTKSK-FDNLYGCRESLIDGIK
T......YPQL..GI.GISEET.TGVHNL.KMMA..ILKVP.INVNDSVTKSK.FDNLYGC.ESLIDG.K
RetrocopyTSSTPSTYPQLMSGI*GISEETKTGVHNLHKMMASAILKVPTINVNDSVTKSK>FDNLYGCQESLIDGTK
ParentalRAT-DVMIAGKVAVVAGYGDVGKGCAQALRGFGARVIITEIDPINALQAAMEGYEVTTMDEACQEGNIFV
....DVMIA.KVAVVAGYG.VGKGCAQAL.GFGA..IITE.DPI.ALQAAMEGYEVTTMDEACQEGNIFV
RetrocopyWTK<DVMIASKVAVVAGYGGVGKGCAQALQGFGACIIITETDPISALQAAMEGYEVTTMDEACQEGNIFV
ParentalTTTGCIDIILGRHFEQMKDDAIVCNIGHFDVEIDVKWLNENAVEKVNIKP-QVDRYRLKNGRRIILLAEG
TTT.C..IILGRHFEQMKDDAI.CN...FDVEIDV..LN.NAVEK.NIKP.Q.D.Y.LKNG..II.LAEG
RetrocopyTTTTCVNIILGRHFEQMKDDAILCNTEQFDVEIDVRCLNNNAVEKANIKP<QADWYWLKNGCHIIVLAEG
ParentalRLVNLGCAMGHPSFVMSNSFTNQVMAQIELWTHPDKYPVGVHFLPKKLDEAVAEA
.LVNLGCAMG.PSFV.SNSF.NQVM.QI.LWTHPDKYP.GVHFLPKKLDEAVAEA
RetrocopyWLVNLGCAMGRPSFVGSNSF-NQVMVQIALWTHPDKYPIGVHFLPKKLDEAVAEA

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 .06 RPM 36 .04 RPM
bodymap2_adrenal 0 .00 RPM 53 .73 RPM
bodymap2_brain 0 .00 RPM 25 .46 RPM
bodymap2_breast 0 .00 RPM 43 .60 RPM
bodymap2_colon 0 .00 RPM 73 .71 RPM
bodymap2_heart 0 .00 RPM 40 .45 RPM
bodymap2_kidney 0 .00 RPM 70 .35 RPM
bodymap2_liver 0 .08 RPM 100 .84 RPM
bodymap2_lung 0 .00 RPM 42 .25 RPM
bodymap2_lymph_node 0 .00 RPM 52 .56 RPM
bodymap2_ovary 0 .00 RPM 89 .17 RPM
bodymap2_prostate 0 .05 RPM 80 .94 RPM
bodymap2_skeletal_muscle 0 .00 RPM 44 .31 RPM
bodymap2_testis 0 .00 RPM 95 .57 RPM
bodymap2_thyroid 0 .21 RPM 97 .56 RPM
bodymap2_white_blood_cells 0 .00 RPM 37 .84 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_4213 was not detected

EST - click to see more details

1 EST(s) were mapped to retro_hsap_4213 retrocopy
EST ID Start End Identity Match Mis-match Score
CV402334 123483463 123483696 98.8 230 3 227

TSS - click to see more details

No TSS is located nearby retro_hsap_4213 retrocopy 5' end.

Lab - click to see more details

retro_hsap_4213 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_4213 has 4 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_2860
Gorilla gorilla retro_ggor_2822
Pongo abelii retro_pabe_3446
Callithrix jacchus retro_cjac_480
Parental genes homology:
Parental genes homology involve 15 parental genes, and 55 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG000000183037 retrocopies
retro_cjac_1028, retro_cjac_1248, retro_cjac_1806, retro_cjac_2132, retro_cjac_2839, retro_cjac_3287, retro_cjac_480,
Echinops telfairi ENSETEG000000025761 retrocopy
retro_etel_444,
Homo sapiens ENSG00000101444 6 retrocopies
retro_hsap_1496, retro_hsap_2325, retro_hsap_2365, retro_hsap_4213 , retro_hsap_571, retro_hsap_803,
Gorilla gorilla ENSGGOG000000146945 retrocopies
retro_ggor_1148, retro_ggor_1795, retro_ggor_2822, retro_ggor_3087, retro_ggor_511,
Monodelphis domestica ENSMODG000000027531 retrocopy
retro_mdom_1974,
Mus musculus ENSMUSG000000275971 retrocopy
retro_mmus_197,
Nomascus leucogenys ENSNLEG000000100414 retrocopies
retro_nleu_1717, retro_nleu_2785, retro_nleu_40, retro_nleu_929,
Oryctolagus cuniculus ENSOCUG000000085921 retrocopy
retro_ocun_1886,
Pongo abelii ENSPPYG000000109359 retrocopies
retro_pabe_1247, retro_pabe_1978, retro_pabe_2108, retro_pabe_2189, retro_pabe_3446, retro_pabe_647, retro_pabe_658, retro_pabe_665, retro_pabe_718,
Pan troglodytes ENSPTRG000000134147 retrocopies
retro_ptro_1015, retro_ptro_1698, retro_ptro_1730, retro_ptro_2860, retro_ptro_3011, retro_ptro_559, retro_ptro_771,
Rattus norvegicus ENSRNOG000000177777 retrocopies
retro_rnor_1142, retro_rnor_1820, retro_rnor_1903, retro_rnor_2120, retro_rnor_569, retro_rnor_647, retro_rnor_839,
Sus scrofa ENSSSCG000000072781 retrocopy
retro_sscr_119,
Tarsius syrichta ENSTSYG000000071633 retrocopies
retro_tsyr_1178, retro_tsyr_1529, retro_tsyr_1582,
Tursiops truncatus ENSTTRG000000036321 retrocopy
retro_ttru_1666,
Xenopus tropicalis ENSXETG000000194861 retrocopy
retro_xtro_62,

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 = 0.09 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 .00 RPM
CEU_NA12751 0 .07 RPM
CEU_NA12760 0 .00 RPM
CEU_NA12827 0 .09 RPM
CEU_NA12872 0 .00 RPM
CEU_NA12873 0 .00 RPM
FIN_HG00183 0 .00 RPM
FIN_HG00277 0 .00 RPM
FIN_HG00315 0 .06 RPM
FIN_HG00321 0 .00 RPM
FIN_HG00328 0 .00 RPM
FIN_HG00338 0 .00 RPM
FIN_HG00349 0 .03 RPM
FIN_HG00375 0 .00 RPM
FIN_HG00377 0 .00 RPM
FIN_HG00378 0 .00 RPM
GBR_HG00099 0 .03 RPM
GBR_HG00111 0 .00 RPM
GBR_HG00114 0 .00 RPM
GBR_HG00119 0 .02 RPM
GBR_HG00131 0 .00 RPM
GBR_HG00133 0 .00 RPM
GBR_HG00134 0 .04 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 .03 RPM
TSI_NA20538 0 .00 RPM
TSI_NA20756 0 .00 RPM
TSI_NA20765 0 .02 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 .05 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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