Skip to another splice site:
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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGTATATGGGCTAATTTTTCTCTTCAAGTGGATACCCGGGGAGAAGGATGAACGGCCTGTTGTCAGAGATCCTAACCCAAACCTTTTCTTTGCGCACCAAgttagttctgttctgtttctgtccctttagctaaccacgtttgctactctgtgcttaacaataacaggatatccttttacttattttcag

Basic information

species Zea mays
transcript GRMZM2G108739_T01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G108739_T01 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os02g57630.2 (Oryza sativa), 5'ss of exon 5
AGTATATGGGCTAATTTTTCTCTTCAAGTGGATACCCGGGGAGAAGGATGAACGGCCTGTTGTCAGAGATCCTAACCCAAACCTTTTCTTTGCGCACCAAgttagttctgttctgtttctgtccctttagctaaccacgtttgctactctgtgcttaacaataacaggatatccttttacttattttcag
||| |||||||||||||||||||||||||||||  | ||||| ||||||||||||||||| |||| |||||| ||||||||||||||||||||   ||| ||||||||  || || |      || ||||||| |   |||    | |  |   |||||| |      | |     | | | | |  |||
AGTTTATGGGCTAATTTTTCTCTTCAAGTGGATGGCTGGGGAAAAGGATGAACGGCCTGTCGTCAAAGATCCAAACCCAAACCTTTTCTTTGCTAGCCAGgttagttccattttgct------ccgttagctacctctgttcagaatt--ggatttaacatttgatcta-actaaatcaatcactgccag

upper sequence: GRMZM2G108739_T01 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os02g57630.3 (Oryza sativa), 5'ss of exon 5
AGTATATGGGCTAATTTTTCTCTTCAAGTGGATACCCGGGGAGAAGGATGAACGGCCTGTTGTCAGAGATCCTAACCCAAACCTTTTCTTTGCGCACCAAgttagttctgttctgtttctgtccctttagctaaccacgtttgctactctgtgcttaacaataacaggatatccttttacttattttcag
  | |||||||||||||||||||||||||||||  | ||||| ||||||||||||||||| |||| |||||| ||||||||||||||||||||   ||| ||||||||  || || |      || ||||||| |   |||    | |  |   |||||| |      | |     | | | | |  |||
--TTTATGGGCTAATTTTTCTCTTCAAGTGGATGGCTGGGGAAAAGGATGAACGGCCTGTCGTCAAAGATCCAAACCCAAACCTTTTCTTTGCTAGCCAGgttagttccattttgct------ccgttagctacctctgttcagaatt--ggatttaacatttgatcta-actaaatcaatcactgccag
















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|71437430|gb|DR818480.1|DR818480
EST:     AACGGCCTGTTGTCAGAGATCCTAACCCAAACCTTTTCTTTGCGCACCAA                         GTCATCACTAATGCATGTGCTACTCAAGCTATTCTCTCAGTTCTCATGAAT
genomic: AACGGCCTGTTGTCAGAGATCCTAACCCAAACCTTTTCTTTGCGCACCAAgttagttctg ... ttattttcagGTCATCACTAATGCATGTGCTACTCAAGCTATTCTCTCAGTTCTCATGAAT
EST: gi|37361488|gb|CF602777.1|CF602777
EST:     AACGGCCTGTTGTCAGAGATCCTAACCCAAACCTTTTCTTTGCGCACCAA                         GTCATCACTAATGCATGTGCTACTCAAGCTATTCTCTCAGTTCTCATGAAT
genomic: AACGGCCTGTTGTCAGAGATCCTAACCCAAACCTTTTCTTTGCGCACCAAgttagttctg ... ttattttcagGTCATCACTAATGCATGTGCTACTCAAGCTATTCTCTCAGTTCTCATGAAT
EST: gi|18649335|gb|BM498154.1|BM498154
EST:     AACGGCCTGTTGTCAGAGATCCTAACCCAAACCTTTTCTTTGCGCACCAA                         GTCATCACTAATGCATGTGCTACTCAAGCTATTCTCTCAGTTCTCATGAAT
genomic: AACGGCCTGTTGTCAGAGATCCTAACCCAAACCTTTTCTTTGCGCACCAAgttagttctg ... ttattttcagGTCATCACTAATGCATGTGCTACTCAAGCTATTCTCTCAGTTCTCATGAAT
EST: gi|19058669|gb|BM737336.1|BM737336
EST:     AACGGCCTGTTGTCAGAGATCCTAACCCAAACCTTTTCTTTGCGCACCAA                         GTCATCACTAATGCATGTGCTACTCAAGCTATTCTCTCAGNTCTCATGAAT
genomic: AACGGCCTGTTGTCAGAGATCCTAACCCAAACCTTTTCTTTGCGCACCAAgttagttctg ... ttattttcagGTCATCACTAATGCATGTGCTACTCAAGCTATTCTCTCAGTTCTCATGAAT
EST: gi|18450451|gb|BM428729.1|BM428729
EST:     AACGGCCTGTTGTCAGAGATCCTAACCCAAACCTTTTCTTTGCGCNCCAA                         GTCATCACTAATGCATGTGCTACTCAAGCTATTCTCTCAGTTCTCATGAAT
genomic: AACGGCCTGTTGTCAGAGATCCTAACCCAAACCTTTTCTTTGCGCACCAAgttagttctg ... ttattttcagGTCATCACTAATGCATGTGCTACTCAAGCTATTCTCTCAGTTCTCATGAAT
EST: gi|32936153|gb|CF040965.1|CF040965
EST:     AACGGCCTGTTGTCAGAGATCCTAACCCAAACCTTTTCTTTGCGCACCAA                         GTCATCACTAATGCATGTGCTACTCAAGCTATTCTCTCAGTTCTCATGAAT
genomic: AACGGCCTGTTGTCAGAGATCCTAACCCAAACCTTTTCTTTGCGCACCAAgttagttctg ... ttattttcagGTCATCACTAATGCATGTGCTACTCAAGCTATTCTCTCAGTTCTCATGAAT
EST: gi|32937762|gb|CF042581.1|CF042581
EST:     AACGGCCTGTTGTCAGAGATCCTAACCCAAACCTTTTCTTTGCGCACCAA                         GTCATCACTAATGCATGTGCTACTCAAGCTATTCTCTCAGTTCTCATGAAT
genomic: AACGGCCTGTTGTCAGAGATCCTAACCCAAACCTTTTCTTTGCGCACCAAgttagttctg ... ttattttcagGTCATCACTAATGCATGTGCTACTCAAGCTATTCTCTCAGTTCTCATGAAT
EST: gi|18649482|gb|BM498301.1|BM498301
EST:     AACGGCCTGTTGTCAGAGATCCTAACCCAAACCTTTTCTTTGCGCACCAN                         GTCATCACTAATGCATGTGCTACTCA-GCTATTCTCTCAGTTCTCATGAAT
genomic: AACGGCCTGTTGTCAGAGATCCTAACCCAAACCTTTTCTTTGCGCACCAAgttagttctg ... ttattttcagGTCATCACTAATGCATGTGCTACTCAAGCTATTCTCTCAGTTCTCATGAAT
EST: gi|18649277|gb|BM498096.1|BM498096
EST:     AACGGCCTGTTGTCAGAGATCCTAACCCAAACCTTTTCTTTGCGCACCAA                         GTCATCACTAATGCATGTGCTACTCA-GCTATTCTCTCAGTTCTCATGAAT
genomic: AACGGCCTGTTGTCAGAGATCCTAACCCAAACCTTTTCTTTGCGCACCAAgttagttctg ... ttattttcagGTCATCACTAATGCATGTGCTACTCAAGCTATTCTCTCAGTTCTCATGAAT
EST: gi|18450400|gb|BM428678.1|BM428678
EST:     AACGGCCTGTTGTCAGAGATCCTAACCCAAACCTTTTCTTTGCGCACCAA                         GTCATCACTAATGCATGTGCTACTCAAGCTATTCTCTCAGTTCTCATGAAT
genomic: AACGGCCTGTTGTCAGAGATCCTAACCCAAACCTTTTCTTTGCGCACCAAgttagttctg ... ttattttcagGTCATCACTAATGCATGTGCTACTCAAGCTATTCTCTCAGTTCTCATGAAT
EST: gi|211120940|gb|FL408170.1|FL408170
EST:     AACGGCCTGTTGTCAGAGATCCTAACCCAAACCTTTTCTTTGCGCACCAA                         GTCATCACTAATGCATGTGCTACTCAAGCTATTCTCTCAGTTCTCATGAAT
genomic: AACGGCCTGTTGTCAGAGATCCTAACCCAAACCTTTTCTTTGCGCACCAAgttagttctg ... ttattttcagGTCATCACTAATGCATGTGCTACTCAAGCTATTCTCTCAGTTCTCATGAAT
EST: gi|211288445|gb|FL410142.1|FL410142
EST:     AACGGCCTGTTGTCAGAGATCCTAACCTAAACCTTTTCTTTGCGCACCAA                         GTCATCACTAATGCATGTGCTACTCAAGCTATTCTCTCAGTTCTCATGAAT
genomic: AACGGCCTGTTGTCAGAGATCCTAACCCAAACCTTTTCTTTGCGCACCAAgttagttctg ... ttattttcagGTCATCACTAATGCATGTGCTACTCAAGCTATTCTCTCAGTTCTCATGAAT
EST: gi|5055707|gb|AI734594.1|AI734594
EST:     AACGGCCTGTTGTCAGAGATCCTAACCCAAACCTTTTCTTTGCGCACCAA                         GTCATCACTAATGCATGTGCTACTCAAGCTATTCTCTCAGTTCTCATGAAT
genomic: AACGGCCTGTTGTCAGAGATCCTAACCCAAACCTTTTCTTTGCGCACCAAgttagttctg ... ttattttcagGTCATCACTAATGCATGTGCTACTCAAGCTATTCTCTCAGTTCTCATGAAT
EST: gi|31664378|gb|CD573103.1|CD573103
EST:     AACGGCCTGTTGTCAGAGATCCTAACCCAAACCTTTTCTTTGCGCACCAA                         GTCATCACTAATGCATGTGCTACTCAAGCTATTCTCTCAGTTCTCATGAAT
genomic: AACGGCCTGTTGTCAGAGATCCTAACCCAAACCTTTTCTTTGCGCACCAAgttagttctg ... ttattttcagGTCATCACTAATGCATGTGCTACTCAAGCTATTCTCTCAGTTCTCATGAAT
EST: gi|211490322|gb|FL377881.1|FL377881
EST:     AACGGCCTGTTGTCAGAGATCCTAACCCAAACCTTTTCTTTGCGCACCAA                         GTCATCACTAATGCATGTGCTACTCAAGCTATTCTCTCAGTTCTCATGAAT
genomic: AACGGCCTGTTGTCAGAGATCCTAACCCAAACCTTTTCTTTGCGCACCAAgttagttctg ... ttattttcagGTCATCACTAATGCATGTGCTACTCAAGCTATTCTCTCAGTTCTCATGAAT
EST: gi|211132915|gb|FL391880.1|FL391880
EST:     AACGGCCTGTTGTCAGAGATCCTAACCCAAACCTTTTCTTTGCGCACCAA                         GTCATCACTAATGCATGTGCTACTCAAGCTATTCTCTCAGTTCTCATGAAT
genomic: AACGGCCTGTTGTCAGAGATCCTAACCCAAACCTTTTCTTTGCGCACCAAgttagttctg ... ttattttcagGTCATCACTAATGCATGTGCTACTCAAGCTATTCTCTCAGTTCTCATGAAT
EST: gi|211156337|gb|FL380332.1|FL380332
EST:     AACGGCCTGTTGTCAGAGATCCTAACCCAAACCTTTTCTTTGCGCACCAA                         GTCATCACTAATGCATGTGCTACTCAAGCTATTCTCTCAGTTCTCATGAAT
genomic: AACGGCCTGTTGTCAGAGATCCTAACCCAAACCTTTTCTTTGCGCACCAAgttagttctg ... ttattttcagGTCATCACTAATGCATGTGCTACTCAAGCTATTCTCTCAGTTCTCATGAAT
EST: gi|30306470|gb|CD001143.1|CD001143
EST:     AACGGCCTGTTGTCAGAGATCCTAACCCAAACCTTTTCTTTGCGCACCAA                         GTCATCACTAATGCATGTGCTACTCAAGCTATTCTCTCAGTTCTCATGAAT
genomic: AACGGCCTGTTGTCAGAGATCCTAACCCAAACCTTTTCTTTGCGCACCAAgttagttctg ... ttattttcagGTCATCACTAATGCATGTGCTACTCAAGCTATTCTCTCAGTTCTCATGAAT
EST: gi|211102481|gb|FL395954.1|FL395954
EST:     AACGGCCTGTTGTCAGAGATCCTAACCCAAACCTTTTCTTTGCGCACCAA                         GTCATCACTAATGCATGTGCTACTCAAGCTATTCTCTCAGTTCTCATGAAT
genomic: AACGGCCTGTTGTCAGAGATCCTAACCCAAACCTTTTCTTTGCGCACCAAgttagttctg ... ttattttcagGTCATCACTAATGCATGTGCTACTCAAGCTATTCTCTCAGTTCTCATGAAT
EST: gi|93013476|gb|EB638996.1|EB638996
EST:     AACGGCCTGTTGTCAGAGATCCTAACCCAAACCTTTTCTTTGCGCACCAA                         GTCATCACTAATGCATGTGCTACTCCAGCTATTCTCTCAGTTCTCATGAAT
genomic: AACGGCCTGTTGTCAGAGATCCTAACCCAAACCTTTTCTTTGCGCACCAAgttagttctg ... ttattttcagGTCATCACTAATGCATGTGCTACTCAAGCTATTCTCTCAGTTCTCATGAAT
EST: gi|211392419|gb|FL378726.1|FL378726
EST:     AACGGCCTGTTGTCAGAGATCCTAACCCAAACCTTTTCTTTGCGCACCAA                         GTCATCACTAATGCATGTGCTACTCAAGCTATTCTCTCAGTTCTCATGAAT
genomic: AACGGCCTGTTGTCAGAGATCCTAACCCAAACCTTTTCTTTGCGCACCAAgttagttctg ... ttattttcagGTCATCACTAATGCATGTGCTACTCAAGCTATTCTCTCAGTTCTCATGAAT
EST: gi|76929348|gb|DV171972.1|DV171972
EST:     AACGGCCTGTTGTCAGAGATCCTAACCCAAACCTTTTCTTTGCGCACCAA                         GTCATCACTAATGCATGTGCTACTCAAGCTATTCTCTCAGTTCTCATGAAT
genomic: AACGGCCTGTTGTCAGAGATCCTAACCCAAACCTTTTCTTTGCGCACCAAgttagttctg ... ttattttcagGTCATCACTAATGCATGTGCTACTCAAGCTATTCTCTCAGTTCTCATGAAT
EST: gi|211045017|gb|FL382448.1|FL382448
EST:     AACGGCCTGTTGTCAGAGATCCTAACCCAAACCTTTTCTTTGCGCACCAA                         GTCATCACTAATGCATGTGCTACTCAAGCTATTCTCTCAGTTCTCATGAAT
genomic: AACGGCCTGTTGTCAGAGATCCTAACCCAAACCTTTTCTTTGCGCACCAAgttagttctg ... ttattttcagGTCATCACTAATGCATGTGCTACTCAAGCTATTCTCTCAGTTCTCATGAAT
EST: gi|211474315|gb|FL411624.1|FL411624
EST:     AACGGCCTGTTGTCAGAGATCCTAACCCAAACCTTTTCTTTGCGCACCAA                         GTCATCACTAATGCATTTGCYACTCAAGCTATTCTCTCAGTTCTCATGAAT
genomic: AACGGCCTGTTGTCAGAGATCCTAACCCAAACCTTTTCTTTGCGCACCAAgttagttctg ... ttattttcagGTCATCACTAATGCATGTGCTACTCAAGCTATTCTCTCAGTTCTCATGAAT
EST: gi|18650000|gb|BM498819.1|BM498819
EST:     AACGGCCTGTTGTCAGAGATCCTAACCCAAACCTTTTCTTTGCGCACCAA                         GTCATCACTAATGCAT
genomic: AACGGCCTGTTGTCAGAGATCCTAACCCAAACCTTTTCTTTGCGCACCAAgttagttctg ... ttattttcagGTCATCACTAATGCAT
EST: gi|18649234|gb|BM498053.1|BM498053
EST:     AACGGCCTGTTGTCAGAGATCCTAACCCAAACCTTTTCTTTGCGC-CCAA                         GTCATCACTAATGCATGTGCTACTCAAGCTATTCTCTCAGTTCTCATGAAT
genomic: AACGGCCTGTTGTCAGAGATCCTAACCCAAACCTTTTCTTTGCGCACCAAgttagttctg ... ttattttcagGTCATCACTAATGCATGTGCTACTCAAGCTATTCTCTCAGTTCTCATGAAT
EST: gi|78092543|gb|DV520917.1|DV520917
EST:     AACGGCCTGTTGTCAGAGATCCTAACCCAAACCTTTTCTTTGCGCACCAA                         GTCATCACTAATGCATGTGCTACTCAAGCTATTCTCTCAGTTCTCATGAAT
genomic: AACGGCCTGTTGTCAGAGATCCTAACCCAAACCTTTTCTTTGCGCACCAAgttagttctg ... ttattttcagGTCATCACTAATGCATGTGCTACTCAAGCTATTCTCTCAGTTCTCATGAAT
EST: gi|78084624|gb|DV513017.1|DV513017
EST:     AACGGCCTGTTGTCAGAGATCCTAACCCAAACCTTTTCTTTGCGCACCAA                         GTCATCACTAATGCATGTGCTACTCAAGCTATTCTCTCAGTTCTCATGAAT
genomic: AACGGCCTGTTGTCAGAGATCCTAACCCAAACCTTTTCTTTGCGCACCAAgttagttctg ... ttattttcagGTCATCACTAATGCATGTGCTACTCAAGCTATTCTCTCAGTTCTCATGAAT
EST: gi|211491468|gb|FL425155.1|FL425155
EST:     AACGGCCTGTTGTCAGAGATCCTAACCCAAACCTTTTCTTTGCGCACCAA                         GTCATCACTAATGCATGTGCTACTCAAGCTATTCTCTCAGTTCTCATGAAT
genomic: AACGGCCTGTTGTCAGAGATCCTAACCCAAACCTTTTCTTTGCGCACCAAgttagttctg ... ttattttcagGTCATCACTAATGCATGTGCTACTCAAGCTATTCTCTCAGTTCTCATGAAT
EST: gi|19822485|gb|BQ048509.1|BQ048509
EST:     AACGGCCTGTTGTCAGAGATCCTAACCCAAACCTTTTCTTTGCGCACCAA                         GTCATCACTAATGCATGTGCTACTCAAGCTATTCTCTCAGTTCTCATGAAT
genomic: AACGGCCTGTTGTCAGAGATCCTAACCCAAACCTTTTCTTTGCGCACCAAgttagttctg ... ttattttcagGTCATCACTAATGCATGTGCTACTCAAGCTATTCTCTCAGTTCTCATGAAT
EST: gi|211201385|gb|FL369966.1|FL369966
EST:     AACGGCCTGTTGTCAGAGATCCTAACCCAAACCTTTTCTTTGCGCACCAA                         GTCATCACTAATGCATGTGCTACTCAAGCTATTCTCTCAGTTCTCATGAAT
genomic: AACGGCCTGTTGTCAGAGATCCTAACCCAAACCTTTTCTTTGCGCACCAAgttagttctg ... ttattttcagGTCATCACTAATGCATGTGCTACTCAAGCTATTCTCTCAGTTCTCATGAAT

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), 47 (downstream exon)
Score: 331

AGTATATGGGCTAATTTTTCTCTTCAAGTGGATACCCGGGGAGAAGGATGAACGGCCTGTTGTCAGAGATCCTAACCCAAACCTTTTCTTTGCGCACCAAgttagttctg ... ttattttcagGTCATCACTAATGCATGTGCTACTCAAGCTATTCTCTCAGTTCTCATGAATCGCCCTGAAATTGACATTGGCCCAGAATTATCTCAATTGAAGGAATTCA


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

AGTATATGGGCTAATTTTTCTCTTCAAGTGGATACCCGGGGAGAAGGATGAACGGCCTGTTGTCAGAGATCCTAACCCAAACCTTTTCTTTGCGCACCAAgttagttctg ... ttattttcagGTCATCACTAATGCATGTGCTACTCAAGCTATTCTCTCAGTTCTCATGAATCGCCCTGAAATTGACATTGGCCCAGAATTATCTCAATTGAAGGAATTCA


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 98

AGTATATGGGCTAATTTTTCTCTTCAAGTGGATACCCGGGGAGAAGGATGAACGGCCTGTTGTCAGAGATCCTAACCCAAACCTTTTCTTTGCGCACCAAgttagttctg ... ttattttcagGTCATCACTAATGCATGTGCTACTCAAGCTATTCTCTCAGTTCTCATGAATCGCCCTGAAATTGACATTGGCCCAGAATTATCTCAATTGAAGGAATTCA


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 290

AGTATATGGGCTAATTTTTCTCTTCAAGTGGATACCCGGGGAGAAGGATGAACGGCCTGTTGTCAGAGATCCTAACCCAAACCTTTTCTTTGCGCACCAAgttagttctg ... ttattttcagGTCATCACTAATGCATGTGCTACTCAAGCTATTCTCTCAGTTCTCATGAATCGCCCTGAAATTGACATTGGCCCAGAATTATCTCAATTGAAGGAATTCA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGTATATGGGCTAATTTTTCTCTTCAAGTGGATACCCGGGGAGAAGGATGAACGGCCTGTTGTCAGAGATCCTAACCCAAACCTTTTCTTTGCGCACCAAgttagttctgttctgtttctgtccctttagctaaccacgtttgctactctgtgcttaacaataacaggatatccttttacttattttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC