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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgtccgtttttcttttaatgtggtagtaagatgatgtgttttcagagattatgtttcttcatcgttttgactgtaatccttcaattcttttttgttccagTATGGTTCTCACTCAAAGAAGAGGCCCAACAATCTTGTTTTGGGGAGGACTTATGATCACCACATATATGATCTTGTTGAAGTAGGAGTTGAAAACTACA

Basic information

species Oryza sativa
transcript LOC_Os01g33030.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g33030.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G069518_T01 (Zea mays), 3'ss of exon 2
----tgtccgtttttcttttaatgtggtag-taagatgatgtgttttcagagattatgtttcttc-atcgtttt-gactgtaatccttcaattcttttttgttccagTATGGTTCTCACTCAAAGAAGAGGCCCAACAATCTTGTTTTGGGGAGGACTTATGATCACCACATATATGATCTTGTTGAAGTAGGAGTTGAAAACTACA
    ||||  || |   || || ||||| | |   |   |  ||||  ||||||||| || |||| || |||||  ||||||    || ||    ||| || | |||||||||||||| |||||||||||||||||||||||  ||||||  || || ||||| |||||||||||||| |||||||||||||||||||| |||||||
attatgtc-attgtatcttaaacgtggtgggttgtacccttggtttaaagagattatcttacttccattgttttcaactgta---ttttaa---atttatgatgcagTATGGTTCTCATTCAAAGAAGAGGCCCAACAATCTGATTTTGGCTAGAACGTATGACCACCACATATATGACCTTGTTGAAGTAGGAGTTGAGAACTACA

upper sequence: LOC_Os01g33030.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G359874_T01 (Zea mays), 3'ss of exon 2
----tgtccgtttttcttttaatgtggtagtaag-atgatgtgttttcagagattatgtttcttc-atcgtttt-gactgtaatccttcaattcttttttgttccagTATGGTTCTCACTCAAAGAAGAGGCCCAACAATCTTGTTTTGGGGAGGACTTATGATCACCACATATATGATCTTGTTGAAGTAGGAGTTGAAAACTACA
    |||   || |   || ||  |||| ||  | |   |  ||||  ||||||||| || |||| || |||||  ||||||    || ||    ||| || | |||||||||||||| |||||||||||||||||||||||  ||||||| || || ||||| |||||||||||||| |||||||||||||||||||| |||||||
attatgtt-attgtatcttaaacatggtggtttgtacccttagtttaaagagattatattacttccattgttttcaactgta---ttttaa---atttatgatgcagTATGGTTCTCATTCAAAGAAGAGGCCCAACAATCTGATTTTGGGTAGAACGTATGACCACCACATATATGACCTTGTTGAAGTAGGAGTTGAGAACTACA

upper sequence: LOC_Os01g33030.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA10G07630.1 (Glycine max), 3'ss of exon 2
tgtccgtttttcttttaatgtggtagtaagatgatgtgttttcagagattatgtttcttcatcgttttgactgtaatccttcaattct----ttt---ttgttccagTATGGTTCTCACTCAAAGAAGAGGCCCAACAATCTTGTTTTGGGGAGGACTTATGATCACCACATATATGATCTTGTTGAAGTAGGAGTTGAAAACTACA
         | |||| ||| |  |   ||| |||  |  | ||  | | | |     |  |        |||       ||   || |    |||   ||||| |||||||| |||||||| |||||| ||||  | || |||||| | ||||| ||||||||||| || || |||||| | || || || ||||||||||| |  |
-------gctgctttaaatttacttaaaagttgaattcctgtctaaaaatttccccatctaaacacaccactaaggctttttggttttggtgtttgtattgttgcagTATGGATCTCACTCGAAGAAGCGGCCTGATAACCTTGTTATTGGGAGAACTTATGATCATCATATCTATGATTTAGTGGAGGTTGGAGTTGAAAATTTTA

upper sequence: LOC_Os01g33030.1 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv08s0007g03890.t01 (Vitis vinifera), 3'ss of exon 3
tgtccgtttttcttttaatgtggtagtaagatgatgtgttttcagagattatgtttcttcatcgttttgactgtaat---ccttcaattcttttttgttccagTATGGTTCTCACTCAAAGAAGAGGCCCAACAATCTTGTTTTGGGGAGGACTTATGATCACCACATATATGATCTTGTTGAAGTAGGAGTTGAAAACTACA
     |  |   || | |     |  ||  | | |   |||    |   |   ||| || |  ||    |   ||||   | |  |   ||| | | ||  ||| ||||||||| ||||||||| ||||| | ||||||||| | ||| | ||||| ||||| |||||||||||||| || || || || |||||||| |  |
---tggagtagattctgagaaattcttattagggttcttttgtttactctggatttttttaatgtaaatatcttaatatacttctatggcttctgttttgtagTTTGGTTCTCATTCAAAGAAGCGGCCCGATAATCTTGTTATTGGGCGAACTTACGATCATCACATATATGATCTCGTAGAGGTTGGTGTTGAAAATTTTA

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|117244410|gb|CT848406.1|CT848406
EST:     AAACTTCTCTCGAGTTCTTCTCCCTCAAGACGGATTGCAGCCTTATAGTG                         TATGGTTCTCACTCAAAGAAGAGGCCCAACAATCTTGTTTTGGGGAGGACT
genomic: AAACTTCTCTCGAGTTCTTCTCCCTCAAGACGGATTGCAGCCTTATAGTGgtaaagctca ... tttgttccagTATGGTTCTCACTCAAAGAAGAGGCCCAACAATCTTGTTTTGGGGAGGACT
EST: gi|25797109|gb|CA753070.1|CA753070
EST:     AAACTTCTCTCGAGTTCTTCTCCCTCAAGACGGATTGCAGCCTTATAGTG                         TATGGTTCTCACTCAAAGAAGAGGCCCAACAATCTTGTTTTGGGGAGGACT
genomic: AAACTTCTCTCGAGTTCTTCTCCCTCAAGACGGATTGCAGCCTTATAGTGgtaaagctca ... tttgttccagTATGGTTCTCACTCAAAGAAGAGGCCCAACAATCTTGTTTTGGGGAGGACT
EST: gi|29658373|gb|CB654648.1|CB654648
EST:     AAACTTCTCTCGAGTTCTTCTCCCTCAAGACGGATTGCAGCCTTATAGTG                         TATGGTTCTCACTCAAAGAAGAGGCCCAACAATCTTGTTTTGGGGAGGACT
genomic: AAACTTCTCTCGAGTTCTTCTCCCTCAAGACGGATTGCAGCCTTATAGTGgtaaagctca ... tttgttccagTATGGTTCTCACTCAAAGAAGAGGCCCAACAATCTTGTTTTGGGGAGGACT
EST: gi|88405693|gb|CI609592.1|CI609592
EST:     AAACTTCTCTCGAGTTCTTCTCCCTCAAGACGGATTGCAGCCTTATAGTG                         TATGGTTCTCACTCAAAGAAGAGGCCCAACAATCTTGTTTTGGGGAGGACT
genomic: AAACTTCTCTCGAGTTCTTCTCCCTCAAGACGGATTGCAGCCTTATAGTGgtaaagctca ... tttgttccagTATGGTTCTCACTCAAAGAAGAGGCCCAACAATCTTGTTTTGGGGAGGACT
EST: gi|33793838|gb|CF322807.1|CF322807
EST:     AAACTTCTCTCGAGTTCTTCTCCCTCAAGACGGATTGCAGCCTTATAGTG                         TATGGTTCTCACTCAAAGAAGAGGCCCAACAATCTTGTTTTGGGGAGGACT
genomic: AAACTTCTCTCGAGTTCTTCTCCCTCAAGACGGATTGCAGCCTTATAGTGgtaaagctca ... tttgttccagTATGGTTCTCACTCAAAGAAGAGGCCCAACAATCTTGTTTTGGGGAGGACT
EST: gi|88331639|gb|CI675987.1|CI675987
EST:     AAACTTCTCTCGAGTTCTTCTCCCTCAAGACGGATTGCAGCCTTATAGTG                         TATGGTTCTCACTCAAAGAAGAGGCCCAA
genomic: AAACTTCTCTCGAGTTCTTCTCCCTCAAGACGGATTGCAGCCTTATAGTGgtaaagctca ... tttgttccagTATGGTTCTCACTCAAAGAAGAGGCCCAA
EST: gi|218479735|gb|FG953410.1|FG953410
EST:     TCGAGTTCTTCTCCCTCAAGACGGATTGCAGCCTTATAGTG                         TATGGTTCTCACTCAAAGAAGAGGCCCAACAATCTTGTTTTGGGGAGGACT
genomic: TCGAGTTCTTCTCCCTCAAGACGGATTGCAGCCTTATAGTGgtaaagctca ... tttgttccagTATGGTTCTCACTCAAAGAAGAGGCCCAACAATCTTGTTTTGGGGAGGACT
EST: gi|88403868|gb|CI611523.1|CI611523
EST:     AAAATTATCTCGAGTTCTTCTCC-TCAAGACGGATTGCCGACTTATAGTG                         TATGGTTCTCAATCAA
genomic: AAACTTCTCTCGAGTTCTTCTCCCTCAAGACGGATTGCAGCCTTATAGTGgtaaagctca ... tttgttccagTATGGTTCTCACTCAA
EST: gi|2310605|gb|C26760.1|C26760
EST:     AAACTTCTCTCGAGTTCTTCTCCCTCAAGACGGATTGCAGCCTTATAGTG                         TATGGTTCTCACTCAAAGAAGAGGCC-AACAATCTTGTTTT
genomic: AAACTTCTCTCGAGTTCTTCTCCCTCAAGACGGATTGCAGCCTTATAGTGgtaaagctca ... tttgttccagTATGGTTCTCACTCAAAGAAGAGGCCCAACAATCTTGTTTT
EST: gi|218502254|gb|FG960361.1|FG960361
EST:     AACTTCTTCGCGAGTTCTTCTCCCTCAAGACGGATTGCAGCCTTATAGTG                         TATGGTTCTCAGTCGGAGAAGAGGCCCAACAATCTTGTTATGGGGAGGACT
genomic: AACTTCT-CTCGAGTTCTTCTCCCTCAAGACGGATTGCAGCCTTATAGTGgtaaagctca ... tttgttccagTATGGTTCTCACTCAAAGAAGAGGCCCAACAATCTTGTTTTGGGGAGGACT
EST: gi|29675589|gb|CB671864.1|CB671864
EST:     AAACTTCTCTCGAGTTCTTCTCCCTCAAGACGGATTGCAGCCTTATAGTG                         TATGGTTCTCACTCAAAGAAGAGGCCCAACAATCTTGTTTTGGGGAGGACT
genomic: AAACTTCTCTCGAGTTCTTCTCCCTCAAGACGGATTGCAGCCTTATAGTGgtaaagctca ... tttgttccagTATGGTTCTCACTCAAAGAAGAGGCCCAACAATCTTGTTTTGGGGAGGACT
EST: gi|88571250|gb|CI662623.1|CI662623
EST:     AAACTTCTCTCGAGTTCTTCTCCCTCAAGACGGATTGCAGCCTTATAGTG                         TATGGTTCTCACTCAAAG
genomic: AAACTTCTCTCGAGTTCTTCTCCCTCAAGACGGATTGCAGCCTTATAGTGgtaaagctca ... tttgttccagTATGGTTCTCACTCAAAG
EST: gi|163929082|gb|EG710963.1|EG710963
EST:     AAACTTCTCTCGAGTTCTTCTCCCTCAAGACGGATTGCAGCCTTATAGTG                         TATGGTTCTCACTCAAAGAAGAGGCCCAACAATCTTGTTTTGGGGAGGACT
genomic: AAACTTCTCTCGAGTTCTTCTCCCTCAAGACGGATTGCAGCCTTATAGTGgtaaagctca ... tttgttccagTATGGTTCTCACTCAAAGAAGAGGCCCAACAATCTTGTTTTGGGGAGGACT
EST: gi|58687729|gb|CK076416.1|CK076416
EST:     TGCAGCCTTATAGTG                         TATGGTTCTCACTCAAAGAAGAGGCCCAACAATCTTGTTTGGGGGAGGACT
genomic: TGCAGCCTTATAGTGgtaaagctca ... tttgttccagTATGGTTCTCACTCAAAGAAGAGGCCCAACAATCTTGTTTTGGGGAGGACT
EST: gi|88360195|gb|CI610309.1|CI610309
EST:     AAACTTCTCTCGAGTTCTTCTCCCTCAAGACGGATTGCAGCCTTATAGTG                         TATGGTTCTCACTCAAAGAAGAGGCCCAACAATCTTGTTTTG
genomic: AAACTTCTCTCGAGTTCTTCTCCCTCAAGACGGATTGCAGCCTTATAGTGgtaaagctca ... tttgttccagTATGGTTCTCACTCAAAGAAGAGGCCCAACAATCTTGTTTTG
EST: gi|66914740|gb|CX101588.1|CX101588
EST:     AAACTTCTCTCGAGTTCTTCTCCCTCAAGACGGATTGCAGCCTTATAGTG                         TATGGTTCTCACTCAAAGAAGAGGCCCAACAATCTTGTTTTGGGGAGGACT
genomic: AAACTTCTCTCGAGTTCTTCTCCCTCAAGACGGATTGCAGCCTTATAGTGgtaaagctca ... tttgttccagTATGGTTCTCACTCAAAGAAGAGGCCCAACAATCTTGTTTTGGGGAGGACT
EST: gi|88369711|gb|CI680379.1|CI680379
EST:     AAACTTCTCTCGAGTTCTTCTCCCTCAAGACGGATTGCAGCCTTATAGTG                         TATGGTTCTCACTCAAAGAAGAGG
genomic: AAACTTCTCTCGAGTTCTTCTCCCTCAAGACGGATTGCAGCCTTATAGTGgtaaagctca ... tttgttccagTATGGTTCTCACTCAAAGAAGAGG

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: 66 (upstream exon), 69 (downstream exon)
Score: 20

CAAGTACTCCAAGAAGAATGACAACATCAGGCCGTTCGAGAGCGGCGGCGAAACTTCTCTCGAGTTCTTCTCCCTCAAGACGGATTGCAGCCTTATAGTGgtaaagctca ... tttgttccagTATGGTTCTCACTCAAAGAAGAGGCCCAACAATCTTGTTTTGGGGAGGACTTATGATCACCACATATATGATCTTGTTGAAGTAGGAGTTGAAAACTACA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agattatgtttcttcatcgttttgactgtaatccttcaattcttttttgttccagTATGGTTCTCACTCAAAGAAGAGGCCCAACAATCTTGTTTTGGGGAGGACTTATGATCACCACATATATGATCTTGTTGAAGTAGGAGTTGAAAACTACA
                   ttttgac  putative branch site (score: 20)
                               tccttcaattcttttt  putative PPT
                                  ttcaattctttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgtccgtttttcttttaatgtggtagtaagatgatgtgttttcagagattatgtttcttcatcgttttgactgtaatccttcaattcttttttgttccagTATGGTTCTCACTCAAAGAAGAGGCCCAACAATCTTGTTTTGGGGAGGACTTATGATCACCACATATATGATCTTGTTGAAGTAGGAGTTGAAAACTACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - atgatgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tccttca