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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tatgcaacatttcctcagcctggcagtgcaaagcttgcttgcttatttttcttctgttgtttgatcatcttctatcttctgaaatctcgtctttatttagGCTAGCAGAGGACTTGGTCTCACAGCACATATTATTGATCACTGCAAGCTGGTCCTTAAATTTCCTGAAGGGACCAACAGCACCTGG

Basic information

species Zea mays
transcript GRMZM2G119791_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G119791_T03 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os11g36420.1 (Oryza sativa), 3'ss of exon 2
tatgcaacattt-cctcagcctggcagtgcaaagcttgcttgcttatt-tttcttctgttgtttgatcatcttctatcttctgaaatctcgtctttatttagGCTAGCAGAGGACTTGGTCTCACAGCACATATTATTGATCACTGCAAGCTGGTCCTTAAATTTCCTGAAGGGACCAACAGCACCTGG
  |||| ||||| |||  |    |||||  ||   |   || | | || |||  ||| ||| ||  |      ||  |||||||||||||  |||||||||||| || || |||||||| ||||||||| ||||||||||||| |||||||| ||||||| ||||||| |||| ||||||||||| |||
--tgcagcattttcctttgatcagcagtagaagtttcatttacatgttctttactctcttgcttcttttctagcttgcttctgaaatctcaactttatttagGCAAGAAGGGGACTTGGCCTCACAGCAGATATTATTGATCATTGCAAGCTAGTCCTTAGATTTCCTAAAGGAACCAACAGCACTTGG

upper sequence: GRMZM2G119791_T03 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA19G27570.1 (Glycine max), 3'ss of exon 2
tatgcaacatttcctcagcctggcagtgcaaagcttgcttgcttatttttcttctgttgtttgatcatcttc-----tatcttctgaaatctcgtctttatttagGCTAGCAGAGGACTTGGTCTCACAGCACATATTATTGATCACTGCAAGCTGGTCCTTAAATTTCCTGAAGGGACCAACAGCACCTGG
     ||||   ||  |       | || |  |  | |  | ||  |  | ||    | ||  |  |   |      ||   |||||  |   |  |  |   ||| || ||| || ||||| ||||| ||||||||||||||||| |||||| |  | |||||||  |||||||| ||||||||||| |||
-----aacaacaccgaaaatatctaatgaattgtatccaagttttgtcctttttaacttttaaaaaaaaataaaaaatagaatctgaggttgggaatgaaaacagGATAACAGGGGGCTTGGACTCACTGCACATATTATTGATCATTGCAAGTTAATTCTTAAATACCCTGAAGGTACCAACAGCACTTGG

upper sequence: GRMZM2G119791_T03 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA19G27570.2 (Glycine max), 3'ss of exon 2
-----------------------------------------------------------tatgcaacatttcctcagcctggcagtgcaaagcttgcttgcttatttttcttctgttgtttgatcatcttc-----tatcttctgaaatctcgtctttatttagGCTAGCAGAGGACTTGGTCTCACAGCACATATTATTGATCACTGCAAGCTGGTCCTTAAATTTCCTGAAGGGACCAACAGCACCTGG
                                                           |    ||||   ||  |       | || |  |  | |  | ||  |  | ||    | ||  |  |   |      ||   |||||  |   |  |  |   ||| || ||| || ||||| ||||| ||||||||||||||||| |||||| |  | |||||||  |||||||| ||||||||||| |||
gtttgcattaaatgtcaacatagattattgatgtctaacttcaattctgaatttcttattggagaacaacaccgaaaatatctaatgaattgtatccaagttttgtcctttttaacttttaaaaaaaaataaaaaatagaatctgaggttgggaatgaaaacagGATAACAGGGGGCTTGGACTCACTGCACATATTATTGATCATTGCAAGTTAATTCTTAAATACCCTGAAGGTACCAACAGCACTTGG

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|148936990|gb|EC881159.2|EC881159
EST:     ACGACGTGCGCGAGCTCGCGGGGTTCCAGTCCCGCGTCCAGCAGTGCGTG                         GCTAGCAGAGGACTTGGTCTCACAGCACATATTATTGATCACTGCAAGCTG
genomic: ACGACGTGCGCGAGCTCGCGGGGTTCCAGTCCCGCGTCCAGCAGTGCGTGgtacgtctcc ... ctttatttagGCTAGCAGAGGACTTGGTCTCACAGCACATATTATTGATCACTGCAAGCTG
EST: gi|78092057|gb|DV520431.1|DV520431
EST:     ACGACGTGCGCGAGCTCGCGGGGTTCCAGTCCCGCGTCCAGCAGTGCGTG                         GCTAGCAGAGGACTTGGTCTCACAGCACATATTATTGATCACTGCAAGCTG
genomic: ACGACGTGCGCGAGCTCGCGGGGTTCCAGTCCCGCGTCCAGCAGTGCGTGgtacgtctcc ... ctttatttagGCTAGCAGAGGACTTGGTCTCACAGCACATATTATTGATCACTGCAAGCTG
EST: gi|211356321|gb|FL081349.1|FL081349
EST:     ACGACGTGCGCGAGCTCGCGGGGTTCCAGTCCCGCGTCCAGCAGTGCGTG                         GCTAGCAGAGGACTTGGTCTCACAGCACATATTATTGATCACTGCAAGCTG
genomic: ACGACGTGCGCGAGCTCGCGGGGTTCCAGTCCCGCGTCCAGCAGTGCGTGgtacgtctcc ... ctttatttagGCTAGCAGAGGACTTGGTCTCACAGCACATATTATTGATCACTGCAAGCTG
EST: gi|149080539|gb|EE169577.2|EE169577
EST:     ACGACGTGCGCGAGCTCGCGGGGTTCCAGTCCCGCGTCCAGCAGTGCGTG                         GCTAGCAGAGGACTTGGTCTCACAGCACATATTATTGATCACTGCAAGCTG
genomic: ACGACGTGCGCGAGCTCGCGGGGTTCCAGTCCCGCGTCCAGCAGTGCGTGgtacgtctcc ... ctttatttagGCTAGCAGAGGACTTGGTCTCACAGCACATATTATTGATCACTGCAAGCTG
EST: gi|76288008|gb|DV027576.1|DV027576
EST:     ACGACGTGCGCGAGCTCGCGGGGTTCCAGTCCCGCGTCCAGCAGTGCGTG                         GCTAGCAGAGGACTTGGTCTCACAGCACATATTATTGATCACTGCAAGCTG
genomic: ACGACGTGCGCGAGCTCGCGGGGTTCCAGTCCCGCGTCCAGCAGTGCGTGgtacgtctcc ... ctttatttagGCTAGCAGAGGACTTGGTCTCACAGCACATATTATTGATCACTGCAAGCTG
EST: gi|211356320|gb|FL081348.1|FL081348
EST:     ACGACGTGCGCGAGCTCGCGGGGTTCCAGTCCCGCGTCCAGCAGTGCGTG                         GCTAGCAGAGGACTTGGTCTCACAGCACATATTATTGATCACTGCAAGCTG
genomic: ACGACGTGCGCGAGCTCGCGGGGTTCCAGTCCCGCGTCCAGCAGTGCGTGgtacgtctcc ... ctttatttagGCTAGCAGAGGACTTGGTCTCACAGCACATATTATTGATCACTGCAAGCTG
EST: gi|149082841|gb|EE172066.2|EE172066
EST:     ACGACGTGCGCGAGCTCGCGGGGTTCCAGTCCCGCGTCCAGCAGTGCGTG                         GCTAGCAGAGCACTTGGTCTCACACCACATATTATTGATCACTGCCAGCTG
genomic: ACGACGTGCGCGAGCTCGCGGGGTTCCAGTCCCGCGTCCAGCAGTGCGTGgtacgtctcc ... ctttatttagGCTAGCAGAGGACTTGGTCTCACAGCACATATTATTGATCACTGCAAGCTG
EST: gi|78082688|gb|DV511091.1|DV511091
EST:     ACGACGTGCGCGAGCTCGCGGGGTTCCAGTCCCGCGTCCAGCAGTGCGTG                         GCTAGCAGAGGACTTGGTCTCACAGCACATATTATTGATCACTGCAAGCTG
genomic: ACGACGTGCGCGAGCTCGCGGGGTTCCAGTCCCGCGTCCAGCAGTGCGTGgtacgtctcc ... ctttatttagGCTAGCAGAGGACTTGGTCTCACAGCACATATTATTGATCACTGCAAGCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttttcttctgttgtttgatcatcttctatcttctgaaatctcgtctttatttagGCTAGCAGAGGACTTGGTCTCACAGCACATATTATTGATCACTGCAAGCTGGTCCTTAAATTTCCTGAAGGGACCAACAGCACCTGG
             gtttgat  putative branch site (score: 5)
                                       tctcgtctttattt  putative PPT
                                            tctttattta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tatgcaacatttcctcagcctggcagtgcaaagcttgcttgcttatttttcttctgttgtttgatcatcttctatcttctgaaatctcgtctttatttagGCTAGCAGAGGACTTGGTCTCACAGCACATATTATTGATCACTGCAAGCTGGTCCTTAAATTTCCTGAAGGGACCAACAGCACCTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG