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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaggcaacttcttagagacaaatattttaaacatcttgatatgaaatgaaaggaagactatcctgttatatagaaccatgcatttgctgactacaatatattgatgcatgttcttgttcgctctgcagAGAGGCAAAGTAAAACCTGTTCATGTTGTTGACGTTCCTGGTCATGCAAGGCTCAAACCCAAACTTGATGAAGTCCTGCCTCAAGCAGCTGGAATAGTTT

Basic information

species Oryza sativa
transcript LOC_Os08g41250.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g41250.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G059260_T01 (Zea mays), 3'ss of exon 3
gtaaggcaacttcttagagacaaatattttaaacatcttgatatgaaatgaaaggaagactatcctgttatatagaaccatgcatttgctgactacaatatat-tgatgcatgttcttgtt----cgctctgcagAGAGGCAAAGTAAAACCTGTTCATGTTGTTGACGTTCCTGGTCATGCAAGGCTCAAACCCAAACTTGATGAAGTCCTGCCTCAAGCAGCTGGAATAGTTT
                                   |  || || | |||| ||  |    | |  | || |  | || ||||||| | |||||| | |||| | || |  |  ||| ||||      | ||||||| ||  |||||||||| ||| |||||| |||| |||||||||||||| ||||||||||||||||||||||||||||||||| |||  |||  | | || |
---------------------------------agttctgcta-gtaatgtaaatagttttgtt-tcttgtgaaaaaacatgcatatcctgactgcgatatttctgctaaaccttcctgttgtccttccctgcagAAAGAAAAAGTAAAACTTGTGCATGTTATTGATGTTCCTGGTCATGCTAGGCTCAAACCCAAACTTGATGAAGTCCTGCCTAAAGTTGCTACAGTTGTCT

upper sequence: LOC_Os08g41250.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G175054_T01 (Zea mays), 3'ss of exon 6
gtaaggcaacttcttagagacaaatattttaaacatcttgatatgaaatgaaaggaagactatcctgttatatagaaccatgcatttgctgactacaatatat-tgatgcatgttcttgtt----cgctctgcagAGAGGCAAAGTAAAACCTGTTCATGTTGTTGACGTTCCTGGTCATGCAAGGCTCAAACCCAAACTTGATGAAGTCCTGCCTCAAGCAGCTGGAATAGTTT
                                   |  || || | |||| ||  |    | |  | || |  | || ||||||| | |||||| | |||| | || |  |  ||| ||||      | ||||||| || ||||||||||||||| |||||| |||| |||||||||||||| ||||||||||||||||||||||||||||||||| |||  ||||   | || |
---------------------------------agttctgcta-gtaatgtaaatagttttgtt-tcttgtgaaaaaacatgcatatcctgactgcgatatttctgctaaaccttcatgttgtccttccctgcagAAAGACAAAGTAAAACCTGTGCATGTTATTGATGTTCCTGGTCATGCTAGGCTCAAACCCAAACTTGATGAAGTCCTGCCTAAAGTTGCTGCGGTTGTCT

upper sequence: LOC_Os08g41250.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G091503_T04 (Zea mays), 3'ss of exon 4
gtaaggcaacttcttagagacaaatatttta--aacatcttgatatgaaatgaaaggaagactatcctgtt----atatagaaccatgcatttgctgactacaatatat-tgatgcatgttcttgtt----cgctctgcagAGAGGCAAAGTAAAACCTGTTCATGTTGTTGACGTTCCTGGTCATGCAAGGCTCAAACCCAAACTTGATGAAGTCCTGCCTCAAGCAGCTGGAATAGTTT
||| |  ||||||| ||||   | | ||||   ||||| |||| | |||| | || | |||   |  ||||    ||  | || ||||||| | |||||| | |||| | || |  |  ||| ||||      | ||||||| || ||||||||||||||| ||| || |||| |||||||||||||| ||||||||||||||||||||||||||||||||| |||| ||||   | || |
gtatgcaaacttct-agagctcattctttttccaacatattgaga-gaaaagtaatgtagatagttttgtttcttatgaaaaaacatgcatatcctgactgcgatatttctgctaaaccttcctgttgtccttccctgcagAAAGACAAAGTAAAACCTGTGCATATTATTGATGTTCCTGGTCATGCTAGGCTCAAACCCAAACTTGATGAAGTCCTGCCTAAAGCTGCTGCGGTTGTCT

upper sequence: LOC_Os08g41250.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G014704_T01 (Zea mays), 3'ss of exon 1
gtaaggcaacttcttagagacaaatatttta--aacatcttgatatgaaatgaaaggaagactatcctgtt----atatagaaccatgcatttgctgactacaatatat-tgatgcatgttcttgtt----cgctctgcagAGAGGCAAAGTAAAACCTGTTCATGTTGTTGACGTTCCTGGTCATGCAAGGCTCAAACCCAAACTTGATGAAGTCCTGCCTCAAGCAGCTGGAATAGTTT
||| |  ||||||| ||||   | | ||||   ||||| |||| | |||| | || | | |   |  ||||     |  | || || |||| | |||| | | |||| | || |  |  ||| ||||      | ||||||| || ||||||||||||||| ||| || |||| |||||||||||||| ||||||||||||||||||||||||||||||||| |||| ||||  || || |
gtatgcaaacttct-agagttcattctttttccaacatattgaga-gaaaagtaatgtaaatagttttgtttcttgtgaaaaaacacgcatatcctgattgcgatatttctgctaaaccttcctgttgtccttccctgcagAAAGACAAAGTAAAACCTGTGCATATTATTGATGTTCCTGGTCATGCTAGGCTCAAACCCAAACTTGATGAAGTCCTGCCTAAAGCTGCTGCGATTGTCT

upper sequence: LOC_Os08g41250.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G015642_T01 (Zea mays), 3'ss of exon 4
gtaaggcaacttcttagagacaaatatttta--aacatcttgatatgaaa-tgaaaggaaga--ctatcctgttatatagaaccatgcatttgctgactacaata-tattgatgcatgttcttgttcgctct----gcagAGAGGCAAAGTAAAACCTGTTCATGTTGTTGACGTTCCTGGTCATGCAAGGCTCAAACCCAAACTTGATGAAGTCCTGCCTCAAGCAGCTGGAATAGTTT
||| || ||||||| ||||   | | ||||   ||||| |||| || ||| ||||  ||| |   | | || ||||  |||| |||||||||||||||| ||||| |  || |  |  ||| ||||  |  |    ||||| |||||||||||||||||| ||| ||||||| |||||||||||||| |||||||| ||||| |||||||||||||||||| |||| |||||  | || |
gtatggaaacttct-agagctcattctttttccaacatattgagataaaaatgaagtgaatagctttttctcttatgaagaaacatgcatttgctgactgcaatagttctgctaaaccttcctgttgcccttccgtgcagAAAGGCAAAGTAAAACCTGTGCATATTGTTGATGTTCCTGGTCATGCTAGGCTCAAGCCCAAGCTTGATGAAGTCCTGCCTAAAGCTGCTGGGGTTGTCT

upper sequence: LOC_Os08g41250.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G466947_T01 (Zea mays), 3'ss of exon 8
gtaaggcaacttcttagagacaaatattttaaacatcttgatatgaaatgaaaggaagactatcctgttatatagaaccatgcatttgctgactacaatatat-tgatgcatgttcttgtt----cgctctgcagAGAGGCAAAGTAAAACCTGTTCATGTTGTTGACGTTCCTGGTCATGCAAGGCTCAAACCCAAACTTGATGAAGTCCTGCCTCAAGCAGCTGGAATAGTTT
                                   |  || || | |||| ||  |    | |  | || |  | || ||| ||| | |||||| | |||| | || |  |  ||| ||||      | ||||||| || ||||||||||||| | |||||| |||| |||||||||||||| ||||||||||||||||||||||||||||||||| |||  ||||   | || |
---------------------------------agttctgcta-gtaatgtaaatagttttgtt-tcttgtgaaaaaacatccatatcctgactgcgatatttctgctaaaccttcctgttgtccttccctgcagAAAGACAAAGTAAAACCTATGCATGTTATTGATGTTCCTGGTCATGCTAGGCTCAAACCCAAACTTGATGAAGTCCTGCCTAAAGTTGCTGCGGTTGTCT

upper sequence: LOC_Os08g41250.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM5G886354_T01 (Zea mays), 3'ss of exon 1
gtaaggcaacttcttagagacaaatatttta-aacatcttgatatgaaatgaaaggaa---gactatcctgttatatagaaccatgcatttgctgactacaatatat-tgatgcatgttcttgtt----cgctctgcagAGAGGCAAAGTAAAACCTGTTCATGTTGTTGACGTTCCTGGTCATGCAAGGCTCAAACCCAAACTTGATGAAGTCCTGCCTCAAGCAGCTGGAATAGTTT
||| |  |||||||      ||    ||||  ||||| |||| |  |||  || | ||   |  |    | || |  | || ||||||| | |||||| | |||| | || |  |  ||| ||||      | ||| ||| || ||||||||||||||| ||| || |||| |||||||||||||| ||||||||||||||||||||||||||||||||| ||||  |||   | || |
gtatgcaaacttctggagttcattctttttccaacatattgagagaaaagtaatgtaaatagttttatttcttgtgaaaaaacatgcatatcctgactgcgatatttctgctagaccttcctgttgtccttccctgtagAAAGACAAAGTAAAACCTGTGCATATTATTGATGTTCCTGGTCATGCTAGGCTCAAACCCAAACTTGATGAAGTCCTGCCTAAAGCTCCTGCGGTTGTCT

upper sequence: LOC_Os08g41250.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G701405_T01 (Zea mays), 3'ss of exon 1
gtaaggcaacttcttagagacaaatatttta-aacatcttgatatgaaatgaaaggaagactatcctgtt----atatagaaccatgcatttgctgactacaatatat-tgatgcatgttcttgtt----cgctctgcagAGAGGCAAAGTAAAACCTGTTCATGTTGTTGACGTTCCTGGTCATGCAAGGCTCAAACCCAAACTTGATGAAGTCCTGCCTCAAGCAGCTGGAATAGTTT
||| |  |||||||      ||    ||||  ||||| |||| | |||| | || | | |   |  ||||     |  | || ||||||| | |||||| | |||| | || |  |  ||| ||||      | || |||| || ||||||||||| ||| ||| || |||| |||||||||||||| ||||||||||||||||||||||||||||||||| |||| ||||   | || |
gtatgcaaacttctggagttcattctttttccaacatattgaga-gaaaagtaatgtaaatagttttgtttcttgtgaaaaaacatgcatatcctgactgcgatatttctgctaaaccttcctgttgtccttccctacagAAAGACAAAGTAAAACATGTGCATATTATTGATGTTCCTGGTCATGCTAGGCTCAAACCCAAACTTGATGAAGTCCTGCCTAAAGCTGCTGCGGTTGTCT

upper sequence: LOC_Os08g41250.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G325453_T01 (Zea mays), 3'ss of exon 8
gtaaggcaacttcttagagacaaatattttaaacatcttgatatgaaatgaaaggaagactatcctgttatatagaaccatgcatttgctgactacaatatat-tgatgcatgttcttgtt----cgctctgcagAGAGGCAAAGTAAAACCTGTTCATGTTGTTGACGTTCCTGGTCATGCAAGGCTCAAACCCAAACTTGATGAAGTCCTGCCTCAAGCAGCTGGAATAGTTT
                                   |  || || | |||| ||  |    | |  | || |  | || ||||||| | |||||| | |||| | || |  |  ||| ||||      | ||||||| ||  |||||||||| ||| |||||| |||| |||||| ||||||| ||||||||||||||||||||||||||||||||| |||  ||||   | || |
---------------------------------agttctgcta-gtaatgtaaatagttttgtt-tcttgtgaaaaaacatgcatatcctgactgcgatatttctgctaaaccttcctgttgtccttccctgcagAAAGATAAAGTAAAACTTGTGCATGTTATTGATGTTCCTAGTCATGCTAGGCTCAAACCCAAACTTGATGAAGTCCTGCCTAAAGTTGCTGCGGTTGTCT

upper sequence: LOC_Os08g41250.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM5G800070_T01 (Zea mays), 3'ss of exon 1
gtaaggcaacttcttagagacaaatatttta-aacatcttgatatgaaatgaaaggaagactatcctgtt----atatagaaccatgcatttgctgactacaatatat-tgatgcatgttcttgtt----cgctctgcagAGAGGCAAAGTAAAACCTGTTCATGTTGTTGACGTTCCTGGTCATGCAAGGCTCAAACCCAAACTTGATGAAGTCCTGCCTCAAGCAGCTGGAATAGTTT
||| |  |||||||      ||    ||||  ||||| |||| | |||| | || | | |   |  ||||     |  | || ||||||| | |||||| |||||| | || |  |  ||| ||||      | ||||||| || ||||||||||||| | ||| || |||| |||||||||||||| ||||||||||||||||||||||||||||||||| |||| ||||   | || |
gtatgcaaacttctggagttcattctttttccaacatattgaga-gaaaagtaatgtaaatagttttgtttcttgtgaaaaaacatgcatatcctgactgcaatatttctgctaaaccttcctgttgtccttccctgcagAAAGACAAAGTAAAACCTATGCATATTATTGATGTTCCTGGTCATGCTAGGCTCAAACCCAAACTTGATGAAGTCCTGCCTAAAGCTGCTGCGGTTGTCT

upper sequence: LOC_Os08g41250.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA02G04110.1 (Glycine max), 3'ss of exon 3
gtaaggcaacttcttagagacaaatattttaaacatcttgatatgaaatgaaaggaagactatcctgttatatagaaccatgcatttgctgactacaatatattgatgcatgttcttgttcgctctgcagAGAGGCAAAGTAAAACCTGTTCATGTTGTTGACGTTCCTGGTCATGCAAGGCTCAAACCCAAACTTGATGAAGTCCTGCCTCAAGCAGCTGGAATAGTTT
                            | ||  || |  || | |  | | | |     | |  || | | | ||| ||  || | |      || | || |||    || ||  | |    |   ||||  |||||  |||| ||||||||||||||||| |||||||| ||| |  ||||   ||||||||| |||||   | ||||||||||||||||  ||||||
---------------------------ctgaattatatcaatcttatttcatatgtttgtt-tgttgat-tgtggaatcagacaataga-attgactaaatgttgtcttatatttctttgattttaacagAAGGGCAAGATAAAGCCTGTTCATGTTGTTGATGTTCCTGGGCATTCTCGGCTTCGACCCAAACTGGATGAGTACTTGCCTCAAGCAGCTGGGGTAGTTT

upper sequence: LOC_Os08g41250.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA01G03540.1 (Glycine max), 3'ss of exon 3
gtaaggcaacttcttagagacaaatattttaaacatcttgatatgaaatgaaaggaagactatcctgttatatagaaccatgcatttgct-gactacaata--tattgatgcatgttcttgttcgctctgcagAGAGGCAAAGTAAAACCTGTTCATGTTGTTGACGTTCCTGGTCATGCAAGGCTCAAACCCAAACTTGATGAAGTCCTGCCTCAAGCAGCTGGAATAGTTT
                              | |  ||||  |   |  |||||  |   | ||| ||||  |||      |   |    | || |  | ||  | |||    || ||    |    |   ||||  |||||  |||||||||||||||||||||| |||||||| ||| |  ||||   ||||||||| |||||   | |||||||||||||||| |||||||
------------------------------agatgtcttagt---agctgaaattatatcaatcgtgtttcatatgtttgtttgtacaatagaattgagtaaatgttgtctaatatttccttgattttaacagAAGGGCAAGATAAAACCTGTTCATGTTGTTGATGTTCCTGGGCATTCTCGGCTTCGACCCAAACTGGATGAGTACTTGCCTCAAGCAGCTGGGATAGTTT

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|163925831|gb|EG709627.1|EG709627
EST:     CAATGGAACAAAACAACGATACTTTCGTGCTTCATTCTGAGCTGGAGAGG                         AGAGGCAAAGTAAAACC--TTCATGTTGTTGACGTTCCTGGTCATGCAAGG
genomic: CAATGGAACAAAACAACGATACTTTCGTGCTTCATTCTGAGCTGGAGAGGgtaaggcaac ... cgctctgcagAGAGGCAAAGTAAAACCTGTTCATGTTGTTGACGTTCCTGGTCATGCAAGG
EST: gi|33685924|gb|CF314163.1|CF314163
EST:     CAATGGAACAAAACAACGATACTTTCGTGCTTCATTCTGAGCTGGAGAGG                         AGAGGCAAAGTAAAACCTGTTCATGTTGTTGACGTTCCTGGTCATGCAAGG
genomic: CAATGGAACAAAACAACGATACTTTCGTGCTTCATTCTGAGCTGGAGAGGgtaaggcaac ... cgctctgcagAGAGGCAAAGTAAAACCTGTTCATGTTGTTGACGTTCCTGGTCATGCAAGG
EST: gi|10931045|gb|AU161319.1|AU161319
EST:     CTGAGCTGGAGAGG                         AGAGGCAAAGTNAAACCCTGTTCATGTTGTTGACGTTCCTGGTCATGCAAG
genomic: CTGAGCTGGAGAGGgtaaggcaac ... cgctctgcagAGAGGCAAAGT-AAAACCTGTTCATGTTGTTGACGTTCCTGGTCATGCAAG
EST: gi|218481364|gb|FG954015.1|FG954015
EST:     CAATGGAACAAAACAACGATACTTTCGTGCTTCATTCTGAGCTGGAGAGG                         AGAGGCAAAGTAAAACCTGTTCATGTTGTTGACGTTCCTGGTCATGCAAGG
genomic: CAATGGAACAAAACAACGATACTTTCGTGCTTCATTCTGAGCTGGAGAGGgtaaggcaac ... cgctctgcagAGAGGCAAAGTAAAACCTGTTCATGTTGTTGACGTTCCTGGTCATGCAAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaccatgcatttgctgactacaatatattgatgcatgttcttgttcgctctgcagAGAGGCAAAGTAAAACCTGTTCATGTTGTTGACGTTCCTGGTCATGCAAGGCTCAAACCCAAACTTGATGAAGTCCTGCCTCAAGCAGCTGGAATAGTTT
                                     ttcttgttcgctct  CT-rich tract
                  tacaatatattgat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaggcaacttcttagagacaaatattttaaacatcttgatatgaaatgaaaggaagactatcctgttatatagaaccatgcatttgctgactacaatatattgatgcatgttcttgttcgctctgcagAGAGGCAAAGTAAAACCTGTTCATGTTGTTGACGTTCCTGGTCATGCAAGGCTCAAACCCAAACTTGATGAAGTCCTGCCTCAAGCAGCTGGAATAGTTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA