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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtgtaccttaacaataaattgttgcaaatcatctatatttactaatttactgtgctcactaattaagccttccattttagTTAAGTGTGTCGATTGAAGTCCCTGGAGAGGAGCCGTACCATTTTCAGCCTCGTCTGTTTTCTAAG

Basic information

species Oryza sativa
transcript LOC_Os01g43540.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g43540.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G149704_T02 (Zea mays), 3'ss of exon 5
gtgtgtaccttaacaataaattgttgcaaatcatctatattta-ctaatttactgtgctcactaattaagccttccattttagTTAAGTGTGTCGATTGAAGTCCCTGGAGAGGAGCCGTACCATTTTCAGCCTCGTCTGTTTTCTAAG
  ||||   ||    || | || |      || |  || |||  ||  ||||||||  ||||||||   |  |  |||||||||| ||||| || |||||||| ||||| || || ||||||||||||||||| |||||||||||||||
--gtgtgttttgctcatta-ttatcattgttctttcatctttgtcttttttactgtattcactaatcttgtttctcattttagTTGAGTGTATCCATTGAAGTACCTGGTGAAGAACCGTACCATTTTCAGCCCCGTCTGTTTTCTAAG

upper sequence: LOC_Os01g43540.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G105019_T01 (Zea mays), 3'ss of exon 5
gtgtgtaccttaacaataa-attgttgcaaatcatctatatttactaatttactgtgctcactaattaagccttccattttagTTAAGTGTGTCGATTGAAGTCCCTGGAGAGGAGCCGTACCATTTTCAGCCTCGTCTGTTTTCTAAG
  ||||    |    |||  ||| ||  || |  ||| | | |  |  ||||||||  ||||||||   |  |  |||| ||||| ||||| || |||||||| ||||| || || || |||||||||||||| |||||||||||||||
--gtgtgttctgctcatattattattataa-ttgtct-tgtctgtt--tttactgtattcactaatcttgtttctcattctagTTGAGTGTATCCATTGAAGTTCCTGGTGAAGAACCATACCATTTTCAGCCCCGTCTGTTTTCTAAG
















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|29661449|gb|CB657724.1|CB657724
EST:     CAAAGGGTGTTCCTGCTGAGAATGTTGTTGTTGATTTTGGTGAACAAATG                         TTAAGTGTGTCGATTGAAGTCCCTGGAGAGGAGCCGTACCATTTTCAGCCT
genomic: CAAAGGGTGTTCCTGCTGAGAATGTTGTTGTTGATTTTGGTGAACAAATGgtgtgtacct ... tccattttagTTAAGTGTGTCGATTGAAGTCCCTGGAGAGGAGCCGTACCATTTTCAGCCT
EST: gi|87008059|gb|CI297037.1|CI297037
EST:     CAAAGGGTGTTCCTGCTGAGAATGTTGTTGTTGATTTTGGTGAACAAATG                         TTAAGTGTGTCGATTGAAGTCCCTGGAGAGGAGCCGTACCATTTTCAGCCT
genomic: CAAAGGGTGTTCCTGCTGAGAATGTTGTTGTTGATTTTGGTGAACAAATGgtgtgtacct ... tccattttagTTAAGTGTGTCGATTGAAGTCCCTGGAGAGGAGCCGTACCATTTTCAGCCT
EST: gi|29661448|gb|CB657723.1|CB657723
EST:     CAAAGGGTGTTCCTGCTGAGAATGTTGTTGTTGATTTTGGTGAACAAATG                         TTAAGTGTGTCGATTGAAGTCCCTGGAGAGGAGCCGTACCATTTTCAGCCT
genomic: CAAAGGGTGTTCCTGCTGAGAATGTTGTTGTTGATTTTGGTGAACAAATGgtgtgtacct ... tccattttagTTAAGTGTGTCGATTGAAGTCCCTGGAGAGGAGCCGTACCATTTTCAGCCT
EST: gi|58662717|gb|CK051403.1|CK051403
EST:     CAAAGGGTGTTCCTGCTGAGAATGTTGTTGTTGATTTTGGTGAACAAATG                         TTAAGTGTGTCGATTGAAGTCCCTGGAGAGGAGCCGTACCATTTTCAGCCT
genomic: CAAAGGGTGTTCCTGCTGAGAATGTTGTTGTTGATTTTGGTGAACAAATGgtgtgtacct ... tccattttagTTAAGTGTGTCGATTGAAGTCCCTGGAGAGGAGCCGTACCATTTTCAGCCT
EST: gi|58593415|gb|CF991723.1|CF991723
EST:     CAAAGGGTGTTCCTGCTGAGAATGTTGTTGTTGATTTTGGTGAACAAATG                         TTAAGTGTGTCGATTGAAGTCCCTGGAGAGGAGCCGTACCATTTTCAGCCT
genomic: CAAAGGGTGTTCCTGCTGAGAATGTTGTTGTTGATTTTGGTGAACAAATGgtgtgtacct ... tccattttagTTAAGTGTGTCGATTGAAGTCCCTGGAGAGGAGCCGTACCATTTTCAGCCT
EST: gi|29660562|gb|CB656837.1|CB656837
EST:     CAAAGGGTGTTCCTGCTGAGAATGTTGTTGTTGATTTTGGTGAACAAATG                         TTAAGTGTGTCGATTGAAGTCCCTGGAGAGGAGCCGTACCATTTTCAGCCT
genomic: CAAAGGGTGTTCCTGCTGAGAATGTTGTTGTTGATTTTGGTGAACAAATGgtgtgtacct ... tccattttagTTAAGTGTGTCGATTGAAGTCCCTGGAGAGGAGCCGTACCATTTTCAGCCT
EST: gi|29625917|gb|CB630928.1|CB630928
EST:     CAAAGGGTGTTCCTGCTGAGAATGTTGTTGTTGATTTTGGTGAACAAATG                         TTAAGTGTGTCGATTGAAGTCCCTGGAGAGGAGCCGTACCATTTTCAGCCT
genomic: CAAAGGGTGTTCCTGCTGAGAATGTTGTTGTTGATTTTGGTGAACAAATGgtgtgtacct ... tccattttagTTAAGTGTGTCGATTGAAGTCCCTGGAGAGGAGCCGTACCATTTTCAGCCT
EST: gi|33797195|gb|CF324461.1|CF324461
EST:     CAAAGGGTGTTCCTGCTGAGAATGTTGTTGTTGATTTTGGTGAACAAATG                         TTAAGTGTGTCGATTGAAGTCCCTGGAGAGGAGCCGTACCATTTTCAGCCT
genomic: CAAAGGGTGTTCCTGCTGAGAATGTTGTTGTTGATTTTGGTGAACAAATGgtgtgtacct ... tccattttagTTAAGTGTGTCGATTGAAGTCCCTGGAGAGGAGCCGTACCATTTTCAGCCT
EST: gi|29669130|gb|CB665405.1|CB665405
EST:     CAAAGGGTGTTCCTGCTGAGAATGTTGTTGTTGATTTTGGTGAACAAATG                         TTAAGTGTGTCGATTGAAGTCCCTGGAGAGGAGCCGTACCATTTTCAGCCT
genomic: CAAAGGGTGTTCCTGCTGAGAATGTTGTTGTTGATTTTGGTGAACAAATGgtgtgtacct ... tccattttagTTAAGTGTGTCGATTGAAGTCCCTGGAGAGGAGCCGTACCATTTTCAGCCT
EST: gi|27578357|gb|CB001052.1|CB001052
EST:     CAAAGGGTGTTCCTGCTGAGAATGTTGTTGTTGATTTTGGTGAACAAATG                         TTAAGTGTGTCGATTGAAGTCCCTGGAGAGGAGCCGTACCATTTTCAGCCT
genomic: CAAAGGGTGTTCCTGCTGAGAATGTTGTTGTTGATTTTGGTGAACAAATGgtgtgtacct ... tccattttagTTAAGTGTGTCGATTGAAGTCCCTGGAGAGGAGCCGTACCATTTTCAGCCT
EST: gi|29660561|gb|CB656836.1|CB656836
EST:     CAAAGGGTGTTCCTGCTGAGAATGTTGTTGTTGATTTTGGTGAACAAATG                         TTAAGTGTGTCGATTGAAGTCCCTGGAGAGGAGCCGTACCATTTTCAGCCT
genomic: CAAAGGGTGTTCCTGCTGAGAATGTTGTTGTTGATTTTGGTGAACAAATGgtgtgtacct ... tccattttagTTAAGTGTGTCGATTGAAGTCCCTGGAGAGGAGCCGTACCATTTTCAGCCT
EST: gi|29655865|gb|CB652140.1|CB652140
EST:     CAAAGGGTGTTCCTGCTGAGAATGTTGTTGTTGATTTTGGTGAACAAATG                         TTAAGTGTGTCGATTGAAGTCCCTGGAGAGGAGCCGTGCCATTTTCAGCCT
genomic: CAAAGGGTGTTCCTGCTGAGAATGTTGTTGTTGATTTTGGTGAACAAATGgtgtgtacct ... tccattttagTTAAGTGTGTCGATTGAAGTCCCTGGAGAGGAGCCGTACCATTTTCAGCCT
EST: gi|4714313|gb|AU058280.1|AU058280
EST:     GTTCCTGCTGAGAATGTTGTTGTTGATTTTGGTGAACAAATG                         TTAAGTGTGTCGATTGAAGTCCCTGGAGAGGAGCCGTACCATTTTCAGCCT
genomic: GTTCCTGCTGAGAATGTTGTTGTTGATTTTGGTGAACAAATGgtgtgtacct ... tccattttagTTAAGTGTGTCGATTGAAGTCCCTGGAGAGGAGCCGTACCATTTTCAGCCT
EST: gi|163920381|gb|EG714468.1|EG714468
EST:     CAAAGGGTGTTCCTGCTGAGAATGTTGTTGTTGATTTTGGTGAACAAATG                         TTAAGTGTGTCGATTGAAGTCCCTGGAGAGGAGCCGTACCATTTTCAGCCT
genomic: CAAAGGGTGTTCCTGCTGAGAATGTTGTTGTTGATTTTGGTGAACAAATGgtgtgtacct ... tccattttagTTAAGTGTGTCGATTGAAGTCCCTGGAGAGGAGCCGTACCATTTTCAGCCT
EST: gi|33686913|gb|CF315152.1|CF315152
EST:     CAAAGGGTGTTCCTGCTGAGAATGTTGTTGTTGATTTTGGTGAACAGATG                         TTAAGTGTGTCGATTGAAGTCCCTGGAGAGGAGCCGTACCATTTTCAGCCT
genomic: CAAAGGGTGTTCCTGCTGAGAATGTTGTTGTTGATTTTGGTGAACAAATGgtgtgtacct ... tccattttagTTAAGTGTGTCGATTGAAGTCCCTGGAGAGGAGCCGTACCATTTTCAGCCT
EST: gi|58594119|gb|CF992427.1|CF992427
EST:     CAAAGGGTGTTCCTGCTGAGAATGTTGTTGTTGATTTTGGTGAACAAATG                         TTAAGTGTGTCGATTGAAGTCCCTGGAGAGGAGCCGTACCATTTTCAGCCT
genomic: CAAAGGGTGTTCCTGCTGAGAATGTTGTTGTTGATTTTGGTGAACAAATGgtgtgtacct ... tccattttagTTAAGTGTGTCGATTGAAGTCCCTGGAGAGGAGCCGTACCATTTTCAGCCT
EST: gi|218487981|gb|FG959844.1|FG959844
EST:     CAAAGGGTGTTCCTGCTGAGAATGTTGTTGTTGATTTTGGTGAACAAATG                         TTAAGTGTGTCGATTGAAGTCCCTGGAGAGGAGCCGTACCATTTTCAGCCT
genomic: CAAAGGGTGTTCCTGCTGAGAATGTTGTTGTTGATTTTGGTGAACAAATGgtgtgtacct ... tccattttagTTAAGTGTGTCGATTGAAGTCCCTGGAGAGGAGCCGTACCATTTTCAGCCT
EST: gi|29659289|gb|CB655564.1|CB655564
EST:     CAAAGGGTGTTCCTGCTGAGAATGTTGTTGTTGATTTTGGTGAACAAATG                         TTAAGTGTGTCGATTGAAGTCCCTGGAGAGGAGCCGTACCATTTTCAGCCT
genomic: CAAAGGGTGTTCCTGCTGAGAATGTTGTTGTTGATTTTGGTGAACAAATGgtgtgtacct ... tccattttagTTAAGTGTGTCGATTGAAGTCCCTGGAGAGGAGCCGTACCATTTTCAGCCT
EST: gi|29669129|gb|CB665404.1|CB665404
EST:     CAAAGGGTGTTCCTGCTGAGAATGTTGATGTTGATTTTGGTGAACAAATG                         TTAAGTGTGTCGATTGAAGTCCCTGGAGAGGAGCCGTACCATTTTCAGCCT
genomic: CAAAGGGTGTTCCTGCTGAGAATGTTGTTGTTGATTTTGGTGAACAAATGgtgtgtacct ... tccattttagTTAAGTGTGTCGATTGAAGTCCCTGGAGAGGAGCCGTACCATTTTCAGCCT
EST: gi|29658976|gb|CB655251.1|CB655251
EST:     CAAAGGGTGTTCCTGCTGAGAATGTTGTTGTTGATTTTGGTGAACAAATG                         TTAAGTGTGTCGATTGAAGTCCCTGGAGAGGAGCCGTACCATTTTCAGCCT
genomic: CAAAGGGTGTTCCTGCTGAGAATGTTGTTGTTGATTTTGGTGAACAAATGgtgtgtacct ... tccattttagTTAAGTGTGTCGATTGAAGTCCCTGGAGAGGAGCCGTACCATTTTCAGCCT
EST: gi|33678214|gb|CF306453.1|CF306453
EST:     CAAAGGGTGTTCCTGCTGAGAATGTTGTTGTTGATTTTGGTGAACAAATG                         TTAAGTGTGTCGATT
genomic: CAAAGGGTGTTCCTGCTGAGAATGTTGTTGTTGATTTTGGTGAACAAATGgtgtgtacct ... tccattttagTTAAGTGTGTCGATT

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: 74 (upstream exon), 66 (downstream exon)
Score: 90

GCACGACTTCTACAACAGTGCTACAGAAGTTGTATTGACAATTTTTGCAAAGGGTGTTCCTGCTGAGAATGTTGTTGTTGATTTTGGTGAACAAATGgtgtgtacct ... tccattttagTTAAGTGTGTCGATTGAAGTCCCTGGAGAGGAGCCGTACCATTTTCAGCCTCGTCTGTTTTCTAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaatcatctatatttactaatttactgtgctcactaattaagccttccattttagTTAAGTGTGTCGATTGAAGTCCCTGGAGAGGAGCCGTACCATTTTCAGCCTCGTCTGTTTTCTAAG
                                          ccttccatttt  CT-rich tract
     atctatatttactaat  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgtgtaccttaacaataaattgttgcaaatcatctatatttactaatttactgtgctcactaattaagccttccattttagTTAAGTGTGTCGATTGAAGTCCCTGGAGAGGAGCCGTACCATTTTCAGCCTCGTCTGTTTTCTAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG