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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgtgggaaatgtatgagtatgacatattttaagggcagcaaatttcgattcaaaatagcaaaatgttgactgcagtcgctaatttattccatgcatacagGTACTGGTGGAAATCCTAATTTGGGAGAGCAAGCTGCTGAGGAATCAAAAGAAGCCATAGCCAATGCCCTGAAGGATTCTGACCTTGTCTTCATAACGGC

Basic information

species Oryza sativa
transcript LOC_Os04g56970.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g56970.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G119773_T01 (Zea mays), 3'ss of exon 2
tgtgggaaatgtatgagtatgacatattttaagggcagcaaatttcgattcaaaatagca-aaatgttgactgcagtcgctaatt---------tattccatgcatacagGTACTGGTGGAAATCCTAATTTGGGAGAGCAAGCTGCTGAGGAATCAAAAGAAGCCATAGCCAATGCCCTGAAGGATTCTGACCTTGTCTTCATAACGGC
          |    |  |  |   ||  | |   | | ||||||| ||| |||||     | | |||| ||  | ||  ||| |           |  ||     |||||| | ||||||||||| |||||||||||||| |||||||||||||||| |||| ||||||||| |||||||| |||||| || |||||||||||||| ||
----------gccctataacaatgcatcatcaaaactgtaaatttccattgaaaatgtttcagaggttggctagattcagtaaatatgatactacgtaacacatgcacagGTGCCGGTGGAAATCCGAATTTGGGAGAGCAGGCTGCTGAGGAATCAAGAGAAACCATAGCCACTGCCCTGAGGGATTCAGATCTTGTCTTCATAACAGC

upper sequence: LOC_Os04g56970.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA08G43500.1 (Glycine max), 3'ss of exon 2
----------------------------------------------tgtgggaaatgtatgagtatgacatattttaagggcagcaaatttcgattcaaaatagcaaaatgttgactgcagtcgctaattta--ttccatgc-----atacagGTACTGGTGGAAATCCTAATTTGGGAGAGCAAGCTGCTGAGGAATCAAAAGAAGCCATAGCCAATGCCCTGAAGGATTCTGACCTTGTCTTCATAACGGC
                                              | ||  |    |||  || ||  ||| | | |     |      |   |   |  ||||   ||  | | ||    |  | ||| |  || | ||      || |||||||||| || |||||   |||||| || |||||||||||||||||||||||||| || || ||||| ||  | |  || ||  | || ||  |||| ||
gtcaggcacttgcattttatgcctaggtggttcctttgtgcttgattatgacatgcatatatgt-tgctatagtgtgatttgtgtgtgcctgtgtggtacttagcttcattctaa-tgtgtcctttgattcaagttgcttgagagagatgcagGTACTGGAGGGAATCCGCTTTTGGGGGAACAAGCTGCTGAGGAATCAAAAGAAGCTATTGCTAATGCTCTTCAAGGCTCGGATTTAGTGTTTGTAACTGC

upper sequence: LOC_Os04g56970.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA18G10030.1 (Glycine max), 3'ss of exon 2
--------------------------------------------tgtgggaaatgtatgagtatgacatattttaagggcagcaaatttcgattcaaaatagcaa---aatgttgactgcagtcgctaatttattccatgcatacagGTACTGGTGGAAATCCTAATTTGGGAGAGCAAGCTGCTGAGGAATCAAAAGAAGCCATAGCCAATGCCCTGAAGGATTCTGACCTTGTCTTCATAACGGC
                                              |   | ||| ||   | |  || ||  |  |  |   |  | |   |         ||    |||||   ||    |      |   |   |   || ||||||||||||| |||||   |||||| || |||||||||||||||||||||||||| || |||||||| ||  | |  || ||  | || ||  |||| ||
gtcaggaagttgcattttatgcctagggggttcctttgtacttgattataacatgcatatatgttgca-atcatgtgatctatatgtgtgtgtgtgtggcttcactccaatgtgacctttgattcgagttgcttgatagagatgcagGTACTGGTGGGAATCCACTTTTGGGGGAACAAGCTGCTGAGGAATCAAAAGAAGCTATTGCCAATGCTCTTCAAGGATCAGATTTAGTGTTTGTAACTGC

upper sequence: LOC_Os04g56970.1 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv19s0090g01320.t01 (Vitis vinifera), 3'ss of exon 2
-------tgtgggaaatgtatgagtatgacatattttaagggcagcaaatttcgattcaaaatagcaaaatgttgactgcagtcgctaatttattccatgcatacagGTACTGGTGGAAATCCTAATTTGGGAGAGCAAGCTGCTGAGGAATCAAAAGAAGCCATAGCCAATGCCCTGAAGGATTCTGACCTTGTCTTCATAACGGC
       | ||||   | ||   |  |    | | ||| | |  |   |  | |       || | |   | ||||||  |  | || | |      |   || ||||||| ||||| |||||   |||||| || || ||||||||||||||||| |||||||| || ||||| || |||| ||| || ||||| || ||||| ||
acttttatatgggtggtatagctgcttttgttttcttatgtgttgaggaccttgtggttgtattgtatcct-ttgactcaaaccacttaat------agagatgcagGTACGGGTGGGAATCCACTTTTGGGGGAACAGGCTGCTGAGGAATCAAAGGAAGCCATTGCAAATGCTCTCAAGGGTTCAGATCTTGTGTTTATAACAGC

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|29655620|gb|CB651895.1|CB651895
EST:     GCAAGCGCAATACCCGCTACAAATTGGAGAGCATTTAACTCGTGGACTAC                         GTACTGGTGGAAATCCTAATTTGGGAGAGCAAGCTGCTGAGGAATCAAAAG
genomic: GCAAGCGCAATACCCGCTACAAATTGGAGAGCAGTTAACTCGTGGACTAGgtaatatttg ... atgcatacagGTACTGGTGGAAATCCTAATTTGGGAGAGCAAGCTGCTGAGGAATCAAAAG
EST: gi|29655649|gb|CB651924.1|CB651924
EST:     GCAAGCGCAATACCCGCTACAAATTGGAGAGCAGTTAACTCGTGGACTAG                         GTACTGGTGGAAATCCTAATTTGGGAGAGCAAGCTGCTGAGGAATCAAAAG
genomic: GCAAGCGCAATACCCGCTACAAATTGGAGAGCAGTTAACTCGTGGACTAGgtaatatttg ... atgcatacagGTACTGGTGGAAATCCTAATTTGGGAGAGCAAGCTGCTGAGGAATCAAAAG
EST: gi|58687955|gb|CK076642.1|CK076642
EST:     GCAAGCGCAATACCCGCTACAAATTGGAGAGCAGTTAACTCGTGGACTAG                         GTACTGGTGGAAATCCTAATTTGGGAGAGCAAGCTGCTGAGGAATCAAAAG
genomic: GCAAGCGCAATACCCGCTACAAATTGGAGAGCAGTTAACTCGTGGACTAGgtaatatttg ... atgcatacagGTACTGGTGGAAATCCTAATTTGGGAGAGCAAGCTGCTGAGGAATCAAAAG
EST: gi|86885639|gb|CI309766.1|CI309766
EST:     GCAAGCGCAATACCCGCTACAAATTGGAGAGCAGTTAACTCGTGGACTAG                         GTACTGGTGGAAGTCCTAATTTGGGAGAGCAAGCTGCTG
genomic: GCAAGCGCAATACCCGCTACAAATTGGAGAGCAGTTAACTCGTGGACTAGgtaatatttg ... atgcatacagGTACTGGTGGAAATCCTAATTTGGGAGAGCAAGCTGCTG
EST: gi|58688695|gb|CK077382.1|CK077382
EST:     GCAAGCGCAATACCCGCTACAAATTGGAGAGCAGTTAACTCGTGGACTAG                         GTACTGGTGGAAATCCTAATTTGGGAGAGCAAGCTGCTGAGGAATCAAAAG
genomic: GCAAGCGCAATACCCGCTACAAATTGGAGAGCAGTTAACTCGTGGACTAGgtaatatttg ... atgcatacagGTACTGGTGGAAATCCTAATTTGGGAGAGCAAGCTGCTGAGGAATCAAAAG
EST: gi|29655650|gb|CB651925.1|CB651925
EST:     GCAAGCGCAATACCCGCTACAAATTGGAGAGCAGTTAACTCGTGGACTAG                         GTACTGGTGGAAATCCTAATTTGGGAGAGCAAGCTGCTGAGGAATCAAAAG
genomic: GCAAGCGCAATACCCGCTACAAATTGGAGAGCAGTTAACTCGTGGACTAGgtaatatttg ... atgcatacagGTACTGGTGGAAATCCTAATTTGGGAGAGCAAGCTGCTGAGGAATCAAAAG
EST: gi|88316287|gb|CI621526.1|CI621526
EST:     GCAAGCGCAATACCCGCTACAAATTGGAGAGCAGTTAACTCGTGGACTAG                         GTACTGGTGGAAATC-TAATTTGGGAGAGCAAGCTGCTGAGGAATCAAAAG
genomic: GCAAGCGCAATACCCGCTACAAATTGGAGAGCAGTTAACTCGTGGACTAGgtaatatttg ... atgcatacagGTACTGGTGGAAATCCTAATTTGGGAGAGCAAGCTGCTGAGGAATCAAAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgattcaaaatagcaaaatgttgactgcagtcgctaatttattccatgcatacagGTACTGGTGGAAATCCTAATTTGGGAGAGCAAGCTGCTGAGGAATCAAAAGAAGCCATAGCCAATGCCCTGAAGGATTCTGACCTTGTCTTCATAACGGC
                               cgctaat  putative branch site (score: 3)
                                  taatttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgtgggaaatgtatgagtatgacatattttaagggcagcaaatttcgattcaaaatagcaaaatgttgactgcagtcgctaatttattccatgcatacagGTACTGGTGGAAATCCTAATTTGGGAGAGCAAGCTGCTGAGGAATCAAAAGAAGCCATAGCCAATGCCCTGAAGGATTCTGACCTTGTCTTCATAACGGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG