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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttaacacttaaacaaagtagcagtaagatgtatgttgcttgttatagtttactgttgttctattatatgctgatttgcagtttccctctactatcatagTGTATACAAGGCTTGCCCGAAGGAGCACTTCGCCGCATTATTTTGACTGCATCAGGTGGTGCTTTCAG

Basic information

species Oryza sativa
transcript LOC_Os01g01710.2
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g01710.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G056975_T02 (Zea mays), 3'ss of exon 6
------tttaacacttaaacaaagtagcag--taagatgtatgttgcttgttatagtttactgttgttctattatatgctgatttgcagtttccctctactatcatagTGTATACAAGGCTTGCCCGAAGGAGCACTTCGCCGCATTATTTTGACTGCATCAGGTGGTGCTTTCAG
      |  |||| |    | |      |   | | ||      |||   ||||||||||          ||| | |||| ||| |   |    ||||  || ||  |||||||||||||||| ||||||| |||||||| ||||||||| | |||||||||||||||||||||||
agggagtacaacattcgtgccatccctgaacttgaaataagaaatgcactttatagtttatgac------attctttgcttattagagctgcttctcttgtacca--gTGTATACAAGGCTTGTCCGAAGGTGCACTTCGTCGCATTATTCTAACTGCATCAGGTGGTGCTTTCAG

upper sequence: LOC_Os01g01710.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G036290_T01 (Zea mays), 3'ss of exon 6
-tttaacacttaaacaaagtagcagtaagatgtatgttgcttgttatagtttac-tgttgttctattatatgctgatttgcagtttccctctactatcatagTGTATACAAGGCTTGCCCGAAGGAGCACTTCGCCGCATTATTTTGACTGCATCAGGTGGTGCTTTCAG
 |  |||| |      |  |   |    ||  ||   ||    |   | ||||  |||| |   ||| | | || ||| | | | | | ||   | |   |||| || ||||||||| |||||||||||||||| ||||||||| | |||||||||||||||||||||||
atagaacagtagtgttatctctgaacttgaaataatgtggaaat-gcattttatgtgttatggcattcttttcttattag-aatctgcttcccttgtaccagTGCATCCAAGGCTTGTCCGAAGGAGCACTTCGTCGCATTATTCTAACTGCATCAGGTGGTGCTTTCAG

upper sequence: LOC_Os01g01710.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G036290_T02 (Zea mays), 3'ss of exon 7
tttaacacttaaacaaagtagcagtaagatgtatgttgcttgttatagtttactgttgttctattatatgctgatttgcagtttccctctactatcatagTGTATACAAGGCTTGCCCGAAGGAGCACTTCGCCGCATTATTTTGACTGCATCAGGTGGTGCTTTCAG----------------------------------------------------------------------------------------------------
                                                                    | || ||| | | | | | ||   | |   |||| || ||||||||| |||||||||||||||| ||||||||| | |||||||||||||||||||||||                                                                                                    
-------------------------------------------------------------------tttcttattag-aatctgcttcccttgtaccagtgcatccaaggcttgtccgaaggagcacttcgtcgcattattctaactgcatcaggtggtgctttcagGCAAGTCCATCCATATGTGTTATATGTACTTCGGTAAACATGCGAATCCATCTCATATCAAATGCTCATGACAGGGACTGGCCAGTTGACAGGCTGAAAG

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|29613664|gb|CB618677.1|CB618677
EST:     ACAAAGTGAAAATACTTCCTGCTGATTCTGAGCACTCTGCTATATTTCAG                         TGTATACAAGGCTTGCCCGAAGGAGCACTTCGCCGCATTATTTTGACTGCA
genomic: ACAAAGTGAAAATACTTCCTGCTGATTCTGAGCACTCTGCTATATTTCAGgtaccacaga ... actatcatagTGTATACAAGGCTTGCCCGAAGGAGCACTTCGCCGCATTATTTTGACTGCA
EST: gi|29688464|gb|CB684739.1|CB684739
EST:     ACAAAGTGANAATACTTCCTGCTGATTCTGAGCACTCTGCTATATTTCAG                         TGTATACAAGGCTTGCCCGAAGGAGCACTTCGCCGCATTATTTTGACTGCA
genomic: ACAAAGTGAAAATACTTCCTGCTGATTCTGAGCACTCTGCTATATTTCAGgtaccacaga ... actatcatagTGTATACAAGGCTTGCCCGAAGGAGCACTTCGCCGCATTATTTTGACTGCA
EST: gi|29681868|gb|CB678143.1|CB678143
EST:     ACAAAGTGAAAATACTTCCTGCTGATTCTGAGCACTCTGCTATATTTCAG                         TGTATACAAAGCTTGCCCGAAAGAGCACTTCGCCGCATTATTTTGACTGCA
genomic: ACAAAGTGAAAATACTTCCTGCTGATTCTGAGCACTCTGCTATATTTCAGgtaccacaga ... actatcatagTGTATACAAGGCTTGCCCGAAGGAGCACTTCGCCGCATTATTTTGACTGCA
EST: gi|29617049|gb|CB622061.1|CB622061
EST:     ACAAAGTGAAAATACTTCCTGCTGATTCTGAGCACTCTGCTATATTTCAG                         TGTATACAAGGCTTGCCCGAAGGAGCACTTCGCCGCATTATTTTGACTGCA
genomic: ACAAAGTGAAAATACTTCCTGCTGATTCTGAGCACTCTGCTATATTTCAGgtaccacaga ... actatcatagTGTATACAAGGCTTGCCCGAAGGAGCACTTCGCCGCATTATTTTGACTGCA
EST: gi|58669161|gb|CK057847.1|CK057847
EST:     ACAAAGTGAAAATACTTCCTGCTGATTCTGAGCACTCTGCTATATTTCAG                         TGTATACAAGGCTTGCCCGAAGGAGCACTTCGCCGCATTATTTTGACTGCA
genomic: ACAAAGTGAAAATACTTCCTGCTGATTCTGAGCACTCTGCTATATTTCAGgtaccacaga ... actatcatagTGTATACAAGGCTTGCCCGAAGGAGCACTTCGCCGCATTATTTTGACTGCA
EST: gi|29620626|gb|CB625637.1|CB625637
EST:     ACAAAGTGAAAATACTTCCTGCTGATTCTGAGCACTCTGCTATATTTCAG                         TGTATACAAGGCTTGCCCGAAGGAGCACTTCGCCGCATTATTTTGACTGCA
genomic: ACAAAGTGAAAATACTTCCTGCTGATTCTGAGCACTCTGCTATATTTCAGgtaccacaga ... actatcatagTGTATACAAGGCTTGCCCGAAGGAGCACTTCGCCGCATTATTTTGACTGCA
EST: gi|29620641|gb|CB625652.1|CB625652
EST:     ACAAAGTGAAAATACTTCCTGCTGATTCTGAGCACTCTGCTATATTTCAG                         TGTATACAAGGCTTTGCCCGAAAGAGCACTTCGCCGC
genomic: ACAAAGTGAAAATACTTCCTGCTGATTCTGAGCACTCTGCTATATTTCAGgtaccacaga ... actatcatagTGTATACAAGGCTT-GCCCGAAGGAGCACTTCGCCGC
EST: gi|58694512|gb|CK083199.1|CK083199
EST:     ACAAAGTGAAAATACTTCCTGCTGATTCTGAGCACTCTGCTATATTTCAG                         TGTATACAAGGCTTGCCCGAAGGAGCACTTCGCCGCATTATTTTGACTGCA
genomic: ACAAAGTGAAAATACTTCCTGCTGATTCTGAGCACTCTGCTATATTTCAGgtaccacaga ... actatcatagTGTATACAAGGCTTGCCCGAAGGAGCACTTCGCCGCATTATTTTGACTGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagtttactgttgttctattatatgctgatttgcagtttccctctactatcatagTGTATACAAGGCTTGCCCGAAGGAGCACTTCGCCGCATTATTTTGACTGCATCAGGTGGTGCTTTCAG
                       tgctgat  putative branch site (score: 3)
                                    tttccctctactatc  putative PPT
          ttgttctattatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttaacacttaaacaaagtagcagtaagatgtatgttgcttgttatagtttactgttgttctattatatgctgatttgcagtttccctctactatcatagTGTATACAAGGCTTGCCCGAAGGAGCACTTCGCCGCATTATTTTGACTGCATCAGGTGGTGCTTTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA