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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgcacaatttatattatcatgctgttctgaaccagtttgccaacttgtcccatgcatgagagatgagatgagccacaactatttgttaattttgtttcagGTACAACTGTTGTTTGGTGCTTGTCCAGCTAGGACAGCCGAGTGAAGTGCCAGCATGGGTGGCATCCTTGGACGCCATGACACCATGAAGAGGAGCTCTC

Basic information

species Oryza sativa
transcript LOC_Os06g40720.1
intron # 1
splice site 3'
intron type U2

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|88688075|gb|CI731651.1|CI731651
EST:     CCGATCTGGGCCGCCGGCGACGGCGAAACACAGGCAAAGCAAAGATAAAG                         GTACAACTGTTGTTTGGTGCTTGTCCAGCTAGGACAGCCGAGTGAAGTGCC
genomic: CCGATCTGGGCCGCCGGCGACGGCGAAACACAGGCAAAGCAAAGATAAAGgttcttttct ... tttgtttcagGTACAACTGTTGTTTGGTGCTTGTCCAGCTAGGACAGCCGAGTGAAGTGCC
EST: gi|88670009|gb|CI724125.1|CI724125
EST:     CCGATCTGGGCCGCCGGNGACGGCGAAACACAGGCAAAGCAAAGATAAAG                         GTACAACTGTTGTTTGGTGCTTGTCCAGCTAGGACAGCCGAGTGAAGTGCC
genomic: CCGATCTGGGCCGCCGGCGACGGCGAAACACAGGCAAAGCAAAGATAAAGgttcttttct ... tttgtttcagGTACAACTGTTGTTTGGTGCTTGTCCAGCTAGGACAGCCGAGTGAAGTGCC
EST: gi|88672156|gb|CI726272.1|CI726272
EST:     CCGATCTGGGCCGCCGGCGACGGCGAAACACAGGCAAAGCAAAGATAAAG                         GTACAACTGTTGTTTGGTGCTTGTCCAGCTAGGACAGCCGAGTGAAGTGCC
genomic: CCGATCTGGGCCGCCGGCGACGGCGAAACACAGGCAAAGCAAAGATAAAGgttcttttct ... tttgtttcagGTACAACTGTTGTTTGGTGCTTGTCCAGCTAGGACAGCCGAGTGAAGTGCC
EST: gi|88670336|gb|CI724452.1|CI724452
EST:     CCGATCTGGGCCGCCGGCGACGGCGAAACACAGGCAAAGCAAAGATAAAG                         GTACAACTGTTGTTTGGTGCTTGTCCACCTAGGACAGCCGAGTGAAGTGCC
genomic: CCGATCTGGGCCGCCGGCGACGGCGAAACACAGGCAAAGCAAAGATAAAGgttcttttct ... tttgtttcagGTACAACTGTTGTTTGGTGCTTGTCCAGCTAGGACAGCCGAGTGAAGTGCC
EST: gi|88415313|gb|CI586519.1|CI586519
EST:     CCGATCTGGGCCGCCGGCGACGGCGAAACACAGGCAAAGCAAAGATAAAG                         GTACAACTGTTGTTTGGTGCTTGTCCAGCTAGGACAGCCGAGTGAAGTGCC
genomic: CCGATCTGGGCCGCCGGCGACGGCGAAACACAGGCAAAGCAAAGATAAAGgttcttttct ... tttgtttcagGTACAACTGTTGTTTGGTGCTTGTCCAGCTAGGACAGCCGAGTGAAGTGCC
EST: gi|88373009|gb|CI640460.1|CI640460
EST:     CCGATCTGGGCCGCCGGCGACGGCGAAACACAGGCAAAGCAAAGATAAAG                         GTACAACTGTTGTTTGGTGCTTGTCCAGCTAGGACAGCCGAGTGAAGTGCC
genomic: CCGATCTGGGCCGCCGGCGACGGCGAAACACAGGCAAAGCAAAGATAAAGgttcttttct ... tttgtttcagGTACAACTGTTGTTTGGTGCTTGTCCAGCTAGGACAGCCGAGTGAAGTGCC
EST: gi|88904947|gb|CI712246.1|CI712246
EST:     CCGATCTGGGCCGCCGGCGACGGCGAAACACAGGCAAAGCAAAGATAAAG                         GTACAACTGTTGTTTGGTGCTTGTCCAGCTAGGACAGCCGAGTGAAGTGCC
genomic: CCGATCTGGGCCGCCGGCGACGGCGAAACACAGGCAAAGCAAAGATAAAGgttcttttct ... tttgtttcagGTACAACTGTTGTTTGGTGCTTGTCCAGCTAGGACAGCCGAGTGAAGTGCC
EST: gi|88302426|gb|CI668272.1|CI668272
EST:     CCGATCTGGGCCGCCGGCGACGGCGAAACACAGGCAAAGCAAAGATAAAG                         GTACAACTGTTGTTTGGTGCTTGTCCAGCTAGGACAGCCGAGTGAAGTGCC
genomic: CCGATCTGGGCCGCCGGCGACGGCGAAACACAGGCAAAGCAAAGATAAAGgttcttttct ... tttgtttcagGTACAACTGTTGTTTGGTGCTTGTCCAGCTAGGACAGCCGAGTGAAGTGCC
EST: gi|88368777|gb|CI649985.1|CI649985
EST:     CCGATCTGGGCCGCCGGCGACGGCGAAACACAGGCAAAGCAAAGATAAAG                         GTACAACTGTTGTTTGGTGCTTGTCCAGCTAGGACAGCCGAGTGAAGTGCC
genomic: CCGATCTGGGCCGCCGGCGACGGCGAAACACAGGCAAAGCAAAGATAAAGgttcttttct ... tttgtttcagGTACAACTGTTGTTTGGTGCTTGTCCAGCTAGGACAGCCGAGTGAAGTGCC
EST: gi|88594383|gb|CI714341.1|CI714341
EST:     CCGATCTGGGCCGNCGGCGACGGCGAAACACAGGCAAAGCAAAGATAAAG                         GTACAACTGTTGTTTGGTGCTTGTCCAGCTAGGACAGCCGAGTGAAGTGCC
genomic: CCGATCTGGGCCGCCGGCGACGGCGAAACACAGGCAAAGCAAAGATAAAGgttcttttct ... tttgtttcagGTACAACTGTTGTTTGGTGCTTGTCCAGCTAGGACAGCCGAGTGAAGTGCC
EST: gi|88673974|gb|CI728087.1|CI728087
EST:     CCGATCTGGGCCGCCGGCGACGGCGAAACACAGGCAAAGCAAAGATAAAG                         GTACAACTGTTGTTTGGTGCTTGTCCAGCTAGGACAGCCGAGTGAAGTGCC
genomic: CCGATCTGGGCCGCCGGCGACGGCGAAACACAGGCAAAGCAAAGATAAAGgttcttttct ... tttgtttcagGTACAACTGTTGTTTGGTGCTTGTCCAGCTAGGACAGCCGAGTGAAGTGCC
EST: gi|88667293|gb|CI715451.1|CI715451
EST:     CCGATCTGGGCCGCCGGCGACGGCGAAACACAGGCAAAGCAAAGATAAAG                         GTACAACTGTTGTTTGGTGCTTGTCCAGCTAGGACAGCCGAGTGAAGTGCC
genomic: CCGATCTGGGCCGCCGGCGACGGCGAAACACAGGCAAAGCAAAGATAAAGgttcttttct ... tttgtttcagGTACAACTGTTGTTTGGTGCTTGTCCAGCTAGGACAGCCGAGTGAAGTGCC
EST: gi|88593480|gb|CI713434.1|CI713434
EST:     CCGATCTGGGCCGCCGGCGACGGGGAAACACAGGCAAAGCAAAGATAAAG                         GTACAACTGTTGTTTGGTGCTTGTCCAGCTAGGACAGCCGAGTGAAGTGCC
genomic: CCGATCTGGGCCGCCGGCGACGGCGAAACACAGGCAAAGCAAAGATAAAGgttcttttct ... tttgtttcagGTACAACTGTTGTTTGGTGCTTGTCCAGCTAGGACAGCCGAGTGAAGTGCC
EST: gi|88673365|gb|CI727478.1|CI727478
EST:     CCGATCTGGGCCGCCGGCGACGGCGAAACACAGGCAAAGCAAAGATAAAG                         GTACAACTGTTGTTTGGTGCTTGTCCAGCTAGGACAGCCGAGTGAAGTGCC
genomic: CCGATCTGGGCCGCCGGCGACGGCGAAACACAGGCAAAGCAAAGATAAAGgttcttttct ... tttgtttcagGTACAACTGTTGTTTGGTGCTTGTCCAGCTAGGACAGCCGAGTGAAGTGCC
EST: gi|88670643|gb|CI724759.1|CI724759
EST:     CCGATCTGGGCCGCCGGCGACGGCGAAACACAGGCAAAGCAAAGATAAAG                         GTACAACTGTTGTTTGGTGCTTGTCCAGCTAGGACAGCCGAGTGAAGTGCC
genomic: CCGATCTGGGCCGCCGGCGACGGCGAAACACAGGCAAAGCAAAGATAAAGgttcttttct ... tttgtttcagGTACAACTGTTGTTTGGTGCTTGTCCAGCTAGGACAGCCGAGTGAAGTGCC
EST: gi|88904636|gb|CI711935.1|CI711935
EST:     CCGATCTGGGCCGCCGGCGACGGCGAAACACAGGCAAAGCAAAGATAAAG                         GTACAACTGTTGTTTGGTGCTTGTCCAGCTAGGACAGCCGAGTGAAGTGCC
genomic: CCGATCTGGGCCGCCGGCGACGGCGAAACACAGGCAAAGCAAAGATAAAGgttcttttct ... tttgtttcagGTACAACTGTTGTTTGGTGCTTGTCCAGCTAGGACAGCCGAGTGAAGTGCC
EST: gi|88665950|gb|CI716106.1|CI716106
EST:     CCGATCTGGGCCGCCGGCGACGGCGAAACACAGGCAAAGCAAAGATAAAG                         GTACAACTGTTGTTTGGTGCTTGTCCAGCTAGGACAGCCGAGTGAAGTGCC
genomic: CCGATCTGGGCCGCCGGCGACGGCGAAACACAGGCAAAGCAAAGATAAAGgttcttttct ... tttgtttcagGTACAACTGTTGTTTGGTGCTTGTCCAGCTAGGACAGCCGAGTGAAGTGCC
EST: gi|89172319|gb|CI721378.1|CI721378
EST:     CCGATCTGGGCCGCCGGCGACGGNGAAACACAGGCAAAGCAAAGATAAAG                         GTACAACTGTTGTTTGGTGCTTGTCCAGCTAGGACAGCCGAGTGAAGTGCC
genomic: CCGATCTGGGCCGCCGGCGACGGCGAAACACAGGCAAAGCAAAGATAAAGgttcttttct ... tttgtttcagGTACAACTGTTGTTTGGTGCTTGTCCAGCTAGGACAGCCGAGTGAAGTGCC
EST: gi|88973647|gb|CI718075.1|CI718075
EST:     CCGATCTGGGCCGCCGGCGACGGCGAAACACAGGCAAAGCAAAGATAAAG                         GTACAACTGTTGTTTGGTGCTTGTCCAGCTAGGACAGCCGAGTGAAGTGCC
genomic: CCGATCTGGGCCGCCGGCGACGGCGAAACACAGGCAAAGCAAAGATAAAGgttcttttct ... tttgtttcagGTACAACTGTTGTTTGGTGCTTGTCCAGCTAGGACAGCCGAGTGAAGTGCC
EST: gi|88673254|gb|CI726029.1|CI726029
EST:     CCGATCTGGGCCGCCGGCGACGGCGAAACACAGGCAAAGCAAAGATAAAG                         GTACAANTGTTGTTTGGTGCTTGTCCAGCTAGGACAGNCGAGTGAAGTGCC
genomic: CCGATCTGGGCCGCCGGCGACGGCGAAACACAGGCAAAGCAAAGATAAAGgttcttttct ... tttgtttcagGTACAACTGTTGTTTGGTGCTTGTCCAGCTAGGACAGCCGAGTGAAGTGCC
EST: gi|88677204|gb|CI729862.1|CI729862
EST:     CCGATCTGGGCCGCCGGCGACGGCGAAACACAGGCAAAGCAAAGATAAAG                         GTACAACTGTTGTTTGGTGCTTGTCCAGCTAGGACAGCCGAGTGAAGTGCC
genomic: CCGATCTGGGCCGCCGGCGACGGCGAAACACAGGCAAAGCAAAGATAAAGgttcttttct ... tttgtttcagGTACAACTGTTGTTTGGTGCTTGTCCAGCTAGGACAGCCGAGTGAAGTGCC
EST: gi|89171456|gb|CI720515.1|CI720515
EST:     CCGATCTGGGCCGCCGGCGACGGCGAAACACAGGCAAAGCAAAGATAAAG                         GTACAACTGTTGTTTGGTGCTTGTCCAGCTAGGACAGCCGAGTGAAGTGCC
genomic: CCGATCTGGGCCGCCGGCGACGGCGAAACACAGGCAAAGCAAAGATAAAGgttcttttct ... tttgtttcagGTACAACTGTTGTTTGGTGCTTGTCCAGCTAGGACAGCCGAGTGAAGTGCC
EST: gi|88673646|gb|CI727759.1|CI727759
EST:     CCGATCTGGGCCGCCGGCGACGGCGAAACACAGGCAAAGCAAAGATAAAG                         GTACAACTGTTGTTTGGTGCTTGTCCAGCTAGGACAGCCGAGTGAAGTGCC
genomic: CCGATCTGGGCCGCCGGCGACGGCGAAACACAGGCAAAGCAAAGATAAAGgttcttttct ... tttgtttcagGTACAACTGTTGTTTGGTGCTTGTCCAGCTAGGACAGCCGAGTGAAGTGCC
EST: gi|88667277|gb|CI715536.1|CI715536
EST:     CCGATCTGGGCCGCCGGCGACGGCGAAACACAGGCAAAGCAAAGATAAAG                         GTACAACTGTTGTTTGGTGCTTGTCCAGCTAGGACAGCCGAGTGAAGTGCC
genomic: CCGATCTGGGCCGCCGGCGACGGCGAAACACAGGCAAAGCAAAGATAAAGgttcttttct ... tttgtttcagGTACAACTGTTGTTTGGTGCTTGTCCAGCTAGGACAGCCGAGTGAAGTGCC
EST: gi|88671406|gb|CI725522.1|CI725522
EST:     CCGATCTGGGCCGCCGGCGACGGCGAAACACAGGCAAAGCAAAGATAAAG                         GTACAACTGTTGTTTGGTGCTTGTCCAGCTAGGACAGCCGAGTGAAGTGCC
genomic: CCGATCTGGGCCGCCGGCGACGGCGAAACACAGGCAAAGCAAAGATAAAGgttcttttct ... tttgtttcagGTACAACTGTTGTTTGGTGCTTGTCCAGCTAGGACAGCCGAGTGAAGTGCC
EST: gi|88973511|gb|CI717939.1|CI717939
EST:     CCGATCTGGGCCGCCGGCGACGGCGAAACACAGGCAAAGCAAAGATAAAG                         GTACAACTGTTGTTTGGTGCTTGTCCCGCTAGGACAGCCGAGTGAAGTGCC
genomic: CCGATCTGGGCCGCCGGCGACGGCGAAACACAGGCAAAGCAAAGATAAAGgttcttttct ... tttgtttcagGTACAACTGTTGTTTGGTGCTTGTCCAGCTAGGACAGCCGAGTGAAGTGCC
EST: gi|88441153|gb|CI602175.1|CI602175
EST:     CCGATCTGGGCCGCCGGCGACGGCGAAACACAGGCAAAGCAAAGATAAAG                         GTACAAGTGTTGTTTGGTGCTTGTCCAGCTAGGACAGCCGAGTGAAGTGCC
genomic: CCGATCTGGGCCGCCGGCGACGGCGAAACACAGGCAAAGCAAAGATAAAGgttcttttct ... tttgtttcagGTACAACTGTTGTTTGGTGCTTGTCCAGCTAGGACAGCCGAGTGAAGTGCC
EST: gi|88973656|gb|CI718084.1|CI718084
EST:     CCGATCTGGGCCGNCGGCGACGGCGAAACACAGGCAAAGCAAAGATAAAG                         GTACAACTGTTGTTTGGTGCTTGTCCAGCTAGGACAGCCGAGTGAAGTGCC
genomic: CCGATCTGGGCCGCCGGCGACGGCGAAACACAGGCAAAGCAAAGATAAAGgttcttttct ... tttgtttcagGTACAACTGTTGTTTGGTGCTTGTCCAGCTAGGACAGCCGAGTGAAGTGCC
EST: gi|88673461|gb|CI727574.1|CI727574
EST:     CCGATCTGGGCCGCCGGCGACGGCGAAACACAGGCAAAGCAAAGATAAAG                         GTACAACTGTTGTTTGGTGCTTGTCCAGCTAGGACAGCCGAGTGAAGTGCC
genomic: CCGATCTGGGCCGCCGGCGACGGCGAAACACAGGCAAAGCAAAGATAAAGgttcttttct ... tttgtttcagGTACAACTGTTGTTTGGTGCTTGTCCAGCTAGGACAGCCGAGTGAAGTGCC
EST: gi|88578280|gb|CI687200.1|CI687200
EST:     CCGATCTGGGCCGCCGGCGACGGCGAAACACAGGCAAAGCAAAGATAAAG                         GTACAACTGTTGTTTGGTGCTTGTCCAGCTAGGACAGCCGAGTGAAGTGCC
genomic: CCGATCTGGGCCGCCGGCGACGGCGAAACACAGGCAAAGCAAAGATAAAGgttcttttct ... tttgtttcagGTACAACTGTTGTTTGGTGCTTGTCCAGCTAGGACAGCCGAGTGAAGTGCC
EST: gi|88580296|gb|CI697213.1|CI697213
EST:     CCGATCTGGGCCGCCGGCGACGGCGAAACACAGGCAAAGCAAAGATAAAG                         GTACAACTGTTGTTTGGTGCTTGTCCAGCTAGGACAGCCGAGTGAAGTGCC
genomic: CCGATCTGGGCCGCCGGCGACGGCGAAACACAGGCAAAGCAAAGATAAAGgttcttttct ... tttgtttcagGTACAACTGTTGTTTGGTGCTTGTCCAGCTAGGACAGCCGAGTGAAGTGCC
EST: gi|88670231|gb|CI723479.1|CI723479
EST:     CCGATCTGGGCCGCCGGCGACGGNGAAACACAGGCAAAGCAAAGATAAAG                         GTACAACTGTTGTTTGGTGCTTGTCCAGCTAGGACAGCCGAGTGAAGTGCC
genomic: CCGATCTGGGCCGCCGGCGACGGCGAAACACAGGCAAAGCAAAGATAAAGgttcttttct ... tttgtttcagGTACAACTGTTGTTTGGTGCTTGTCCAGCTAGGACAGCCGAGTGAAGTGCC
EST: gi|58671024|gb|CK059710.1|CK059710
EST:     CCGATCTGGGCCGCCGGCGACGGCGAAACACAGGCAAAGCAAAGATAAAG                         GTACAACTGTTGTTTGGTGCTTGTCCAGCTAGGACAGCCGAGTGAAGTGCC
genomic: CCGATCTGGGCCGCCGGCGACGGCGAAACACAGGCAAAGCAAAGATAAAGgttcttttct ... tttgtttcagGTACAACTGTTGTTTGGTGCTTGTCCAGCTAGGACAGCCGAGTGAAGTGCC

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: 67 (upstream exon), 72 (downstream exon)
Score: 35

TCGATCGAAGCTACCACCCATCCCACCTTGCCCTTCCTTCGCCGCCGATTCCGATCTGGGCCGCCGGCGACGGCGAAACACAGGCAAAGCAAAGATAAAGgttcttttct ... tttgtttcagGTACAACTGTTGTTTGGTGCTTGTCCAGCTAGGACAGCCGAGTGAAGTGCCAGCATGGGTGGCATCCTTGGACGCCATGACACCATGAAGAGGAGCTCTC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtcccatgcatgagagatgagatgagccacaactatttgttaattttgtttcagGTACAACTGTTGTTTGGTGCTTGTCCAGCTAGGACAGCCGAGTGAAGTGCCAGCATGGGTGGCATCCTTGGACGCCATGACACCATGAAGAGGAGCTCTC
                                      tgttaat  putative branch site (score: 35)
                                            ttttgtttc  CT-rich tract
                               aactatttgttaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgcacaatttatattatcatgctgttctgaaccagtttgccaacttgtcccatgcatgagagatgagatgagccacaactatttgttaattttgtttcagGTACAACTGTTGTTTGGTGCTTGTCCAGCTAGGACAGCCGAGTGAAGTGCCAGCATGGGTGGCATCCTTGGACGCCATGACACCATGAAGAGGAGCTCTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
tgcacaa
- - - - - - - - - -tgctgtt
- - - - - - - - - - - - - ctgaacc
- - - - - - - - - - - - - - - - - - - - - - - - - - tgcatga