RetrogeneDB ID:

retro_hsap_4826

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:X:47577748..47578498(-)
Located in intron of:ENSG00000187893
Retrocopy
information
Ensembl ID:ENSG00000224656
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:SMS
Ensembl ID:ENSG00000102172
Aliases:SMS, MRSR, SPMSY, SRS, SpS
Description:spermine synthase [Source:HGNC Symbol;Acc:11123]


Retrocopy-Parental alignment summary:






>retro_hsap_4826
ATGGCAGCGGCATGGCACAGCACACTCGACTTCATGCTCAGCGCCAAAGCTGATGGCGAGACCATTCTAAAAGGGCTCCA
GTCCATTTTCCAGGAGCAGGGGATGGCAGAACCGGTGGACACCGGGCAGGACCACACCGCTGTTTAGCAACCTGCACACA
CACAAAAAAACGGCAGCTTTGCCAATTTGAGAATTTACTCACATAGATTGGAGTTATTGGACCTTCAGAGTTACGATGGT
GATGCACAAGGCAAAGAAGAGATCGACAGTCTTTTGAACAAAGGAGAAGAAAGAATGAAAGAATTGAGTCAGGACAGTAG
TTGGCAGATGAGGCAATTACCACCTATAGTTCCAGGAGGAGCCATCGACAGATACTGGCCCACCGCAGATGGACTCCTGG
TTGAATACAACATAGATGAAGTGGTATATGATGAAGATTCACCTTATCAGAACATTAAAATTCTACACTCGAAGCAATTT
GGAAATATTCTCATCCTTAGTGGGAATGTTAATTTGGCATAGAGTGATTTGACATATACCTGGGCCATCATGGGCAGTGG
CAAAGTTTGCATCGGCAAAGATGTACTCATTCTGGGAGGCCGAGATGGGGGCATATTGTGTGAAATAGCCGAACTAAAAC
TAAAGATGGTCACTATGATAGAGATTGACGAAATGGTGATTGATGGATGTAGGAAATATATGTGAAAAACTTGTGGTGAT
GTCTTAGATAATCTTAAAGGAGACTGCTAT

ORF - retro_hsap_4826 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 82.47 %
Parental protein coverage: 68.03 %
Number of stop codons detected: 3
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMAAARHSTLDFMLGAKADGETILKGLQSIFQEQGMAESVHTWQDHGYL--ATYTNKNGSFANLRIYPHGL
MAAA.HSTLDFML.AKADGETILKGLQSIFQEQGMAE.V.T.QDH........T.KNGSFANLRIY.H.L
RetrocopyMAAAWHSTLDFMLSAKADGETILKGLQSIFQEQGMAEPVDTGQDHTAV*QPAHTQKNGSFANLRIYSHRL
ParentalVLLDLQSYDGDAQGKEEIDSILNKVEERMKELSQDSTGRVKRLPPIVRGGAIDRYWPTADGRLVEYDIDE
.LLDLQSYDGDAQGKEEIDS.LNK.EERMKELSQDS......LPPIV.GGAIDRYWPTADG.LVEY.IDE
RetrocopyELLDLQSYDGDAQGKEEIDSLLNKGEERMKELSQDSSWQMRQLPPIVPGGAIDRYWPTADGLLVEYNIDE
ParentalVVYDEDSPYQNIKILHSKQFGNILILSGDVNLAESDLAYTRAIMGSGKEDYTGKDVLILGGGDGGILCEI
VVYDEDSPYQNIKILHSKQFGNILILSG.VNLA.SDL.YT.AIMGSGK....GKDVLILGG.DGGILCEI
RetrocopyVVYDEDSPYQNIKILHSKQFGNILILSGNVNLA*SDLTYTWAIMGSGKV-CIGKDVLILGGRDGGILCEI
ParentalVKLKPKMVTMVEIDQMVIDGCKKYMRKTCGDVLDNLKGDCY
..LK.KMVTM.EID.MVIDGC.KYM.KTCGDVLDNLKGDCY
RetrocopyAELKLKMVTMIEIDEMVIDGCRKYM*KTCGDVLDNLKGDCY

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 44 .17 RPM
bodymap2_adrenal 0 .00 RPM 35 .90 RPM
bodymap2_brain 0 .00 RPM 60 .12 RPM
bodymap2_breast 0 .00 RPM 49 .55 RPM
bodymap2_colon 0 .00 RPM 96 .64 RPM
bodymap2_heart 0 .00 RPM 24 .28 RPM
bodymap2_kidney 0 .00 RPM 89 .51 RPM
bodymap2_liver 0 .00 RPM 18 .59 RPM
bodymap2_lung 0 .00 RPM 68 .78 RPM
bodymap2_lymph_node 0 .00 RPM 39 .25 RPM
bodymap2_ovary 0 .00 RPM 85 .65 RPM
bodymap2_prostate 0 .00 RPM 99 .38 RPM
bodymap2_skeletal_muscle 0 .00 RPM 18 .12 RPM
bodymap2_testis 0 .00 RPM 98 .75 RPM
bodymap2_thyroid 0 .00 RPM 115 .28 RPM
bodymap2_white_blood_cells 0 .00 RPM 62 .80 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_4826 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_4826 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_4826 retrocopy 5' end.

Lab - click to see more details

retro_hsap_4826 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_4826 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pongo abelii retro_pabe_3752
Parental genes homology:
Parental genes homology involve 13 parental genes, and 40 retrocopies.

Species Parental gene accession Retrocopies number
Canis familiaris ENSCAFG000000132843 retrocopies
retro_cfam_1076, retro_cfam_1995, retro_cfam_613,
Cavia porcellus ENSCPOG000000061762 retrocopies
retro_cpor_729, retro_cpor_889,
Echinops telfairi ENSETEG000000100982 retrocopies
retro_etel_1066, retro_etel_1540,
Homo sapiens ENSG00000102172 5 retrocopies
retro_hsap_243, retro_hsap_3168, retro_hsap_3193, retro_hsap_3611, retro_hsap_4826 ,
Gorilla gorilla ENSGGOG000000031233 retrocopies
retro_ggor_1335, retro_ggor_2437, retro_ggor_3009,
Myotis lucifugus ENSMLUG000000131853 retrocopies
retro_mluc_471, retro_mluc_530, retro_mluc_92,
Macaca mulatta ENSMMUG000000203922 retrocopies
retro_mmul_2003, retro_mmul_2574,
Monodelphis domestica ENSMODG000000078971 retrocopy
retro_mdom_412,
Mus musculus ENSMUSG000000717086 retrocopies
retro_mmus_2162, retro_mmus_2170, retro_mmus_2837, retro_mmus_3502, retro_mmus_3628, retro_mmus_994,
Nomascus leucogenys ENSNLEG000000099554 retrocopies
retro_nleu_1664, retro_nleu_2200, retro_nleu_2208, retro_nleu_2755,
Pongo abelii ENSPPYG000000201824 retrocopies
retro_pabe_2649, retro_pabe_2810, retro_pabe_3752, retro_pabe_38,
Rattus norvegicus ENSRNOG000000076882 retrocopies
retro_rnor_1934, retro_rnor_938,
Tupaia belangeri ENSTBEG000000121093 retrocopies
retro_tbel_1630, retro_tbel_1893, retro_tbel_3570,

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 = 0.02 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 .02 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).





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