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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagacttagttccttttaatgaaattatggatgttgaagataacatgatcgattcttctacatggtggctggcatagttacatctagacaaattgtttagctattaatttgtagataatggggacattatagtaatatacacctgtctcgttgtcctcattttgcagATTGAGCCAGAATCACAAACTCAACTTCTGGATGCCACTATGAATATGGAGGGTGTTCTACTAGCTGGAGTTCCTGGGGCCGGTGGCTTTGATGCAGTTT

Basic information

species Oryza sativa
transcript LOC_Os03g14830.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g14830.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G030839_T02 (Zea mays), 3'ss of exon 10
gtaagacttagttccttttaatgaaattatggatgttgaag-ataacatgatcgat-------tcttctacatggtggctggcatagttacatctagacaaattgtttagctattaatttgtag-------ataatggggacattatagtaatatacacctgtct-----cgttgtcctcattttgcagATTGAGCCAGAATCACAAACTCAACTTCTGGATGCCACTATGAATATGGAGGGTGTTCTACTAGCTGGAGTTCCTGGGGCCGGTGGCTTTGATGCAGTTT
       | || |||  |  |   || |     |  || || ||| |||| ||||        | |||   |||  |  ||||||| | ||| |   |    |   | || ||  || ||||||       ||||  ||| || |||  | ||  |  | ||| |     | ||| ||| |||||| ||||||||||||| |||||||| |  || || ||||||||||||||||||||||||||| |||| ||||||||||| || || |||||||| |||||||| |
------gtaaggtcccctatacataactgcaagtactgtagtatagcatgctcgaaggaagtatattcagtatgacgtttggcataatcacagcagtatgggtgactaagttacgaaattgtaggtataatataacagggtcaatattcttattcaatcttgtttgacatctttgccctaattttgtagATTGAGCCAGATTCACAAACACGGCTACTAGATGCCACTATGAATATGGAGGGTGTTTTACTGGCTGGAGTTCCGGGAGCTGGTGGCTTCGATGCAGTGT

upper sequence: LOC_Os03g14830.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G030839_T01 (Zea mays), 3'ss of exon 11
gtaagacttagttccttttaatgaaattatggatgttgaag-ataacatgatcgat-------tcttctacatggtggctggcatagttacatctagacaaattgtttagctattaatttgtag-------ataatggggacattatagtaatatacacctgtct-----cgttgtcctcattttgcagATTGAGCCAGAATCACAAACTCAACTTCTGGATGCCACTATGAATATGGAGGGTGTTCTACTAGCTGGAGTTCCTGGGGCCGGTGGCTTTGATGCAGTTT
          || || | ||    || |     |  || || ||| |||| ||||        | |||   |||  |  ||||||| | ||| |   |    |   | || ||  || ||||||       ||||  ||| || |||  | ||  |  | ||| |     | ||| ||| |||||| ||||||||||||| |||||||| |  || || ||||||||||||||||||||||||||| |||| ||||||||||| || || |||||||| |||||||| |
----------gtcccctata-cataactgcaagtactgtagtatagcatgctcgaaggaagtatattcagtatgacgtttggcataatcacagcagtatgggtgactaagttacgaaattgtaggtataatataacagggtcaatattcttattcaatcttgtttgacatctttgccctaattttgtagATTGAGCCAGATTCACAAACACGGCTACTAGATGCCACTATGAATATGGAGGGTGTTTTACTGGCTGGAGTTCCGGGAGCTGGTGGCTTCGATGCAGTGT

upper sequence: LOC_Os03g14830.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G030839_T03 (Zea mays), 3'ss of exon 11
gtaagacttagttccttttaatgaaattatggatgttgaagataacatgatcgattcttctacatggtggctggcatagttacatctagacaaattgtttagctattaatttgtagataatggggacattatagtaatatacacctgtct-----cgttgtcctcattttgcagATTGAGCCAGAATCACAAACTCAACTTCTGGATGCCACTATGAATATGGAGGGTGTTCTACTAGCTGGAGTTCCTGGGGCCGGTGGCTTTGATGCAGTTT
                                                                                                          ||  |   | ||||  ||| || |||  | ||  |  | ||| |     | ||| ||| |||||| ||||||||||||| |||||||| |  || || ||||||||||||||||||||||||||| |||| ||||||||||| || || |||||||| |||||||| |
---------------------------------------------------------------------------------------------------------gtaggtataatataacagggtcaatattcttattcaatcttgtttgacatctttgccctaattttgtagATTGAGCCAGATTCACAAACACGGCTACTAGATGCCACTATGAATATGGAGGGTGTTTTACTGGCTGGAGTTCCGGGAGCTGGTGGCTTCGATGCAGTGT

upper sequence: LOC_Os03g14830.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G019260_T01 (Zea mays), 3'ss of exon 9
gtaagacttagttccttttaatgaaattatggatgttgaagataacatgatcgattcttctacatggtggctggcatagttacatctagacaaattgtttagctattaatttgtagata--atggggacattatagtaatatacacctgtct-----cgttgtcctcattttgcagATTGAGCCAGAATCACAAACTCAACTTCTGGATGCCACTATGAATATGGAGGGTGTTCTACTAGCTGGAGTTCCTGGGGCCGGTGGCTTTGATGCAGTTT
                                                                            || | ||| | | |   ||   | || ||| || |||||||||  || ||| || |||  | ||  |  | ||| |     | ||| ||| |||||| ||||||||||||| |||||||| |  || || || |||||||||||||||||||||||| |||| ||||||||||| || || |||||||| |||||||| |
----------------------------------------------------------------------------taatcacagcaacatggatcactaagttatgaaattgtagatataatagggtcaatattcttattcaaccttgtttgatatctttgccctaattttgtagATTGAGCCAGATTCACAAACACGGCTACTTGACGCCACTATGAATATGGAGGGTGTTTTACTTGCTGGAGTTCCGGGAGCTGGTGGCTTCGATGCAGTAT

upper sequence: LOC_Os03g14830.1 (Oryza sativa), 3'ss of exon 9
lower sequence: AT1G31910.1 (Arabidopsis thaliana), 3'ss of exon 11
gtaag--acttagttcc-ttttaatgaa-attatggatgttga-agataa------catgatcgatt----cttctacatggtgg--ctggcatagttaca---tctagacaaattgtttagctattaatttgtagataatggggacattatagtaatatacacctgtctcgttgtcctcatt-----------ttgcagATTGAGCCAGAATCACAAACTCAACTTCTGGATGCCACTATGAATATGGAGGGTGTTCTACTAGCTGGAGTTCCTGGGGCCGGTGGCTTTGATGCAGTTT
|||||  | || ||||  |||| ||      |   ||| |  |  ||  |      ||||||   ||    ||  | |||  |    || |  | | |  |   |||  |||   |   |          ||  | | | |  | |  |   |  |||  ||  |    |  ||| ||||              |||||||| ||||| ||||| |||||||||||| ||||| | || |||| |   || || |||||||| ||||| |||||||| || ||||| ||||||||  | |
gtaagtgattttgttctgttttgatagttgcttcagatctcaacggaccatttgtgcatgattacttagtgctgttgcataataatactcgtctggctgtagaatcttaacagcatacatgatatacgggttccacaaattccgcatttagaacaaattgacttcatcataattgacctcgagggaccatggaattgcagATAGAGCCTGAATCTCAAACTCAACTTTTGGATTCTACAATGAGTGCTGAAGGAGTTCTACTTGCTGGTGTTCCTGGAGCTGGTGGATTTGATGCCATAT

upper sequence: LOC_Os03g14830.1 (Oryza sativa), 3'ss of exon 9
lower sequence: Vv02s0012g02530.t01 (Vitis vinifera), 3'ss of exon 9
gtaagacttagttccttttaatgaaattatggatgttgaagataacatgatcgattcttctacatggtggctggcatagttacatctagacaaattgtttagctattaatttgtagataatggggacattatagtaatatacacctgtctcgttgtcctcattttgcagATTGAGCCAGAATCACAAACTCAACTTCTGGATGCCACTATGAATATGGAGGGTGTTCTACTAGCTGGAGTTCCTGGGGCCGGTGGCTTTGATGCAGTTT
                                                                  |||| ||   ||  |    ||| |     | |  |||  |   | |    |  |||  |   |   |||   ||  |  | | |   | |||| | || |||||| || ||  | || |||||||  ||| ||||||| |||||| | ||||| || |||||| | ||||||||||| || || ||||| ||||||||| |||
------------------------------------------------------------------gtgggtgatctaaatttcacta-atgtgctttcaagccctccctattatcaccatgctgttctatcagtt-catcaatttcttttactttcctaaatt-gcagATAGAACCCAATTCTCAAACTCGGCTTTTGGATGCTACTATGGACATGGAAGGAGTTCTATTGGCTGGAGTTCCAGGAGCAGGTGGATTTGATGCAATTT

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|88958473|gb|CI095989.1|CI095989
EST:     TGCGAGAGATGGGCATAGCAGCTGGTGTTCCA                         ATTGAGCCAGAATCACAAACTCAACTTCTGGATGCCACTATGAATATGGAG
genomic: TGCGAGAGATGGGCATAGCAGCTGGTGTTCCAgtaagactta ... cattttgcagATTGAGCCAGAATCACAAACTCAACTTCTGGATGCCACTATGAATATGGAG
EST: gi|86863992|gb|CI332922.1|CI332922
EST:     TTGAAATAAGGCTTCATATGCGAGAGATGGGCATAGCAGCTGGTGTTCCA                         ATTGAGCCAGAATCACAAACTCAACTTCTGGATGCCACTATGAATATGGAG
genomic: TTGAAATAAGGCTTCATATGCGAGAGATGGGCATAGCAGCTGGTGTTCCAgtaagactta ... cattttgcagATTGAGCCAGAATCACAAACTCAACTTCTGGATGCCACTATGAATATGGAG
EST: gi|88968305|gb|CI098547.1|CI098547
EST:     TTGAAATAAGGCTTCATATGCGAGAGATGGGCATAGCAGCTGGTGTTCCA                         ATTGAGCCAGAATCACCAACTCAAGTTCTGGATGCCACTATGAATATGGAG
genomic: TTGAAATAAGGCTTCATATGCGAGAGATGGGCATAGCAGCTGGTGTTCCAgtaagactta ... cattttgcagATTGAGCCAGAATCACAAACTCAACTTCTGGATGCCACTATGAATATGGAG
EST: gi|88225815|gb|CI225731.1|CI225731
EST:     ATAAGGCTTCATATGCGAGAGATGGGCATAGCAGCTGGTGTTCCA                         ATTGAGCCAGAATCACAAACTCAACTTCTGGATGCCACTATGAATATGGAG
genomic: ATAAGGCTTCATATGCGAGAGATGGGCATAGCAGCTGGTGTTCCAgtaagactta ... cattttgcagATTGAGCCAGAATCACAAACTCAACTTCTGGATGCCACTATGAATATGGAG
EST: gi|86436947|gb|CI118669.1|CI118669
EST:     TTGAAATAAGGCTTCATATGCGAGAGATGGGCATAGCAGCTGGTGTTCCC                         ATTGAGCCAGAATCACAAACTCAACTTCTGGATGCCACTATGAATATGGAG
genomic: TTGAAATAAGGCTTCATATGCGAGAGATGGGCATAGCAGCTGGTGTTCCAgtaagactta ... cattttgcagATTGAGCCAGAATCACAAACTCAACTTCTGGATGCCACTATGAATATGGAG
EST: gi|86492705|gb|CI135338.1|CI135338
EST:     TTGAAATAAGGCTTCATATGCGAGAGATGGGCATAGCAGCTGGTGTTCCA                         ATTGAGCCAGAATCACAAACTCAACTTCTGGATGCCACTATGAATATGGAG
genomic: TTGAAATAAGGCTTCATATGCGAGAGATGGGCATAGCAGCTGGTGTTCCAgtaagactta ... cattttgcagATTGAGCCAGAATCACAAACTCAACTTCTGGATGCCACTATGAATATGGAG
EST: gi|88842761|gb|CI371661.1|CI371661
EST:     ATGCGAGAGATGGGCATAGCAGCTGGTGTTCCA                         ATTGAGCCAGAATCACAAACTCAACTTCTGGATGCCACTATGAATATGGAG
genomic: ATGCGAGAGATGGGCATAGCAGCTGGTGTTCCAgtaagactta ... cattttgcagATTGAGCCAGAATCACAAACTCAACTTCTGGATGCCACTATGAATATGGAG
EST: gi|88961521|gb|CI096802.1|CI096802
EST:     TTGAAATAAGGCTTCATATGCGAGAGATGGGCATAGCAGCTGGTGTTCCA                         ATTGAGCCAGAATCACCAACTCAACTTCTGGATGCCACTATGAATATGGAG
genomic: TTGAAATAAGGCTTCATATGCGAGAGATGGGCATAGCAGCTGGTGTTCCAgtaagactta ... cattttgcagATTGAGCCAGAATCACAAACTCAACTTCTGGATGCCACTATGAATATGGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agataatggggacattatagtaatatacacctgtctcgttgtcctcattttgcagATTGAGCCAGAATCACAAACTCAACTTCTGGATGCCACTATGAATATGGAGGGTGTTCTACTAGCTGGAGTTCCTGGGGCCGGTGGCTTTGATGCAGTTT
                                         tcctcatttt  CT-rich tract
           acattatagtaatata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagacttagttccttttaatgaaattatggatgttgaagataacatgatcgattcttctacatggtggctggcatagttacatctagacaaattgtttagctattaatttgtagataatggggacattatagtaatatacacctgtctcgttgtcctcattttgcagATTGAGCCAGAATCACAAACTCAACTTCTGGATGCCACTATGAATATGGAGGGTGTTCTACTAGCTGGAGTTCCTGGGGCCGGTGGCTTTGATGCAGTTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA