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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atatgtgtatggctctctgttgatgtcaatatcttctatgtatggtggtatagtacaactacctgcaaaattcaaggtttaacaattattccatctgcagGCTGCCATTGTGAATTCTCAGACACTTGAGGAGGTTGCAAGGCTTGAAAAG

Basic information

species Oryza sativa
transcript LOC_Os02g13990.3
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g13990.3 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA10G24350.1 (Glycine max), 3'ss of exon 6
atatgtgtatggctctctgttgatgtcaatatcttctatgtatggtggtatagtacaactacctgcaaa-attcaaggtttaacaa--ttattccatctgcagGCTGCCATTGTGAATTCTCAGACACTTGAGGAGGTTGCAAGGCTTGAAAAG
   ||  | |     | |      || |   |||  ||    | |    ||    ||||||  |      | | | ||||| |||   || | |  | |||||||||||||||||||||||||||| ||||| |||||||| || |||||||||
---tgactgtattcatataccagagttaccttctcttagaagttggtacatcaagcaactaattctggttacttatggtttgacatgtttctgctttatgcagGCTGCCATTGTGAATTCTCAGACTCTTGAAGAGGTTGCTAGACTTGAAAAG

upper sequence: LOC_Os02g13990.3 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA20G18440.1 (Glycine max), 3'ss of exon 6
atatgtgtatggctctctgttgatgtcaatatcttctatgtatggtggtatagtacaactacctgcaaaattcaaggtttaacaa--ttattccatctgcagGCTGCCATTGTGAATTCTCAGACACTTGAGGAGGTTGCAAGGCTTGAAAAG
  |||  | |     |    |   || ||  |||  ||      |    ||    || |||  |       || | | || |||   || | |  | |||||||||||||||||||||||||||| ||||| |||||||| ||||||||||||
--atgactgtattcataaactagagttaacttctcttagaagctggtacatcaggcagctaattttggttatctatggttgacatgtttgtgctttatgcagGCTGCCATTGTGAATTCTCAGACTCTTGAAGAGGTTGCTAGGCTTGAAAAG

upper sequence: LOC_Os02g13990.3 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv01s0150g00590.t01 (Vitis vinifera), 3'ss of exon 5
atatgtgtatggctctctgttgatgtcaatatcttctatgtatggtggtatagtacaactacctgcaaaattcaaggttta-----acaattattccatctgcagGCTGCCATTGTGAATTCTCAGACACTTGAGGAGGTTGCAAGGCTTGAAAAG
 | |   |||   |      |||   |   ||||| | | | |  | | ||  |  ||||      |||||||| | |||      | | ||  |   | ||||||| || ||||||||||| ||||| ||||| |||||||||||||||||||||
ttttacttattctttgtcagtgaaagctgcatcttttctct-tcattgcatgcttgaactt----aaaaattcatgttttccgtccatattttgttgttgtgcagGCCGCAATTGTGAATTCACAGACTCTTGAAGAGGTTGCAAGGCTTGAAAAG

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|29681479|gb|CB677754.1|CB677754
EST:     AGGGTCCAAAAGTAGTTGCTCCAACACCTGAGCAAATCACAGCTATCAAG                         GCTGCCATTGTGAATTCTCAGACACTTGAGGAGGTTGCAAGGCTTGAAAAG
genomic: AGGGTCCAAAAGTAGTTGCTCCAACACCTGAGCAAATCACAGCTATCAAGgtactattgc ... ccatctgcagGCTGCCATTGTGAATTCTCAGACACTTGAGGAGGTTGCAAGGCTTGAAAAG
EST: gi|88201604|gb|CI201959.1|CI201959
EST:     TCCAACACCTGAGCAAATCACAGCTATCAAG                         GCTGCCATTGTGAATTCTCAGACACTTGAGGAGGTTGCAAGGCTTGAAAAG
genomic: TCCAACACCTGAGCAAATCACAGCTATCAAGgtactattgc ... ccatctgcagGCTGCCATTGTGAATTCTCAGACACTTGAGGAGGTTGCAAGGCTTGAAAAG
EST: gi|86545114|gb|CI185320.1|CI185320
EST:     AGGGTCCAAAAGTAGTTGCTCCAACACCTGAGCAAATCACAGCTATCAAG                         GCTGCCATTGTGAATTCTCAGACACTTGAGGAGGTTGCAAGGCTTGAAAAG
genomic: AGGGTCCAAAAGTAGTTGCTCCAACACCTGAGCAAATCACAGCTATCAAGgtactattgc ... ccatctgcagGCTGCCATTGTGAATTCTCAGACACTTGAGGAGGTTGCAAGGCTTGAAAAG
EST: gi|88227188|gb|CI228301.1|CI228301
EST:     TCCAACACCTGAGCAAATCACAGCTATCAAG                         GCTGCCATTGTGAATTCTCAGACACTTGAGGAGGTTGCAAGGCTTGAAAAG
genomic: TCCAACACCTGAGCAAATCACAGCTATCAAGgtactattgc ... ccatctgcagGCTGCCATTGTGAATTCTCAGACACTTGAGGAGGTTGCAAGGCTTGAAAAG
EST: gi|86500747|gb|CI143380.1|CI143380
EST:     AGGGTCCAAAAGTAGTTGCTCCAACACCTGAGCAAATCACAGCTATCAAG                         GCTGCCATTGTGAATTCTCAGACACTTGAGGAGGTTGCAAGGCTTGAAAAG
genomic: AGGGTCCAAAAGTAGTTGCTCCAACACCTGAGCAAATCACAGCTATCAAGgtactattgc ... ccatctgcagGCTGCCATTGTGAATTCTCAGACACTTGAGGAGGTTGCAAGGCTTGAAAAG
EST: gi|86421117|gb|CI057106.1|CI057106
EST:     ACCTGAGCAAATCACAGCTATCAAG                         GCTGCCATTGTGAATTCTCAGACACTTGAGGAGGTTGCAAGGCTTGAAAAG
genomic: ACCTGAGCAAATCACAGCTATCAAGgtactattgc ... ccatctgcagGCTGCCATTGTGAATTCTCAGACACTTGAGGAGGTTGCAAGGCTTGAAAAG
EST: gi|86536011|gb|CI176217.1|CI176217
EST:     AGGGTCCAAAAGTAGTTGCTCCAACACCTGAGCAAATCACAGCTATCAAG                         GCTGCCATTGTGAATTCTCAGACACTTGAGGAGGTTGCAAGGCTTGAAAAG
genomic: AGGGTCCAAAAGTAGTTGCTCCAACACCTGAGCAAATCACAGCTATCAAGgtactattgc ... ccatctgcagGCTGCCATTGTGAATTCTCAGACACTTGAGGAGGTTGCAAGGCTTGAAAAG
EST: gi|29645677|gb|CB650684.1|CB650684
EST:     AGGGTCCAAAAGTAGTTGCTCCAACACCTGAGCAAATCACAGCTATCAAG                         GCTGCCATTGTGAATTCTCAGACACTTGAGGAGGTTGCAAGGCTTGAAAAG
genomic: AGGGTCCAAAAGTAGTTGCTCCAACACCTGAGCAAATCACAGCTATCAAGgtactattgc ... ccatctgcagGCTGCCATTGTGAATTCTCAGACACTTGAGGAGGTTGCAAGGCTTGAAAAG
EST: gi|86503360|gb|CI145993.1|CI145993
EST:     AGGGTCCAAAAGTAGTTGCTCCAACACCTGAGCAAATCATAGCTATCAAG                         GCTGCCATTGTGAATTCTCAGACACTTGAGGAGGTTGCCAAGGCTTGAAAA
genomic: AGGGTCCAAAAGTAGTTGCTCCAACACCTGAGCAAATCACAGCTATCAAGgtactattgc ... ccatctgcagGCTGCCATTGTGAATTCTCAGACACTTGAGGAGGTTG-CAAGGCTTGAAAA
EST: gi|5005007|gb|AU068324.1|AU068324
EST:     AGGGTCCAAAAGTAGTTGCTCCAACACCTGAGCAAATCACAGCTATCAAG                         GCTGCCATTGTGAATTCTCAGACACTTGAGGAGGTTGCAAGGCTTGAAAAG
genomic: AGGGTCCAAAAGTAGTTGCTCCAACACCTGAGCAAATCACAGCTATCAAGgtactattgc ... ccatctgcagGCTGCCATTGTGAATTCTCAGACACTTGAGGAGGTTGCAAGGCTTGAAAAG
EST: gi|88223197|gb|CI223046.1|CI223046
EST:     CAACACCTGAGCAAATCACAGCTATCAAG                         GCTGCCATTGTGAATTCTCAGACACTTGAGGAGGTTGCAAGGCTTGAAAAG
genomic: CAACACCTGAGCAAATCACAGCTATCAAGgtactattgc ... ccatctgcagGCTGCCATTGTGAATTCTCAGACACTTGAGGAGGTTGCAAGGCTTGAAAAG
EST: gi|88830705|gb|CI078149.1|CI078149
EST:     AGGGTCCAAAAGTAGTTGCTCCAACACCTGAGCAAATCACAGCTATCAAG                         GCTGCCATTGTGAATTCTCAGACACTTGAGGAGGTTGCAAGGCTTGAAAAG
genomic: AGGGTCCAAAAGTAGTTGCTCCAACACCTGAGCAAATCACAGCTATCAAGgtactattgc ... ccatctgcagGCTGCCATTGTGAATTCTCAGACACTTGAGGAGGTTGCAAGGCTTGAAAAG
EST: gi|88252358|gb|CI350786.1|CI350786
EST:     ACAGCTATCAAG                         GCTGCCATTGTGAATTCTCAGACACTTGAGGAGGTTGCAAGGCTTGAAAAG
genomic: ACAGCTATCAAGgtactattgc ... ccatctgcagGCTGCCATTGTGAATTCTCAGACACTTGAGGAGGTTGCAAGGCTTGAAAAG
EST: gi|86505850|gb|CI148483.1|CI148483
EST:     CTGAGCAAATCACAGCTATCAAG                         GCTGCCATTGTGAATTCTCAGACACTTGAGGAGGTTGCAAGGCTTGAAAAG
genomic: CTGAGCAAATCACAGCTATCAAGgtactattgc ... ccatctgcagGCTGCCATTGTGAATTCTCAGACACTTGAGGAGGTTGCAAGGCTTGAAAAG
EST: gi|116875219|gb|EC365727.1|EC365727
EST:     AGGGTCCAAAAGTAGTTGCTCCAACACCTGAGCAAATCACAGCTATCAAG                         GCTGCCATTGTGAATCCTCAGACACTTGAGGAGGTTGCAAGGCTTGAAAAG
genomic: AGGGTCCAAAAGTAGTTGCTCCAACACCTGAGCAAATCACAGCTATCAAGgtactattgc ... ccatctgcagGCTGCCATTGTGAATTCTCAGACACTTGAGGAGGTTGCAAGGCTTGAAAAG
EST: gi|86496623|gb|CI139256.1|CI139256
EST:     AGGGTCCAAAAGTAGTTGCTCCAACACCTGAGCAAATCACAGCTATCAAG                         GCTGCCATTGTGAATTCTCAGACACTTGAGGAGGTTGCAAGGCTTGAAAAG
genomic: AGGGTCCAAAAGTAGTTGCTCCAACACCTGAGCAAATCACAGCTATCAAGgtactattgc ... ccatctgcagGCTGCCATTGTGAATTCTCAGACACTTGAGGAGGTTGCAAGGCTTGAAAAG
EST: gi|86500143|gb|CI142776.1|CI142776
EST:     AGGGTCCAAAAGTAGTTGCTCCAACACCTGAGCAAATCACAGCTATCAAG                         GCTGCCATTGTGAATTCTCAGACACTTGAGGAGGTTGCAAGGCTTGAAAAG
genomic: AGGGTCCAAAAGTAGTTGCTCCAACACCTGAGCAAATCACAGCTATCAAGgtactattgc ... ccatctgcagGCTGCCATTGTGAATTCTCAGACACTTGAGGAGGTTGCAAGGCTTGAAAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggtatagtacaactacctgcaaaattcaaggtttaacaattattccatctgcagGCTGCCATTGTGAATTCTCAGACACTTGAGGAGGTTGCAAGGCTTGAAAAG
                               gtttaac  putative branch site (score: 3)
                                           ttccatct  putative PPT
                                tttaacaattatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atatgtgtatggctctctgttgatgtcaatatcttctatgtatggtggtatagtacaactacctgcaaaattcaaggtttaacaattattccatctgcagGCTGCCATTGTGAATTCTCAGACACTTGAGGAGGTTGCAAGGCTTGAAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG