RetrogeneDB ID:

retro_hsap_547

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:10:20639162..20640029(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000228339
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:AMD1
Ensembl ID:ENSG00000123505
Aliases:AMD1, ADOMETDC, AMD, SAMDC
Description:adenosylmethionine decarboxylase 1 [Source:HGNC Symbol;Acc:457]


Retrocopy-Parental alignment summary:






>retro_hsap_547
TTGATAAATGTGCAATGTTCAATCCTAAGCCTGACAAAAACTGACAAATAGGAAGCTTATGTACGCAGTGAGAGTAGCAT
GTTTGTCTTCAAGAGATGTCTCGTTTTGCAGACATGTGGAACTACCCTCTTTCTGCAAGCACTGGTTCCCATATTGAAGC
TTGCTAGACATGACAATGGGTTTGACTCAATTAAAGCTTCTTTTATTCGCATAAGAATTTCATGAAGCTTCTTCACCAAG
GATACTCACGCCAGAATTTCCAGGAAGAAATAGAGATTCTTAATGCAATTTTCCCAAATGGAGCAGCATATTGTATGAGA
TGTATGAGTTGTGATGTTGGTACTTATATGTACTGGGTTTCCCAGGGAGTGGGGTAATCAGTCAGACAGATTAAACCCTG
GAAATTCTGATGAGTGTGCTTGACCCAGCAGTTATGGACCAGTTCTGCATGAAAGATGGTGTTACTGTAGATGACGTCAC
TCTCTAGAATGAAATTCATGACTTGATACCAGATCCTGTCATTGAGGCCACACTGTTCAATCCTTGGGGGATCTGATGAA
TGGAATGAAATAAGATAGAACTTATTGGACTATTCATATCACTCCAGAACCAGAATTTTCTTACTTTAGTTTTAAAAGAA
ACTTAGGTCATACCTCCTATGATGACCTAATCGGGACAGTTGTGAAAGTCTTCAAGACAGGAAAATTTGTGACCACCTTG
TTAGCTAATCAGAGCTCTAAATGTCACACCATGTTTTCTTCACCCCAGCAGACTGAAGGTTTTAAATGTCTTGATTGCCA
GAATGCTGTGTTCAATGATTACAATTTTGTTTTTACCGGTTTTGCAAAGCAGCAATGACAACAGAGA

ORF - retro_hsap_547 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 72.7 %
Parental protein coverage: 86.83 %
Number of stop codons detected: 5
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalLKDVQCSIISVTKTDKQEAYVLSESSMFVSKRRFILKTCGTTLLLKALVPLLKLARDYSGFDSIQ-SFFY
L..VQCSI.S.TKTDK.EAYV.SESSMFV.KR...L.TCGTTL.L.ALVP.LKLAR...GFDSI..SFFY
RetrocopyLINVQCSILSLTKTDK*EAYVRSESSMFVFKRCLVLQTCGTTLFLQALVPILKLARHDNGFDSIK<SFFY
ParentalSRKNFMKPSHQGYPHRNFQEEIEFLNAIFPNGAAYCMGRMNSD-CWYLYTLDFPESRVISQPDQTLEILM
S.KNFMK..HQGY...NFQEEIE.LNAIFPNGAAYCM..M..D.CWYLY.L.FP.S.VISQ.D.TLEILM
RetrocopySHKNFMKLLHQGYSRQNFQEEIEILNAIFPNGAAYCMRCMSCD<CWYLYVLGFPGSGVISQTD*TLEILM
ParentalSELDPAVMDQFYMKDGVTAKDVTRESGIRDLIPGSVIDATMFNPCGY-SMNGMKSDGTYWTIHITPEPEF
S.LDPAVMDQF.MKDGVT..DVT....I.DLIP..VI.AT.FNP.G...MNGMK.D.TYWTIHITPEPEF
RetrocopySVLDPAVMDQFCMKDGVTVDDVTL*NEIHDLIPDPVIEATLFNPWGI<LMNGMK*DRTYWTIHITPEPEF
ParentalSYVSFETNLSQTSYDDLIRKVVEVFKPGKFVTTLFVNQSSKCRTVLASPQKIEGFKRLDCQSAMFNDYNF
SY.SF..NL..TSYDDLI..VV.VFK.GKFVTTL..NQSSKC.T...SPQ..EGFK.LDCQ.A.FNDYNF
RetrocopySYFSFKRNLGHTSYDDLIGTVVKVFKTGKFVTTLLANQSSKCHTMFSSPQQTEGFKCLDCQNAVFNDYNF
ParentalVFTSFAKKQQQQQ
VFT.FAK.Q.QQ.
RetrocopyVFTGFAKQQ*QQR

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 .14 RPM 58 .02 RPM
bodymap2_adrenal 0 .00 RPM 90 .07 RPM
bodymap2_brain 0 .05 RPM 150 .72 RPM
bodymap2_breast 0 .00 RPM 59 .32 RPM
bodymap2_colon 0 .00 RPM 120 .06 RPM
bodymap2_heart 0 .00 RPM 115 .40 RPM
bodymap2_kidney 0 .00 RPM 147 .31 RPM
bodymap2_liver 0 .00 RPM 62 .06 RPM
bodymap2_lung 0 .00 RPM 118 .23 RPM
bodymap2_lymph_node 0 .00 RPM 121 .81 RPM
bodymap2_ovary 0 .02 RPM 156 .72 RPM
bodymap2_prostate 0 .00 RPM 138 .75 RPM
bodymap2_skeletal_muscle 0 .00 RPM 36 .28 RPM
bodymap2_testis 0 .00 RPM 156 .33 RPM
bodymap2_thyroid 0 .00 RPM 165 .70 RPM
bodymap2_white_blood_cells 0 .00 RPM 154 .92 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_547 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_547 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_547 retrocopy 5' end.

Lab - click to see more details

retro_hsap_547 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_547 has 4 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_411
Gorilla gorilla retro_ggor_498
Pongo abelii retro_pabe_505
Macaca mulatta retro_mmul_2383
Parental genes homology:
Parental genes homology involve 23 parental genes, and 87 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000035001 retrocopy
retro_amel_797,
Bos taurus ENSBTAG000000033421 retrocopy
retro_btau_1545,
Canis familiaris ENSCAFG000000039052 retrocopies
retro_cfam_1526, retro_cfam_2056,
Choloepus hoffmanni ENSCHOG000000091719 retrocopies
retro_chof_1327, retro_chof_2200, retro_chof_238, retro_chof_2691, retro_chof_332, retro_chof_425, retro_chof_628, retro_chof_74, retro_chof_968,
Callithrix jacchus ENSCJAG000000052576 retrocopies
retro_cjac_1600, retro_cjac_1738, retro_cjac_2452, retro_cjac_3020, retro_cjac_631, retro_cjac_850,
Dasypus novemcinctus ENSDNOG0000000686710 retrocopies
retro_dnov_1736, retro_dnov_1796, retro_dnov_185, retro_dnov_2436, retro_dnov_2653, retro_dnov_315, retro_dnov_357, retro_dnov_63, retro_dnov_752, retro_dnov_770,
Equus caballus ENSECAG000000111984 retrocopies
retro_ecab_1110, retro_ecab_173, retro_ecab_57, retro_ecab_681,
Felis catus ENSFCAG000000280331 retrocopy
retro_fcat_1175,
Homo sapiens ENSG00000123505 5 retrocopies
retro_hsap_3315, retro_hsap_3630, retro_hsap_3922, retro_hsap_4917, retro_hsap_547 ,
Gorilla gorilla ENSGGOG000000064665 retrocopies
retro_ggor_1304, retro_ggor_2448, retro_ggor_2640, retro_ggor_3070, retro_ggor_498,
Loxodonta africana ENSLAFG000000132032 retrocopies
retro_lafr_1040, retro_lafr_770,
Macropus eugenii ENSMEUG000000106301 retrocopy
retro_meug_1558,
Myotis lucifugus ENSMLUG000000056664 retrocopies
retro_mluc_1675, retro_mluc_1687, retro_mluc_2625, retro_mluc_538,
Macaca mulatta ENSMMUG000000005356 retrocopies
retro_mmul_1606, retro_mmul_1742, retro_mmul_1841, retro_mmul_2076, retro_mmul_2383, retro_mmul_2648,
Mus musculus ENSMUSG000000752321 retrocopy
retro_mmus_47,
Nomascus leucogenys ENSNLEG000000128184 retrocopies
retro_nleu_2758, retro_nleu_2983, retro_nleu_720, retro_nleu_812,
Otolemur garnettii ENSOGAG000000301507 retrocopies
retro_ogar_1108, retro_ogar_1152, retro_ogar_1608, retro_ogar_1962, retro_ogar_3163, retro_ogar_354, retro_ogar_366,
Pongo abelii ENSPPYG000000169244 retrocopies
retro_pabe_2977, retro_pabe_3194, retro_pabe_3826, retro_pabe_505,
Pan troglodytes ENSPTRG000000185015 retrocopies
retro_ptro_2157, retro_ptro_2453, retro_ptro_2667, retro_ptro_3280, retro_ptro_411,
Rattus norvegicus ENSRNOG000000005851 retrocopy
retro_rnor_1050,
Sorex araneus ENSSARG000000143873 retrocopies
retro_sara_274, retro_sara_614, retro_sara_760,
Sus scrofa ENSSSCG000000043921 retrocopy
retro_sscr_1042,
Ictidomys tridecemlineatus ENSSTOG000000002054 retrocopies
retro_itri_1402, retro_itri_1859, retro_itri_598, retro_itri_943,

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 = 0.03 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .02 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 .03 RPM
FIN_HG00277 0 .00 RPM
FIN_HG00315 0 .00 RPM
FIN_HG00321 0 .03 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 .03 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 .02 RPM

Indel association:

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





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