RetrogeneDB ID:

retro_hsap_3568

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:6:29044352..29044945(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000228364
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:SAR1A
Ensembl ID:ENSG00000079332
Aliases:SAR1A, SAR1, SARA1, Sara, masra2
Description:SAR1 homolog A (S. cerevisiae) [Source:HGNC Symbol;Acc:10534]


Retrocopy-Parental alignment summary:






>retro_hsap_3568
ATGTCTTTCCTCTTTGAGTGGATCTACAATGGCTTCAGCAGTGTGCTCCAGTTCCTAGGACTCTACAAGAAATTTGGAAA
ACTTGTATTTTTCGGTTTGGACAACGCAGGCAAAACCACTCTTCTTCACATGCTCAAAGATGACAGATTGGGTCAACATG
TTCCAACACTACATCCGACATCAGAAAAGCTATTAATTGCTGGAATGACTTTTACAACTCTTGATCTTGGTGGACACAAG
CAAGCATGTCAGGTTTGAAAAAATTATCTCCAAGCAATTAATGAGATTGTTTTTCTGGTGGATTCTGCAGATCATTCTGG
CCTCATGGAATCTAAAGTTGAGCTTAATGCTTTAATGACTGATGAAATAATATCCAATGTGCCAATCCTTATATTGGGTA
ACAAAATAGACAGAACAATGCAATAAGTGAAGAAAAACTCTTTGAGATATTTGGGCTTTCTGGACAGACCACAGGAAAGA
GGAACATGGCCCTTTAGGAGCTGAACGCTCACCCCACTGAAGTGTTCATGTGCAGTGTGCTCAAGAGGCAAGGCTAGGGC
GAGGGATTCTGCTGGCTCTCCCAATGTATTGAC

ORF - retro_hsap_3568 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 85.43 %
Parental protein coverage: 100. %
Number of stop codons detected: 3
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMSFIFEWIYNGFSSVLQFLGLYKKSGKLVFLGLDNAGKTTLLHMLKDDRLGQHVPTLHPTSEELTIAGMT
MSF.FEWIYNGFSSVLQFLGLYKK.GKLVF.GLDNAGKTTLLHMLKDDRLGQHVPTLHPTSE.L.IAGMT
RetrocopyMSFLFEWIYNGFSSVLQFLGLYKKFGKLVFFGLDNAGKTTLLHMLKDDRLGQHVPTLHPTSEKLLIAGMT
ParentalFTTFDLGGHEQARRVWKNYLPAINGIVFLVDCADHSRLVESKVELNALMTDETISNVPILILGNKIDRT-
FTT.DLGGH.QA..V.KNYL.AIN.IVFLVD.ADHS.L.ESKVELNALMTDE.ISNVPILILGNKIDRT.
RetrocopyFTTLDLGGHKQACQV*KNYLQAINEIVFLVDSADHSGLMESKVELNALMTDEIISNVPILILGNKIDRT<
ParentalDAISEEKLREIFGLYGQTTGKGNVTLKELNARPMEVFMCSVLKRQGYGEGFRWLSQYID
.AISEEKL.EIFGL.GQTTGK.N..L.ELNA.P.EVFMCSVLKRQG.GEGF.WLSQ.ID
RetrocopyNAISEEKLFEIFGLSGQTTGKRNMAL*ELNAHPTEVFMCSVLKRQG*GEGFCWLSQCID

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 242 .79 RPM
bodymap2_adrenal 0 .00 RPM 150 .57 RPM
bodymap2_brain 0 .00 RPM 104 .99 RPM
bodymap2_breast 0 .00 RPM 384 .15 RPM
bodymap2_colon 0 .00 RPM 125 .88 RPM
bodymap2_heart 0 .00 RPM 84 .81 RPM
bodymap2_kidney 0 .00 RPM 143 .81 RPM
bodymap2_liver 0 .00 RPM 73 .89 RPM
bodymap2_lung 0 .00 RPM 178 .71 RPM
bodymap2_lymph_node 0 .00 RPM 127 .46 RPM
bodymap2_ovary 0 .02 RPM 203 .16 RPM
bodymap2_prostate 0 .00 RPM 123 .58 RPM
bodymap2_skeletal_muscle 0 .00 RPM 75 .32 RPM
bodymap2_testis 0 .68 RPM 129 .37 RPM
bodymap2_thyroid 0 .00 RPM 149 .65 RPM
bodymap2_white_blood_cells 0 .00 RPM 148 .31 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_3568 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_3568 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_3568 retrocopy 5' end.

Lab - click to see more details

retro_hsap_3568 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_3568 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_2423
Pongo abelii retro_pabe_2940
Macaca mulatta retro_mmul_1825
Parental genes homology:
Parental genes homology involve 12 parental genes, and 40 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG000000163535 retrocopies
retro_cjac_1006, retro_cjac_2242, retro_cjac_2305, retro_cjac_4081, retro_cjac_957,
Homo sapiens ENSG00000079332 4 retrocopies
retro_hsap_2976, retro_hsap_3568 , retro_hsap_4714, retro_hsap_639,
Gorilla gorilla ENSGGOG000000248793 retrocopies
retro_ggor_144, retro_ggor_2408, retro_ggor_2929,
Myotis lucifugus ENSMLUG000000066262 retrocopies
retro_mluc_1317, retro_mluc_1996,
Nomascus leucogenys ENSNLEG000000112434 retrocopies
retro_nleu_1987, retro_nleu_2231, retro_nleu_2311, retro_nleu_2759,
Otolemur garnettii ENSOGAG000000050403 retrocopies
retro_ogar_1447, retro_ogar_1981, retro_ogar_2467,
Pongo abelii ENSPPYG000000023744 retrocopies
retro_pabe_2468, retro_pabe_2940, retro_pabe_3661, retro_pabe_565,
Pan troglodytes ENSPTRG000000025844 retrocopies
retro_ptro_2011, retro_ptro_2423, retro_ptro_3133, retro_ptro_465,
Ictidomys tridecemlineatus ENSSTOG000000127802 retrocopies
retro_itri_1191, retro_itri_590,
Tupaia belangeri ENSTBEG000000086575 retrocopies
retro_tbel_1060, retro_tbel_14, retro_tbel_2319, retro_tbel_2366, retro_tbel_2846,
Tarsius syrichta ENSTSYG000000059552 retrocopies
retro_tsyr_1204, retro_tsyr_2099,
Vicugna pacos ENSVPAG000000026312 retrocopies
retro_vpac_5, retro_vpac_77,

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 = 0.04 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 .04 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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