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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ataaatcattttccttcacttgccattctgagtagattgcaatccaaataaggaatcatgttgatgctaacaattttttcctctccttttaatataacagGCCTTCCCCAAAGCGAATTGAAGGTCCAAATGGAAGAACTCTGCAACTCGAATTCCGAACAAGGCTGTCACTTCCCCTTTTTACTGGAGGAAAAGTTGAA

Basic information

species Zea mays
transcript GRMZM2G018837_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G018837_T04 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os02g08120.1 (Oryza sativa), 3'ss of exon 4
ataaatcattttccttcacttgccattctgagtagattgcaatccaaataaggaatcatgttgatgctaaca-attttttcctctccttttaatataacagGCCTTCCCCAAAGCGAATTGAAGGTCCAAATGGAAGAACTCTGCAACTCGAATTCCGAACAAGGCTGTCACTTCCCCTTTTTACTGGAGGAAAAGTTGAA
  ||    |  |    | |       | |   || ||    ||  | |||   |   || |  ||    | | || |||| ||    ||  ||||   |||| ||||||| |||||||||||||||||  ||||||||| |||||||||| | ||| | ||||| ||||| ||||| ||||||||||||||||||||||||
-caacctttggtagaacccacattgatatatatatatatatatatatatatatatatatatatatatatatatatattttgctactgttggaataattcagGTCTTCCCCGAAGCGAATTGAAGGTCCTGATGGAAGAAATCTGCAACTCCAGTTCAGGACAAGACTGTCTCTTCCTCTTTTTACTGGAGGAAAAGTTGAA

upper sequence: GRMZM2G018837_T04 (Zea mays), 3'ss of exon 4
lower sequence: Vv11s0052g01380.t01 (Vitis vinifera), 3'ss of exon 3
ataaatcattttccttcacttgccat-tctgagtagattgcaatccaaataaggaatcatgttgatgctaacaattttttcctctc--cttttaatataacagGCCTTCCCCAAAGCGAATTGAAGGTCCAAATGGAAGAACTCTGCAACTCGAATTCCGAACAAGGCTGTCACTTCCCCTTTTTACTGGAGGAAAAGTTGAA
 |  | | | |||| |   |   ||| ||| | |    ||  |    | |   |  |||| |      |     ||||||  |     |  ||   ||  |||| ||||||| || ||||||||||| ||  ||||||| |   ||||  |  | ||  |  | |||||||| |||||||||||||| ||||||||||| || 
-tttaccttcttccctatttgatcatatctcactgctatggtaaatgactt--gtttcatatctggcttggtggttttttatttctaacaattgccatttcagGTCTTCCCCTAAACGAATTGAAGGACCTGATGGAAGGAACTTGCAGTTGCAGTTTAGGTCCAGGCTGTCTCTTCCCCTTTTTACAGGAGGAAAAGTAGAG
















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|149075355|gb|EE163864.2|EE163864
EST:     GAAGTGGAGCGCGCACTGGGCAAACTTGGCCCTGCAACAATCGGTGGAAG                         GCCTTCCCCAAAGCGAATTGAAGGTCCAAATGGAAGAACTCTGCAACTCGA
genomic: GAAGTGGAGCGCGCACTGGGCAAACTTGGCCCTGCAACAATCGGTGGAAGgtaagctatt ... aatataacagGCCTTCCCCAAAGCGAATTGAAGGTCCAAATGGAAGAACTCTGCAACTCGA
EST: gi|211057553|gb|FL294376.1|FL294376
EST:     GAAGTGGAGCGTGCACTGGGCAAACTTGGCCCTGCAACAATCGGTGGAAG                         GCCTTCCCCAAAGAGAATTGAAGGTCCAAATGGAAGAACTCTGCAACTCGA
genomic: GAAGTGGAGCGCGCACTGGGCAAACTTGGCCCTGCAACAATCGGTGGAAGgtaagctatt ... aatataacagGCCTTCCCCAAAGCGAATTGAAGGTCCAAATGGAAGAACTCTGCAACTCGA
EST: gi|211057556|gb|FL294379.1|FL294379
EST:     GAAGTGGAGCGCGCACCGCGCAAACTTGGCCCTGCAACAATCGGTGGAAG                         GCCTTCCCCAAAGCGAATTGAAGGTCCAAATGGAAGAACTCTGCAACTCGA
genomic: GAAGTGGAGCGCGCACTGGGCAAACTTGGCCCTGCAACAATCGGTGGAAGgtaagctatt ... aatataacagGCCTTCCCCAAAGCGAATTGAAGGTCCAAATGGAAGAACTCTGCAACTCGA
EST: gi|211057557|gb|FL294380.1|FL294380
EST:     GAAGTGGAGCGCGCACTGGGCAAACTTGGCCCTGCAACAATCGGTGGAAG                         GCCTTCCCCAAAGCGAATTGAAGGTCCAAATGGAAGAACTCTGCAACTCGA
genomic: GAAGTGGAGCGCGCACTGGGCAAACTTGGCCCTGCAACAATCGGTGGAAGgtaagctatt ... aatataacagGCCTTCCCCAAAGCGAATTGAAGGTCCAAATGGAAGAACTCTGCAACTCGA
EST: gi|26557412|gb|CA829647.1|CA829647
EST:     GAAGTGGAGCGCGCACTGGGCAAACTTGGCCCTGCAACAATCGGTGGAAG                         GCCTTCCCCAAAGCGAATTGAAGGTCCAAATGGAAGAACTCTGCAACTCGA
genomic: GAAGTGGAGCGCGCACTGGGCAAACTTGGCCCTGCAACAATCGGTGGAAGgtaagctatt ... aatataacagGCCTTCCCCAAAGCGAATTGAAGGTCCAAATGGAAGAACTCTGCAACTCGA
EST: gi|211054587|gb|FL294369.1|FL294369
EST:     GAAGTGGAGCGCGCACTGGGCAAACTTGGCCCTGCAACAATCGGTGGAAG                         GCCTTCCCCAAAGCGAATTGAAGGTCCAAATGGAAGAACTCTGCAACTCGA
genomic: GAAGTGGAGCGCGCACTGGGCAAACTTGGCCCTGCAACAATCGGTGGAAGgtaagctatt ... aatataacagGCCTTCCCCAAAGCGAATTGAAGGTCCAAATGGAAGAACTCTGCAACTCGA
EST: gi|76937510|gb|DV175167.1|DV175167
EST:     GAAGTGGAGCGCGCACTGGGCAAACTTGGCCCTGCAACAATCGGTGGAAG                         GCCTTCCCCAAAGCGAATTGAAGGTCCAAATGGAAGAACTCTGCAACTCGA
genomic: GAAGTGGAGCGCGCACTGGGCAAACTTGGCCCTGCAACAATCGGTGGAAGgtaagctatt ... aatataacagGCCTTCCCCAAAGCGAATTGAAGGTCCAAATGGAAGAACTCTGCAACTCGA
EST: gi|149000276|gb|EE037432.2|EE037432
EST:     GAAGTGGAGCGCGCACTGGGCAAACTTGGCCCTGCAACAATCGGTGGAAG                         GCCTTCCCCAAAGCGAATTGAAGGTCCAAATGGAAGAACTCTGCAACTCGA
genomic: GAAGTGGAGCGCGCACTGGGCAAACTTGGCCCTGCAACAATCGGTGGAAGgtaagctatt ... aatataacagGCCTTCCCCAAAGCGAATTGAAGGTCCAAATGGAAGAACTCTGCAACTCGA
EST: gi|76910443|gb|DV163876.1|DV163876
EST:     GAAGTGGAGCGCGCACTGGGCAAACTTGGCCCTGCAACAATCGGTGGAAG                         GCCTTCCCCAAAGCGAATTGAAGGTCCAAATGGAAGAACTCTGCAACTCGA
genomic: GAAGTGGAGCGCGCACTGGGCAAACTTGGCCCTGCAACAATCGGTGGAAGgtaagctatt ... aatataacagGCCTTCCCCAAAGCGAATTGAAGGTCCAAATGGAAGAACTCTGCAACTCGA
EST: gi|211057550|gb|FL294373.1|FL294373
EST:     GAAGTGGAGCGCGCACTGGGCAAACTTGGCCCTGCAACAATCGGTGGAAG                         GCCTTCCCCAAAGCGAATTGAAGGTCCAAATGGAAGAACTCTGCAACTCGA
genomic: GAAGTGGAGCGCGCACTGGGCAAACTTGGCCCTGCAACAATCGGTGGAAGgtaagctatt ... aatataacagGCCTTCCCCAAAGCGAATTGAAGGTCCAAATGGAAGAACTCTGCAACTCGA
EST: gi|211054585|gb|FL294367.1|FL294367
EST:     GAAGTGGAGCGTGCACTGGGCAAACTTGGCCCTGCAACAATCGGTGGAAG                         GCCTTCCCCAAAGAGAATTGAAGGTCCAAATGGAAGAACTCTGCAACTCGA
genomic: GAAGTGGAGCGCGCACTGGGCAAACTTGGCCCTGCAACAATCGGTGGAAGgtaagctatt ... aatataacagGCCTTCCCCAAAGCGAATTGAAGGTCCAAATGGAAGAACTCTGCAACTCGA
EST: gi|211057551|gb|FL294374.1|FL294374
EST:     GAAGTGGAGCGTGCACTGGGCAAACTTGGCCCTGCAACAATCGGTGGAAG                         GCCTTCCCCAAAGAGAATTGAAGGTCCAAATGGAAGAACTCTGCAACTCGA
genomic: GAAGTGGAGCGCGCACTGGGCAAACTTGGCCCTGCAACAATCGGTGGAAGgtaagctatt ... aatataacagGCCTTCCCCAAAGCGAATTGAAGGTCCAAATGGAAGAACTCTGCAACTCGA
EST: gi|148974485|gb|EE025268.2|EE025268
EST:     GAAGTGGAGCGCGCACTGGGCAAACTTGGCCCTGCAACAATCGGTGGAAG                         GCCTTCCCCAAAGCGAATTGAAGGTCCAAATGGAAGAACTCTGCAACTCGA
genomic: GAAGTGGAGCGCGCACTGGGCAAACTTGGCCCTGCAACAATCGGTGGAAGgtaagctatt ... aatataacagGCCTTCCCCAAAGCGAATTGAAGGTCCAAATGGAAGAACTCTGCAACTCGA
EST: gi|148956501|gb|EC902338.2|EC902338
EST:     GAAGTGGAGCGCGCACTGGGCAAACTTGGCCCTGCAACAATCGGTGGAAG                         GCCTTCCCCAAAGCGAATTGAAGGTCCAAATGGAAGAACTCTGCAACTCGA
genomic: GAAGTGGAGCGCGCACTGGGCAAACTTGGCCCTGCAACAATCGGTGGAAGgtaagctatt ... aatataacagGCCTTCCCCAAAGCGAATTGAAGGTCCAAATGGAAGAACTCTGCAACTCGA
EST: gi|211054577|gb|FL294359.1|FL294359
EST:     GAAGTGGAGTGCGCACTGGGCAAACTTGGCCCTGCAACAATCGGTGGAAG                         GCCTTCCCCAAAGCGAATTGAAGGTCCAAATGGAAGAACTCTGCAACTCGA
genomic: GAAGTGGAGCGCGCACTGGGCAAACTTGGCCCTGCAACAATCGGTGGAAGgtaagctatt ... aatataacagGCCTTCCCCAAAGCGAATTGAAGGTCCAAATGGAAGAACTCTGCAACTCGA
EST: gi|149014700|gb|EE044372.2|EE044372
EST:     GAAGTGGAGCGCGCACTGGGCAAACTTGGCCCTGCAACAATCGGTGGAAG                         GCCTTCCCCAAAGCGAATTGAAGGTCCAAATGGAAGAACTCTGCAACTCGA
genomic: GAAGTGGAGCGCGCACTGGGCAAACTTGGCCCTGCAACAATCGGTGGAAGgtaagctatt ... aatataacagGCCTTCCCCAAAGCGAATTGAAGGTCCAAATGGAAGAACTCTGCAACTCGA
EST: gi|211057549|gb|FL294372.1|FL294372
EST:     GAAGTGGAGCGTGCACTGGGCAAACTTGGCCCTGCAACAATCGGTGGAAG                         GCCTTCCCCAAAGAGAATTGAAGGTCCAAATGGAAGAACTCTGCAACTCGA
genomic: GAAGTGGAGCGCGCACTGGGCAAACTTGGCCCTGCAACAATCGGTGGAAGgtaagctatt ... aatataacagGCCTTCCCCAAAGCGAATTGAAGGTCCAAATGGAAGAACTCTGCAACTCGA
EST: gi|37420242|gb|CF647811.1|CF647811
EST:     GAAGTGGAGCGCGCACTGGGCAAACTTGGCCCTGCAACAATCGGTGGAAG                         GCCTTCCCCAAAGCGAATTGAAGGTCCAAATGGA
genomic: GAAGTGGAGCGCGCACTGGGCAAACTTGGCCCTGCAACAATCGGTGGAAGgtaagctatt ... aatataacagGCCTTCCCCAAAGCGAATTGAAGGTCCAAATGGA
EST: gi|211054586|gb|FL294368.1|FL294368
EST:     GAAGTGGAGCGCGCACTGGGCAAACTTGGCCCTGCAACAATCGGTGGAAG                         GCCTTCCCCAAAGCGAATTGAAGGTCCAAATGGAAGAACTCTGCAACTCGA
genomic: GAAGTGGAGCGCGCACTGGGCAAACTTGGCCCTGCAACAATCGGTGGAAGgtaagctatt ... aatataacagGCCTTCCCCAAAGCGAATTGAAGGTCCAAATGGAAGAACTCTGCAACTCGA
EST: gi|76015275|gb|DT942445.1|DT942445
EST:     GAAGTGGAGCGCGCACTGGGCAAACTTGGCCCTGCAACAATCGGTGGAAG                         GCCTTCCCCAAAGCGAATTGAAGGTCCAAATGGAAGAACTCTGCAACTCGA
genomic: GAAGTGGAGCGCGCACTGGGCAAACTTGGCCCTGCAACAATCGGTGGAAGgtaagctatt ... aatataacagGCCTTCCCCAAAGCGAATTGAAGGTCCAAATGGAAGAACTCTGCAACTCGA

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 131

GTCAGTGAAGAAGTGGAGCGCGCACTGGGCAAACTTGGCCCTGCAACAATCGGTGGAAGgtaagctatt ... aatataacagGCCTTCCCCAAAGCGAATTGAAGGTCCAAATGGAAGAACTCTGCAACTCGAATTCCGAACAAGGCTGTCACTTCCCCTTTTTACTGGAGGAAAAGTTGAA


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 202

GTCAGTGAAGAAGTGGAGCGCGCACTGGGCAAACTTGGCCCTGCAACAATCGGTGGAAGgtaagctatt ... aatataacagGCCTTCCCCAAAGCGAATTGAAGGTCCAAATGGAAGAACTCTGCAACTCGAATTCCGAACAAGGCTGTCACTTCCCCTTTTTACTGGAGGAAAAGTTGAA


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 176

GTCAGTGAAGAAGTGGAGCGCGCACTGGGCAAACTTGGCCCTGCAACAATCGGTGGAAGgtaagctatt ... aatataacagGCCTTCCCCAAAGCGAATTGAAGGTCCAAATGGAAGAACTCTGCAACTCGAATTCCGAACAAGGCTGTCACTTCCCCTTTTTACTGGAGGAAAAGTTGAA


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 86

GTCAGTGAAGAAGTGGAGCGCGCACTGGGCAAACTTGGCCCTGCAACAATCGGTGGAAGgtaagctatt ... aatataacagGCCTTCCCCAAAGCGAATTGAAGGTCCAAATGGAAGAACTCTGCAACTCGAATTCCGAACAAGGCTGTCACTTCCCCTTTTTACTGGAGGAAAAGTTGAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaataaggaatcatgttgatgctaacaattttttcctctccttttaatataacagGCCTTCCCCAAAGCGAATTGAAGGTCCAAATGGAAGAACTCTGCAACTCGAATTCCGAACAAGGCTGTCACTTCCCCTTTTTACTGGAGGAAAAGTTGAA
                            ttttttcctctccttt  CT-rich tract
                                         ttttaatataaca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ataaatcattttccttcacttgccattctgagtagattgcaatccaaataaggaatcatgttgatgctaacaattttttcctctccttttaatataacagGCCTTCCCCAAAGCGAATTGAAGGTCCAAATGGAAGAACTCTGCAACTCGAATTCCGAACAAGGCTGTCACTTCCCCTTTTTACTGGAGGAAAAGTTGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - ccttcac
- - - - - - - - - - -gccattc
- - - - - - - - - - - - - - - - - - - - - -ccaaataa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgatgct