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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tagcttcaattgaacacatatagtgaaataaatagaagtaatgtcggtgctcatttgtattgtttttctttattgttctgatgaaatcctgtttgaatagGGGTATTTATCCACCAGCTGAGGAGTACATTATCCATGCTGAGAGGCCCAATGAGACTCTGGTGGAAGCTTTCAAAAGTATGCATATACATCTAGAGGAG

Basic information

species Oryza sativa
transcript LOC_Os02g11840.2
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g11840.1 (Oryza sativa), 3'ss of exon 13
lower sequence: GRMZM2G124886_T04 (Zea mays), 3'ss of exon 22
------------------------------------------------------------tagcttcaattg--aacac-atatagtgaaataaat-agaagtaatgtcggtgctcatttgtattg------tttttctttattgtt-ctgatgaaatcct--gtttgaatagGGGTATTTATCCACCAGCTGAGGAGTACATTATCCATGCTGAGAGGCCCAATGAGACTCTGGTGGAAGCTTTCAAAAGTATGCATATACATCTAGAGGAG
                                                            | || |||  ||  |   | ||||  |     |||| |||||| |||||  | ||||| | | ||       || || ||||||||  || |  |  |  |  |||||||||||| ||| |||||||| |||||||||||||| || |||||||| ||| | ||||||| | | ||||||||||| ||||  |||||| ||||   ||||  |
gtatttgttccttttattttcatatatattgtatccctttgcattgtctccgattacctcttgcatcagatggcagtgctatattctcttgaaaatcagaagtgatgtcaatactcatattttttcaatcttttattttttattgtcactcacaattttttttgtttgaatagGGTTATCTATCCACCGGCTGAGGAGTACATGATTCATGCTGAAAGGTCAAATGAGAATTTAGTGGAAGCTTTTAAAAACATGCATGTACAGGAAGAGATG

upper sequence: LOC_Os02g11840.1 (Oryza sativa), 3'ss of exon 13
lower sequence: GRMZM2G141587_T03 (Zea mays), 3'ss of exon 22
------------------------------------------------------------------------------tagcttcaattgaacacatatagtgaaataaatagaagtaatgtcggtgctcatttgt---------attgtttttctttattgttct------gatgaaatcctgtttgaatagGGGTATTTATCCACCAGCTGAGGAGTACATTATCCATGCTGAGAGGCCCAATGAGACTCTGGTGGAAGCTTTCAAAAGTATGCATATACATCTAGAGGAG
                                                                                |||| |||||    ||| |  |||||  |   |||||  ||||  |  |||| | |         ||  |  |  ||| ||| |         | ||||    ||||||| ||| |||| |||||| | || ||||||||||| || |||||||| ||| | ||||||| | | ||||||||||| |||| ||||||| |||||  ||||  |
gtttttttgttctttttgtcttcatctataactgtatccttttgtattgtctctgattacctcttgcatcagatgatggcgctttaattgcgttcatctgttgaaa--atcggaagtggtgtcaatattcatatttttccaaactatcatcatcttttgttgatactcacaaaaagaaaattcgtttgaaaagGAGTATCTATCCATCGGCCGAGGAGTACATGATTCATGCTGAAAGGTCAAATGAGAGTTTAGTGGAAGCTTTTAAAAATATGCATGTACATGAAGAGATG
















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|29644063|gb|CB649070.1|CB649070
EST:     GAAGACTGGCAAATTGCTCTCAATGTAGAAGCTAATGTCGCGCCCAAAAG                         GGGTATTTATCCACCAGCTGAGGAGTACATTATCCATGCTGAGAGGCCCAA
genomic: GAAGACTGGCAAATTGCTCTCAATGTAGAAGCTAATGTCGCGCCCAAAAGgtatgttcgt ... gtttgaatagGGGTATTTATCCACCAGCTGAGGAGTACATTATCCATGCTGAGAGGCCCAA
EST: gi|87021165|gb|CI271972.1|CI271972
EST:     GAAGACTGGCAAATTGCTCTCAATGTAGAAGCTAATGTCGCGCCCAAAAG                         GGGTATTTATCCACCAGCTGAGGAGTACATTATCCATGCTGAGAGGCCCAA
genomic: GAAGACTGGCAAATTGCTCTCAATGTAGAAGCTAATGTCGCGCCCAAAAGgtatgttcgt ... gtttgaatagGGGTATTTATCCACCAGCTGAGGAGTACATTATCCATGCTGAGAGGCCCAA
EST: gi|86481559|gb|CI124192.1|CI124192
EST:     GAAGACTGGCAAATGGCTCTCAATGTAGAAGCTAATGTCGCGCCCAAAAG                         GGGTATTTATCCACCAGCTGAGGAGTACATTATCCATGCTGAGAGGCCCAA
genomic: GAAGACTGGCAAATTGCTCTCAATGTAGAAGCTAATGTCGCGCCCAAAAGgtatgttcgt ... gtttgaatagGGGTATTTATCCACCAGCTGAGGAGTACATTATCCATGCTGAGAGGCCCAA
EST: gi|86478917|gb|CI121550.1|CI121550
EST:     AAGACTGGCAAATTGCTCTCAATGTAGAAGCTAATGTCGCGCCCAAAAG                         GGGTATTTATCCACCAGCTGAGGAGTACATTATCCATGCTGAGAGGCCCAA
genomic: AAGACTGGCAAATTGCTCTCAATGTAGAAGCTAATGTCGCGCCCAAAAGgtatgttcgt ... gtttgaatagGGGTATTTATCCACCAGCTGAGGAGTACATTATCCATGCTGAGAGGCCCAA
EST: gi|2797452|gb|AA750746.1|AA750746
EST:     GAAGACTGGCAAATTGCTCTCAATGTAGAAGCTAATGTCGCGCCCAAAAG                         GGGTATTTATCCACCAGCTGAGGAGTACATTATCCATGCTGAGAGGCCCAA
genomic: GAAGACTGGCAAATTGCTCTCAATGTAGAAGCTAATGTCGCGCCCAAAAGgtatgttcgt ... gtttgaatagGGGTATTTATCCACCAGCTGAGGAGTACATTATCCATGCTGAGAGGCCCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggtgctcatttgtattgtttttctttattgttctgatgaaatcctgtttgaatagGGGTATTTATCCACCAGCTGAGGAGTACATTATCCATGCTGAGAGGCCCAATGAGACTCTGGTGGAAGCTTTCAAAAGTATGCATATACATCTAGAGGAG
                              ttctgat  putative branch site (score: 3)
                                         tcctgttt  putative PPT
       atttgtattgtttttc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tagcttcaattgaacacatatagtgaaataaatagaagtaatgtcggtgctcatttgtattgtttttctttattgttctgatgaaatcctgtttgaatagGGGTATTTATCCACCAGCTGAGGAGTACATTATCCATGCTGAGAGGCCCAATGAGACTCTGGTGGAAGCTTTCAAAAGTATGCATATACATCTAGAGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
-agcttca
- - - - - -gaacaca
- - - - - - - - - - - - -aaataaa
- - - - - - - - - - - - - - - - - - - - - - -ggtgctc
- - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtattg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gatgaaa