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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatttaggaaatgcggagccggagctccagaatattttgccggtcgcttgctgcactcattgtgcttagtgccttagtaccacctgttggcaatgttctttacaatgtttgccatgcagGAAGCTGTTGCGATGACTAGATCCATTAAGGACCCAGAAGAGGCTGCAAAGATGCTCTTGCAAGAGGCGTACAAGAGGGAGAGCAGTGACAACATAACTT

Basic information

species Zea mays
transcript GRMZM2G056572_T01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G056572_T02 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os04g56450.2 (Oryza sativa), 3'ss of exon 7
gtaatttaggaaatgcggagccggagctccagaatattttgccggtcgcttgctgcactcattgtgcttagtgccttagtaccacctgttggcaatgttctttacaatgtttgccatgcagGAAGCTGTTGCGATGACTAGATCCATTAAGGACCCAGAAGAGGCTGCAAAGATGCTCTTGCAAGAGGCGTACAAGAGGGAGAGCAGTGACAACATAACTT
|||| ||    ||   | |     ||    |||| |||||   |     |    | | || ||||||||  ||   |||  || ||| |||    || ||||             |||||||| ||||| |  ||||| ||||| ||| | ||||||||||| |||||||||| ||||||||||||||| |||||||||||||||||||||||||||||||
gtaaattcaagaaaatgaaa----ag----agaagatttttatgtatcttaatcgtattccttgtgcttgatg---tag--cccccttttgcatttgctctt-------------atgcagGAGGCTGTCGACATGACCAGATCGATTCATGACCCAGAAGAAGCTGCAAAGAAGCTCTTGCAAGAGGCCTACAAGAGGGAGAGCAGTGACAACATAACTT
















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|71762691|gb|DR960628.1|DR960628
EST:     AGTTTCTTATCCTTGCAAGTGATGGGCTGTGGGATGTGGTCTCTAACGAG                         GAAGCTGTTGCGATGACTAGATCCATTAAGGACCCAGAAGAGGCTGCAAAG
genomic: AGTTTCTTATCCTTGCAAGTGATGGGCTGTGGGATGTGGTCTCTAACGAGgtaatttagg ... tgccatgcagGAAGCTGTTGCGATGACTAGATCCATTAAGGACCCAGAAGAGGCTGCAAAG
EST: gi|6095655|gb|AW120322.1|AW120322
EST:     AGTTTCTTATCCTTGCAAGTGATGGGCTGTGGGATGTGGTCTCTAACGAG                         GAAGCTGTCGCGATGACTAGATCCATTCAGGACCCAGAAGAGGCTGCAAAG
genomic: AGTTTCTTATCCTTGCAAGTGATGGGCTGTGGGATGTGGTCTCTAACGAGgtaatttagg ... tgccatgcagGAAGCTGTTGCGATGACTAGATCCATTAAGGACCCAGAAGAGGCTGCAAAG
EST: gi|211036167|gb|FL457683.1|FL457683
EST:     AGTTTCTTATCCTTGCAAGTGATGGGCTGTGGGATGTGGTCTCTAACGAG                         GAAGCTGTTGCGATGACTAGATCCATTAAGGACCCAGAAGAGGCTGCAAAG
genomic: AGTTTCTTATCCTTGCAAGTGATGGGCTGTGGGATGTGGTCTCTAACGAGgtaatttagg ... tgccatgcagGAAGCTGTTGCGATGACTAGATCCATTAAGGACCCAGAAGAGGCTGCAAAG
EST: gi|5124063|gb|AI745904.1|AI745904
EST:     AGTTTCTTATCCTTGCAAGTGATGGGCTGTGGGATGTGGTCTCTAACGAG                         GAAGCTGTTGCGATGACTAGATCCATTAAGGACCCAGAAGAGGCTGCAAAG
genomic: AGTTTCTTATCCTTGCAAGTGATGGGCTGTGGGATGTGGTCTCTAACGAGgtaatttagg ... tgccatgcagGAAGCTGTTGCGATGACTAGATCCATTAAGGACCCAGAAGAGGCTGCAAAG
EST: gi|76016318|gb|DT943488.1|DT943488
EST:     AGTTTCTTATCCTTGCAAGTGATGGGCTGTGGGATGTGGTCTCTAACGAG                         GAAGCTGTTGCGATGACTAGATCCATTAAGGACCCAGAAGAGGCTGCAAAG
genomic: AGTTTCTTATCCTTGCAAGTGATGGGCTGTGGGATGTGGTCTCTAACGAGgtaatttagg ... tgccatgcagGAAGCTGTTGCGATGACTAGATCCATTAAGGACCCAGAAGAGGCTGCAAAG
EST: gi|67024109|gb|CO452858.1|CO452858
EST:     AGTTTCTTATCCTTGCAAGTGATGGGTTGTGGGATGTGGTCTCTAACGAG                         GAAGCTGTCGCGATGACCAGATCCATCCAGGACCCAGAAGAAGCTGCAAAG
genomic: AGTTTCTTATCCTTGCAAGTGATGGGCTGTGGGATGTGGTCTCTAACGAGgtaatttagg ... tgccatgcagGAAGCTGTTGCGATGACTAGATCCATTAAGGACCCAGAAGAGGCTGCAAAG
EST: gi|211036166|gb|FL457682.1|FL457682
EST:     AGTTTCTTATCCTTGCAAGTGATGGGCTGTGGGATGTGGTCTCTAACGAG                         GAAGCTGTTGCGATGACTAGATCCATTAAGGACCCAGAAGAGGCTGCAAAG
genomic: AGTTTCTTATCCTTGCAAGTGATGGGCTGTGGGATGTGGTCTCTAACGAGgtaatttagg ... tgccatgcagGAAGCTGTTGCGATGACTAGATCCATTAAGGACCCAGAAGAGGCTGCAAAG
EST: gi|76016319|gb|DT943489.1|DT943489
EST:     AGTTTCTTATCCTTGCAAGTGATGGGCTGTGGGATGTGGTCTCTAACGAG                         GAAGCTGTTGCGATGACTAGATCCATTAAGGACCCAGAAGAGGCTGCAAAG
genomic: AGTTTCTTATCCTTGCAAGTGATGGGCTGTGGGATGTGGTCTCTAACGAGgtaatttagg ... tgccatgcagGAAGCTGTTGCGATGACTAGATCCATTAAGGACCCAGAAGAGGCTGCAAAG
EST: gi|5901101|gb|AW042201.1|AW042201
EST:     AGTTTCTTATCCTTGCAAGTGATGGGCTGTGGGATGTGGTCTCTAACGAG                         GAAGCTGTCGCGATGACTAGATCCATTCAGGACCCAGAAGAGGCTGCAAAG
genomic: AGTTTCTTATCCTTGCAAGTGATGGGCTGTGGGATGTGGTCTCTAACGAGgtaatttagg ... tgccatgcagGAAGCTGTTGCGATGACTAGATCCATTAAGGACCCAGAAGAGGCTGCAAAG
EST: gi|94472146|gb|EB701104.1|EB701104
EST:     GTTTCTTATCCTTTGCA-GTGATGGGCTGTGGGATGTGGTCTCTAACGAG                         GAAGCTGTTGCGATGA
genomic: GTTTCTTATCCTT-GCAAGTGATGGGCTGTGGGATGTGGTCTCTAACGAGgtaatttagg ... tgccatgcagGAAGCTGTTGCGATGA
EST: gi|76290021|gb|DV029589.1|DV029589
EST:     AGTTTCTTATCCTTGCAAGTGATGGGCTGTGGGATGTGGTCTCTAACGAG                         GAAGCTGTTGCGATGACT
genomic: AGTTTCTTATCCTTGCAAGTGATGGGCTGTGGGATGTGGTCTCTAACGAGgtaatttagg ... tgccatgcagGAAGCTGTTGCGATGACT
EST: gi|76288714|gb|DV028282.1|DV028282
EST:     AGTTTCTTATCCTTGCAAGTGATGGGCTGTGGGATGTGGTCTCTAACGAG                         GAAGCTGTTGCGATGACTAGATCCATTAAGGACCCAGAAGAGGCTGCAAAG
genomic: AGTTTCTTATCCTTGCAAGTGATGGGCTGTGGGATGTGGTCTCTAACGAGgtaatttagg ... tgccatgcagGAAGCTGTTGCGATGACTAGATCCATTAAGGACCCAGAAGAGGCTGCAAAG
EST: gi|60340995|gb|DN207968.1|DN207968
EST:     AGTTTCTTATCCTTGCAAGTGATGGGCTGTGGGATGTGGTCTCTAACGAG                         GAAGCTGTTGCGATGACTAGATCCATTAAGGACCCAGAAGAGGCTGCAAAG
genomic: AGTTTCTTATCCTTGCAAGTGATGGGCTGTGGGATGTGGTCTCTAACGAGgtaatttagg ... tgccatgcagGAAGCTGTTGCGATGACTAGATCCATTAAGGACCCAGAAGAGGCTGCAAAG
EST: gi|60357297|gb|DN224270.1|DN224270
EST:     AGTTTCTTATCCTTGCAAGTGATGGGCTGTGGGATGTGGTCTCTAACGAG                         GAAGCTGTTGCGATGACTAGATCCATTAAGGACCCAGAAGAGGGTGCAAAG
genomic: AGTTTCTTATCCTTGCAAGTGATGGGCTGTGGGATGTGGTCTCTAACGAGgtaatttagg ... tgccatgcagGAAGCTGTTGCGATGACTAGATCCATTAAGGACCCAGAAGAGGCTGCAAAG
EST: gi|60359261|gb|DN226234.1|DN226234
EST:     AGTTTCTTATCCTTGCAAGTGATGGGCTGTGGGATGTGGTCTCTAACGAG                         GAAGCTGTTGCGATGACTAGAT
genomic: AGTTTCTTATCCTTGCAAGTGATGGGCTGTGGGATGTGGTCTCTAACGAGgtaatttagg ... tgccatgcagGAAGCTGTTGCGATGACTAGAT
EST: gi|60354881|gb|DN221854.1|DN221854
EST:     AGTTTCTTATCCTTGCAAGTGATGGGCTGTGGGATGTGGTCTCTAACGAG                         GAAGCTGTTGCGATGACTAGATCCATTAAGGACCCAGAAGAGGCTGCAAAG
genomic: AGTTTCTTATCCTTGCAAGTGATGGGCTGTGGGATGTGGTCTCTAACGAGgtaatttagg ... tgccatgcagGAAGCTGTTGCGATGACTAGATCCATTAAGGACCCAGAAGAGGCTGCAAAG
EST: gi|60338245|gb|DN205218.1|DN205218
EST:     AGTTTCTTATCCTTGCAAGTGATGGGCTGTGGGATGTGGTCTCTAACGAG                         GAAGCTGTTGCGATGACTAGATCCATTAAGGACCCAGAAGAGGCTGCAAAG
genomic: AGTTTCTTATCCTTGCAAGTGATGGGCTGTGGGATGTGGTCTCTAACGAGgtaatttagg ... tgccatgcagGAAGCTGTTGCGATGACTAGATCCATTAAGGACCCAGAAGAGGCTGCAAAG
EST: gi|166579571|gb|EG295241.1|EG295241
EST:     GTGGTCTCTAACGAG                         GAAGCTGTCGCGATGACTAGATCCATTAAGGACCCAGAAGAGGCTGCAAAG
genomic: GTGGTCTCTAACGAGgtaatttagg ... tgccatgcagGAAGCTGTTGCGATGACTAGATCCATTAAGGACCCAGAAGAGGCTGCAAAG
EST: gi|67021956|gb|CO450705.1|CO450705
EST:     AGTTTCTTATCCTTGCAAGTGATGGGTTGTGGGATGTGGTCTCTAACGAG                         GAAGCTGTCGCGATGACCAGATCCATCCAGGACCCAGAAGAAGCTGCAAAG
genomic: AGTTTCTTATCCTTGCAAGTGATGGGCTGTGGGATGTGGTCTCTAACGAGgtaatttagg ... tgccatgcagGAAGCTGTTGCGATGACTAGATCCATTAAGGACCCAGAAGAGGCTGCAAAG
EST: gi|31406343|gb|CD485075.1|CD485075
EST:     AGTTTCTTATCCTTGCAAGTGATGGGCTGTGGGATGTGGTCTCTAACGAG                         GAAGCTGTTGCGATGACTAGATCCATTAAGGACCCAGAAGAGGCTGCAAAG
genomic: AGTTTCTTATCCTTGCAAGTGATGGGCTGTGGGATGTGGTCTCTAACGAGgtaatttagg ... tgccatgcagGAAGCTGTTGCGATGACTAGATCCATTAAGGACCCAGAAGAGGCTGCAAAG
EST: gi|149111015|gb|EE294514.2|EE294514
EST:     AGTTTTTTATCCTTGCAAGTGATGGGCTGTGGGATGTGGTCTTTAACGAG                         GAAGCTGTTGCGATGACTAGATCCATTAAGGACCCAGAAGAGGCTGCAAAG
genomic: AGTTTCTTATCCTTGCAAGTGATGGGCTGTGGGATGTGGTCTCTAACGAGgtaatttagg ... tgccatgcagGAAGCTGTTGCGATGACTAGATCCATTAAGGACCCAGAAGAGGCTGCAAAG

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), 49 (downstream exon)
Score: 375

GAGGAAGTTGTTGATGACACACTCGAGTTTCTTATCCTTGCAAGTGATGGGCTGTGGGATGTGGTCTCTAACGAGgtaatttagg ... tgccatgcagGAAGCTGTTGCGATGACTAGATCCATTAAGGACCCAGAAGAGGCTGCAAAGATGCTCTTGCAAGAGGCGTACAAGAGGGAGAGCAGTGACAACATAACTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 394

GAGGAAGTTGTTGATGACACACTCGAGTTTCTTATCCTTGCAAGTGATGGGCTGTGGGATGTGGTCTCTAACGAGgtaatttagg ... tgccatgcagGAAGCTGTTGCGATGACTAGATCCATTAAGGACCCAGAAGAGGCTGCAAAGATGCTCTTGCAAGAGGCGTACAAGAGGGAGAGCAGTGACAACATAACTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 679

GAGGAAGTTGTTGATGACACACTCGAGTTTCTTATCCTTGCAAGTGATGGGCTGTGGGATGTGGTCTCTAACGAGgtaatttagg ... tgccatgcagGAAGCTGTTGCGATGACTAGATCCATTAAGGACCCAGAAGAGGCTGCAAAGATGCTCTTGCAAGAGGCGTACAAGAGGGAGAGCAGTGACAACATAACTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 426

GAGGAAGTTGTTGATGACACACTCGAGTTTCTTATCCTTGCAAGTGATGGGCTGTGGGATGTGGTCTCTAACGAGgtaatttagg ... tgccatgcagGAAGCTGTTGCGATGACTAGATCCATTAAGGACCCAGAAGAGGCTGCAAAGATGCTCTTGCAAGAGGCGTACAAGAGGGAGAGCAGTGACAACATAACTT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttagtgccttagtaccacctgttggcaatgttctttacaatgtttgccatgcagGAAGCTGTTGCGATGACTAGATCCATTAAGGACCCAGAAGAGGCTGCAAAGATGCTCTTGCAAGAGGCGTACAAGAGGGAGAGCAGTGACAACATAACTT
                                  tttacaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatttaggaaatgcggagccggagctccagaatattttgccggtcgcttgctgcactcattgtgcttagtgccttagtaccacctgttggcaatgttctttacaatgtttgccatgcagGAAGCTGTTGCGATGACTAGATCCATTAAGGACCCAGAAGAGGCTGCAAAGATGCTCTTGCAAGAGGCGTACAAGAGGGAGAGCAGTGACAACATAACTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG