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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtttccctgcatacaaactgaagaatgttcatgctttctcaaagcgtagtagtttcttgttgttttttttttacattttaactatttcattatgttgtccttactgtgatacttccttgcggatgcagGATTTATTGCCATGTATGCTACTCTTGCAAGCAGAGATGTG

Basic information

species Zea mays
transcript GRMZM5G879882_T03
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G879882_T03 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os01g53680.1 (Oryza sativa), 3'ss of exon 9
gtaagtttccctgcatacaaactgaagaatgttcatgctttctcaaagcgtagtagtttcttgttgttttttttttacattttaactatttcattatgttgtccttactgtgatacttccttgcggatgcagGATTTATTGCCATGTATGCTACTCTTGCAAGCAGAGATGTG
                               ||||    |||   | | | |    |      ||  |   |||||   |||||  |||||||||||  |||||||| |    | ||    | |   |||||| |||||||| |||||||||||||||||||||||||| |||
------------------------------attcacatattcctcatgtgaatccatgatgaatttctaacttttt-tgttttagttatttcattatactgtccttattccttttctatggtacct-tgcagGGTTTATTGCAATGTATGCTACTCTTGCAAGCAGAGACGTG

upper sequence: GRMZM5G879882_T03 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA06G09320.1 (Glycine max), 3'ss of exon 8
gtaagtttccctgcatacaaactgaagaatgttcatgctttctcaaagcgtagtagtttcttgttgttttttttttacattttaactatttcattatgttgtccttactgtgatacttccttgcggatgcagGATTTATTGCCATGTATGCTACTCTTGCAAGCAGAGATGTG-----------------------------------------------------------
                      | |  | |||   ||  || |   | |||   |||        |||  ||||    || |  |   |||  || |  |||      | ||||   | ||   |  |||||| |||||||| |||||||| |||||||| ||||||||||||                                                           
----------------------taacaattgtaagtgtatttt---atcgtctaagtgcacca--gttgcttttgaggatctggatctttttcttttcctgt----gttatgatgaatact-atgactgcagGTTTTATTGCAATGTATGCCACTCTTGCTAGCAGAGATGTGGACTGTTGCTTGATTCCAGAGTCACCCTTCTACCTTGAAGGAAAGGGTGGACTTTTTGA

upper sequence: GRMZM5G879882_T03 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA13G42990.1 (Glycine max), 3'ss of exon 9
------------gtaagtttccctgcata-caaactgaagaatgttcatgctttctcaaagcgtagtagtttcttgttgttttttttttacattttaactatttcattatgttgtccttactgtgatacttccttgcggatgcagGATTTATTGCCATGTATGC----TACTCTTGCAAGCAGAGATGTG---------------
             | |   |  ||||  | ||||   |  |    ||  ||| |||  ||   |||| ||||   ||       | || |||||| |  |     ||| | | | | |   ||  |  ||| |  || |      |  || |||||   |   |     || |||  |    |||                    
ttatcattaatcatgacagtttctgctgagcaaaacaagaagaaatctagctatcttgaat--tagttgtttacagtcaccaaatattgacatttca--tgcagGATT-TATCGCCATGTATGCAACTCTTGCCAGCCGTGATGTGGATTGTTGCCTGATTCCCGAATCACCCTTTTACCTGGAGGGTCCAGGAGGCCTGTTGGA

upper sequence: GRMZM5G879882_T03 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA01G00870.1 (Glycine max), 3'ss of exon 9
gtaagtttccctgcatacaaactgaagaatgttcatgctttctcaaagcgtagtagtt-tcttgttgttttttttttacattttaactatttcattatgttgtccttactgtgatacttccttgcggatgcagGATTTATTGCCATGTATGCTACTCTTGCAAGCAGAGATGTG-----------------------------------------------------------
                       ||| |   ||  || | |    |||   |  |||| |    |||    | ||    |  || | | || | | || |   | ||| | ||  ||||       ||| ||||||||||||| ||||||||||||||||| ||  |||| |||                                                           
----------------------agaaaagaattgctgttat----aagttcaaaagttattccattgaagctgttagcgaaattgatt-ttgcttcatatatgctttattttgg-acttat-----gatacagGATTTATTGCAATGTATGCTACTCTTGCGAGTCGAGACGTGGATTGTTGCTTAATTCCAGAGTCACCCTTTTACCTTGAAGGTCCTGGTGGACTCTATGA

upper sequence: GRMZM5G879882_T03 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA07G15170.4 (Glycine max), 3'ss of exon 9
gtaagtttccctgcatacaaactgaagaatgttcatgctttctcaaagcgtagtagtttcttgttgttttttttttacattttaactatttcattatgttgtccttactgtgatacttccttgcggatgcagGATTTATTGCCATGTATGCTACTCTTGCAAGCAGAGATGTG-----------------------------------------------------------
                   ||  |||        ||| | |   ||||        | |    |||   || |  |  |  || ||| || | | || |   | ||| | ||  | ||       ||||||||||||||||| ||||||||||| ||||||||  |||| |||                                                           
------------------gaaaagaacggctagtatgatattcaaaagt-------tcttccattgacattgtcatcaaacttgact-ttgcttcatatatgctttattttgg-atttat-----gatgcagGATTTATTGCAATGTATGCTACACTTGCAAGTCGAGACGTGGACTGTTGCTTAATTCCAGAGTCACCCTTTTACCTTGAAGGTACTGGTGGACTCTATGA

upper sequence: GRMZM5G879882_T03 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA15G02400.1 (Glycine max), 3'ss of exon 9
-------------gtaagtttccctgcata-caaactgaagaatgttcatgctttctcaaagc----gtagtagtttcttgttgttttttttttacattttaactatt-tcat-tatgttgtccttact----gtgatact--tccttgcg-gatgcagGATTTATTGCCATGTATGCTACTCTTGCAAGCAGAGATGTG
              | |   |   |||  | ||||   |  |    || |||| |||  ||      ||   |||  |    | ||    ||| |      |  |||   ||| ||||     ||| |     |||||  |  |  ||||  ||| |  || | |      |   ||           || |  | ||  
tttatcattaatcatgacagttgttgctgagcaaaacaagaagaaatcttgctatcttgaattagttgttacagtgaccaaatattgacatttcatgcagGATTTATCGCCATGTATGCAACTCTTGCCAGCCGTGATGTTGATTGTTGCTTGATTCCAGAATCACCCTTTTACCTGGAGGGTCCAGGAGGACTGTTGGA

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|40334982|gb|CK369052.1|CK369052
EST:     AAGTGCTGAAAATGGAATAGGTTTAGTGAAGCTTATGGGTCGCTATAGTG                         GATTTATTGCCATGTTTGCTACTCTTGCAAGCAGAGATGTG
genomic: AAGTGCTGAAAATGGAATAGGTTTAGTGAAGCTTATGGGTCGCTATAGTGgtaagtttcc ... gcggatgcagGATTTATTGCCATGTATGCTACTCTTGCAAGCAGAGATGTG
EST: gi|87153557|gb|DY398346.1|DY398346
EST:     AAGTGCTGAAAATGGAATAGGTTTAGTGAAGCTTATGGGTCGCTATAGTG                         GATTTATTGCCATGTATGCTACTCTTGCAAGCAGAGATGTG
genomic: AAGTGCTGAAAATGGAATAGGTTTAGTGAAGCTTATGGGTCGCTATAGTGgtaagtttcc ... gcggatgcagGATTTATTGCCATGTATGCTACTCTTGCAAGCAGAGATGTG
EST: gi|19351112|gb|BM895644.1|BM895644
EST:     AAGTGCTGAAAATGGAATAGGTTTAGTGAAGCTTATGGGTCGCTATAGTG                         GATTTATTGCCATGTATGCTACTCTCGCAAGCAGAGATGTG
genomic: AAGTGCTGAAAATGGAATAGGTTTAGTGAAGCTTATGGGTCGCTATAGTGgtaagtttcc ... gcggatgcagGATTTATTGCCATGTATGCTACTCTTGCAAGCAGAGATGTG
EST: gi|108954346|gb|EC365109.1|EC365109
EST:     AAGTGCTGAAAATGGAATAGGTTTAGTGAAGCTTATGGGTCGCTATAGTG                         GATTTATTGCCATGTATGCTACTCTTGCAAGCAGAGATGTG
genomic: AAGTGCTGAAAATGGAATAGGTTTAGTGAAGCTTATGGGTCGCTATAGTGgtaagtttcc ... gcggatgcagGATTTATTGCCATGTATGCTACTCTTGCAAGCAGAGATGTG
EST: gi|22491553|gb|BU051476.1|BU051476
EST:     AAGTGCTGAAAATGGAATAGGTTTAGTGAAGCTTATGGGTCGCTATAGTG                         GATTTTATTGCCATGTATGCTACTCTTGCAAGCAGAGATGTG
genomic: AAGTGCTGAAAATGGAATAGGTTTAGTGAAGCTTATGGGTCGCTATAGTGgtaagtttcc ... gcggatgcagGATTT-ATTGCCATGTATGCTACTCTTGCAAGCAGAGATGTG
EST: gi|33942634|gb|CF349234.1|CF349234
EST:     AAGTGCTGAAAATGGAATAGGTTTAGTGAAGCTTATGGGTCGCTATAGTG                         GATTTATTGCCATGTATGCTACTCTTGCAAGCAGAGATGTG
genomic: AAGTGCTGAAAATGGAATAGGTTTAGTGAAGCTTATGGGTCGCTATAGTGgtaagtttcc ... gcggatgcagGATTTATTGCCATGTATGCTACTCTTGCAAGCAGAGATGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cattttaactatttcattatgttgtccttactgtgatacttccttgcggatgcagGATTTATTGCCATGTATGCTACTCTTGCAAGCAGAGATGTG
                        tccttac  putative branch site (score: 2)
                                      cttccttgc  putative PPT
     taactatttcattat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtttccctgcatacaaactgaagaatgttcatgctttctcaaagcgtagtagtttcttgttgttttttttttacattttaactatttcattatgttgtccttactgtgatacttccttgcggatgcagGATTTATTGCCATGTATGCTACTCTTGCAAGCAGAGATGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG