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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gaaaatgcttgtaacaaaaacaaacttagttatacatcgttgtgtttttcctttaatttggcatattatgttgttaagtcctcaattttgcttttgacagGTGAGATGTGTAGCATCGGACCTGGATCGGAAAAGAATCTGCAGCGGTGGTCGCAACGGACTTCTTCGGCTTTGGGATGCCACCACGAGTATCTAAGTTA

Basic information

species Oryza sativa
transcript LOC_Os01g39380.1
intron # 31
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g39380.1 (Oryza sativa), 3'ss of exon 31
lower sequence: GRMZM2G074466_T01 (Zea mays), 3'ss of exon 11
gaaaatgcttgtaacaaaaacaaacttagttatacatcgttgtgtttttcctttaatttggcatattat-gttgtt--aagtcctcaattttgcttttgacagGTGAGATGTGTAGCATCGGACCTGGATCGGAAAAGAATCTGCAGCGGTGGTCGCAACGGACTTCTTCGGCTTTGGGATGCCACCACGAGTATCTAAGTTA
      |  ||     |          |||  |   |  || |||| ||    | || |     ||||| | || |  || |  |     || | | |  |||||||||||| ||||||| ||||||||| |||||||||| || || ||||||||||||||||| || |||||||||||||| || || || ||||| |   
--gggcgactgctcttatgctctgaacagtcgtgt-tttttttgttcttttcgtgatattctgaattatcgatgctcaaaatattttgaattacatgttgcagGTGAGATGTATAGCATCTGACCTGGATAGGAAAAGAATATGTAGTGGTGGTCGCAACGGACTCCTGCGGCTTTGGGATGCAACTACAAGCATCTAGGACT

upper sequence: LOC_Os01g39380.1 (Oryza sativa), 3'ss of exon 31
lower sequence: GLYMA05G35210.1 (Glycine max), 3'ss of exon 14
gaaaatgcttgtaacaaaaacaaacttagttatacatcgttgtgtttttcctttaat--ttggcatattatgttgttaagtcctcaattttgcttttgacagGTGAGATGTGTAGCATCGGACCTGGATCGGAAAAGAATCTGCAGCGGTGGTCGCAACGGACTTCTTCGGCTTTGGGATGCCACCACGAGTATCTAAGTTA
|   || | ||     | ||     ||   |     | ||| |||   |   ||| |  |||   |  |  |||| |     |   ||| ||   |   ||||| |||||||| || || ||| ||||  ||||||| || ||||||||||||||||| || |||||  |||| |||||||| || |  | ||| | || | 
gtgcatacatggctggagaatgttattttatgcctgttgttatgtccatttgttattggttgttttcctgggttgattttggccgtattatgacatc--cagGTTAGATGTGTTGCTTCAGACTTGGAAAGGAAAAGGATATGCAGCGGTGGTCGCAATGGGCTTCTAAGGCTGTGGGATGCAACTATTAATATTTGAGCTT
















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|86504094|gb|CI146727.1|CI146727
EST:     AAGTTGCAGGATGGCAGCTTTACAGAACTCCCCAGAAAACTGCTGCTATG                         GTGAGATGTGTAGCATCGGACCTGGATCGGAAAAGAATCTGCAGCGGTGGT
genomic: AAGTTGCAGGATGGCAGCTTTACAGAACTCCCCAGAAAACTGCTGCTATGgtatgaaact ... cttttgacagGTGAGATGTGTAGCATCGGACCTGGATCGGAAAAGAATCTGCAGCGGTGGT
EST: gi|86893144|gb|CI333425.1|CI333425
EST:     AAGTTGCAGGATGGCAGCTTTACAGAACTCCCCAGAAAACTGCTGCTATG                         GTGAGATGTGTAGCATCGGACCTGGATCGGAAAAGAATCTGCAGCGGTGGT
genomic: AAGTTGCAGGATGGCAGCTTTACAGAACTCCCCAGAAAACTGCTGCTATGgtatgaaact ... cttttgacagGTGAGATGTGTAGCATCGGACCTGGATCGGAAAAGAATCTGCAGCGGTGGT
EST: gi|29628945|gb|CB633956.1|CB633956
EST:     AAGTTGCAGGATGGCAGCTTTACAGAACTCCCCAGAAAACTGCTGCTATG                         GTGAGATGTGTAGCATCGGACCTGGATCGGAAAAGAATTTGCAGCGGTGGT
genomic: AAGTTGCAGGATGGCAGCTTTACAGAACTCCCCAGAAAACTGCTGCTATGgtatgaaact ... cttttgacagGTGAGATGTGTAGCATCGGACCTGGATCGGAAAAGAATCTGCAGCGGTGGT
EST: gi|29641895|gb|CB646902.1|CB646902
EST:     AAGTTGCAGGATGGCAGCTTTACAGAACTCCCCAGAAAACTGCTGCTATG                         GTGAGATGTGTAGCATCGGACCTGGATCGGAAAAGAATCTGCAGCGGTGGT
genomic: AAGTTGCAGGATGGCAGCTTTACAGAACTCCCCAGAAAACTGCTGCTATGgtatgaaact ... cttttgacagGTGAGATGTGTAGCATCGGACCTGGATCGGAAAAGAATCTGCAGCGGTGGT
EST: gi|86884600|gb|CI312979.1|CI312979
EST:     AAGTTGCAGGATGCCAGCTTTACAGAACTCCCCAAAAAACTGCTGCTATG                         TTGAGATGTTTAGCATCGGACCTGGATCGGAAAAGAATCTGCAGCGGTGGT
genomic: AAGTTGCAGGATGGCAGCTTTACAGAACTCCCCAGAAAACTGCTGCTATGgtatgaaact ... cttttgacagGTGAGATGTGTAGCATCGGACCTGGATCGGAAAAGAATCTGCAGCGGTGGT
EST: gi|86257231|gb|CI004049.1|CI004049
EST:     AAGTTGCAGGATGGCAGCTTTACAGAACTCCCCAGAAAACTGCTGCTATG                         GTGAGATGTGTAGCATCGGACCTGGATCGGAAAAGAATCTGCAGCGGTGGT
genomic: AAGTTGCAGGATGGCAGCTTTACAGAACTCCCCAGAAAACTGCTGCTATGgtatgaaact ... cttttgacagGTGAGATGTGTAGCATCGGACCTGGATCGGAAAAGAATCTGCAGCGGTGGT
EST: gi|29639658|gb|CB644667.1|CB644667
EST:     AAGTTGCAGGATGGCAGCTTTACAGAACTCCCCAGAAAACTGCTGCTATG                         GTGAGATGTGTAGCATCGGACCTGGATCGGAAAAGAATCTGCAGCGGTGGT
genomic: AAGTTGCAGGATGGCAGCTTTACAGAACTCCCCAGAAAACTGCTGCTATGgtatgaaact ... cttttgacagGTGAGATGTGTAGCATCGGACCTGGATCGGAAAAGAATCTGCAGCGGTGGT
EST: gi|88523777|gb|CI451629.1|CI451629
EST:     AAGTTGCAGGATGGCAGCTTTACAGAACTCCCCAGAAAACTGCTGCTATG                         GTGAGATGTGTAGCATCGGACCTGGATCGGAAAAGAATCTGCAGCGGTGGT
genomic: AAGTTGCAGGATGGCAGCTTTACAGAACTCCCCAGAAAACTGCTGCTATGgtatgaaact ... cttttgacagGTGAGATGTGTAGCATCGGACCTGGATCGGAAAAGAATCTGCAGCGGTGGT
EST: gi|58694575|gb|CK083262.1|CK083262
EST:     AAGTTGCAGGATGGCAGCTTTACAGAACTCCCCAGAAAACTGCTGCTATG                         GTGAGATGTGTAGCATCGGACCTGGATCGGAAAAGAATCTGCAGCGGTGGT
genomic: AAGTTGCAGGATGGCAGCTTTACAGAACTCCCCAGAAAACTGCTGCTATGgtatgaaact ... cttttgacagGTGAGATGTGTAGCATCGGACCTGGATCGGAAAAGAATCTGCAGCGGTGGT
EST: gi|88323639|gb|CI556270.1|CI556270
EST:     AAGTTGCAGGATGGCAGGTTTACAGAACTCCCCAGAAAACTGCTGGTATG                         GTGAAATTTGTAGCATCGGACCTGGATCGGAAAAGAATCTGCAGCGGTGGT
genomic: AAGTTGCAGGATGGCAGCTTTACAGAACTCCCCAGAAAACTGCTGCTATGgtatgaaact ... cttttgacagGTGAGATGTGTAGCATCGGACCTGGATCGGAAAAGAATCTGCAGCGGTGGT
EST: gi|88537567|gb|CI466525.1|CI466525
EST:     AAGTTGCAGGATGGCAGCTTTACAGAACTCCCCAGAAAACTGCTGCTATG                         GTGAGATGTGTAGCATCGGACCTGGATCGGAAAAGAATGTGCAGCGGTGGT
genomic: AAGTTGCAGGATGGCAGCTTTACAGAACTCCCCAGAAAACTGCTGCTATGgtatgaaact ... cttttgacagGTGAGATGTGTAGCATCGGACCTGGATCGGAAAAGAATCTGCAGCGGTGGT
EST: gi|27547319|gb|CA765549.2|CA765549
EST:     AAGNTGCAGGATGGCAGCTTTACAGAACTNCCCANAAAACTGCTGCTATG                         GTGAGATGTGTAGCATCGGACCTGGATCGGAAAANAATCTGCAGCGGNGGT
genomic: AAGTTGCAGGATGGCAGCTTTACAGAACTCCCCAGAAAACTGCTGCTATGgtatgaaact ... cttttgacagGTGAGATGTGTAGCATCGGACCTGGATCGGAAAAGAATCTGCAGCGGTGGT
EST: gi|88535510|gb|CI464314.1|CI464314
EST:     AAGTTGCAGGATGGCAGCTTTACAGAACTCCCCAGAAAACTGCTGCTATG                         GTGAGATGTGTAGCATCGGACCTGGATCGGAAAAGAATCTGCAGCGGTGGT
genomic: AAGTTGCAGGATGGCAGCTTTACAGAACTCCCCAGAAAACTGCTGCTATGgtatgaaact ... cttttgacagGTGAGATGTGTAGCATCGGACCTGGATCGGAAAAGAATCTGCAGCGGTGGT
EST: gi|22304904|gb|BQ906126.1|BQ906126
EST:     AAGTTGCAGGATGGCAGCTTTACAGAACTCCCCAGAAAACTGCTGCTATG                         GTGAGATGTGTAGCATCGGACCTGGATCGGAAAAGAATCTGCAGCGGTGGT
genomic: AAGTTGCAGGATGGCAGCTTTACAGAACTCCCCAGAAAACTGCTGCTATGgtatgaaact ... cttttgacagGTGAGATGTGTAGCATCGGACCTGGATCGGAAAAGAATCTGCAGCGGTGGT
EST: gi|8324548|gb|AU091694.1|AU091694
EST:     AAGTTGCAGGATGGCAGCTTTACAGAACTCCCCAGAAAACTGCTGCTATG                         GTGAGATGTGTAGCATCGGACCTGGATCGGAAAAGAATCTGCAGCGGTGGT
genomic: AAGTTGCAGGATGGCAGCTTTACAGAACTCCCCAGAAAACTGCTGCTATGgtatgaaact ... cttttgacagGTGAGATGTGTAGCATCGGACCTGGATCGGAAAAGAATCTGCAGCGGTGGT
EST: gi|88522363|gb|CI450117.1|CI450117
EST:     AGTNTGCAGGATGGCAGCGTTACAGAACTCCCCAGAAAACTGCTGCTATG                         GTGAGATGTGTAGCATCGGACCTGGATCGGAAAAGAATGTGGCAGCGGTGG
genomic: AGT-TGCAGGATGGCAGCTTTACAGAACTCCCCAGAAAACTGCTGCTATGgtatgaaact ... cttttgacagGTGAGATGTGTAGCATCGGACCTGGATCGGAAAAGAATCT-GCAGCGGTGG
EST: gi|88845811|gb|CI084541.1|CI084541
EST:     AAGTTGCAGGATGGCAGCTTTACAGAACTCCCCAGAAAACTGCTGCTATG                         GTGAGATGTGTAGCATCGGACCTGGATCGGAAAAGAATCTGCAGCGGTGGT
genomic: AAGTTGCAGGATGGCAGCTTTACAGAACTCCCCAGAAAACTGCTGCTATGgtatgaaact ... cttttgacagGTGAGATGTGTAGCATCGGACCTGGATCGGAAAAGAATCTGCAGCGGTGGT
EST: gi|88319523|gb|CI518367.1|CI518367
EST:     AAGTTGCAGGATGGCAGCTTTACAGAACTCCCCAGAAAACTGCTGCTATG                         GTGAGATGTGTAGCATCGGACCTGGATCGGAAAAGAATCTGCAGCGGTGGT
genomic: AAGTTGCAGGATGGCAGCTTTACAGAACTCCCCAGAAAACTGCTGCTATGgtatgaaact ... cttttgacagGTGAGATGTGTAGCATCGGACCTGGATCGGAAAAGAATCTGCAGCGGTGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttcctttaatttggcatattatgttgttaagtcctcaattttgcttttgacagGTGAGATGTGTAGCATCGGACCTGGATCGGAAAAGAATCTGCAGCGGTGGTCGCAACGGACTTCTTCGGCTTTGGGATGCCACCACGAGTATCTAAGTTA
     ctttaat  putative branch site (score: 4)
                                        ttttgctttt  putative PPT
                 atattatgttgttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gaaaatgcttgtaacaaaaacaaacttagttatacatcgttgtgtttttcctttaatttggcatattatgttgttaagtcctcaattttgcttttgacagGTGAGATGTGTAGCATCGGACCTGGATCGGAAAAGAATCTGCAGCGGTGGTCGCAACGGACTTCTTCGGCTTTGGGATGCCACCACGAGTATCTAAGTTA

- - atgcttg
- - - - - - - - -aaacaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -atgttgt