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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatttgttcattgcaatctttttaacccagataagattctgctatttggacaacattttttttttaacaaaatggaaacctggatgcctaacttgcaattcgtatagGGTGTTCTGCACTGGGTTGCTCAGCCAGCACCTGGAGTTGAACCACTTAAGGTGGAAGTAAGATTATTTGATAAATTATTCCTCTCTGAG

Basic information

species Oryza sativa
transcript LOC_Os01g09000.1
intron # 19
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g09000.1 (Oryza sativa), 3'ss of exon 19
lower sequence: GRMZM2G048012_T01 (Zea mays), 3'ss of exon 18
gtatttgttcattgcaatctttttaa-cccagataagattctgctatttggaca-----------acattttttt------tttaacaaaatggaaacctggatgcctaacttg-----caattcgtatagGGTGTTCTGCACTGGGTTGCTCAGCCAGCACCTGGAGTTGAACCACTTAAGGTGGAAGTAAGATTATTTGATAAATTATTCCTCTCTGAG
|||   |||||  | ||| | || ||  |  | |  ||||||||||| | || |           | || |  ||       |||| ||||  | || || |||| || |||||     | |||  || ||||||||||||||||||||||| ||||||||||||| || |||||| | ||||||||||||||| |||| || ||||| ||| | || |||
gtaacagttcaccggaatttcttgaaatctgggtttgattctgctatctagatatttttcaagataaatctagttgggccccttaaaaaaaatgcaatctagatgactgacttggcttgcgatttatacagGGTGTTCTGCACTGGGTTGCTGAGCCAGCACCTGGTGTCGAACCATTGAAGGTGGAAGTAAGACTATTCGAGAAATTGTTCATGTCAGAG

upper sequence: LOC_Os01g09000.1 (Oryza sativa), 3'ss of exon 19
lower sequence: GRMZM2G032049_T01 (Zea mays), 3'ss of exon 19
gtatttgttcattgcaatctttttaa-cccagataagattctgctatttggacaacattttttttttaacaaaatggaaacctggatgcctaacttgcaattcgtatagGGTGTTCTGCACTGGGTTGCTCAGCCAGCACCTGGAGTTGAACCACTTAAGGTGGAAGTAAGATTATTTGATAAATTATTCCTCTCTGAG
|||   | | | || ||| | || ||  |  | |  || | ||||||      || |  |         |||  | ||   ||   | | |  ||||| ||| ||| |||||||||| |||||| ||||| ||||||||||||| || || ||| | |||||||||||||||||||| || ||||| ||| | || |||
gtaacagatgactgaaatttcttaaaatctgggtttgaatttgctatccactaaaaaagt--------gcaacctagatggct---tacttggcttgcgatttgtacagGGTGTTCTTCACTGGATTGCTGAGCCAGCACCTGGTGTAGAGCCATTGAAGGTGGAAGTAAGATTATTCGAGAAATTGTTCATGTCAGAG

upper sequence: LOC_Os01g09000.1 (Oryza sativa), 3'ss of exon 19
lower sequence: GLYMA10G41920.1 (Glycine max), 3'ss of exon 20
gtatttgttcattgcaatctttttaacccagataagattctgctatttggacaacattttttttttaacaaaatggaaacctggatgcctaacttgcaattcgtat--agGGTGTTCTGCACTGGGTTGCTCAGCCAGCACCTGGAGTTGAACCACTTAAGGTGGAAGTAAGATTATTTGATAAATTATTCCTCTCTGAG
   ||||   | |    |  || |   |  | ||| | |   |||   |         ||  |   | || | |||  | ||  ||||  |  |||   || || |  |||| ||||| || ||||||||||| ||  | ||||||||||| ||| | ||||||||||| ||||| ||||| |   | ||||| |  |||
--gtttgccaactttgctgattctg--ctggttaaaaatagtctacaagag-------ttggtaagatcagattggtgatct--atgca-attttgttttttgtttttagGGGGTTCTCCATTGGGTTGCTCAACCTTCTCCTGGAGTTGATCCATTAAAGGTGGAAGTCAGATTGTTTGAGAGGCTGTTCCTATTAGAG

upper sequence: LOC_Os01g09000.1 (Oryza sativa), 3'ss of exon 19
lower sequence: GLYMA20G25120.1 (Glycine max), 3'ss of exon 20
gtatttgttcattgcaatctttttaacccagataagattctgctatttggacaacatttttttt--ttaacaaaatggaaacctggatgcct---aacttgcaattcgtatagGGTGTTCTGCACTGGGTTGCTCAGCCAGCACCTGGAGTTGAACCACTTAAGGTGGAAGTAAGATTATTTGATAAATTATTCCTCTCTGAG
                   ||   |||   |  |  ||||||||  ||  | |   | |       ||   || ||   |     |||   |   || ||    ||  | ||||| ||||| || ||||||||||| ||  | ||||||||||| ||| | ||||||||||| ||||| ||||| |   ||||||| || |||
-----------------gtttgccaactttgcca--attctgctggttaaaaatagtctacaagagttggtaagattcgattggtgatctttgcaaaatttttgtt--tttagGGGGTTCTCCATTGGGTTGCTCAACCTTCTCCTGGAGTTGATCCATTGAAGGTGGAAGTCAGATTGTTTGAGAGGCTATTCCTATCAGAG

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|88197986|gb|CI197836.1|CI197836
EST:     TCATTGAAATTCGAGCTGAATATGACCCTTCAAAGACTACTAAACCTAAG                         GGTGTTCTGCACTGGGTTGCTCAGCCAGCACCTGGAGTTGAACCACTTAAG
genomic: TCATTGAAATTCGAGCTGAATATGACCCTTCAAAGACTACTAAACCTAAGgtatttgttc ... attcgtatagGGTGTTCTGCACTGGGTTGCTCAGCCAGCACCTGGAGTTGAACCACTTAAG
EST: gi|29673631|gb|CB669906.1|CB669906
EST:     TCATTGAAATTCGAGCTGAATATGACCCTTCAAAGACTACTAAACCTAAG                         GGTGTTCTGCACTGGGTTGCTCAGCCAGCACCTGGAGTTGAACCACTTAAG
genomic: TCATTGAAATTCGAGCTGAATATGACCCTTCAAAGACTACTAAACCTAAGgtatttgttc ... attcgtatagGGTGTTCTGCACTGGGTTGCTCAGCCAGCACCTGGAGTTGAACCACTTAAG
EST: gi|86495415|gb|CI138048.1|CI138048
EST:     TCATTGAAATTCGAGCTGAATATGACCCTTCAAAGACTACTAAACCTAAG                         GGTGTTCTGCACTGGGTTGCTCAGCCAGCACCTGGAGTTGAACCACTTAAG
genomic: TCATTGAAATTCGAGCTGAATATGACCCTTCAAAGACTACTAAACCTAAGgtatttgttc ... attcgtatagGGTGTTCTGCACTGGGTTGCTCAGCCAGCACCTGGAGTTGAACCACTTAAG
EST: gi|87017890|gb|CI273912.1|CI273912
EST:     TCATTGAAATTCGAGCTGAATATGACCCTTCAAAGACTACTAAACCTAAG                         GGTGTTCTGCACTGGGTTGCTCAGCCAGCACCTGGAGTTGAACCACTTAAG
genomic: TCATTGAAATTCGAGCTGAATATGACCCTTCAAAGACTACTAAACCTAAGgtatttgttc ... attcgtatagGGTGTTCTGCACTGGGTTGCTCAGCCAGCACCTGGAGTTGAACCACTTAAG
EST: gi|86478328|gb|CI120961.1|CI120961
EST:     TCATTGAAATTCGAGCTGAATATGACCCTTCAAAGACTACTAAACCTAAG                         GGTGTTCTGCACTGGGTTGCTCAGCCAGCACCTGGAGTTGAACCACTTAAG
genomic: TCATTGAAATTCGAGCTGAATATGACCCTTCAAAGACTACTAAACCTAAGgtatttgttc ... attcgtatagGGTGTTCTGCACTGGGTTGCTCAGCCAGCACCTGGAGTTGAACCACTTAAG
EST: gi|29660827|gb|CB657102.1|CB657102
EST:     TCATTGAAATTCGAGCTGAATATGACCCTTCAAAGACTACTAAACCTAAG                         GGTGTTCTGCACTGGGTTGCTCAGCCAGCACCTGGAGTTGAACCACTTAAG
genomic: TCATTGAAATTCGAGCTGAATATGACCCTTCAAAGACTACTAAACCTAAGgtatttgttc ... attcgtatagGGTGTTCTGCACTGGGTTGCTCAGCCAGCACCTGGAGTTGAACCACTTAAG
EST: gi|29660828|gb|CB657103.1|CB657103
EST:     TCATTGAAATTCGAGCTGAATATGACCCTTCAAAGACTACTAAACCTAAG                         GGTGTTCTGCACTGGGTTGCTCAGCCAGCACCTGGAGTTGAACCACTTAAG
genomic: TCATTGAAATTCGAGCTGAATATGACCCTTCAAAGACTACTAAACCTAAGgtatttgttc ... attcgtatagGGTGTTCTGCACTGGGTTGCTCAGCCAGCACCTGGAGTTGAACCACTTAAG
EST: gi|87030255|gb|CI270265.1|CI270265
EST:     TCATTGAAATTCGAGCTGAATATGACCCTTCAAAGACTACTAAACCTAAG                         GGTGTTCTGCACTGGGTTGCTCAGCCAGCACCTGGAGTTGAACCACTTAAG
genomic: TCATTGAAATTCGAGCTGAATATGACCCTTCAAAGACTACTAAACCTAAGgtatttgttc ... attcgtatagGGTGTTCTGCACTGGGTTGCTCAGCCAGCACCTGGAGTTGAACCACTTAAG
EST: gi|86482312|gb|CI124945.1|CI124945
EST:     TCATTGAAATTCGAGCTGAATATGACCCTTCAAAGACTACTAAACCTAAG                         GGTGTTCTGCACTGGGTTGCTCAGCCAGCACCTGGAGTTGAACCACTTAAG
genomic: TCATTGAAATTCGAGCTGAATATGACCCTTCAAAGACTACTAAACCTAAGgtatttgttc ... attcgtatagGGTGTTCTGCACTGGGTTGCTCAGCCAGCACCTGGAGTTGAACCACTTAAG
EST: gi|88197825|gb|CI197675.1|CI197675
EST:     TCATTGAAATTCGAGCTGAATATGACCCTTCAAAGACTACTAAACCTAAG                         GGTGTTCTGCACTGGGTTGCTCAGCCAGCACCTGGAGTTGAACCACTTAAG
genomic: TCATTGAAATTCGAGCTGAATATGACCCTTCAAAGACTACTAAACCTAAGgtatttgttc ... attcgtatagGGTGTTCTGCACTGGGTTGCTCAGCCAGCACCTGGAGTTGAACCACTTAAG
EST: gi|33677551|gb|CF305790.1|CF305790
EST:     TCATTGAAATTCGAGCTGAATATGACCCTTCAAAGACTACTAAACCTAAG                         GGTGTTCTGCACTGGGTTGCTCAGCCAGCACCTGGAGTTGAACCACTTAAG
genomic: TCATTGAAATTCGAGCTGAATATGACCCTTCAAAGACTACTAAACCTAAGgtatttgttc ... attcgtatagGGTGTTCTGCACTGGGTTGCTCAGCCAGCACCTGGAGTTGAACCACTTAAG
EST: gi|87041341|gb|CI195963.1|CI195963
EST:     TCATTGAAATTCGAGCTGAATATGACCCTTCAAAGACTACTAAACCTAAG                         GGTGTTCTGCACTGGGTTGCTCAGCCAGCACCTGGAGTTGAACCACTTAAG
genomic: TCATTGAAATTCGAGCTGAATATGACCCTTCAAAGACTACTAAACCTAAGgtatttgttc ... attcgtatagGGTGTTCTGCACTGGGTTGCTCAGCCAGCACCTGGAGTTGAACCACTTAAG
EST: gi|58587067|gb|CF985375.1|CF985375
EST:     TCATTGAAATTCGAGCTGAATATGACCCTTCAAAGACTACTAAACCTAAG                         GGTGTTCTGCACTGGGTTGCTCAGCCAGCACCTGGAGTTGAACCACTTAAG
genomic: TCATTGAAATTCGAGCTGAATATGACCCTTCAAAGACTACTAAACCTAAGgtatttgttc ... attcgtatagGGTGTTCTGCACTGGGTTGCTCAGCCAGCACCTGGAGTTGAACCACTTAAG
EST: gi|86597706|gb|CI274697.1|CI274697
EST:     TCATTGAAATTCGAGCTGAATATGACCCTTCAAAGACTACTAAACCTAAG                         GGTGTTCTGCACTGGGTTGCTCAGCCAGCACCTGGAGTTGAACCACTTAAG
genomic: TCATTGAAATTCGAGCTGAATATGACCCTTCAAAGACTACTAAACCTAAGgtatttgttc ... attcgtatagGGTGTTCTGCACTGGGTTGCTCAGCCAGCACCTGGAGTTGAACCACTTAAG
EST: gi|88966267|gb|CI119402.1|CI119402
EST:     TCATTGAAATTCGAGCTGAATATGACCCTTCAAAGACTACTAAACCTAAG                         GGTGTTCTGCACTGGGTTGCTCAGCCAGCACCTGGAGTTGAACCACTTAAG
genomic: TCATTGAAATTCGAGCTGAATATGACCCTTCAAAGACTACTAAACCTAAGgtatttgttc ... attcgtatagGGTGTTCTGCACTGGGTTGCTCAGCCAGCACCTGGAGTTGAACCACTTAAG

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: 75 (upstream exon), 72 (downstream exon)
Score: 96

ATTCCCCATTAAATGTACCGAGGTTGTTTATGGTGACAATCCAGATGACATCATTGAAATTCGAGCTGAATATGACCCTTCAAAGACTACTAAACCTAAGgtatttgttc ... attcgtatagGGTGTTCTGCACTGGGTTGCTCAGCCAGCACCTGGAGTTGAACCACTTAAGGTGGAAGTAAGATTATTTGATAAATTATTCCTCTCTGAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acattttttttttaacaaaatggaaacctggatgcctaacttgcaattcgtatagGGTGTTCTGCACTGGGTTGCTCAGCCAGCACCTGGAGTTGAACCACTTAAGGTGGAAGTAAGATTATTTGATAAATTATTCCTCTCTGAG
                                 gcctaac  putative branch site (score: 96)
     ttttttttaacaaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatttgttcattgcaatctttttaacccagataagattctgctatttggacaacattttttttttaacaaaatggaaacctggatgcctaacttgcaattcgtatagGGTGTTCTGCACTGGGTTGCTCAGCCAGCACCTGGAGTTGAACCACTTAAGGTGGAAGTAAGATTATTTGATAAATTATTCCTCTCTGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG