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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttattttcctttgcatatcctctcatttgagactttggtgagaaataggcatatgcatatgtttattctgatgtggcttgttttttttcatggatgtagACAATGGCGTGGATACTTGACGAATACTCAAAGTTTCATGGTTATTCACCTGCTGTGGTGACTGGAAAACCTGTT

Basic information

species Oryza sativa
transcript LOC_Os03g58040.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g58040.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G178415_T02 (Zea mays), 3'ss of exon 4
gttattttcctttgcatatcctctcatttgagactttggtgagaaataggcat----atgcatatgtttattctgatgtggcttgtttttttt----catggatgtagACAATGGCGTGGATACTTGACGAATACTCAAAGTTTCATGGTTATTCACCTGCTGTGGTGACTGGAAAACCTGTT
|||||||||||||   |||| | ||||    ||||||  |||||| |||  ||    |   ||||||||||||| || |||| | |||| |||     ||||||| |||||||||| |||||||||||||||||||||||||| |||||||| ||||||||||| ||||| ||||| ||||| 
gttattttcctttatgtatcatttcatgaaggactttcatgagaattagttatcaataaatatatgtttattctaatatggcctattttgtttgctttatggatgcagACAATGGCATGGATACTTGACGAATACTCAAAGTTCCATGGTTACTCACCTGCTGTTGTGACAGGAAAGCCTGTG

upper sequence: LOC_Os03g58040.2 (Oryza sativa), 3'ss of exon 3
lower sequence: AT3G03910.1 (Arabidopsis thaliana), 3'ss of exon 3
gttattttcctttgcatatcctctcatttgagactttggtgagaaataggcatatgcatatgtttattctgatgtggcttgttttttttcatggatgtagACAATGGCGTGGATACTTGACGAATACTCAAAGTTTCATGGTTATTCACCTGCTGTGGTGACTGGAAAACCTGTT
          |||  | | | |    ||  || |||      | | |   | | |         | ||||  | ||   | |  |  |  |    |  |||||||||| ||||| ||||| ||||||||||| || |||||  |||| |||||||| || |||||||||||  ||
---------gtttcgaaaacatgatcttgaagtcttcatcttgtattttacgtgt---------tgttcttgtctgaaatatagtgatgaaaattttcagACAATGGCTTGGATTCTTGATGAATACTCAAAATTCCATGGACATTCTCCTGCTGTTGTCACTGGAAAACCCATT

upper sequence: LOC_Os03g58040.2 (Oryza sativa), 3'ss of exon 3
lower sequence: AT5G18170.1 (Arabidopsis thaliana), 3'ss of exon 3
gttattttcctttgcatatcctctcatttgagactttggtgagaaataggcatatgcatatgtttattctgatgtggcttgttttttttcatgga---tgtagACAATGGCGTGGATACTTGACGAATACTCAAAGTTTCATGGTTATTCACCTGCTGTGGTGACTGGAAAACCTGTT
            | | ||  ||||| ||    || ||    | |  |     | |   | | |  |  |   | |    | |||   ||  ||||   || |||||||||| ||||| ||||| |||||||| ||||||||||| || || ||||| || ||||||||||||||  ||
-----------gttcttaaactctc-ttcagaacgtttccaaaatgttc-tgtgtttttttttgaaaccatctttcaactttttcccttggtggaatttgcagACAATGGCTTGGATTCTTGATGAATACTCTAAGTTTCATGGATACTCGCCTGCAGTTGTGACTGGAAAACCCATT

upper sequence: LOC_Os03g58040.2 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv08s0007g07400.t01 (Vitis vinifera), 3'ss of exon 5
-gttattttcctttgcatatcctctcatttgagactttggtgagaaataggcatatgcatatgtttattctgatgtggcttgttttttt-tcatggatgtagACAATGGCGTGGATACTTGACGAATACTCAAAGTTTCATGGTTATTCACCTGCTGTGGTGACTGGAAAACCTGTT
 |              |  |  |   || |  |  ||   ||   ||     || || |     |    ||  |||  || ||| || | |  | ||   |||| ||||| |||||||| || || ||||| || |||||||| || ||||||||||||||||||||||| ||| ||
agaaggaaaaaaaaaaaagttatggtatctttggtttgaatgttcaacca-tatttgaactaactgtggcttttgtttctggttcttgtgttgttga-acagACCATGGCATGGATACTAGATGAGTACTCGAAATTTCATGGCTACTCACCTGCTGTGGTGACTGGAAAGCCTATT

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|29674431|gb|CB670706.1|CB670706
EST:     TTGGCATTCATACAGATGTTCCAGCTCCAGATATGGGAACCAACTCTCAG                         ACAATGGCGTGGATACTTGACGAATACTCAAAGTTTCATGGTTATTCACCT
genomic: TTGGCATTCATACAGATGTTCCAGCTCCAGATATGGGAACCAACTCTCAGgttattttcc ... atggatgtagACAATGGCGTGGATACTTGACGAATACTCAAAGTTTCATGGTTATTCACCT
EST: gi|88428743|gb|CI599459.1|CI599459
EST:     TTGGCATTCATACAGATGTTCCAGCTCCAGATATGGGAACCAACTCTCAG                         ACAATGGCGTGGATACTTGACGAATACTCAAAGTTT-ATGGTTATTCAC-T
genomic: TTGGCATTCATACAGATGTTCCAGCTCCAGATATGGGAACCAACTCTCAGgttattttcc ... atggatgtagACAATGGCGTGGATACTTGACGAATACTCAAAGTTTCATGGTTATTCACCT
EST: gi|29673988|gb|CB670263.1|CB670263
EST:     TTGGCATTCATACAGATGTTCCAGCTCCAGATATGGGAACCAACTCTCAG                         ACAATGGCGTGGATACTTGACGAATACTCAAAGTTTCATGGTTATTCACCT
genomic: TTGGCATTCATACAGATGTTCCAGCTCCAGATATGGGAACCAACTCTCAGgttattttcc ... atggatgtagACAATGGCGTGGATACTTGACGAATACTCAAAGTTTCATGGTTATTCACCT
EST: gi|163928511|gb|EG711396.1|EG711396
EST:     TTGGCATTCATACAGATGTTCCAGCTCCAGATATGGGAACCAACTCTCAG                         ACAATGGCGTGGATACTTGACGAATACTCAAAGTTTCATGGTTATTCACCT
genomic: TTGGCATTCATACAGATGTTCCAGCTCCAGATATGGGAACCAACTCTCAGgttattttcc ... atggatgtagACAATGGCGTGGATACTTGACGAATACTCAAAGTTTCATGGTTATTCACCT
EST: gi|29679310|gb|CB675585.1|CB675585
EST:     TTGGCATTCATACAGATGTTCCAGCTCCAGATATGGGAACCAACTCTCAG                         ACAATGGCGTGGATACTTGACGAATACTCAAAGTTTCATGGTTATTCACCT
genomic: TTGGCATTCATACAGATGTTCCAGCTCCAGATATGGGAACCAACTCTCAGgttattttcc ... atggatgtagACAATGGCGTGGATACTTGACGAATACTCAAAGTTTCATGGTTATTCACCT
EST: gi|88314120|gb|CI602452.1|CI602452
EST:     CATTCATACAGATGTTCCAGCTCCAGATATGGGAACCAACTCTCAG                         ACAATGGCGTGGATACTTGACGAATACTCAAAGTTTCATGGTTATTCACCT
genomic: CATTCATACAGATGTTCCAGCTCCAGATATGGGAACCAACTCTCAGgttattttcc ... atggatgtagACAATGGCGTGGATACTTGACGAATACTCAAAGTTTCATGGTTATTCACCT
EST: gi|33675066|gb|CF303305.1|CF303305
EST:     TTGGCATTCATACAGATGTTCCAGCTCCAGATATGGGAACCAACTCTCAG                         ACAATGGCGTGGATACTTGACGAATACTCAAAGTTTCATGGTTATTCACCT
genomic: TTGGCATTCATACAGATGTTCCAGCTCCAGATATGGGAACCAACTCTCAGgttattttcc ... atggatgtagACAATGGCGTGGATACTTGACGAATACTCAAAGTTTCATGGTTATTCACCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ataggcatatgcatatgtttattctgatgtggcttgttttttttcatggatgtagACAATGGCGTGGATACTTGACGAATACTCAAAGTTTCATGGTTATTCACCTGCTGTGGTGACTGGAAAACCTGTT
                     ttctgat  putative branch site (score: 3)
                                cttgttttttttcat  putative PPT
                                 ttgttttttttcat  TA-rich tract