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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtgctagaattttgattattgtttctagaaattgaagtgaacggttcggaggacagtcttaatggttggatcgttgagtagGTCAATTGTGCTGATTCTATTGTTGGTGATGCAAAAGTTCGTGGAATAAGTGGGGGTGAGAAGAAGCGCCTCTCACTTGCATGTGAGTTGATTGCTAGCC

Basic information

species Zea mays
transcript GRMZM2G119345_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G119345_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os01g03144.1 (Oryza sativa), 3'ss of exon 3
----gtgagtgctagaattttgattattgtttctagaaa-----------ttgaagtgaacggttcggaggacagtcttaatggttggatcgttgagtagGTCAATTGTGCTGATTCTATTGTTGGTGATGCAAAAGTTCGTGGAATAAGTGGGGGTGAGAAGAAGCGCCTCTCACTTGCATGTGAGTTGATTGCTAGCC
       |     | ||| |  ||   ||| | |  ||            ||    || |      ||     | |  |  |  ||  | |     |||||| || |||||||| || ||||| |||||||||||||| |||||||||||||||||||| |||||||| ||||| ||||| |||||  ||||||||||||
gggcagaacctacataatatctatcgctgtctgttcaagtatttccctttttattttgtatcaccaggtatttatttctttttattataactggttgtagGTTAACTGTGCTGACTCAATTGTGGGTGATGCAAAAGTACGTGGAATAAGTGGGGGTGAAAAGAAGCGTCTCTCCCTTGCGTGTGAACTGATTGCTAGCC

upper sequence: GRMZM2G119345_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA20G26160.1 (Glycine max), 3'ss of exon 3
-------------gtgagtgctagaattttgattattgtttctagaaattg--aagtgaacggttcggaggacagtcttaatggttggatcgttgagtagGTCAATTGTGCTGATTCTATTGTTGGTGATGCAAAAGTTCGTGGAATAAGTGGGGGTGAGAAGAAGCGCCTCTCACTTGCATGTGAGTTGATTGCTAGCC
              |   || | |||  |   ||  | ||  | || | |   | || |  | | |        |  |   |       |  || |  |||| |  ||||||||| | | ||||||||||||||||||||||||||| ||||| ||||| ||||| ||| | ||  | ||||||||  |  |||| ||||
tttcctctttcaaatttatgattgaaaatgtgttgctcttgttggatagtcctatgttactgatactccctttggcatctgtatgctttttcttcaaaagGTTAGCTGTGCTGATACCAATGTTGGTGATGCAAAAGTTCGTGGAATTAGTGGTGGTGAAAAGAAACGCTTATCCATGGCATGTGAACTACTTGCAAGCC

upper sequence: GRMZM2G119345_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA10G41110.1 (Glycine max), 3'ss of exon 3
-------------gtgagtgctagaattttgattattgtttctagaaattg--aagtgaacggttcggaggacagtcttaatggttggatcgttgagtagGTCAATTGTGCTGATTCTATTGTTGGTGATGCAAAAGTTCGTGGAATAAGTGGGGGTGAGAAGAAGCGCCTCTCACTTGCATGTGAGTTGATTGCTAGCC
              |   || | |||  |   ||  | ||  | || | |   | || |  | | |        |  |   |       |  || |  |||| |  ||||||||| | | ||||||||||||||||||||||||||| ||||| ||||| ||||| ||| | ||  | ||||||||  || |||| ||||
attcctctttcaaatttatgattgaaaatgtgttgctcttgttggatagtcctatgttactgatactccctgtggcatctgtatgctttttcttcaaaagGTTAGCTGTGCTGATACCAATGTTGGTGATGCAAAAGTTCGTGGAATTAGTGGTGGTGAAAAGAAACGCTTATCCATGGCATGTGAACTGCTTGCAAGCC

upper sequence: GRMZM2G119345_T01 (Zea mays), 3'ss of exon 3
lower sequence: AT2G01320.2 (Arabidopsis thaliana), 3'ss of exon 3
----------gtgagtgctagaattttgattattgtttctagaaattgaagtgaacggttcggaggacagtcttaatggttg-gatcgttgagtagGTCAATTGTGCTGATTCTATTGTTGGTGATGCAAAAGTTCGTGGAATAAGTGGGGGTGAGAAGAAGCGCCTCTCACTTGCATGTGAGTTGATTGCTAGCC
           |   |    | ||||||  |  | ||     | |||||| |    |  |       |    |      ||| |    |  |  ||||||  ||||| |||||   |||||| ||||| ||||||||||| || || || || ||||||||||| || |||||||| ||||| ||||| ||||| |
gtgaggtttcattgatctctgcattttggatgatattgtggtagattgaaatcctggaattatgtttcttgatcgtcttttgtggctctccaaaagGTCAGCTGTGCAGATTCATGTGTTGGCGATGCTAAAGTTCGTGGGATCAGCGGTGGAGAGAAGAAGCGGCTGTCACTTGCGTGTGAATTGATCGCTAGTC

upper sequence: GRMZM2G119345_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv01s0011g04670.t01 (Vitis vinifera), 3'ss of exon 3
-----------gtgagtgctagaattttga--ttattgtttctagaaattgaagtgaacggttcggaggacagtcttaatggttgga----tcgttgagtagGTCAATTGTGCTGATTCTATTGTTGGTGATGCAAAAGTTCGTGGAATAAGTGGGGGTGAGAAGAAGCGCCTCTCACTTGCATGTGAGTTGATTGCTAGCC
           | || |    |||  |  |   | |      ||  ||||   |||| |  ||           | | ||||||       |  || |  ||||||  ||||||||||| | ||||||||||||||||||||||||||| ||||| ||||| ||||| ||  | ||||||||||||||  ||||||| ||||
ttttttgttttgagaataactgaaaatgaaagctgtcacacttacgaatttttgtgatctttttttct--tttcccttatggttattctctttcttcaaaagGTCAGCTGTGCTGATTCCAATGTTGGTGATGCAAAAGTTCGTGGAATCAGTGGTGGTGAAAAGAAACGTTTGTCACTTGCATGTGAACTGATTGCAAGCC

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|32863377|gb|CF003059.1|CF003059
EST:     CTGAGAGAAAGGAGGGCTATGTCAATGATCTTTTGTTACGTATGGGGTTG                         GTCAATTGTGCTGATTCTATTGTTGGTGATGCAAAAGTTCGTGGAATAAGT
genomic: CTGAGAGAAAGGAGAGCTATGTCAATGATCTTTTGTTACGTATGGGGTTGgtgagtgcta ... cgttgagtagGTCAATTGTGCTGATTCTATTGTTGGTGATGCAAAAGTTCGTGGAATAAGT
EST: gi|211452481|gb|FL182655.1|FL182655
EST:     CTGAGAGAAAGGAGAGCTATGTCAATGATCTTTTGTTACGTATGGGGTTG                         GTCAATTGTGCTGATTCTATTGTTGGTGATGCAAAAGTTCGTGGAATAAGT
genomic: CTGAGAGAAAGGAGAGCTATGTCAATGATCTTTTGTTACGTATGGGGTTGgtgagtgcta ... cgttgagtagGTCAATTGTGCTGATTCTATTGTTGGTGATGCAAAAGTTCGTGGAATAAGT
EST: gi|32863127|gb|CF002809.1|CF002809
EST:     CTGAGAGAAAGGAGGGCTATGTCAATGATCTTTTGTTACGTATGGGGTTG                         GTCAATTGTGCTGATTCTATTGTTGGTGATGCAAAAGTTCGTGGAATAAGT
genomic: CTGAGAGAAAGGAGAGCTATGTCAATGATCTTTTGTTACGTATGGGGTTGgtgagtgcta ... cgttgagtagGTCAATTGTGCTGATTCTATTGTTGGTGATGCAAAAGTTCGTGGAATAAGT
EST: gi|211450348|gb|FL182649.1|FL182649
EST:     CTGAGAGAAAGGAGAGCTATGTCAATGATCTTTTGTTACGTATGGGGTTG                         GCCAATTGTGCTGATTCTATTGTTGG
genomic: CTGAGAGAAAGGAGAGCTATGTCAATGATCTTTTGTTACGTATGGGGTTGgtgagtgcta ... cgttgagtagGTCAATTGTGCTGATTCTATTGTTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agaaattgaagtgaacggttcggaggacagtcttaatggttggatcgttgagtagGTCAATTGTGCTGATTCTATTGTTGGTGATGCAAAAGTTCGTGGAATAAGTGGGGGTGAGAAGAAGCGCCTCTCACTTGCATGTGAGTTGATTGCTAGCC
                              tcttaat  putative branch site (score: 3)
                              tcttaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtgctagaattttgattattgtttctagaaattgaagtgaacggttcggaggacagtcttaatggttggatcgttgagtagGTCAATTGTGCTGATTCTATTGTTGGTGATGCAAAAGTTCGTGGAATAAGTGGGGGTGAGAAGAAGCGCCTCTCACTTGCATGTGAGTTGATTGCTAGCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC