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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttttgagttattggagtgccttttgtacgcgatttccttggtaaccattccatgccaaatttgtacctaatctcattcatttgtggaaacctctttgcagAACTTTGACACCTGGCCATGATCCTGTCCAAAAGGTTACCTTAATCCCAAGGGGTCAAGCTCGTGGTCTTACATGGTTTATCCCGATGGATGACCCAACA

Basic information

species Zea mays
transcript GRMZM2G110408_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G110408_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os06g45820.1 (Oryza sativa), 3'ss of exon 3
-ttttgagttattggagtgccttttgtacgcgatttccttggtaaccattccatgccaaatttgtacctaatctcattcatttgtggaaac---ctctttgcagAACTTTGACACCTGGCCATGATCCTGTCCAAAAGGTTACCTTAATCCCAAGGGGTCAAGCTCGTGGTCTTACATGGTTTATCCCGATGGATGACCCAACA
 |      | ||  |  |   |  |    | | |||  ||  | ||  || |||  |||| ||      ||    |||||| | ||||||     |||||| ||||||||||| |||||||| || ||||||||||||||||| || ||||| |||||||||||||||||||| |||||||| || || ||||| |||||||| 
gtaagagataatctgcatatttgctaactgtgcttttgtttattac--ttgcatatcaaaattccgtgcaact--attcatatctggaaatgtattctttgtagAACTTTGACGCCTGGCCACGACCCTGTCCAAAAGGTTACTTTGATCCCGAGGGGTCAAGCTCGTGGTCTCACATGGTTCATTCCAATGGACGACCCAACG

upper sequence: GRMZM2G110408_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os06g45820.4 (Oryza sativa), 3'ss of exon 3
-----ttttgagttattggagtgccttttgtacgcgatttccttggtaaccattccatgccaaatttgtacctaatctcattcatttgtggaaac---ctctttgcagAACTTTGACACCTGGCCATGATCCTGTCCAAAAGGTTACCTTAATCCCAAGGGGTCAAGCTCGTGGTCTTACATGGTTTATCCCGATGGATGACCCAACA
     |      | ||  |  |   |  |    | | |||  ||  | ||  || |||  |||| ||      ||    |||||| | ||||||     |||||| ||||||||||| |||||||| || ||||||||||||||||| || ||||| |||||||||||||||||||| |||||||| || || ||||| |||||||| 
gtgggtaagagataatctgcatatttgctaactgtgcttttgtttattac--ttgcatatcaaaattccgtgcaact--attcatatctggaaatgtattctttgtagAACTTTGACGCCTGGCCACGACCCTGTCCAAAAGGTTACTTTGATCCCGAGGGGTCAAGCTCGTGGTCTCACATGGTTCATTCCAATGGACGACCCAACG

upper sequence: GRMZM2G110408_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os06g45820.3 (Oryza sativa), 3'ss of exon 3
----------------------------------ttttgagttat---tggagtgcct-tttgtacgcgatttccttggtaacca-ttccatgccaaatttgtacctaatctcattcatttgtggaaac---ctctttgcagAACTTTGACACCTGGCCATGATCCTGTCCAAAAGGTTACCTTAATCCCAAGGGGTCAAGCTCGTGGTCTTACATGGTTTATCCCGATGGATGACCCAACA----------------------------------
                                  || || || |    |    ||| | ||||    |  |    ||| | |  | || |||  |||| ||      ||    |||||| | ||||||     |||||| ||||||||||| |||||||| || ||||||||||||||||| || ||||| |||||||||||||||||||| |||||||| || || ||||| ||||||||                                   
gtcttgttgcttaccatgaagttgggcatgcaatttgtgggtaagagataatctgcatatttgctaactgtgcttttgtttattacttgcatatcaaaattccgtgcaact--attcatatctggaaatgtattctttgtagaactttgacgcctggccacgaccctgtccaaaagGTTACTTTGATCCCGAGGGGTCAAGCTCGTGGTCTCACATGGTTCATTCCAATGGACGACCCAACGCTCATCTCCAGGCAACAACTGTTCGCCAGAATTG

upper sequence: GRMZM2G110408_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA05G26230.1 (Glycine max), 3'ss of exon 3
ttttgagttattggagtgccttttgtacgcgatttccttggtaaccattccatgccaaatttgt-----acctaatctcattcatttgtggaaacctctttgcagAACTTTGACACCTGGCCATGATCCTGTCCAAAAGGTTACCTTAATCCCAAGGGGTCAAGCTCGTGGTCTTACATGGTTTATCCCGATGGATGACCCAACA
     |   |   |     || ||    |  |     |    | || || ||    | | || |     |  |  ||| |  ||| |||    || |  ||||||||||||||| ||||| |||||| |||| |||||||| ||  || | ||  | ||||||||||| |||||||||||||| || || |  ||||| ||||| 
-----aagcaaaagtaccactgttaagtggtaaaatttaaaaagccgtttcagtaaacaattctcaaaaagttgttctaaaacatctgtttttacttgcttgcagAACTTTGACTCCTGGTCATGATGCTGTGCAAAAGGTAACACTAGTTCCTCGTGGTCAAGCTCGGGGTCTTACATGGTTCATTCCTAATGATGATCCAACT

upper sequence: GRMZM2G110408_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA08G09160.1 (Glycine max), 3'ss of exon 3
ttttgagttattggagtgccttttgtacgcgatttccttggtaaccattccatgccaaatttgt-----acctaatctcattcatttgtggaaacctctttgcagAACTTTGACACCTGGCCATGATCCTGTCCAAAAGGTTACCTTAATCCCAAGGGGTCAAGCTCGTGGTCTTACATGGTTTATCCCGATGGATGACCCAACA
     ||  |    |   || ||   | |  |  |  ||   | |  || ||    | | || |     |  |  ||| |  ||| |||  | || |  ||||||||||||||| ||||| |||||| |||| |||||||| ||  || | ||  | |||||||||||||| ||||||||||| || || |  ||||||||||| 
---caagcaaaactaccaccgttaagaggtaacat--ttaaaagcagtttcagtaaacaattctcaaaaagttgttctgaaacatctgtttatacttgcttgcagAACTTTGACTCCTGGTCATGATGCTGTGCAAAAGGTAACACTAGTTCCTCGCGGTCAAGCTCGTGGACTTACATGGTTCATTCCTAACGATGACCCAACT

upper sequence: GRMZM2G110408_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA09G05820.1 (Glycine max), 3'ss of exon 3
-------------ttttgagttattggagtgccttttgtacgcgatttccttggtaaccattccatgccaaatttgtacctaatctcattcatttgtggaaacctctttgcagAACTTTGACACCTGGCCATGATCCTGTCCAAAAGGTTACCTTAATCCCAAGGGGTCAAGCTCGTGGTCTTACATGGTTTATCCCGATGGATGACCCAACA
             |   ||   |     |   ||  |  |   | | |  |||  ||| ||||||    ||| |||| | |||    ||  || |||          ||||||||||||||| ||||| ||||||||||| ||||| || |||||| | ||  | || ||||||||||||||||| ||||| || ||    ||||||||||| 
atataagtaataatccagaaaaaacaatggttctcattcagaagctgtttttgcaaacaattccaa---aaagttgttcttaaa--tatctatctgta--------cttgcagAACTTTGACTCCTGGTCATGATCCTGTACAAAAAGTAACCTTAGTTCCTCGCGGGCAAGCTCGTGGTCTTACTTGGTTCATTCCTGCTGATGACCCAACT

upper sequence: GRMZM2G110408_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA15G17070.1 (Glycine max), 3'ss of exon 3
--------------------------------------------------------------ttttgagttattggagtgccttt---tgtacgcgatttccttggtaaccat----tccatgccaaa-------tttgtacctaatctcat----tcatttgtggaaacctct------ttgcagAACTTTGACACCTGGCCATGATCCTGTCCAAAAGGTTACCTTAATCCCAAGGGGTCAAGCTCGTGGTCTTACATGGTTTATCCCGATGGATGACCCAACA
                                                               | | | ||  ||     | | |   |  | |  ||         ||| ||      ||| |  ||       ||||||   |||  ||     |  ||  |  | |||| |      ||||||||||||||| ||||| ||||||||||| ||||| || |||||| | ||  | || |||||||| |||||||| ||||| || ||    ||||||||||| 
gtaagccaaaaatcagtaaatgtgtacgatatgatggcaatggaagcaaggtgttattgcctatataaattcatgttacacttgtatataaaagtaatccagaaaaaaacaatggttctcattcagaagctgttttttgtaaacaattccaaaaagttgttcttaaatacctatctgtacttgcagAACTTTGACTCCTGGTCATGATCCTGTACAAAAAGTAACCTTAGTTCCTCGTGGGCAAGCTCGGGGTCTTACTTGGTTCATTCCTGCTGATGACCCAACT

upper sequence: GRMZM2G110408_T01 (Zea mays), 3'ss of exon 3
lower sequence: PP1S9_115V6.1 (Physcomitrella patens), 3'ss of exon 4
---------------ttttgagtt---attggagtgccttttgtacgcgatttccttg-gtaaccattccatgccaaatttgtacctaatctcattcatttgtgga--aacctctt----tgcagAACTTTGACACCTGGCCATGATCCTGTCCAAAAGGTTACCTTAATCCCAAGGGGTCAAGCTCGTGGTCTTACATGGTTTATCCCGATGGATGACCCAACA
                 |  | ||   | || ||   || | | |       || |   | |   | |   ||  | ||   |   || ||| | ||   | | ||  ||| |  |    ||||| || |||||||| || |||||| | || |||||||||||| | || || ||||||||||| |||||||| || |||||||||||    || ||||| || 
gtacccctcattcaccatccaattgcaactgcagctgctctggcattttccctcttcctgcagtaaatgtctgtgagatgcttttata-tctaagtctagtatcgatcaactttgtgtggtgcagGACCTTGACACCAGGGCATGATGCGGTGCAAAAGGTTACCCTTATTCCCAGGGGTCAAGCCCGTGGTCTCACCTGGTTTATCCCAGGCGACGACCCTACC

upper sequence: GRMZM2G110408_T01 (Zea mays), 3'ss of exon 3
lower sequence: PP1S156_30V6.1 (Physcomitrella patens), 3'ss of exon 4
--------ttttgagttattggagtgccttt-tgtacgcgatttccttg-----gtaaccattccatgccaaatttgtacctaatctca---ttcatttgtgga--aacctctt----tgcagAACTTTGACACCTGGCCATGATCCTGTCCAAAAGGTTACCTTAATCCCAAGGGGTCAAGCTCGTGGTCTTACATGGTTTATCCCGATGGATGACCCAACA
        | ||     ||   | |||  || |    ||  |||| |||     | ||   ||| | |   |   || |   |     |    | |||  |  |  ||     |    ||||| || |||||||| ||||||||| | || |||||||||||| | || || |||||||||||||||||||| || ||||| || ||    || ||||| || 
gtactttttctttcaccatccaattgcaattgtacctgcagtttcattgtctctggaaaatttctaaggttacggtgcattgacctctaaggcttattaataaattaattgtgtgaggtgcagGACCTTGACACCAGGCCATGATGCAGTGCAAAAGGTTACCCTGATTCCTAGGGGTCAAGCTCGTGGTCTCACCTGGTTCATTCCAGGCGAGGACCCCACC

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|211130729|gb|FL008630.1|FL008630
EST:     AAGAGCAAAAGTCTTGTTGCTTACCATGAAATCGGGCATGCAATTTGCGG                         AACTTTGACACCTGGCCATGATCCTGTCCAAAAGGTTACCTTAATCCCAAG
genomic: AAGAGCAAAAGTCTTGTTGCTTACCATGAAGTCGGGCATGCAATTTGCGGgtaagagatg ... ctctttgcagAACTTTGACACCTGGCCATGATCCTGTCCAAAAGGTTACCTTAATCCCAAG
EST: gi|32924261|gb|CF029073.1|CF029073
EST:     AAGAGCAAAAGTCTTGTTGCTTACCATGAAGTCGGGCATGCAATTTGCGG                         AACTTTGACACCTGGCCATGATCCTGTCCAAAAGGTTACCTTAATCCCAAG
genomic: AAGAGCAAAAGTCTTGTTGCTTACCATGAAGTCGGGCATGCAATTTGCGGgtaagagatg ... ctctttgcagAACTTTGACACCTGGCCATGATCCTGTCCAAAAGGTTACCTTAATCCCAAG
EST: gi|89248872|gb|DY620658.1|DY620658
EST:     AAGAGCAAAAGTCTTGTTGCTTACCATGAAGTCGGGCATGCAATTTGCGG                         AACTTTGACACCTGGCCATGATCCTGTCCAAAAGGTTACCTTAATCCCAAG
genomic: AAGAGCAAAAGTCTTGTTGCTTACCATGAAGTCGGGCATGCAATTTGCGGgtaagagatg ... ctctttgcagAACTTTGACACCTGGCCATGATCCTGTCCAAAAGGTTACCTTAATCCCAAG
EST: gi|37396149|gb|CF635362.1|CF635362
EST:     AAGAGCAAAAGTCTTGTTGCTTACCATGAAGTCGGGCATGCAATTTGCGG                         AACTTTGACACCTGGCCATGATCCTGTCCAAAAGGTTACCTTAATCCCAAG
genomic: AAGAGCAAAAGTCTTGTTGCTTACCATGAAGTCGGGCATGCAATTTGCGGgtaagagatg ... ctctttgcagAACTTTGACACCTGGCCATGATCCTGTCCAAAAGGTTACCTTAATCCCAAG
EST: gi|32924520|gb|CF029332.1|CF029332
EST:     AAGAGCAAAAGTCTTGTTGCTTACCATGAAGTCGGGCATGCAATTTGCGG                         AACTTTGACACCTGGCCATGATCCTGTCCAAAAGGTTACCTTAATCCCAAG
genomic: AAGAGCAAAAGTCTTGTTGCTTACCATGAAGTCGGGCATGCAATTTGCGGgtaagagatg ... ctctttgcagAACTTTGACACCTGGCCATGATCCTGTCCAAAAGGTTACCTTAATCCCAAG
EST: gi|94472629|gb|EB701587.1|EB701587
EST:     AAGAGCAAAAGTCTTGTTGCTTACCATGAAGTCGGGCATGCAATTTGCGG                         AACTTTGACACCTGGCCATGATCCTGTCCAAAAGGTTACCTTAATCCCAAG
genomic: AAGAGCAAAAGTCTTGTTGCTTACCATGAAGTCGGGCATGCAATTTGCGGgtaagagatg ... ctctttgcagAACTTTGACACCTGGCCATGATCCTGTCCAAAAGGTTACCTTAATCCCAAG
EST: gi|67033229|gb|CO461978.1|CO461978
EST:     AAGAGCAAAAGTCTTGTTGCTTACCATGAAGTTGGGCATGCAATTTGCGG                         AACTTTGACACCTGGCCATGATCCTGTCCAAAAGGTTACCTTAATCCCAAG
genomic: AAGAGCAAAAGTCTTGTTGCTTACCATGAAGTCGGGCATGCAATTTGCGGgtaagagatg ... ctctttgcagAACTTTGACACCTGGCCATGATCCTGTCCAAAAGGTTACCTTAATCCCAAG
EST: gi|148945969|gb|EC891262.2|EC891262
EST:     AAGAGCAAAAGTCTTGTTGCTTACCATGAAGTCGGGCATGCAATTTGCGG                         AACTTTGACACCTGGCCATGATCCTGTCCAAAAGGTTACCTTAATCCCAAG
genomic: AAGAGCAAAAGTCTTGTTGCTTACCATGAAGTCGGGCATGCAATTTGCGGgtaagagatg ... ctctttgcagAACTTTGACACCTGGCCATGATCCTGTCCAAAAGGTTACCTTAATCCCAAG
EST: gi|148955091|gb|EC900605.2|EC900605
EST:     AAGAGCAAAAGTCTTGTTGCTTACCATGAAGTCGGGCATGCAATTTGCGG                         AACTTTGACACCTGGCCATGATCCTGTCCAAAAGGTTACCTTAATCCCAAG
genomic: AAGAGCAAAAGTCTTGTTGCTTACCATGAAGTCGGGCATGCAATTTGCGGgtaagagatg ... ctctttgcagAACTTTGACACCTGGCCATGATCCTGTCCAAAAGGTTACCTTAATCCCAAG
EST: gi|32850880|gb|CD990561.1|CD990561
EST:     AAGAGCAAAAGTCTTGTTGCTTACCATGAAGTCGGGCATGCAATTTGCGG                         AACTTTGACACCTGGCCATGATCCTGTCCAAAAGGTTACCTTAATCCCAAG
genomic: AAGAGCAAAAGTCTTGTTGCTTACCATGAAGTCGGGCATGCAATTTGCGGgtaagagatg ... ctctttgcagAACTTTGACACCTGGCCATGATCCTGTCCAAAAGGTTACCTTAATCCCAAG
EST: gi|32924145|gb|CF028957.1|CF028957
EST:     AAGAGCAAAAGTCTTGTTGCTTACCATGAAGTCGGGCATGCAATTTGCGG                         AACTTTGACACCTGGCCATGATCCTGTCCAAAAGGTTACCTTAATCCCAAG
genomic: AAGAGCAAAAGTCTTGTTGCTTACCATGAAGTCGGGCATGCAATTTGCGGgtaagagatg ... ctctttgcagAACTTTGACACCTGGCCATGATCCTGTCCAAAAGGTTACCTTAATCCCAAG
EST: gi|32850859|gb|CD990540.1|CD990540
EST:     AAGAGCAAAAGTCTTGTTGCTTACCATGAAGTCGGGCATGCAATTTGCGG                         AACTTTGACACCTGGCCATGATCCTGTCCAAAAGGTTACCTTAATCCCAAG
genomic: AAGAGCAAAAGTCTTGTTGCTTACCATGAAGTCGGGCATGCAATTTGCGGgtaagagatg ... ctctttgcagAACTTTGACACCTGGCCATGATCCTGTCCAAAAGGTTACCTTAATCCCAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cattccatgccaaatttgtacctaatctcattcatttgtggaaacctctttgcagAACTTTGACACCTGGCCATGATCCTGTCCAAAAGGTTACCTTAATCCCAAGGGGTCAAGCTCGTGGTCTTACATGGTTTATCCCGATGGATGACCCAACA
                   acctaat  putative branch site (score: 3)
                                            cctctttgc  putative PPT
           aaatttgta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttttgagttattggagtgccttttgtacgcgatttccttggtaaccattccatgccaaatttgtacctaatctcattcatttgtggaaacctctttgcagAACTTTGACACCTGGCCATGATCCTGTCCAAAAGGTTACCTTAATCCCAAGGGGTCAAGCTCGTGGTCTTACATGGTTTATCCCGATGGATGACCCAACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA