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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaagatgccttgatatcttgtttcgggcttactgtaatttcctcaagattatgtgaaaaatgggactgtgatgtaacctttggtgtgaatgccaaatgcagGAAGTTGAAGCAACCATAATTAATGGGAAAGGGACTGAAACTGGGCACATAATTGTCACCACTACTGGTGGCAAGAATGGTCAACCAAAACAG

Basic information

species Zea mays
transcript GRMZM2G024151_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G024151_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os01g14860.1 (Oryza sativa), 3'ss of exon 2
gtgaagatgccttgatatcttgtttcgggcttactgtaatttcctcaagattatgtgaaaaatgggactgtgatgtaacct-ttggtgtgaatgccaaatgcagGAAGTTGAAGCAACCATAATTAATGGGAAAGGGACTGAAACTGGGCACATAATTGTCACCACTACTGGTGGCAAGAATGGTCAACCAAAACAG
           |   | | |  |   | |   | | ||||||| || |  |    || ||| | | ||| || |||||| | | |   ||||||  |||| |||||||||||||| || || ||||| || || || || ||||| || |||||||||||||| |||||||||||||  |||||||| || ||||||
----------gtaagtctatcatgatgaga--agtttaatttcttccatgtgccatgtaaatttg-actttgttgtaacatgtcgaactgaatggtaaatccagGAAGTTGAAGCGACTATTATTAACGGCAAGGGAACAGAAACCGGCCACATAATTGTCACAACTACTGGTGGCAGAAATGGTCAGCCGAAACAG
















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|5566746|gb|AI881612.1|AI881612
EST:     CCGAGAAGTTGCAAGATCAGATGAACGAGCTAAAGATTAGAGATGATAAG                         GAAGTTGAAGCAACCATAATTAATGGGAAAGGGACTGAAACTGGGCACATA
genomic: CCGAGAAGTTGCAAGATCAGATGAACGAGCTAAAGATTAGAGATGATAAGgtgaagatgc ... ccaaatgcagGAAGTTGAAGCAACCATAATTAATGGGAAAGGGACTGAAACTGGGCACATA
EST: gi|19822195|gb|BQ048219.1|BQ048219
EST:     CCGAGAAGTTGCAAGATCAGATGAACGAGCTAAAGATTAGAGATGATAAG                         GAAGTTGAAGCAACCATAATTAATGGGAAAGGGACTGAAACTGGGCACATA
genomic: CCGAGAAGTTGCAAGATCAGATGAACGAGCTAAAGATTAGAGATGATAAGgtgaagatgc ... ccaaatgcagGAAGTTGAAGCAACCATAATTAATGGGAAAGGGACTGAAACTGGGCACATA
EST: gi|32928666|gb|CF033478.1|CF033478
EST:     CCGAGAAGTTGCAAGATCAGATGAACGAGCTAAAGACTAGAGATGATAAG                         GAAGTTGAAGCAACCATAATTAATGGGAAAGGGACTGAAACTGGGCACATA
genomic: CCGAGAAGTTGCAAGATCAGATGAACGAGCTAAAGATTAGAGATGATAAGgtgaagatgc ... ccaaatgcagGAAGTTGAAGCAACCATAATTAATGGGAAAGGGACTGAAACTGGGCACATA
EST: gi|32929341|gb|CF034153.1|CF034153
EST:     CCGAGAAGTTGCAAGATCAGATGAACGAGCTAAAGACTAGAGATGATAAG                         GAAGTTGATTCAACCATAATTAATGGGAAAGGGACTGAAACTGGGCACATA
genomic: CCGAGAAGTTGCAAGATCAGATGAACGAGCTAAAGATTAGAGATGATAAGgtgaagatgc ... ccaaatgcagGAAGTTGAAGCAACCATAATTAATGGGAAAGGGACTGAAACTGGGCACATA
EST: gi|32928546|gb|CF033358.1|CF033358
EST:     CCGAGAAGTTGCAAGATCAGATGAACGAGCTAAAGATTAGAGATGATAAG                         GAAGTTGAAGCAACCATAATTAATGGGAAAGGGACTGAAACTGGGCACATA
genomic: CCGAGAAGTTGCAAGATCAGATGAACGAGCTAAAGATTAGAGATGATAAGgtgaagatgc ... ccaaatgcagGAAGTTGAAGCAACCATAATTAATGGGAAAGGGACTGAAACTGGGCACATA
EST: gi|26455791|gb|CA827374.1|CA827374
EST:     CCGAGAAGTTGCAAGATCAGATGAACGAGCTAAAGATTAGAGATGATAAG                         GAAGTTGAAGCAACCATAATTAATGGGAAAGGGACTGAAACTGGGCACATA
genomic: CCGAGAAGTTGCAAGATCAGATGAACGAGCTAAAGATTAGAGATGATAAGgtgaagatgc ... ccaaatgcagGAAGTTGAAGCAACCATAATTAATGGGAAAGGGACTGAAACTGGGCACATA
EST: gi|5566972|gb|AI881883.1|AI881883
EST:     CCGAGAAGTTGCAAGATCAGATGAACGAGCTAAAGATTAGAGATGATAAG                         GAAGTTGAAGCAACCATAATTAATGGGAAAGGGACTGAAACTGGGCACATA
genomic: CCGAGAAGTTGCAAGATCAGATGAACGAGCTAAAGATTAGAGATGATAAGgtgaagatgc ... ccaaatgcagGAAGTTGAAGCAACCATAATTAATGGGAAAGGGACTGAAACTGGGCACATA
EST: gi|6918384|gb|AW399914.1|AW399914
EST:     CCGAGAAGTTGCAAGATCAGATGAACGAGCTAAAGATTAGAGATGATAAG                         GAAGTTGAAGCAACCATAATTAATGGGAAAGGGACTGAAACTGGGCACATA
genomic: CCGAGAAGTTGCAAGATCAGATGAACGAGCTAAAGATTAGAGATGATAAGgtgaagatgc ... ccaaatgcagGAAGTTGAAGCAACCATAATTAATGGGAAAGGGACTGAAACTGGGCACATA
EST: gi|61117964|gb|DN558925.1|DN558925
EST:     CCGAGAAGTTGCAAGATCAGATGAACGAGCTAAAGATTAGAGATGATAAG                         GAAGTTGAAGCAACCATAATTAATGGGAAAGGGACTGAAACTGGGCACATA
genomic: CCGAGAAGTTGCAAGATCAGATGAACGAGCTAAAGATTAGAGATGATAAGgtgaagatgc ... ccaaatgcagGAAGTTGAAGCAACCATAATTAATGGGAAAGGGACTGAAACTGGGCACATA
EST: gi|166552993|gb|EG316842.1|EG316842
EST:     CGAGAAGTTGCAAGATCAGATGAACGAGCTAAAGATTAGAGATGATAAG                         GAAGTTGAAGCAACCATAATTAATGGGAAAGGGACTGAAACTGGGCACATA
genomic: CGAGAAGTTGCAAGATCAGATGAACGAGCTAAAGATTAGAGATGATAAGgtgaagatgc ... ccaaatgcagGAAGTTGAAGCAACCATAATTAATGGGAAAGGGACTGAAACTGGGCACATA
EST: gi|5268665|gb|AI770629.1|AI770629
EST:     CCGAGAAGTTGCAAGATCAGATGAACGAGCTAAAGATTAGAGATGATAAG                         GAAGTTGAAGCAACCATAATTAATGGGAAAGGGACTGAAACTGGGCACATA
genomic: CCGAGAAGTTGCAAGATCAGATGAACGAGCTAAAGATTAGAGATGATAAGgtgaagatgc ... ccaaatgcagGAAGTTGAAGCAACCATAATTAATGGGAAAGGGACTGAAACTGGGCACATA
EST: gi|22542189|gb|BU092627.1|BU092627
EST:     CCGAGAAGTTGCAAGATCAGATGAACGAGCTAAAGACTAGAGATGATAAG                         GAAGTTGAAGCAACCATAATTAATGGGAAAGGGACTGAAACTGGGCACATA
genomic: CCGAGAAGTTGCAAGATCAGATGAACGAGCTAAAGATTAGAGATGATAAGgtgaagatgc ... ccaaatgcagGAAGTTGAAGCAACCATAATTAATGGGAAAGGGACTGAAACTGGGCACATA
EST: gi|33097218|gb|CF057178.1|CF057178
EST:     CCGAGAAGTTGCAAGATCAGATGAACGAGCTAAAGATTAGAGATGATAAG                         GAAGTTGAAGCAACCATAATTAATGGGAAAGGGACTGAAACTGGGCACATA
genomic: CCGAGAAGTTGCAAGATCAGATGAACGAGCTAAAGATTAGAGATGATAAGgtgaagatgc ... ccaaatgcagGAAGTTGAAGCAACCATAATTAATGGGAAAGGGACTGAAACTGGGCACATA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gattatgtgaaaaatgggactgtgatgtaacctttggtgtgaatgccaaatgcagGAAGTTGAAGCAACCATAATTAATGGGAAAGGGACTGAAACTGGGCACATAATTGTCACCACTACTGGTGGCAAGAATGGTCAACCAAAACAG
                        atgtaac  putative branch site (score: 3)
       tgaaaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgaagatgccttgatatcttgtttcgggcttactgtaatttcctcaagattatgtgaaaaatgggactgtgatgtaacctttggtgtgaatgccaaatgcagGAAGTTGAAGCAACCATAATTAATGGGAAAGGGACTGAAACTGGGCACATAATTGTCACCACTACTGGTGGCAAGAATGGTCAACCAAAACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA