RetrogeneDB ID:

retro_hsap_1426

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:14:61386285..61386740(-)
Located in intron of:ENSG00000020426
Retrocopy
information
Ensembl ID:ENSG00000258485
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:SRM
Ensembl ID:ENSG00000116649
Aliases:SRM, PAPT, SPDSY, SPS1, SRML1
Description:spermidine synthase [Source:HGNC Symbol;Acc:11296]


Retrocopy-Parental alignment summary:






>retro_hsap_1426
TCACAGTACTAGGATACCTTTGTCATCTGCAGTAAGACCTATGGCAACATGATGGCGTTGGATGGCATCATCCAGTATAC
AGAGAGGAACAAGTTCTCCTACCAGGAGATTATAGTCAACCTGCCTCTCTGCAGCCACCCCAACCTACAAATGGCGGTGA
TTATTGAGGACAGGAACAAGGGCATCCTGTGCAAGGTGAGGTAGTACCCCTCTGTGAAGTCTATGGTCCAATGTGAGAAT
GATAAGGATGTCATCCAAGTCTCTCAGAAGTTCCTGCCAGGCAAAGCTGTTGGCTACTTTTGCTCAAAGCTGAACTTACA
CATGGGTGATGGGTTTGAATTCATGAAACAGAATTAGGATGCCTTCAGTGTTATCAATGACTCCTCAGACCCCACTGCCT
TGCTAAAAACCTCTTCAAGGAATCCTACTACCAGTTCATGAAGACAGTCCTCAGG

ORF - retro_hsap_1426 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 64.29 %
Parental protein coverage: 50.66 %
Number of stop codons detected: 3
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalSRYQDILVFRSKTYGNVLVLDGVIQCTERDEFSYQEMIANLPLCSHPNPRKVLIIGGGDGGVLREVVKHP
S.Y.D..V..SKTYGN...LDG.IQ.TER..FSYQE.I.NLPLCSHPN.....II.....G.L..V...P
RetrocopySQY*DTFVICSKTYGNMMALDGIIQYTERNKFSYQEIIVNLPLCSHPNLQMAVIIEDRNKGILCKVR*YP
ParentalSVESVVQCEIDEDVIQVSKKFLPGMAIGYSSSKLTLHVGDGFEFMKQNQDAFDVIITDSSDPMG-PAESL
SV.S.VQCE.D.DVIQVS.KFLPG.A.GY..SKL.LH.GDGFEFMKQN.DAF.V.I.DSSDP....A..L
RetrocopySVKSMVQCENDKDVIQVSQKFLPGKAVGYFCSKLNLHMGDGFEFMKQN*DAFSV-INDSSDPTA<LAKNL
ParentalFKESYYQLMKTALK
FKESYYQ.MKT.L.
RetrocopyFKESYYQFMKTVLR

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 26 .46 RPM
bodymap2_adrenal 0 .00 RPM 47 .43 RPM
bodymap2_brain 0 .02 RPM 17 .18 RPM
bodymap2_breast 0 .00 RPM 22 .24 RPM
bodymap2_colon 0 .00 RPM 24 .63 RPM
bodymap2_heart 0 .09 RPM 11 .17 RPM
bodymap2_kidney 0 .06 RPM 20 .89 RPM
bodymap2_liver 0 .00 RPM 22 .71 RPM
bodymap2_lung 0 .00 RPM 13 .80 RPM
bodymap2_lymph_node 0 .00 RPM 32 .38 RPM
bodymap2_ovary 0 .00 RPM 38 .38 RPM
bodymap2_prostate 0 .00 RPM 21 .25 RPM
bodymap2_skeletal_muscle 0 .00 RPM 35 .52 RPM
bodymap2_testis 0 .00 RPM 37 .29 RPM
bodymap2_thyroid 0 .00 RPM 19 .21 RPM
bodymap2_white_blood_cells 0 .00 RPM 18 .53 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_1426 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_1426 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_1426 retrocopy 5' end.

Lab - click to see more details

retro_hsap_1426 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_1426 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_975
Macaca mulatta retro_mmul_2259
Parental genes homology:
Parental genes homology involve 8 parental genes, and 20 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG000000023544 retrocopies
retro_cjac_2131, retro_cjac_2524, retro_cjac_3331, retro_cjac_4025,
Homo sapiens ENSG00000116649 2 retrocopies
retro_hsap_1426 , retro_hsap_2313,
Gorilla gorilla ENSGGOG000000143851 retrocopy
retro_ggor_1756,
Macropus eugenii ENSMEUG000000070022 retrocopies
retro_meug_1330, retro_meug_887,
Macaca mulatta ENSMMUG000000193212 retrocopies
retro_mmul_1500, retro_mmul_2259,
Nomascus leucogenys ENSNLEG000000095323 retrocopies
retro_nleu_1842, retro_nleu_2082, retro_nleu_2778,
Pongo abelii ENSPPYG000000018923 retrocopies
retro_pabe_1181, retro_pabe_1828, retro_pabe_2044,
Pan troglodytes ENSPTRG000000001383 retrocopies
retro_ptro_1403, retro_ptro_1688, retro_ptro_975,

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 = 0.1 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .00 RPM
CEU_NA11843 0 .03 RPM
CEU_NA11930 0 .03 RPM
CEU_NA12004 0 .00 RPM
CEU_NA12400 0 .00 RPM
CEU_NA12751 0 .05 RPM
CEU_NA12760 0 .04 RPM
CEU_NA12827 0 .00 RPM
CEU_NA12872 0 .08 RPM
CEU_NA12873 0 .00 RPM
FIN_HG00183 0 .03 RPM
FIN_HG00277 0 .07 RPM
FIN_HG00315 0 .03 RPM
FIN_HG00321 0 .03 RPM
FIN_HG00328 0 .02 RPM
FIN_HG00338 0 .00 RPM
FIN_HG00349 0 .00 RPM
FIN_HG00375 0 .00 RPM
FIN_HG00377 0 .03 RPM
FIN_HG00378 0 .00 RPM
GBR_HG00099 0 .06 RPM
GBR_HG00111 0 .00 RPM
GBR_HG00114 0 .03 RPM
GBR_HG00119 0 .05 RPM
GBR_HG00131 0 .00 RPM
GBR_HG00133 0 .07 RPM
GBR_HG00134 0 .00 RPM
GBR_HG00137 0 .05 RPM
GBR_HG00142 0 .00 RPM
GBR_HG00143 0 .00 RPM
TSI_NA20512 0 .00 RPM
TSI_NA20513 0 .05 RPM
TSI_NA20518 0 .00 RPM
TSI_NA20532 0 .10 RPM
TSI_NA20538 0 .00 RPM
TSI_NA20756 0 .00 RPM
TSI_NA20765 0 .04 RPM
TSI_NA20771 0 .03 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 .05 RPM
YRI_NA19099 0 .00 RPM
YRI_NA19114 0 .00 RPM
YRI_NA19118 0 .04 RPM
YRI_NA19213 0 .00 RPM
YRI_NA19214 0 .00 RPM
YRI_NA19223 0 .06 RPM

Indel association:

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



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