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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttcatattaccgttacttttatttgttgattttttttcagctaaatcgtgctagtaagtgctttcgatgtaatattctctagCCTGAGTGGATGGCACCAGAAGTTATACGAGATGAGCCATCAAATGAGAAGTCTGATGTCTACAGCTTTGGTGTTATCCTATGGGAGCTCATGACATTGC

Basic information

species Oryza sativa
transcript LOC_Os02g32610.2
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g32610.3 (Oryza sativa), 3'ss of exon 13
lower sequence: GRMZM2G059671_T04 (Zea mays), 3'ss of exon 12
gtaagttcatattaccgttacttttatttgttgattttttttcagctaaatcgtgctagtaagtgct-ttcgatgtaatattctctagCCTGAGTGGATGGCACCAGAAGTTATACGAGATGAGCCATCAAATGAGAAGTCTGATGTCTACAGCTTTGGTGTTATCCTATGGGAGCTCATGACATTGC
||||||| |||||    |   |||  | | ||   |||| ||  || |     ||    |||||| | |||  ||  ||  | ||||||||||||||||||||||||||||| ||||||| ||||| |||||||||||||||||||| |||||||| ||||| ||| |||||||||| ||||||||||
gtaagtt-atattgt--tccgtttagtgtattttgttttgttacgcaattctatgtggctaagtgttattctgtgccatgctatctagCCTGAGTGGATGGCACCAGAAGTTCTACGAGACGAGCCCTCAAATGAGAAGTCTGATGTTTACAGCTTCGGTGTAATCTTATGGGAGCTTATGACATTGC

upper sequence: LOC_Os02g32610.3 (Oryza sativa), 3'ss of exon 13
lower sequence: GLYMA13G21480.1 (Glycine max), 3'ss of exon 12
gtaagttcatattacc----gttacttttatttgttgattttt---tttcagc--taaatcgtgctagtaagtgctt------tcgatgtaatattctctagCCTGAGTGGATGGCACCAGAAGTTATACGAGATGAGCCATCAAATGAGAAGTCTGATGTCTACAGCTTTGGTGTTATCCTATGGGAGCTCATGACATTGC
||||||||| |||  |    | || || | |||  |   | ||   ||||||   ||| |  |   | ||  |  ||      ||    |    | |  ||||||||||||||||| ||||| ||| |  | ||||||||||| ||||||||||| ||||| |||||||||||||| ||| ||||||||||    |||||||
gtaagttcacattgactgcagatatttctgttttgtacgtcttatgtttcagaagtaagttttataactatatttttaatttttctccttttcctcccttagCCTGAGTGGATGGCTCCAGAGGTTCTTTGTGATGAGCCATCGAATGAGAAGTCCGATGTTTACAGCTTTGGTGTAATCTTATGGGAGCTTGCAACATTGC

upper sequence: LOC_Os02g32610.3 (Oryza sativa), 3'ss of exon 13
lower sequence: GLYMA19G37570.2 (Glycine max), 3'ss of exon 13
gtaagttcatatt---accgttacttttatttgttgatttttt--ttcagcta--aatcgtgctagt---aagtgctttcgatgtaatattctcta----gCCTGAGTGGATGGCACCAGAAGTTATACGAGATGAGCCATCAAATGAGAAGTCTGATGTCTACAGCTTTGGTGTTATCCTATGGGAGCTCATGACATTGC
||||||| |  ||   | |||   |     || |  ||| |||  ||||| |   | |  |  |  |   || |   ||  |     | |||||||    ||||||||||||||| ||||||||| | || || |||||||| ||||||||||| ||||| |||||||||||||| ||| | |||||| ||   |||||||
gtaagtttactttcaaaacgtgtatcagccttttgaattgtttgtttcagatgccatttttatttttgcaaattaagttgaactcctttttctctacttagCCTGAGTGGATGGCTCCAGAAGTTCTTCGTGACGAGCCATCCAATGAGAAGTCAGATGTTTACAGCTTTGGTGTCATCTTGTGGGAGATCGCAACATTGC

upper sequence: LOC_Os02g32610.3 (Oryza sativa), 3'ss of exon 13
lower sequence: GLYMA03G34890.1 (Glycine max), 3'ss of exon 13
gtaagttcatatt---accgttacttttatttgttgatttttt--ttcagcta--aatcgtgctagt---aagtgctttcgatgtaatattctcta----gCCTGAGTGGATGGCACCAGAAGTTATACGAGATGAGCCATCAAATGAGAAGTCTGATGTCTACAGCTTTGGTGTTATCCTATGGGAGCTCATGACATTGC
||||||  |  ||   | |||   | ||  || |  ||  |||  ||||| |   | |  |  || |   || |   ||  |     | |||||||    ||||||||||||||| ||||||||| | || ||||||||||| ||||||||||| ||||| |||||||||||||| ||| | |||||||||   |||||||
gtaagtatactttcaaaacgtgtatcttccttttgaatcgtttgattcagatgtcatttttattattgcaaattaagttgaactcctttttctctacttagCCTGAGTGGATGGCTCCAGAAGTTCTTCGTGATGAGCCATCCAATGAGAAGTCAGATGTTTACAGCTTTGGTGTCATCTTGTGGGAGCTCGCAACATTGC

upper sequence: LOC_Os02g32610.3 (Oryza sativa), 3'ss of exon 13
lower sequence: GLYMA10G07610.1 (Glycine max), 3'ss of exon 14
gtaagttcatattacc-------gttacttttatttgttgattttttttcag-----cta-aatcgtgctagtaagtgctttcgatgtaatattctct-agCCTGAGTGGATGGCACCAGAAGTTATACGAGATGAGCCATCAAATGAGAAGTCTGATGTCTACAGCTTTGGTGTTATCCTATGGGAGCTCATGACATTGC
||||||||| |||  |       ||| || || | |  |  || | ||||||      || ||    | |  ||     |||     |  |  || || |||||||||||||||| ||||| ||| | || ||||||||||| ||||||||||||||||| |||||||||||||| ||| ||||||||||    |||||||
gtaagttcacattgactgcagatgtttctgttttgtactacttatgtttcagaagttttataactacgtttttattaatttttctccttttcctcccttagCCTGAGTGGATGGCTCCAGAGGTTCTTCGTGATGAGCCATCGAATGAGAAGTCTGATGTTTACAGCTTTGGTGTAATCTTATGGGAGCTTGCAACATTGC

upper sequence: LOC_Os02g32610.3 (Oryza sativa), 3'ss of exon 13
lower sequence: AT5G03730.1 (Arabidopsis thaliana), 3'ss of exon 12
------------------------gtaagttcatattaccgttacttttatttgttgattttttttcagctaaatcgtgctagtaagtgctttcgatgtaatattctctagCCTGAGTGGATGGCACCAGAAGTTATACGAGATGAGCCATCAAATGAGAAGTCTGATGTCTACAGCTTTGGTGTTATCCTATGGGAGCTCATGACATTGC
                          |    |  |  | ||| |||||  | |   |   | ||| ||    || |    || | | ||  || ||| ||         |||| ||||||||||||||||||||  | ||||||||||| || ||||| ||||| ||||| |||||||| || || ||| | ||||||||    |||||||
gtaagttcagtttgtttgaaactaaaacacgctgaacaacgtaactttcttctag-gtcctatttccaatggaagctaaataattactgactttgatata-------tcagCCCGAGTGGATGGCACCAGAAGTCCTGCGAGATGAGCCGTCTAATGAAAAGTCAGATGTGTACAGCTTCGGGGTCATCTTGTGGGAGCTTGCTACATTGC

upper sequence: LOC_Os02g32610.3 (Oryza sativa), 3'ss of exon 13
lower sequence: Vv08s0007g03910.t01 (Vitis vinifera), 3'ss of exon 12
----------gtaagttc-atattaccgttacttttatttgttgattttttttcagctaaatcgtgct------agtaagtgctttcgatgtaatattctct-agCCTGAGTGGATGGCACCAGAAGTTATACGAGATGAGCCATCAAATGAGAAGTCTGATGTCTACAGCTTTGGTGTTATCCTATGGGAGCTCATGACATTGC
           |||| |  |||  | |   |  |   ||  |||  |||   | |  |  ||| |  |      | ||     |||  || |   |||   | |||||||||||||||||||||||||| | || |||||| |||||||||| ||||| ||  | || ||||||||| | ||| | ||||| ||    |||||||
gtaagttttactaagctagatagcaacacaatctcagttccttgtatttaggtgatatggatcattttgtcacaaatataaaatttacatttttcatttcatcagCCTGAGTGGATGGCACCAGAAGTTCTTCGGGATGAGGCATCAAATGAAAAGTCAGACATATATAGCTTTGGTATAATCTTGTGGGAACTTGCAACATTGC

upper sequence: LOC_Os02g32610.3 (Oryza sativa), 3'ss of exon 13
lower sequence: Vv13s0074g00430.t01 (Vitis vinifera), 3'ss of exon 12
------------------------gtaagttcatattacc-gtta-----cttttatttgttgattttttttcagctaaatcgtgctagtaagtgctttcgatgtaatattctctagCCTGAGTGGATGGCACCAGAAGTTATACGAGATGAGCCATCAAATGAGAAGTCTGATGTCTACAGCTTTGGTGTTATCCTATGGGAGCTCATGACATTGC
                        || | |  |||| | | |||      || |||   |           |    | |||  |||||  |  | | || ||| |  | ||   ||||||||||||||||||||||||||| | || ||||||||||||||||| ||||| ||||| |||||||||||||| ||| | ||||| ||  |||| ||||
gtaagttctattcaaaactgaaaagttaatgtatataatctgttggcatgctattaaaagcgagcaagggatggcttcaat--tgctaagacttacctttgattt--tttttgttagCCTGAGTGGATGGCACCAGAAGTTCTCCGTGATGAGCCATCAAATGAAAAGTCAGATGTTTACAGCTTTGGTGTAATCTTGTGGGAACTTGTGACCTTGC

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|29680443|gb|CB676718.1|CB676718
EST:     CCAGATTGAAGGCAAACACATTTTTGTCTTCCAAGACTGCAGCAGGGACT                         CCTGAGTGGATGGCACCAGAAGTTATACGAGATGAGCCATCAAATGAGAAG
genomic: CCAGATTGAAGGCAAACACATTTTTGTCTTCCAAGACTGCAGCAGGGACTgtaagttcat ... tattctctagCCTGAGTGGATGGCACCAGAAGTTATACGAGATGAGCCATCAAATGAGAAG
EST: gi|29660723|gb|CB656998.1|CB656998
EST:     CCAGATTGAAGGCAAACACATTTTTGTCTTCCAAGACTGCAGCAGGGACT                         CCTGAGTGGATGGCACCAGAAGTTATACGAGATGAGCCATCAAATGAGAAG
genomic: CCAGATTGAAGGCAAACACATTTTTGTCTTCCAAGACTGCAGCAGGGACTgtaagttcat ... tattctctagCCTGAGTGGATGGCACCAGAAGTTATACGAGATGAGCCATCAAATGAGAAG
EST: gi|29639477|gb|CB644486.1|CB644486
EST:     CCAGATTGAAGGCAAACACATTTTTGTCTTCCAAGACTGCAGCAGGGACT                         CCTGAGTGGATGGCACCAGAAGTTATACGAGATGAGCCATCAAATGAGAAG
genomic: CCAGATTGAAGGCAAACACATTTTTGTCTTCCAAGACTGCAGCAGGGACTgtaagttcat ... tattctctagCCTGAGTGGATGGCACCAGAAGTTATACGAGATGAGCCATCAAATGAGAAG
EST: gi|29625152|gb|CB630163.1|CB630163
EST:     CCAGATTGAAGGCAAACACATTTTTGTCTTCCAAGACTGCAGCAGGGACT                         CCTGAGTGGATGGCACCAGAAGTTATACGAGATGAGCCATCAAATGAGAAG
genomic: CCAGATTGAAGGCAAACACATTTTTGTCTTCCAAGACTGCAGCAGGGACTgtaagttcat ... tattctctagCCTGAGTGGATGGCACCAGAAGTTATACGAGATGAGCCATCAAATGAGAAG
EST: gi|29678550|gb|CB674825.1|CB674825
EST:     CCAGATTGAAGGCAAACACATTTTTGTCTTCCAAGACTGCAGCAGGGACT                         CCTGAGTGGATGGCACCAGAAGTTATACGAGATGAGCCATCAAATGAGAAG
genomic: CCAGATTGAAGGCAAACACATTTTTGTCTTCCAAGACTGCAGCAGGGACTgtaagttcat ... tattctctagCCTGAGTGGATGGCACCAGAAGTTATACGAGATGAGCCATCAAATGAGAAG
EST: gi|88585426|gb|CI703056.1|CI703056
EST:     CCAGATTGAAGGCAAACACATCTTTGTCTTCCAAGACTGCAGCAGGGACT                         CCTGAGTGGATGGCACCAGAAGTTATACGAGATGAG
genomic: CCAGATTGAAGGCAAACACATTTTTGTCTTCCAAGACTGCAGCAGGGACTgtaagttcat ... tattctctagCCTGAGTGGATGGCACCAGAAGTTATACGAGATGAG
EST: gi|29662085|gb|CB658360.1|CB658360
EST:     CCAGATTGAAGGCAAACACATTTTTGTCTTCCAAGACTGCAGCAGGGACT                         CCTGAGTGGATGGCACCAGAAGTTATACGAGATGAGCCATCAAATGAGAAG
genomic: CCAGATTGAAGGCAAACACATTTTTGTCTTCCAAGACTGCAGCAGGGACTgtaagttcat ... tattctctagCCTGAGTGGATGGCACCAGAAGTTATACGAGATGAGCCATCAAATGAGAAG
EST: gi|29680716|gb|CB676991.1|CB676991
EST:     CCAGATTGAAGGCAAACACATTTTTGTCTTCCAAGACTGCAGCAGGGACT                         CCTGAGTGGATGGCACCAGAAGTTATACGAGATGAGCCATCAAATGAGAAG
genomic: CCAGATTGAAGGCAAACACATTTTTGTCTTCCAAGACTGCAGCAGGGACTgtaagttcat ... tattctctagCCTGAGTGGATGGCACCAGAAGTTATACGAGATGAGCCATCAAATGAGAAG
EST: gi|29665413|gb|CB661688.1|CB661688
EST:     CCAGATTGAAGGCAAACACATTTTTGTCTTCCAAGACTGCAGCAGGGACT                         CCTGAGTGGATGGCTCCAGAAGTTATACGAGATGAGCCATCAAATGAGAAG
genomic: CCAGATTGAAGGCAAACACATTTTTGTCTTCCAAGACTGCAGCAGGGACTgtaagttcat ... tattctctagCCTGAGTGGATGGCACCAGAAGTTATACGAGATGAGCCATCAAATGAGAAG
EST: gi|29664340|gb|CB660615.1|CB660615
EST:     CCAGATTGAAGGCAAACACATTTTTGTCTTCCAAGACTGCAGCAGGGACT                         CCTGAGTGGATGGCACCAGAAGTTATACGAGATGAGCCATCAAATGAGAAG
genomic: CCAGATTGAAGGCAAACACATTTTTGTCTTCCAAGACTGCAGCAGGGACTgtaagttcat ... tattctctagCCTGAGTGGATGGCACCAGAAGTTATACGAGATGAGCCATCAAATGAGAAG
EST: gi|33675051|gb|CF303290.1|CF303290
EST:     CCAGATTGAAGGCAAACACATTTTTGTCTTCCAAGACTGCAGCAGGGACT                         CCTGAGTGGATGGCACCAGAAGTTATACGAGATGAGCCATCAAATGAGAAG
genomic: CCAGATTGAAGGCAAACACATTTTTGTCTTCCAAGACTGCAGCAGGGACTgtaagttcat ... tattctctagCCTGAGTGGATGGCACCAGAAGTTATACGAGATGAGCCATCAAATGAGAAG
EST: gi|29630303|gb|CB635312.1|CB635312
EST:     CCAGATTGAAGGCAAACACATTTTTGTCTTCCAAGACTGCAGCAGGGACT                         CCTGAGTGGATGGCACCAGAAGTTATACGAGATGAGCCATCAAATGAGAAG
genomic: CCAGATTGAAGGCAAACACATTTTTGTCTTCCAAGACTGCAGCAGGGACTgtaagttcat ... tattctctagCCTGAGTGGATGGCACCAGAAGTTATACGAGATGAGCCATCAAATGAGAAG
EST: gi|29675290|gb|CB671565.1|CB671565
EST:     CCAGATTGAAGGCAAACACATTTTTGTCTTCCAAGACTGCAGCAGGGACT                         CCTGAGTGGATGGCACCAGAAGTTATACGAGATGAGCCATCAAATGAGAAG
genomic: CCAGATTGAAGGCAAACACATTTTTGTCTTCCAAGACTGCAGCAGGGACTgtaagttcat ... tattctctagCCTGAGTGGATGGCACCAGAAGTTATACGAGATGAGCCATCAAATGAGAAG
EST: gi|29672353|gb|CB668628.1|CB668628
EST:     CCAGATTGAAGGCAAACACATTTTTGTCTTCCAAGACTGCAGCAGGGACT                         CCTGAGTGGATGGCACCAGAAGTTATACGAGATGAGCCATCAAATGAGAAG
genomic: CCAGATTGAAGGCAAACACATTTTTGTCTTCCAAGACTGCAGCAGGGACTgtaagttcat ... tattctctagCCTGAGTGGATGGCACCAGAAGTTATACGAGATGAGCCATCAAATGAGAAG
EST: gi|29628356|gb|CB633367.1|CB633367
EST:     CCAGATTGAAGGCAAACACATTTTTGTCTTCCAAGACTGCAGCAGGGACT                         CCTGAGTGGATGGCACCAGAAGTTATACGAGATGAGCCATCAAATGAGAAG
genomic: CCAGATTGAAGGCAAACACATTTTTGTCTTCCAAGACTGCAGCAGGGACTgtaagttcat ... tattctctagCCTGAGTGGATGGCACCAGAAGTTATACGAGATGAGCCATCAAATGAGAAG
EST: gi|87015028|gb|CI273426.1|CI273426
EST:     TCCAAGACTGCAGCA-GGACT                         CCTGAGTGGATGGCACCAGAAGTTATACGAGATGAGCCATCAAATGAGAAG
genomic: TCCAAGACTGCAGCAGGGACTgtaagttcat ... tattctctagCCTGAGTGGATGGCACCAGAAGTTATACGAGATGAGCCATCAAATGAGAAG
EST: gi|58595275|gb|CF993583.1|CF993583
EST:     CCAGATTGAAGGCAAACACATTTTTGTCTTCCAAGACTGCAGCAGGGACT                         CCTGAGTGGATGGCACCAGAAGTTATACGAGATGAGCCATCAAATGAGAAG
genomic: CCAGATTGAAGGCAAACACATTTTTGTCTTCCAAGACTGCAGCAGGGACTgtaagttcat ... tattctctagCCTGAGTGGATGGCACCAGAAGTTATACGAGATGAGCCATCAAATGAGAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gattttttttcagctaaatcgtgctagtaagtgctttcgatgtaatattctctagCCTGAGTGGATGGCACCAGAAGTTATACGAGATGAGCCATCAAATGAGAAGTCTGATGTCTACAGCTTTGGTGTTATCCTATGGGAGCTCATGACATTGC
           agctaaa  putative branch site (score: 3)
                                             tattctct  putative PPT
                                       atgtaatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagttcatattaccgttacttttatttgttgattttttttcagctaaatcgtgctagtaagtgctttcgatgtaatattctctagCCTGAGTGGATGGCACCAGAAGTTATACGAGATGAGCCATCAAATGAGAAGTCTGATGTCTACAGCTTTGGTGTTATCCTATGGGAGCTCATGACATTGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA