RetrogeneDB ID:

retro_hsap_2267

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:2:62779690..62780369(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000232144
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:PSAT1
Ensembl ID:ENSG00000135069
Aliases:PSAT1, EPIP, PSA, PSAT
Description:phosphoserine aminotransferase 1 [Source:HGNC Symbol;Acc:19129]


Retrocopy-Parental alignment summary:






>retro_hsap_2267
TACAAGGTCATTTTTGTGCAAGAAGGTGGGTCTGGCCAGTTCAGTGCTGTCCCCTTAAACCCAAAGTGCCTGAAAGCAGG
AAGGTGTGCCAACTATGTGGTGACAGGAGCTTGGTCAGCTAAAGCTGCAGAAGCATCCAAGAAGTTTGAGATCGTGAATA
TCAGCTACCCTAAACTTGGGAGTTATATGAAAATTCCAGATTCAACACCTGGAACCTCACCCTTACAGCTTCGATGTGTA
ATGCTGCACAAATGACTGGCACAGAGTGGAGTCTGACTTTATATCTGATCTCAGGAAGCACTACTGGTTTGCCACATATC
CTCAAACTTTCTATCGAAGGCAGTGGATGCTTCCAGGTTTGGTGTGATTTTTGCTGGTGCCCAGAAGCATGTTGGTTGTT
TTGGGATGACAGTAGTGATCATCTGCAATGACTGCTGGGGTCACCCTCAGAGAATGGCCCTCCATCCGGGAATACAAAGT
GCATGTTGGAAACAACTTCTTGTACAACATGCAACAGTATTTCAGCAACTATGTCATGGGCTTGTTCCTGGTGTAGATTA
AGAATGATGGCACTGCAGCAGTGGTGGAGAAGCTTAGCTCCATCAAATCTAAAATAATAATTTATGATATTTTTAATAAT
TCTTAAGGATTCTATGAACATCCAGTAGAGCCTCATAAT

ORF - retro_hsap_2267 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 64.96 %
Parental protein coverage: 61.62 %
Number of stop codons detected: 3
Number of frameshifts detected 5


Retrocopy - Parental Gene Alignment:

ParentalYKVIFLQGGGCGQFSAVPLNLIGLKAGRCADYVVTGAWSAKAAEEAKKFGTINIVHPKLGSYTKIPDP-S
YKVIF.Q.GG.GQFSAVPLN...LKAGRCA.YVVTGAWSAKAAE..KKF...NI..PKLGSY.KIPD...
RetrocopyYKVIFVQEGGSGQFSAVPLNPKCLKAGRCANYVVTGAWSAKAAEASKKFEIVNISYPKLGSYMKIPDS<N
ParentalTWNLNPDASY-VYYCANETVHGVEFDFIPDVK-GAVLVCDMSSNFLSKPVDVSKFGVIFAGAQKNVGSAG
TWNL...AS..V..C.N...H.VE.DFI.D....A.LVC..SSNFLSK.VD.S.FGVIFAGAQK.VG..G
RetrocopyTWNLTLTASM<V*CCTNDW-HRVESDFISDLR<EALLVCHISSNFLSKAVDASRFGVIFAGAQKHVGCFG
ParentalVTVVIVRDD-LLG-FALRECPSVLEYKVQAGNSSLYNTPPCFSIYVMGLVLEWIKNNGGAAAMEKLSSIK
.TVVI...D.LLG...LRE.PS..EYKV..GN..LYN....FS.YVMGL.L..IKN.G.AA..EKLSSIK
RetrocopyMTVVIICND<LLG<VTLREWPSIREYKVHVGNNFLYNMQQYFSNYVMGLFLV*IKNDGTAAVVEKLSSIK
ParentalSQ-TIYEIIDNSQGFYVCPVEPQN
S...IY.I..NS.GFY..PVEP.N
RetrocopySKIIIYDIFNNS*GFYEHPVEPHN

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 7 .67 RPM
bodymap2_adrenal 0 .00 RPM 15 .05 RPM
bodymap2_brain 0 .00 RPM 165 .49 RPM
bodymap2_breast 0 .00 RPM 10 .74 RPM
bodymap2_colon 0 .00 RPM 3 .42 RPM
bodymap2_heart 0 .00 RPM 0 .42 RPM
bodymap2_kidney 0 .00 RPM 113 .78 RPM
bodymap2_liver 0 .00 RPM 128 .94 RPM
bodymap2_lung 0 .00 RPM 1 .81 RPM
bodymap2_lymph_node 0 .00 RPM 19 .06 RPM
bodymap2_ovary 0 .02 RPM 49 .72 RPM
bodymap2_prostate 0 .00 RPM 8 .28 RPM
bodymap2_skeletal_muscle 0 .00 RPM 0 .00 RPM
bodymap2_testis 0 .00 RPM 19 .34 RPM
bodymap2_thyroid 0 .00 RPM 10 .87 RPM
bodymap2_white_blood_cells 0 .00 RPM 5 .18 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_2267 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_2267 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_2267 retrocopy 5' end.

Lab - click to see more details

retro_hsap_2267 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_2267 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_1606
Pongo abelii retro_pabe_1950
Callithrix jacchus retro_cjac_1203
Parental genes homology:
Parental genes homology involve 17 parental genes, and 27 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000068981 retrocopy
retro_amel_375,
Bos taurus ENSBTAG000000139601 retrocopy
retro_btau_1658,
Canis familiaris ENSCAFG000000015701 retrocopy
retro_cfam_269,
Choloepus hoffmanni ENSCHOG000000038171 retrocopy
retro_chof_2702,
Callithrix jacchus ENSCJAG000000033191 retrocopy
retro_cjac_1203,
Echinops telfairi ENSETEG000000041581 retrocopy
retro_etel_99,
Homo sapiens ENSG00000135069 3 retrocopies
retro_hsap_2267 , retro_hsap_4054, retro_hsap_412,
Loxodonta africana ENSLAFG000000179172 retrocopies
retro_lafr_1249, retro_lafr_660,
Macaca mulatta ENSMMUG000000118682 retrocopies
retro_mmul_1029, retro_mmul_2341,
Mustela putorius furoENSMPUG000000125661 retrocopy
retro_mputfur_808,
Nomascus leucogenys ENSNLEG000000029893 retrocopies
retro_nleu_1010, retro_nleu_1288, retro_nleu_2805,
Oryctolagus cuniculus ENSOCUG000000077651 retrocopy
retro_ocun_1092,
Pongo abelii ENSPPYG000000193133 retrocopies
retro_pabe_1950, retro_pabe_308, retro_pabe_3328,
Pan troglodytes ENSPTRG000000210452 retrocopies
retro_ptro_1606, retro_ptro_316,
Rattus norvegicus ENSRNOG000000139711 retrocopy
retro_rnor_1663,
Tupaia belangeri ENSTBEG000000129461 retrocopy
retro_tbel_1577,
Tarsius syrichta ENSTSYG000000000932 retrocopies
retro_tsyr_1073, retro_tsyr_1212,

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).





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