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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGAATCATAGCTACGGTGTTTGGAGCTACTGGATTTCTTGGCCGCTACCTTGTCCAACAACTTGgtgagatgataaggctttagacctatagtactacgttgtaatgaataatatcttactgagttatattaccataaaaacaaagtgaaatagtatggtaactcaattatttatttctattcag

Basic information

species Oryza sativa
transcript LOC_Os02g57180.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g57180.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G143651_T01 (Zea mays), 5'ss of exon 3
TGGAATCATAGCTACGGTGTTTGGAGCTACTGGATTTCTTGGCCGCTACCTTGTCCAACAACTTGgtgagatgataaggctttagacctatagtactacgttgtaatgaataatatcttactgagttatattaccataaaaacaaagtgaaatagtatggtaactcaattatttatttctattcag
||||||  |||| |||||||||||||||||||| |||||||| ||||| ||||| ||||||||||||||||  || | ||| || |  |  | |  ||||    |||  |    ||  |     |||| ||     |  |                                              
TGGAATTGTAGCCACGGTGTTTGGAGCTACTGGGTTTCTTGGGCGCTATCTTGTGCAACAACTTGgtgagactatgatgctatataaattgaat-ttacg----aatagaagggatactcaaacgttaaat-gttgtgcag---------------------------------------------

upper sequence: LOC_Os02g57180.1 (Oryza sativa), 5'ss of exon 3
lower sequence: Vv07s0005g04440.t01 (Vitis vinifera), 5'ss of exon 3
TGGAATCATAGCTACGGTGTTTGGAGCTACTGGATTTCTTGGCCGCTACCTTGTCCAACAACTTGgtgagatga-ta-aggctttagacctatagtacta-cgttgtaatgaataatatcttactgagttatat----taccataaaaacaaagtgaaatagta--tggtaactcaattatttatttcta--ttcag------------------------------------------------------------------
||| ||  | |||  ||| |||||||||||||| |||||||| |||||  ||||||| || |||||||||  || || |   |||     ||| | |||| |    |     ||  ||| ||  |    |||||    |    ||    || | |   || |||   |       | || | || ||| |   |  |                                                                  
TGGCATTGTTGCTGTGGTTTTTGGAGCTACTGGGTTTCTTGGTCGCTATGTTGTCCAGCAGCTTGgtgagtggaatataaattttgttattatggaactagcacattggcccatgttatttttgtattgtatatgtgattttgtatctgcatatttctatcgtaaacgtggggaaagttctctaattccaagcttggtggtggaaagtttttgtttctatttttctctaatacatgtttgcttgtattataattttttcccag
















Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|58603608|gb|CK014136.1|CK014136
EST:     GGTGTTTGGAGCTACTGGATTTCTTGGCCGCTACCTTGTCCAACAACTTG                         CAAAGATGGGGTCTCAAGTGCTTGTACCATTCAGAGGTTCTGAGGATTGTC
genomic: GGTGTTTGGAGCTACTGGATTTCTTGGCCGCTACCTTGTCCAACAACTTGgtgagatgat ... ttctattcagCAAAGATGGGGTCTCAAGTGCTTGTACCATTCAGAGGTTCTGAGGATTGTC
EST: gi|88385402|gb|CI630503.1|CI630503
EST:     GGTGTTTGGAGCTACTGGATTTCTTGGCCGCTACCTTGTCCAACAACTTG                         CAAAGATGGGGTCTCAAGTGCT
genomic: GGTGTTTGGAGCTACTGGATTTCTTGGCCGCTACCTTGTCCAACAACTTGgtgagatgat ... ttctattcagCAAAGATGGGGTCTCAAGTGCT
EST: gi|88356997|gb|CI620885.1|CI620885
EST:     GGTGTTTGGAGCTACTGGATTTCTTGGCCGCTACCTTGTCCAACAACTTG                         CAAAGATGGGGTCTCAAGTGCTTGTACCATTCAGAGGTTCTGAGGATTGTC
genomic: GGTGTTTGGAGCTACTGGATTTCTTGGCCGCTACCTTGTCCAACAACTTGgtgagatgat ... ttctattcagCAAAGATGGGGTCTCAAGTGCTTGTACCATTCAGAGGTTCTGAGGATTGTC
EST: gi|58690755|gb|CK079442.1|CK079442
EST:     GTGTTTGGAGCTACTGGATTTCTTGGCCGCTACCTTGTCCAACAACTTG                         CAAAGATGGGGTCTCAAGTGCTTGTACCATTCAGAGGTTCTGAGGATTGTC
genomic: GTGTTTGGAGCTACTGGATTTCTTGGCCGCTACCTTGTCCAACAACTTGgtgagatgat ... ttctattcagCAAAGATGGGGTCTCAAGTGCTTGTACCATTCAGAGGTTCTGAGGATTGTC
EST: gi|88383864|gb|CI631754.1|CI631754
EST:     GGTGTTTGGAGCTACTGGATTTCTTGGCCGCTACCTTGTCCAACAACTTG                         CAAAGATGGGGTCTNAAGTGCTTGTACCACTT-AGAGGTTCTGAGGATTGT
genomic: GGTGTTTGGAGCTACTGGATTTCTTGGCCGCTACCTTGTCCAACAACTTGgtgagatgat ... ttctattcagCAAAGATGGGGTCTCAAGTGCTTGTACCA-TTCAGAGGTTCTGAGGATTGT
EST: gi|88388115|gb|CI590391.1|CI590391
EST:     GGTGTTTGGAGCTACTGGATTTCTTGGCCGCTACCTTGTCCAACAACTTG                         CAAAGATGGGGTCTCAAGTGCTTGTACCATTCAGAGGTTTTGAG
genomic: GGTGTTTGGAGCTACTGGATTTCTTGGCCGCTACCTTGTCCAACAACTTGgtgagatgat ... ttctattcagCAAAGATGGGGTCTCAAGTGCTTGTACCATTCAGAGGTTCTGAG
EST: gi|38565625|gb|CK085078.1|CK085078
EST:     GGTGTTTGGAGCTACTGGATTTCTTGGCCGCTACCTTGTCCAACAACTTG                         CAAAGATGGGGTCTCAAGTGCTTGTACCATTCAGAGGTTCTGAGGATTGTC
genomic: GGTGTTTGGAGCTACTGGATTTCTTGGCCGCTACCTTGTCCAACAACTTGgtgagatgat ... ttctattcagCAAAGATGGGGTCTCAAGTGCTTGTACCATTCAGAGGTTCTGAGGATTGTC
EST: gi|29673108|gb|CB669383.1|CB669383
EST:     GGTGTTTGGAGCTACTGGATTTCTTGGCCGCTACCTTGTCCAACAACTTG                         CAAAGATGGGGTCTCAAGTGCTTGTACCATTCAGAGGTTCTGAGGATTGTC
genomic: GGTGTTTGGAGCTACTGGATTTCTTGGCCGCTACCTTGTCCAACAACTTGgtgagatgat ... ttctattcagCAAAGATGGGGTCTCAAGTGCTTGTACCATTCAGAGGTTCTGAGGATTGTC
EST: gi|29671358|gb|CB667633.1|CB667633
EST:     GGTGTTTGGAGCTACTGGATTTCTTGGCCGCTACCTTGTCCAACAACTTG                         CAAAGATGGGGTCTCAAGTGCTTGTACCATTCAGAGGTTCTGAGGATTGTC
genomic: GGTGTTTGGAGCTACTGGATTTCTTGGCCGCTACCTTGTCCAACAACTTGgtgagatgat ... ttctattcagCAAAGATGGGGTCTCAAGTGCTTGTACCATTCAGAGGTTCTGAGGATTGTC
EST: gi|88443613|gb|CI591838.1|CI591838
EST:     GGTGTTTGGAGCTACTGGATTTCTTGGCCGCTACCTTGTCCAACAACTTG                         CAAAGATGGGGTCTCAAGTGCTTGTACCATTCAGAGGTTCTG
genomic: GGTGTTTGGAGCTACTGGATTTCTTGGCCGCTACCTTGTCCAACAACTTGgtgagatgat ... ttctattcagCAAAGATGGGGTCTCAAGTGCTTGTACCATTCAGAGGTTCTG
EST: gi|58663529|gb|CK052215.1|CK052215
EST:     GGTGTTTGGAGCTACTGGATTTCTTGGCCGCTACCTTGTCCAACAACTTG                         CAAAGATGGGGTCTCAAGTGCTTGTACCATTCAGAGGTTCTGAGGATTGTC
genomic: GGTGTTTGGAGCTACTGGATTTCTTGGCCGCTACCTTGTCCAACAACTTGgtgagatgat ... ttctattcagCAAAGATGGGGTCTCAAGTGCTTGTACCATTCAGAGGTTCTGAGGATTGTC
EST: gi|88377002|gb|CI597786.1|CI597786
EST:     GGTGTTTGGAGCTACTGGATTTCTTGGCCGCTACCTTGTCCAACAACTTG                         CAAAGATGGGGTCTCAAGTGCTTGTAC-ATTCAGAGGTTCTGAGGATTGTC
genomic: GGTGTTTGGAGCTACTGGATTTCTTGGCCGCTACCTTGTCCAACAACTTGgtgagatgat ... ttctattcagCAAAGATGGGGTCTCAAGTGCTTGTACCATTCAGAGGTTCTGAGGATTGTC
EST: gi|88726504|gb|CI750159.1|CI750159
EST:     GGTGTTTGGAGCTACTGGATTTCTTGGCCGCTACCTTGTCCAACAACTTG                         CAAAGATGGGGTCTCAAGTGCTTGTACCATTCAGAGGTTCCTGAGGATTGT
genomic: GGTGTTTGGAGCTACTGGATTTCTTGGCCGCTACCTTGTCCAACAACTTGgtgagatgat ... ttctattcagCAAAGATGGGGTCTCAAGTGCTTGTACCATTCAGAGGTTC-TGAGGATTGT
EST: gi|88447774|gb|CI576970.1|CI576970
EST:     GGTGTTTGGAGCTACTGGATTTCTTGGCCGCTACCTTGTCCAACAACTTG                         CAAAGATGGGGTCTCAAGTGCTTGTACCATTCAGAGGTTCTGAGGATTGTC
genomic: GGTGTTTGGAGCTACTGGATTTCTTGGCCGCTACCTTGTCCAACAACTTGgtgagatgat ... ttctattcagCAAAGATGGGGTCTCAAGTGCTTGTACCATTCAGAGGTTCTGAGGATTGTC
EST: gi|88362216|gb|CI608607.1|CI608607
EST:     GGTGTTTGGAGCTACTGGATTTCTTGGCCGCTACCTTGTCCAACAACTTG                         CAAAGATGGGGTCTCAAGTGCTTGTACCATTCAGAGGTTCTGAGGATTGTC
genomic: GGTGTTTGGAGCTACTGGATTTCTTGGCCGCTACCTTGTCCAACAACTTGgtgagatgat ... ttctattcagCAAAGATGGGGTCTCAAGTGCTTGTACCATTCAGAGGTTCTGAGGATTGTC
EST: gi|88405560|gb|CI588766.1|CI588766
EST:     GGTGTTTGGAGCTACTGGATTTCTTGGCCGCTACCTTGTCCAACAACTTG                         CAAAGATGGGGTCTCAAGTGCTTGTACCATTCAGAGG
genomic: GGTGTTTGGAGCTACTGGATTTCTTGGCCGCTACCTTGTCCAACAACTTGgtgagatgat ... ttctattcagCAAAGATGGGGTCTCAAGTGCTTGTACCATTCAGAGG
EST: gi|88693529|gb|CI737104.1|CI737104
EST:     GGTGTTTGGAGCTACTGGATTTCTTGGCCGCTACCTTGTCCAACAACTTG                         CAAAGATGGGGTCTCAAGTGCTTGTA
genomic: GGTGTTTGGAGCTACTGGATTTCTTGGCCGCTACCTTGTCCAACAACTTGgtgagatgat ... ttctattcagCAAAGATGGGGTCTCAAGTGCTTGTA
EST: gi|58597371|gb|CK007899.1|CK007899
EST:     GGTGTTTGGAGCTACTGGATTTCTTGGCCGCTACCTTGTCCAACAACTTG                         CAAAGATGGGGTCTCAAGTGCTTGTACCATTCAGAGGTTCTGAGGATTGTC
genomic: GGTGTTTGGAGCTACTGGATTTCTTGGCCGCTACCTTGTCCAACAACTTGgtgagatgat ... ttctattcagCAAAGATGGGGTCTCAAGTGCTTGTACCATTCAGAGGTTCTGAGGATTGTC
EST: gi|88362596|gb|CI607354.1|CI607354
EST:     G-TGTTTGGAGCTACTGGATTTCTTGGCCGCTAACT-GTC-AACAACTTG                         CACAGATGGGG
genomic: GGTGTTTGGAGCTACTGGATTTCTTGGCCGCTACCTTGTCCAACAACTTGgtgagatgat ... ttctattcagCAAAGATGGGG
EST: gi|88348839|gb|CI631926.1|CI631926
EST:     GGTGTTTGGAGCTACTGGATTTCTTGGCCGCTACCTTGTCCAACAACTTG                         CAAAGATGGGGTCTCAAGTGCTTGTA
genomic: GGTGTTTGGAGCTACTGGATTTCTTGGCCGCTACCTTGTCCAACAACTTGgtgagatgat ... ttctattcagCAAAGATGGGGTCTCAAGTGCTTGTA
EST: gi|88387570|gb|CI585273.1|CI585273
EST:     GGTGTTTGGAGCTACTGGATTTCTTGGCCGCTACCTTGTCCAACAACTTG                         CAAAGATGGGGTCTCAAGTGCTTGTACCATTCAGAGGTTCTGAGGATTGTC
genomic: GGTGTTTGGAGCTACTGGATTTCTTGGCCGCTACCTTGTCCAACAACTTGgtgagatgat ... ttctattcagCAAAGATGGGGTCTCAAGTGCTTGTACCATTCAGAGGTTCTGAGGATTGTC
EST: gi|88721928|gb|CI743440.1|CI743440
EST:     GGTGTTTGGAGCTACTGGATTTCTTGGCCGCTACCTTGTCCAACAACTTG                         CAAAGATGGGGTCTCAAGTGCTTGTACCATTCAGAG
genomic: GGTGTTTGGAGCTACTGGATTTCTTGGCCGCTACCTTGTCCAACAACTTGgtgagatgat ... ttctattcagCAAAGATGGGGTCTCAAGTGCTTGTACCATTCAGAG
EST: gi|58678182|gb|CK066869.1|CK066869
EST:     GGTGTTTGGAGCTACTGGATTTCTTGGCCGCTACCTTGTCCAACAACTTG                         CAAAGATGGGGTCTCAA
genomic: GGTGTTTGGAGCTACTGGATTTCTTGGCCGCTACCTTGTCCAACAACTTGgtgagatgat ... ttctattcagCAAAGATGGGGTCTCAA
EST: gi|2427794|gb|C72257.1|C72257
EST:     GGTGTTTNGAGCTACTTGATTTCTTGGCCGTTACCTTGTCCAACAACTTT                         CAAAGATTGGGT
genomic: GGTGTTTGGAGCTACTGGATTTCTTGGCCGCTACCTTGTCCAACAACTTGgtgagatgat ... ttctattcagCAAAGATGGGGT
EST: gi|88449234|gb|CI579918.1|CI579918
EST:     GGTGTTTGGAGCTACTGGATTTCTTGGCCGCTACCTTGTCCAACAACTTG                         CAAAGATGGGGTCTCAAGTGCTTGTACCAT
genomic: GGTGTTTGGAGCTACTGGATTTCTTGGCCGCTACCTTGTCCAACAACTTGgtgagatgat ... ttctattcagCAAAGATGGGGTCTCAAGTGCTTGTACCAT
EST: gi|88730270|gb|CI753884.1|CI753884
EST:     GGTGTTTGGAGCTACTGGATTTCTTGGCCGCTACCTTGTCCAACAACTTG                         CAAAGATGGGGTCTCAAGTGCTTG
genomic: GGTGTTTGGAGCTACTGGATTTCTTGGCCGCTACCTTGTCCAACAACTTGgtgagatgat ... ttctattcagCAAAGATGGGGTCTCAAGTGCTTG
EST: gi|33657303|gb|CF279917.1|CF279917
EST:     GGTGTTTGGAGCTACTGGATTTCTTGGCCGCTACCTTGTCCAACAACTTG                         CAAAGATGGGGTCTCAAGTGCTTGTACCATTCAGAGGTTCTGAGGATTGTC
genomic: GGTGTTTGGAGCTACTGGATTTCTTGGCCGCTACCTTGTCCAACAACTTGgtgagatgat ... ttctattcagCAAAGATGGGGTCTCAAGTGCTTGTACCATTCAGAGGTTCTGAGGATTGTC
EST: gi|58652884|gb|CK041564.1|CK041564
EST:     GGTGTTTGGAGCTACTGGATTTCTTGGCCGCTACCTTGTCCAACAACTTG                         CAAAGATGGGGTCTCAAGTGCTTGTACCATTCAGAGGTTCTGAGGATTGTC
genomic: GGTGTTTGGAGCTACTGGATTTCTTGGCCGCTACCTTGTCCAACAACTTGgtgagatgat ... ttctattcagCAAAGATGGGGTCTCAAGTGCTTGTACCATTCAGAGGTTCTGAGGATTGTC
EST: gi|88356495|gb|CI626110.1|CI626110
EST:     GGTGTTTGGAGCTACTGGATTTCTTGGCCGCTACCTTGTCCAACAACTTG                         CAAAGATGGGGTCTCAAGTGCTTGTAC-ATTCAGAGGTT-TGAGGATTGTC
genomic: GGTGTTTGGAGCTACTGGATTTCTTGGCCGCTACCTTGTCCAACAACTTGgtgagatgat ... ttctattcagCAAAGATGGGGTCTCAAGTGCTTGTACCATTCAGAGGTTCTGAGGATTGTC
EST: gi|88358531|gb|CI617617.1|CI617617
EST:     GGTGTTTGGAGCTACTGGATTTCTTGGCCGCTACCTTGTCCAACAACTTG                         CAAAGATGGGGTCTCAAGTGCTTGTACCA
genomic: GGTGTTTGGAGCTACTGGATTTCTTGGCCGCTACCTTGTCCAACAACTTGgtgagatgat ... ttctattcagCAAAGATGGGGTCTCAAGTGCTTGTACCA

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 65 (upstream exon), 75 (downstream exon)
Score: 64

TGGAATCATAGCTACGGTGTTTGGAGCTACTGGATTTCTTGGCCGCTACCTTGTCCAACAACTTGgtgagatgat ... ttctattcagCAAAGATGGGGTCTCAAGTGCTTGTACCATTCAGAGGTTCTGAGGATTGTCACCGACACCTGAAGTTGATGGGTGACCTGGGTCAG




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Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGGAATCATAGCTACGGTGTTTGGAGCTACTGGATTTCTTGGCCGCTACCTTGTCCAACAACTTGgtgagatgataaggctttagacctatagtactacgttgtaatgaataatatcttactgagttatattaccataaaaacaaagtgaaatagtatggtaactcaattatttatttctattcag

- - - - - - - - - - TTGGAG
- - - - - - - - - - - GGAGCT