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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatatttctcagtgtgctctatttcaatccctacagttgtctgattctagaatttttttttgattaaatgtaccattttcttagGGTTCTGACAAGGATAAGAAGAAGGAAAATGCTGAGCGCGATGAGCGTGCCAAGAAG

Basic information

species Oryza sativa
transcript LOC_Os01g52390.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g52390.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G116282_T02 (Zea mays), 3'ss of exon 4
gtatatttctcagtgtgctctatttcaatccctacagttgtctgattctagaatttttttttgattaaatgtaccattttcttagGGTTCTGACAAGGATAAGAAGAAGGAAAATGCTGAGCGCGATGAGCGTGCCAAGAAG
||   ||||   ||      |  ||  || |||  ||||  ||||   | | ||   || ||   ||  | |     | |||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||
gttagtttcctcgtaattaatgctttgataccttaagtttgctgagctttgcatgggttcttcgatat-tcttttgctctcttagGGTTCTGACAAGGATAAGAAGAAGGAAAATGCTGAGCGTGATGAGCGTGCCAAGAAG

upper sequence: LOC_Os01g52390.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G055276_T01 (Zea mays), 3'ss of exon 4
gtatatttctcagtgtgctctatttcaatccctacagttgtctgattctagaatttttttttgattaaatgtaccattttcttagGGTTCTGACAAGGATAAGAAGAAGGAAAATGCTGAGCGCGATGAGCGTGCCAAGAAG
||   |||| | ||      |  ||  || |||  ||||  ||||   | | |    || ||   |   | |    || |||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||
gttagtttccctgtaattaatgctttgataccttaagtttgctgagctttgcacgggttcttcgatgt-tcttttgttctcttagGGTTCTGACAAGGATAAGAAGAAGGAAAATGCTGAGCGTGATGAGCGTGCCAAGAAG

upper sequence: LOC_Os01g52390.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G055276_T03 (Zea mays), 3'ss of exon 4
gtatatttctcagtgtgctctatttcaatccctacagttgtctgattctagaatttttttttgattaaatgtaccattttcttagGGTTCTGACAAGGATAAGAAGAAGGAAAATGCTGAGCGCGATGAGCGTGCCAAGAAG-------------------------------------------
||   |||| | ||      |  ||  || |||  ||||  ||||   | | |    || ||   |   | |    || |||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||                                           
gttagtttccctgtaattaatgctttgataccttaagtttgctgagctttgcacgggttcttcgatgt-tcttttgttctcttagGGTTCTGACAAGGATAAGAAGAAGGAAAATGCTGAGCGTGATGAGCGTGCCAAGAAGGTATGCATTGTAGTTGCAAATCAAAGTAGTTTCTGACATATGG

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|8335069|gb|BE040053.1|BE040053
EST:     TGCAGCCACTTTCTACCAAGAAAGGAAATGATGAAATTTTCATTAAGCTG                         GGTTCTGACAAGGATAAGAAGAAGGAAAATGCTGAGCGCGATGAGCGTGCC
genomic: TGCAGCCACTTTCTACCAAGAAAGGAAATGATGAAATTTTCATTAAGCTGgtatatttct ... attttcttagGGTTCTGACAAGGATAAGAAGAAGGAAAATGCTGAGCGCGATGAGCGTGCC
EST: gi|218486753|gb|FG965219.1|FG965219
EST:     TGCAGCCACTTTCTACCAAGAAAGGAAATGATGAAATTTTCATTAAGCTG                         GGTTCTGACAAGGATAAGAAGAAGGAAAATGCTGAGCGCGATGAGCGTGCC
genomic: TGCAGCCACTTTCTACCAAGAAAGGAAATGATGAAATTTTCATTAAGCTGgtatatttct ... attttcttagGGTTCTGACAAGGATAAGAAGAAGGAAAATGCTGAGCGCGATGAGCGTGCC
EST: gi|218493559|gb|FG968382.1|FG968382
EST:     TGCAGCCACTTTCTACCAAGAAAGGAAATGATGAAATTTTCATTAAGCTG                         GGTTCTGACAAGGATAAGAAGAAGGAAAATGCTGAGCGCGATGAGCGTGCC
genomic: TGCAGCCACTTTCTACCAAGAAAGGAAATGATGAAATTTTCATTAAGCTGgtatatttct ... attttcttagGGTTCTGACAAGGATAAGAAGAAGGAAAATGCTGAGCGCGATGAGCGTGCC
EST: gi|157652089|gb|EX451723.1|EX451723
EST:     TGCAGCCACTTTCTACCAAGAAAGGAAATGATGAAATTTTCATTAAGCTG                         GGTTCTGACAAGGATAAGAAGAAGGAAAATGCTGAGCGCGATGAGCGTGCC
genomic: TGCAGCCACTTTCTACCAAGAAAGGAAATGATGAAATTTTCATTAAGCTGgtatatttct ... attttcttagGGTTCTGACAAGGATAAGAAGAAGGAAAATGCTGAGCGCGATGAGCGTGCC
EST: gi|66913583|gb|CX100431.1|CX100431
EST:     GAAATGATGAAATTTTCATTAAGCTG                         GGTTCTGCCAAGGATAAGAAGAAGGAAAATGCTGAGCGCGATGAGCGTGCC
genomic: GAAATGATGAAATTTTCATTAAGCTGgtatatttct ... attttcttagGGTTCTGACAAGGATAAGAAGAAGGAAAATGCTGAGCGCGATGAGCGTGCC
EST: gi|427517|gb|D23584.1|D23584
EST:     TGCAGCCACTTTCTACCAAGAAAGGAAATGATGAAATTTTCATTAAGCTG                         GGTTCTGACAAGGATAAGAAGA-GGAAAATGCTGAGCGCGATGAGCGT
genomic: TGCAGCCACTTTCTACCAAGAAAGGAAATGATGAAATTTTCATTAAGCTGgtatatttct ... attttcttagGGTTCTGACAAGGATAAGAAGAAGGAAAATGCTGAGCGCGATGAGCGT
EST: gi|58679736|gb|CK068423.1|CK068423
EST:     TGCAGCCACTTTCTACCAAGAAAGGAAATGATGAAATTTTCATTAAGCTG                         GGTTCTGACAAGGATAAGAAGAAGGAAAATGCTGAGCGCGATGAGCGTGCC
genomic: TGCAGCCACTTTCTACCAAGAAAGGAAATGATGAAATTTTCATTAAGCTGgtatatttct ... attttcttagGGTTCTGACAAGGATAAGAAGAAGGAAAATGCTGAGCGCGATGAGCGTGCC
EST: gi|55409956|gb|CV722332.1|CV722332
EST:     TGCAGCCACTTTCTACCAAGAAAGGAAATGATGAAATTTTCATTAAGCTG                         GGTTCTGACAAGGATAAGAAGAAGGAAAAT
genomic: TGCAGCCACTTTCTACCAAGAAAGGAAATGATGAAATTTTCATTAAGCTGgtatatttct ... attttcttagGGTTCTGACAAGGATAAGAAGAAGGAAAAT
EST: gi|58599621|gb|CK010149.1|CK010149
EST:     GCCACTTTCTACCAAGAAAGGAAATGATGAAATGTTCATTAAGCTG                         GGTTCTGACAAGGATAAGAAGAAGGAAAATGCTGAGCGCGATGAGCGTGCC
genomic: GCCACTTTCTACCAAGAAAGGAAATGATGAAATTTTCATTAAGCTGgtatatttct ... attttcttagGGTTCTGACAAGGATAAGAAGAAGGAAAATGCTGAGCGCGATGAGCGTGCC
EST: gi|88830569|gb|CI078013.1|CI078013
EST:     TGCAGCCACTTTCTACCAAGAAAGGAAATGATGAAATTTTCATTAAGCTG                         GGTTCTGACAAGGATAAGAAGAAGGAAAATGCTGAGCGCGATGAGCGTGCC
genomic: TGCAGCCACTTTCTACCAAGAAAGGAAATGATGAAATTTTCATTAAGCTGgtatatttct ... attttcttagGGTTCTGACAAGGATAAGAAGAAGGAAAATGCTGAGCGCGATGAGCGTGCC
EST: gi|29686653|gb|CB682928.1|CB682928
EST:     TGCAGCCACTTTCTACCAAGAAAGGAAATGATGAAATTTTCATTAAGCTG                         GGTTCTGACAAGGATAAGAAGAAGGAAAATGCTGAGCGCGATGAGCGTGCC
genomic: TGCAGCCACTTTCTACCAAGAAAGGAAATGATGAAATTTTCATTAAGCTGgtatatttct ... attttcttagGGTTCTGACAAGGATAAGAAGAAGGAAAATGCTGAGCGCGATGAGCGTGCC
EST: gi|218490755|gb|FG964437.1|FG964437
EST:     TGCAGCCACTTTCTACCAAGAAAGGAAATGATGAAATTTTCATTAAGCTG                         GGTTCTGACAAGGATAAGAAGAAGGAAAATGCTGAGCGCGAT
genomic: TGCAGCCACTTTCTACCAAGAAAGGAAATGATGAAATTTTCATTAAGCTGgtatatttct ... attttcttagGGTTCTGACAAGGATAAGAAGAAGGAAAATGCTGAGCGCGAT
EST: gi|29614482|gb|CB619495.1|CB619495
EST:     TGCAGCCACTTTCTACCAAGAAAGGAAATGATGAAATTTTCATTAAGCTG                         GGTTCTGACAAGGATAAGAAGAAGGAAAATGCTGAGCGCGATGAGCGTGCC
genomic: TGCAGCCACTTTCTACCAAGAAAGGAAATGATGAAATTTTCATTAAGCTGgtatatttct ... attttcttagGGTTCTGACAAGGATAAGAAGAAGGAAAATGCTGAGCGCGATGAGCGTGCC
EST: gi|300216202|gb|HO087987.1|HO087987
EST:     TGCAGCCACTTTCTACCAAGAAAGGAAATGATGAAATTTTCATTAAGCTG                         GGTTCTGACAAGGATAAGAAGAAGGAAAATGCTGAGCGCGATGAGCGTGCC
genomic: TGCAGCCACTTTCTACCAAGAAAGGAAATGATGAAATTTTCATTAAGCTGgtatatttct ... attttcttagGGTTCTGACAAGGATAAGAAGAAGGAAAATGCTGAGCGCGATGAGCGTGCC
EST: gi|38469519|gb|CF953650.1|CF953650
EST:     TGCAGCCACTTTCTACCAAGAAAGGAAATGATGAAATTTTCATTAAGCTG                         GGTTCTGACAAGGATAAGAAGAAGGAAAATGCTGAGCGCGATGAGCGTGCC
genomic: TGCAGCCACTTTCTACCAAGAAAGGAAATGATGAAATTTTCATTAAGCTGgtatatttct ... attttcttagGGTTCTGACAAGGATAAGAAGAAGGAAAATGCTGAGCGCGATGAGCGTGCC
EST: gi|218486771|gb|FG956353.1|FG956353
EST:     TGCAGCCACTTTCTACCAAGAAAGGAAATGATGAAATTTTCATTAAGCTG                         GGTTCTGACAAGGATAAGAAGAAGGAAAATGCTGAGCGCGATGAGCGTGCC
genomic: TGCAGCCACTTTCTACCAAGAAAGGAAATGATGAAATTTTCATTAAGCTGgtatatttct ... attttcttagGGTTCTGACAAGGATAAGAAGAAGGAAAATGCTGAGCGCGATGAGCGTGCC
EST: gi|163928222|gb|EG714626.1|EG714626
EST:     AAGAAAGGAAATGATGAAATTTTCATTAAGCTG                         GGTTCTGACAAGGATAAGAAGAAGGAAAATGCTGAGCGCGATGAGCGTGCC
genomic: AAGAAAGGAAATGATGAAATTTTCATTAAGCTGgtatatttct ... attttcttagGGTTCTGACAAGGATAAGAAGAAGGAAAATGCTGAGCGCGATGAGCGTGCC

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: 72 (upstream exon), 72 (downstream exon)
Score: 55

TTTCAAGGCTGAAGAGAGGAAGGTTGAGGTCGATAAGGACCTGCAGTCTATGCAGCCACTTTCTACCAAGAAAGGAAATGATGAAATTTTCATTAAGCTGgtatatttct ... attttcttagGGTTCTGACAAGGATAAGAAGAAGGAAAATGCTGAGCGCGATGAGCGTGCCAAGAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cctacagttgtctgattctagaatttttttttgattaaatgtaccattttcttagGGTTCTGACAAGGATAAGAAGAAGGAAAATGCTGAGCGCGATGAGCGTGCCAAGAAG
                            ttttgat  putative branch site (score: 55)
                                           ccattttctt  putative PPT
              attctagaattttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatatttctcagtgtgctctatttcaatccctacagttgtctgattctagaatttttttttgattaaatgtaccattttcttagGGTTCTGACAAGGATAAGAAGAAGGAAAATGCTGAGCGCGATGAGCGTGCCAAGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG