RetrogeneDB ID:

retro_hsap_2140

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:2:110490307..110490756(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000233307
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:SRSF3
Ensembl ID:ENSG00000112081
Aliases:None
Description:serine/arginine-rich splicing factor 3 [Source:HGNC Symbol;Acc:10785]


Retrocopy-Parental alignment summary:






>retro_hsap_2140
GTTTATGCAGGCAATCTTGGAAACAATGGCAACAAGACTGAATTGGAACAGACTTTTGGCTACTGTGGACCACTCTGAAG
TGTGTGGGTTGCTAGAAACCCTCCTGGCTTTGCTTTTGTTGAATTTGAAGATCCCCGAGATGCAGCAGGTGTGGTCTGAG
AACTAGATGGAAGAACACTATGTGGCCCCTGTGTAGGAGAGGAACTGTCAAACGGTGAAAAAAGAAGTAGAAATCATGGC
CCACCTCCCTCTTGGGGTCATCGTCCTTGAGATGATTATTGTAGGAGGGGTCTTCCACCTCGTCGCAGACCTCCAAGAAG
GAGAAACTTGTCTTGTAGCCGGAGCAGGTCCCTTTCTGGAGTTAGGAGAAGAGAGAGATCGCTGTCTCGGGAGAGAAATC
ACAAGCCACCTGATCCTTCTCTAGGTTTCGTAGCCCATCTAGGTCAAAT

ORF - retro_hsap_2140 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 80.79 %
Parental protein coverage: 91.46 %
Number of stop codons detected: 4
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPGFAFVEFEDPRDAADAVRELDGRTLCGCRVRVELS
VY.GNLGNNGNKTELE..FGY.GPL.SVWVARNPPGFAFVEFEDPRDAA..V.ELDGRTLCG..V..ELS
RetrocopyVYAGNLGNNGNKTELEQTFGYCGPL*SVWVARNPPGFAFVEFEDPRDAAGVV*ELDGRTLCGPCVGEELS
ParentalNGEKRSRNRGPPPSWGRRPRDDYRRRSPPPRRRSPRRRSFSRSRSRSLSRDRRRERSLSRERNHKP-SRS
NGEKRSRN.GPPPSWG.RP.DDY.RR..PPRRR.PRRR..S.SRSRSLS..RRRERSLSRERNHKP...S
RetrocopyNGEKRSRNHGPPPSWGHRP*DDYCRRGLPPRRRPPRRRNLSCSRSRSLSGVRRRERSLSRERNHKP<T*S
ParentalFSRSRSRSRSN
FSR.RS.SRSN
RetrocopyFSRFRSPSRSN

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 208 .98 RPM
bodymap2_adrenal 0 .04 RPM 309 .56 RPM
bodymap2_brain 0 .07 RPM 159 .23 RPM
bodymap2_breast 0 .00 RPM 213 .85 RPM
bodymap2_colon 0 .00 RPM 155 .50 RPM
bodymap2_heart 0 .00 RPM 112 .87 RPM
bodymap2_kidney 0 .14 RPM 220 .70 RPM
bodymap2_liver 0 .00 RPM 99 .66 RPM
bodymap2_lung 0 .00 RPM 176 .71 RPM
bodymap2_lymph_node 0 .00 RPM 286 .09 RPM
bodymap2_ovary 0 .00 RPM 433 .11 RPM
bodymap2_prostate 0 .00 RPM 401 .19 RPM
bodymap2_skeletal_muscle 0 .00 RPM 74 .72 RPM
bodymap2_testis 0 .06 RPM 270 .24 RPM
bodymap2_thyroid 0 .00 RPM 318 .10 RPM
bodymap2_white_blood_cells 0 .00 RPM 253 .48 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_2140 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_2140 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_2140 retrocopy 5' end.

Lab - click to see more details

retro_hsap_2140 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_2140 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Macaca mulatta retro_mmul_1007
Parental genes homology:
Parental genes homology involve 18 parental genes, and 80 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000400065 retrocopies
retro_btau_1176, retro_btau_1442, retro_btau_1445, retro_btau_1665, retro_btau_1813,
Callithrix jacchus ENSCJAG000000160625 retrocopies
retro_cjac_1035, retro_cjac_1969, retro_cjac_2006, retro_cjac_620, retro_cjac_746,
Homo sapiens ENSG000001117861 retrocopy
retro_hsap_2530,
Homo sapiens ENSG00000112081 4 retrocopies
retro_hsap_2140 , retro_hsap_2299, retro_hsap_2304, retro_hsap_757,
Homo sapiens ENSG000001241931 retrocopy
retro_hsap_1809,
Loxodonta africana ENSLAFG000000181932 retrocopies
retro_lafr_1219, retro_lafr_80,
Microcebus murinus ENSMICG000000046745 retrocopies
retro_mmur_1090, retro_mmur_160, retro_mmur_287, retro_mmur_710, retro_mmur_916,
Myotis lucifugus ENSMLUG000000106716 retrocopies
retro_mluc_1205, retro_mluc_1312, retro_mluc_1554, retro_mluc_2283, retro_mluc_278, retro_mluc_51,
Mustela putorius furoENSMPUG000000142151 retrocopy
retro_mputfur_613,
Mus musculus ENSMUSG000000711729 retrocopies
retro_mmus_100, retro_mmus_1347, retro_mmus_1749, retro_mmus_2294, retro_mmus_2337, retro_mmus_2433, retro_mmus_2654, retro_mmus_2933, retro_mmus_3629,
Otolemur garnettii ENSOGAG000000005026 retrocopies
retro_ogar_1850, retro_ogar_1959, retro_ogar_2131, retro_ogar_2783, retro_ogar_597, retro_ogar_803,
Ochotona princeps ENSOPRG000000060063 retrocopies
retro_opri_1037, retro_opri_158, retro_opri_545,
Rattus norvegicus ENSRNOG0000000052011 retrocopies
retro_rnor_1010, retro_rnor_1283, retro_rnor_1321, retro_rnor_1339, retro_rnor_1647, retro_rnor_1697, retro_rnor_1889, retro_rnor_2424, retro_rnor_634, retro_rnor_728, retro_rnor_790,
Sus scrofa ENSSSCG000000015641 retrocopy
retro_sscr_1038,
Ictidomys tridecemlineatus ENSSTOG000000142805 retrocopies
retro_itri_123, retro_itri_502, retro_itri_664, retro_itri_857, retro_itri_901,
Tarsius syrichta ENSTSYG000000134983 retrocopies
retro_tsyr_1867, retro_tsyr_2163, retro_tsyr_848,
Tursiops truncatus ENSTTRG0000001344711 retrocopies
retro_ttru_105, retro_ttru_1195, retro_ttru_1577, retro_ttru_1628, retro_ttru_1639, retro_ttru_1653, retro_ttru_1677, retro_ttru_1731, retro_ttru_1892, retro_ttru_610, retro_ttru_916,
Vicugna pacos ENSVPAG000000054811 retrocopy
retro_vpac_541,

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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