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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaatgaacatacttacataaagcaacacattaacgtttcccctgatccgaattgaaaaagatatttgatttaaaatgtgctttccttgaaattatgtgtttaaataagaattttgctattgacatgccgaattatctttttcgcagCTTTGATGATCCTGGTCCACATGGAGCAGGTAGATATTCTGAGCATATGCTACCTGAAATTGTGAAGAAAGATTGGAGAAAGGGTGCGCAG

Basic information

species Zea mays
transcript GRMZM2G099255_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G099255_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os06g48700.1 (Oryza sativa), 3'ss of exon 5
gtaaatgaacatacttacataaagcaacacatta-acgtttcccctgatccgaattgaaaaagatatttgatttaaaatgt---gctttccttgaaattatgtgtttaaataag------aattttgctattgacatgccgaattatctttttcgcagCTTTGATGATCCTGGTCCACATGGAGCAGGTAGATATTCTGAGCATATGCTACCTGAAATTGTGAAGAAAGATTGGAGAAAGGGTGCGCAG
|||| || ||    ||| |    | |    |||| | || |   |  |    || |  || |||| ||||||| |  || |   |    ||||  | | |||  |   || |        | |||  | | ||||| ||| || |   ||||   ||| ||||| ||||||||||||||||||||||| ||||||||||| |||||||||||||||||||| |||| |||||||||||| ||||| |||
gtaagtggacgcctttaaaccctgaatgttattacatgtgtagacacacttaaagttgaacagatgtttgattcaggatctccagtgcccctttcattcatgattgctaacagacattatagtttctccactgacacgcc-aactgctttttcttcagTTTTGACGATCCTGGTCCACATGGAGCAGGCAGATATTCTGATCATATGCTACCTGAAATTGTTAAGAGAGATTGGAGAAAAGGTGCACAG

upper sequence: GRMZM2G099255_T01 (Zea mays), 3'ss of exon 5
lower sequence: AT2G19160.1 (Arabidopsis thaliana), 3'ss of exon 5
gtaaatgaacatacttacataaagcaacacattaacgtttcccctgatccgaattgaaaaagatatttgatttaaaatgtgctttccttgaaattatgtgtttaaataagaattttgctattgacatgccgaattatctttttcgcagCTTTGATGATCCTGGTCCACATGGAGCAGGTAGATATTCTGAGCATATGCTACCTGAAATTGTGAAGAAAGATTGGAGAAAGGGTGCGCAG
                                ||| || |  | |    | | ||||  | ||| |  ||  || |||    |   | ||     |  | | |   | |    | |    || ||      | |  | | ||   |||||||||||||||||||||||||||| | || ||  ||   || || ||| | || ||||||   | | ||||||   |||||||||| |||
-------------------------------gtaaagtatttctt----caagttgatga-gatttcagaactataat----tacacatgttgccagatttcttcttgacttctctatacttaactatgatagtgttttattcttcagCTTTGATGATCCTGGTCCACATGGAACGGGCAGGCATATGGACCACATGTTGCCGGAAATTCCAAGGGAAGATTTTCGAAAGGGTGCACAG

upper sequence: GRMZM2G099255_T01 (Zea mays), 3'ss of exon 5
lower sequence: Vv11s0103g00490.t01 (Vitis vinifera), 3'ss of exon 5
--------------------------------------gtaaatgaacatacttacataaagcaacacattaacgtttcccctgatccgaattgaaaaagatatttgatttaaaatgtgctttccttgaaattatgtgtttaaataagaattttgctattgacatgccgaat---------tatctttttcgcagCTTTGATGATCCTGGTCCACATGGAGCAGGTAGATATTCTGAGCATATGCTACCTGAAATTGTGAAGAAAGATTGGAGAAAGGGTGCGCAG
                                      ||   |     |  ||   | ||  ||   |||||| ||   |  |  |  | |  ||       |||| |||||  | |  | |   |   |  || | |    || | | || || | |  | ||  |  ||         | |||| ||| ||||||||| ||||||||||||||||||   || |||||||| || |||||| |||| ||||||| || ||  || |  |||||||| || |||
gtaaactcaatgttcttattaaaggatgtatccctattgttgcttttgttgtttgggtcaataaaagaattaacattaaacaagtgc--actccaatggcccttttggtttaatcttttttgtatattgcaaaatttatcgggatgaaatttctgttttgcatattactgatgcacacccctttcttgttcccagCTTTGAGGATCCTGGTCCACATGGAAATGGCAGATATTCAGAACATATGTTACCGGAAATTGAGATGAGTGACTTTAGAAAGGGCGCACAG

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|78105512|gb|DV523930.1|DV523930
EST:     GATTATATATATAGTTATCTCATGGAGACAAACGTCAGTTTTGTTGACTG                         CTTTGATGATCCTGGTCCACATGGAGCAGGTAGATATTCTGAGCATATGCT
genomic: GATTATATATATAGTTATCTCATGGAGACAAACGTCAGTTTTGTTGACTGgtaaatgaac ... tttttcgcagCTTTGATGATCCTGGTCCACATGGAGCAGGTAGATATTCTGAGCATATGCT
EST: gi|78090001|gb|DV518375.1|DV518375
EST:     GATTATATATATAGTTATCTCATGGAGACAAACGTCAGTTTTGTTGACTG                         CTTTGATGATCCTGGTCCACATGGAGCAGGTAGATATTCTGAGCATATGCT
genomic: GATTATATATATAGTTATCTCATGGAGACAAACGTCAGTTTTGTTGACTGgtaaatgaac ... tttttcgcagCTTTGATGATCCTGGTCCACATGGAGCAGGTAGATATTCTGAGCATATGCT
EST: gi|76018436|gb|DT945606.1|DT945606
EST:     GATTATATATATAGTTATCTCATGGAGACAAACGTCAGTTTTGTTGACTG                         CTTTGATGATCCTGGTCCACATGGAGCAGGTAGATATTCTGAGCATATGCT
genomic: GATTATATATATAGTTATCTCATGGAGACAAACGTCAGTTTTGTTGACTGgtaaatgaac ... tttttcgcagCTTTGATGATCCTGGTCCACATGGAGCAGGTAGATATTCTGAGCATATGCT
EST: gi|101398462|gb|EB821104.1|EB821104
EST:     GATTATATATATAGTTATCTCATGGAGACAAACGTCAGTTTTGTTGACTG                         CTTTGATGATCCTGGTCCACATGGAGCAGGTAGATATTCTGAGCATATGCT
genomic: GATTATATATATAGTTATCTCATGGAGACAAACGTCAGTTTTGTTGACTGgtaaatgaac ... tttttcgcagCTTTGATGATCCTGGTCCACATGGAGCAGGTAGATATTCTGAGCATATGCT
EST: gi|86474172|gb|DY240542.1|DY240542
EST:     GATTATATATATAGTTATCTCATGGAGACAAACGTCAGTTTTGTTGACTG                         CTTTGATGATCCTGGTCCACATGGAGCAGGTAGATATTCTGAGCATATGCT
genomic: GATTATATATATAGTTATCTCATGGAGACAAACGTCAGTTTTGTTGACTGgtaaatgaac ... tttttcgcagCTTTGATGATCCTGGTCCACATGGAGCAGGTAGATATTCTGAGCATATGCT
EST: gi|78093093|gb|DV521467.1|DV521467
EST:     GATTATATATATAGTTATCTCATGGAGACAAACGTCAGTTTTGTTGACTG                         CTTTGATGATCCTGGTCCACATGGAGCAGGTAGATATTCTGAGCATATGCT
genomic: GATTATATATATAGTTATCTCATGGAGACAAACGTCAGTTTTGTTGACTGgtaaatgaac ... tttttcgcagCTTTGATGATCCTGGTCCACATGGAGCAGGTAGATATTCTGAGCATATGCT
EST: gi|86471048|gb|DY237418.1|DY237418
EST:     GATTATATATATAGTTATCTCATGGAGACAAACGTCAGTTTTGTTGACTG                         CTTTGATGATCCTGGTCCACATGGAGCAGGTAGATATTCTGAGCATATGCT
genomic: GATTATATATATAGTTATCTCATGGAGACAAACGTCAGTTTTGTTGACTGgtaaatgaac ... tttttcgcagCTTTGATGATCCTGGTCCACATGGAGCAGGTAGATATTCTGAGCATATGCT
EST: gi|71774867|gb|DR972745.1|DR972745
EST:     GATTATATATATAGTTATCTCATGGAGACAAACGTCAGTTTTGTTGACTG                         CTTTGATGATCCTGGTCCACATGGAGCAGGTAGATATTCTGAGCATATGCT
genomic: GATTATATATATAGTTATCTCATGGAGACAAACGTCAGTTTTGTTGACTGgtaaatgaac ... tttttcgcagCTTTGATGATCCTGGTCCACATGGAGCAGGTAGATATTCTGAGCATATGCT
EST: gi|78077573|gb|DV506007.1|DV506007
EST:     GATTATATATATAGTTATCTCATGGAGACAAACGTCAGTTTTGTTGACTG                         CTTTGATGATCCTGGTCCACATGGAGCAGGTAGATATTCTGAGCATATGCT
genomic: GATTATATATATAGTTATCTCATGGAGACAAACGTCAGTTTTGTTGACTGgtaaatgaac ... tttttcgcagCTTTGATGATCCTGGTCCACATGGAGCAGGTAGATATTCTGAGCATATGCT
EST: gi|101388829|gb|EB816396.1|EB816396
EST:     GATTATATATATAGTTATCTCATGGAGACAAACGTCAGTTTTGTTGACTG                         CTTTGATGATCCTGGTCCACATGGAGCAGGTAGATATTCTGAGCATATGCT
genomic: GATTATATATATAGTTATCTCATGGAGACAAACGTCAGTTTTGTTGACTGgtaaatgaac ... tttttcgcagCTTTGATGATCCTGGTCCACATGGAGCAGGTAGATATTCTGAGCATATGCT
EST: gi|148961000|gb|EE011700.2|EE011700
EST:     GATTATATATATAGTTATCTCATGGAGACAAACGTCAGTTTTGTTGACTG                         CTTTGATGATCCTGGTCCACATGGAGCAGGTAGATATTCTGAGCATATGCT
genomic: GATTATATATATAGTTATCTCATGGAGACAAACGTCAGTTTTGTTGACTGgtaaatgaac ... tttttcgcagCTTTGATGATCCTGGTCCACATGGAGCAGGTAGATATTCTGAGCATATGCT
EST: gi|71767366|gb|DR965303.1|DR965303
EST:     GATTATATATATAGTTATCTCATGGAGACAAACGTCAGTTTTGTTGACTG                         CTTTGATGATCCTGGTCCACATGGAGCAGGTAGATATTCTGAGCATATGCT
genomic: GATTATATATATAGTTATCTCATGGAGACAAACGTCAGTTTTGTTGACTGgtaaatgaac ... tttttcgcagCTTTGATGATCCTGGTCCACATGGAGCAGGTAGATATTCTGAGCATATGCT
EST: gi|211278467|gb|FL480336.1|FL480336
EST:     GAKBATATATATAGTTATCTCATGGAGACAAACGTCAGTTTTGTTGACTG                         CTTTGATGATCCTGGTCCACATGGAGCAGGTAGATATTCTGAGCATATGCT
genomic: GATTATATATATAGTTATCTCATGGAGACAAACGTCAGTTTTGTTGACTGgtaaatgaac ... tttttcgcagCTTTGATGATCCTGGTCCACATGGAGCAGGTAGATATTCTGAGCATATGCT
EST: gi|149106921|gb|EE188822.2|EE188822
EST:     GATTATATATATAGTTATCTCATGGAGACAAACGTCAGTTTTGTTGACTG                         CTTTGATGATCCTGGTCCACATGGAGCAGGTAGATATTCTGAGCATATGCT
genomic: GATTATATATATAGTTATCTCATGGAGACAAACGTCAGTTTTGTTGACTGgtaaatgaac ... tttttcgcagCTTTGATGATCCTGGTCCACATGGAGCAGGTAGATATTCTGAGCATATGCT
EST: gi|71442672|gb|DR823722.1|DR823722
EST:     GATTATATATATAGTTATCTCATGGAGACAAACGTCAGTTTTGTTGACTG                         CTTTGATGATCCTGGTCCACATGGAGCAGGTAGATATTCTGAGCATATGCT
genomic: GATTATATATATAGTTATCTCATGGAGACAAACGTCAGTTTTGTTGACTGgtaaatgaac ... tttttcgcagCTTTGATGATCCTGGTCCACATGGAGCAGGTAGATATTCTGAGCATATGCT
EST: gi|76912823|gb|DV164898.1|DV164898
EST:     GATTATATATATAGTTATCTCATGGAGACAAACGTCAGTTTTGTTGACTG                         CTTTGATGATCCTGGTCCACATGGAGCANGTAGATATTCTGAGCATATGCT
genomic: GATTATATATATAGTTATCTCATGGAGACAAACGTCAGTTTTGTTGACTGgtaaatgaac ... tttttcgcagCTTTGATGATCCTGGTCCACATGGAGCAGGTAGATATTCTGAGCATATGCT
EST: gi|86469460|gb|DY235830.1|DY235830
EST:     GATTATATATATAGTTATCTCATGGAGACAAACGTCAGTTTTGTTGACTG                         CTTTGATGATCCTGGTCCACATGGAGCAGGTAGATATTCTGAGCATATGCT
genomic: GATTATATATATAGTTATCTCATGGAGACAAACGTCAGTTTTGTTGACTGgtaaatgaac ... tttttcgcagCTTTGATGATCCTGGTCCACATGGAGCAGGTAGATATTCTGAGCATATGCT
EST: gi|149082889|gb|EE172120.2|EE172120
EST:     GATTATATATATAGTTATCTCATGGAGACAAACGTCAGTTTTGTTGACTG                         CTTTGATGATCCTGGTCCACATGGAGCAGGTAGATATTCTGAGCATATGCT
genomic: GATTATATATATAGTTATCTCATGGAGACAAACGTCAGTTTTGTTGACTGgtaaatgaac ... tttttcgcagCTTTGATGATCCTGGTCCACATGGAGCAGGTAGATATTCTGAGCATATGCT
EST: gi|50337694|gb|CO532820.1|CO532820
EST:     GATTATATATATAGTTATCTCATGGAGACAAACGTCAGTTTTGTTGACTG                         CTTTGATGATCCTGGTCCACATGGAGCAGGTAGATATTCTGAGCATATGCT
genomic: GATTATATATATAGTTATCTCATGGAGACAAACGTCAGTTTTGTTGACTGgtaaatgaac ... tttttcgcagCTTTGATGATCCTGGTCCACATGGAGCAGGTAGATATTCTGAGCATATGCT
EST: gi|76912822|gb|DV164897.1|DV164897
EST:     GATTATATATATAGTTATCTCATGGAGACAAACGTCAGTTTTGTTGACTG                         CTTTGATGATCCTGGTCCACATGGAGCAGGTAGATATTCTGAGCATATGCT
genomic: GATTATATATATAGTTATCTCATGGAGACAAACGTCAGTTTTGTTGACTGgtaaatgaac ... tttttcgcagCTTTGATGATCCTGGTCCACATGGAGCAGGTAGATATTCTGAGCATATGCT
EST: gi|148963210|gb|EE014187.2|EE014187
EST:     GATTATATATATAGTTATCTCATGGAGACAAACGTCAGTTTTGTTGACTG                         CTTTGATGATCCTGGTCCACATGGAGCAGGTAGATATTCTGAGCATATGCT
genomic: GATTATATATATAGTTATCTCATGGAGACAAACGTCAGTTTTGTTGACTGgtaaatgaac ... tttttcgcagCTTTGATGATCCTGGTCCACATGGAGCAGGTAGATATTCTGAGCATATGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttatgtgtttaaataagaattttgctattgacatgccgaattatctttttcgcagCTTTGATGATCCTGGTCCACATGGAGCAGGTAGATATTCTGAGCATATGCTACCTGAAATTGTGAAGAAAGATTGGAGAAAGGGTGCGCAG
                         tattgac  putative branch site (score: 2)
                                        ttatctttttc  putative PPT
       tttaaataagaatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaatgaacatacttacataaagcaacacattaacgtttcccctgatccgaattgaaaaagatatttgatttaaaatgtgctttccttgaaattatgtgtttaaataagaattttgctattgacatgccgaattatctttttcgcagCTTTGATGATCCTGGTCCACATGGAGCAGGTAGATATTCTGAGCATATGCTACCTGAAATTGTGAAGAAAGATTGGAGAAAGGGTGCGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA