Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtataaattgtgtactaaaagtcagtaccttttcttagtaggagaggatggaataaaatctatgggactgaaacagttgatttcctgcagGTGCATAACATCCGACCTAAAATGGTGTCAGTGCTTCGTGAAAAGTTTGCACACATGAACTTGACATTTTCTATCGGAGGGCAGATTAGTTTTGAT

Basic information

species Zea mays
transcript GRMZM2G165535_T01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G165535_T05 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os04g58580.1 (Oryza sativa), 3'ss of exon 7
gtataaattgtgtactaaaagtcagtaccttttcttagtaggagaggatggaataaaatctatgggactgaaacagttgatttcctgcagGTGCATAACATCCGACCTAAAATGGTGTCAGTGCTTCGTGAAAAGTTTGCACACATGAACTTGACATTTTCTATCGGAGGGCAGATTAGTTTTGAT
||| |||   |    || ||      |   ||| |||  |     | |           | |||  ||| ||     | |||| ||  |||| |||||||| || ||||||||||| |||||||||||||||||||| || ||| ||||||||||||||||||| |||||||||||||||||||||
gtacaaacaattctttacaaagagcaataatttgttatcattcaggca-----------ccatgaaacttaactgacttatttactatagGTACATAACATTCGGCCTAAAATGGTCTCAGTGCTTCGTGAAAAGTTCGCCCACTTGAACTTGACATTTTCTATTGGAGGGCAGATTAGTTTTGAT

upper sequence: GRMZM2G165535_T05 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA18G46390.1 (Glycine max), 3'ss of exon 8
--------------gtataaattgtgtactaaaagtcagtaccttttcttagtaggagaggatggaataaaatctatgggactgaa--acagttgatttcctgcagGTGCATAACATCCGACCTAAAATGGTGTCAGTGCTTCGTGAAAAGTTTGCACACATGAACTTGACATTTTCTATCGGAGGGCAGATTAGTTTTGAT
              || |  ||    | ||  |      |  || | | || |   |    | |     || | ||||  |        || || |  | || ||||| || || || || || |||||||| || || |||||||| |||||||| ||  | ||||||||||| || || ||||| ||||| |||||||| 
ggttatgtattttggtttttatcacattctctagaattttcactatccatattgaaatgttaggcgtataattttatgctaaaagtttgcaatttaagttct-caGGTTCACAATATACGCCCGAAAATGGTTTCTGTACTTCGTGAGAAGTTTGCTCATCTTAACTTGACATTCTCCATTGGAGGACAGATAAGTTTTGA-

upper sequence: GRMZM2G165535_T05 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA09G39800.1 (Glycine max), 3'ss of exon 8
-------------gtataaattgtgtactaaaagtcagtaccttttcttagtaggagaggatggaataaaatcta---tgggactgaaacagttgatttcctgcagGTGCATAACATCCGACCTAAAATGGTGTCAGTGCTTCGTGAAAAGTTTGCACACATGAACTTGACATTTTCTATCGGAGGGCAGATTAGTTTTGAT
             || |  ||  | | ||  |      |  || | | || |   |    | |     || | ||   |   | |     | || | |||   ||||| || ||||| || || |||||||| || || |||||||| |||||||| ||  | ||||||||||| || || ||||| ||||| |||||||||
gttatgtattttggtttttatcatattctctagaattttcactatccatattgaaatgttaggtgtataactttaccctaaaagtttgcaatttaagttct--cagGTTCACAACATACGCCCAAAAATGGTTTCTGTACTTCGTGAGAAGTTTGCTCATCTTAACTTGACATTCTCCATTGGAGGACAGATAAGTTTTGAT

upper sequence: GRMZM2G165535_T05 (Zea mays), 3'ss of exon 8
lower sequence: Vv15s0046g03520.t01 (Vitis vinifera), 3'ss of exon 7
-----------------------------gtataaattgtgtactaaaagtcagtaccttttcttagtaggagaggatggaataaaatctatgggac---tgaaacagttgat--ttcctgcagGTGCATAACATCCGACCTAAAATGGTGTCAGTGCTTCGTGAAAAGTTTGCACACATGAACTTGACATTTTCTATCGGAGGGCAGATTAGTTTTGAT
                             |  | || |||  | |     |     |  |   ||  | | |   |    || |       ||  ||     | ||| || ||  |     ||| | || ||||| || || || ||||| || ||||||||||| |||||||| ||| | ||| ||||||||||||| ||||| || || || ||||||
gtataaacttcagatccttcgaagcaaaagattgaactgtcaatttgtgtttgtggcaataaattgattgtatttggataaacatgcatcctgaaacaaacaacacaatttataatcatatcagATTCACAACATACGTCCGAAGATGGTTTCTGTGCTTCGTGAGAAGTTTGCTCACCTAAACCTGACATTTTCTATTGGAGGACAAATAAGCTTTGAT

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|6020771|gb|AW065579.1|AW065579
EST:     GAAGAAACTGTAGCCAAGAAGAACGGGATGAATTTGAGAAGTACGATAAG                         GTGCATAACATCCGACCTAAAATGGTGTCAGTGCTTCGTGAAAAGTTTGCA
genomic: GAAGAAACTGTAGCCAAGAAGAACGGGATGAATTTGAGAAGTACGATAAGgtataaattg ... tttcctgcagGTGCATAACATCCGACCTAAAATGGTGTCAGTGCTTCGTGAAAAGTTTGCA
EST: gi|78118501|gb|DV536885.1|DV536885
EST:     GAAGAAACTGTAGCCAAGAAGAACGGGATGAATTTGAGAAGTACGATAAG                         GTGCATAACATCCGACCTAAAATGGTGTCAGTGCTTCGTGAAAAGTTTGCA
genomic: GAAGAAACTGTAGCCAAGAAGAACGGGATGAATTTGAGAAGTACGATAAGgtataaattg ... tttcctgcagGTGCATAACATCCGACCTAAAATGGTGTCAGTGCTTCGTGAAAAGTTTGCA
EST: gi|86471496|gb|DY237866.1|DY237866
EST:     GAAGAAACTGTAGCCAAGAAGAACGGGATGAATTTGAGAAGTACGATAAG                         GTGCATAACATCCGACCTAAAATGGTGTCAGTGCTTCGTGAAAAGTTTGCA
genomic: GAAGAAACTGTAGCCAAGAAGAACGGGATGAATTTGAGAAGTACGATAAGgtataaattg ... tttcctgcagGTGCATAACATCCGACCTAAAATGGTGTCAGTGCTTCGTGAAAAGTTTGCA
EST: gi|85151824|gb|DW587525.1|DW587525
EST:     GAAGAAACTGTAGCCCAGAAGAACGTGATGAATTTGAGAAGTACGATAAG                         GTGCATAACATCCGACCTAAAATGGTGTCAGTGCTTCGTGAAAAGTTTGCA
genomic: GAAGAAACTGTAGCCAAGAAGAACGGGATGAATTTGAGAAGTACGATAAGgtataaattg ... tttcctgcagGTGCATAACATCCGACCTAAAATGGTGTCAGTGCTTCGTGAAAAGTTTGCA
EST: gi|40334667|gb|CK368737.1|CK368737
EST:     GAAGAAACTGTAGCCAAGAAGAACGTGATGAATTTGAGAAGTACGATAAG                         GTGCATAACATCCGACCTAAAATGGTGTCAGTGCTTCGTGAAAAGTTTGCA
genomic: GAAGAAACTGTAGCCAAGAAGAACGGGATGAATTTGAGAAGTACGATAAGgtataaattg ... tttcctgcagGTGCATAACATCCGACCTAAAATGGTGTCAGTGCTTCGTGAAAAGTTTGCA
EST: gi|76011520|gb|DT938690.1|DT938690
EST:     GAAGAAACTGTAGCCAAGAAGAACGGGATGAATTTGAGAAGTACGATAAG                         GTGCATAACATCCGACCTAAAATGGTGTCAGTGCTTCGTGAAAAGTTTGCA
genomic: GAAGAAACTGTAGCCAAGAAGAACGGGATGAATTTGAGAAGTACGATAAGgtataaattg ... tttcctgcagGTGCATAACATCCGACCTAAAATGGTGTCAGTGCTTCGTGAAAAGTTTGCA
EST: gi|71449147|gb|DR830197.1|DR830197
EST:     GAAGAAACTGTAGCCAAGAAGAACGGGATGAATTTGAGAAGTACGATAAG                         GTGCATAACATCCGACCTAAAATGGTGTCAGTGCTTCGTGAAAAGTTTGCA
genomic: GAAGAAACTGTAGCCAAGAAGAACGGGATGAATTTGAGAAGTACGATAAGgtataaattg ... tttcctgcagGTGCATAACATCCGACCTAAAATGGTGTCAGTGCTTCGTGAAAAGTTTGCA
EST: gi|71763428|gb|DR961365.1|DR961365
EST:     GAAGAAACTGTAGCCAAGAAGAACGGGATGAATTTGAGAAGTACGATAAG                         GTGCATAACATCCGACCTAAAATGGTGTCAGTGCTTCGTGAAAAGTTTGCA
genomic: GAAGAAACTGTAGCCAAGAAGAACGGGATGAATTTGAGAAGTACGATAAGgtataaattg ... tttcctgcagGTGCATAACATCCGACCTAAAATGGTGTCAGTGCTTCGTGAAAAGTTTGCA
EST: gi|74245816|gb|DT653730.1|DT653730
EST:     GAAGAAACTGTAGCCAAGAAGAACGGGATGAATTTGAGAAGTACGATAAG                         GTGCATAACATCCGACCTAAAATGGTGTCAGTGCTTCGTGAAAAGTTTGCA
genomic: GAAGAAACTGTAGCCAAGAAGAACGGGATGAATTTGAGAAGTACGATAAGgtataaattg ... tttcctgcagGTGCATAACATCCGACCTAAAATGGTGTCAGTGCTTCGTGAAAAGTTTGCA
EST: gi|45846830|gb|CN070773.1|CN070773
EST:     GAAGAAACTGTAGCCAAGAAGAACGGGATGAATTTGAGAAGTACGATAAG                         GTGCATAACATCCGACCTAAAATGGTGTCAGTGCTTCGTGAAAAGTTTGCA
genomic: GAAGAAACTGTAGCCAAGAAGAACGGGATGAATTTGAGAAGTACGATAAGgtataaattg ... tttcctgcagGTGCATAACATCCGACCTAAAATGGTGTCAGTGCTTCGTGAAAAGTTTGCA
EST: gi|71299719|gb|DR785870.1|DR785870
EST:     GAAGAAACTGTAGCCAAGAAGAACGGGATGAATTTGAGAAGTACGATAAG                         GTGCATAACATCCGACCTAAAATGGTGTCAGTGCTTCGTGAAAAGTTTG
genomic: GAAGAAACTGTAGCCAAGAAGAACGGGATGAATTTGAGAAGTACGATAAGgtataaattg ... tttcctgcagGTGCATAACATCCGACCTAAAATGGTGTCAGTGCTTCGTGAAAAGTTTG
EST: gi|14700950|gb|BI233368.1|BI233368
EST:     TTGAGAAGTACGATAAG                         GTGCATAACATCCGACCTAAAATGGTGTCAGTGCTTCGTGAAAAGTTTGCA
genomic: TTGAGAAGTACGATAAGgtataaattg ... tttcctgcagGTGCATAACATCCGACCTAAAATGGTGTCAGTGCTTCGTGAAAAGTTTGCA
EST: gi|148947648|gb|EC893128.2|EC893128
EST:     GAAGAAACTGTAGCCAAGAAGAACGGGATGAATTTGAGAAGTACGATAAG                         GTGCATAACATCCGACCTAAAATGGTGTCAGTGCTTCGTGAAAAGTTTGCA
genomic: GAAGAAACTGTAGCCAAGAAGAACGGGATGAATTTGAGAAGTACGATAAGgtataaattg ... tttcctgcagGTGCATAACATCCGACCTAAAATGGTGTCAGTGCTTCGTGAAAAGTTTGCA
EST: gi|71773498|gb|DR971398.1|DR971398
EST:     GAAGAAACTGTAGCCAAGAAGAACGGGATGAATTTGAGAAGTACGATAAG                         GTGCATAACATCCGACCTAAAATGGTGTCAGTGCTTCGTGAAAAGTTTGCA
genomic: GAAGAAACTGTAGCCAAGAAGAACGGGATGAATTTGAGAAGTACGATAAGgtataaattg ... tttcctgcagGTGCATAACATCCGACCTAAAATGGTGTCAGTGCTTCGTGAAAAGTTTGCA
EST: gi|148943662|gb|EC888726.2|EC888726
EST:     GAAGAAACTGTAGCCAAGAAGAACGGGATGAATTTGAGAAGTACGATAAG                         GTGCATAACATCCGACCTAAAATGGTGTCAGTGCTTCGTGAAAAGTTTGCA
genomic: GAAGAAACTGTAGCCAAGAAGAACGGGATGAATTTGAGAAGTACGATAAGgtataaattg ... tttcctgcagGTGCATAACATCCGACCTAAAATGGTGTCAGTGCTTCGTGAAAAGTTTGCA
EST: gi|5871104|gb|AW017545.1|AW017545
EST:     GATGAATTTGAGAAGTACGATAAG                         GTGCATACCATCCGACCTAAAATGGTGTCAGTGCTTCGTGAAAAGTTTGCA
genomic: GATGAATTTGAGAAGTACGATAAGgtataaattg ... tttcctgcagGTGCATAACATCCGACCTAAAATGGTGTCAGTGCTTCGTGAAAAGTTTGCA
EST: gi|6056459|gb|AW090849.1|AW090849
EST:     GAAGAAACTGTAGCCAAGAAGAACGGGATGAATTTGAGAAGTACGATAAG                         GTGCATAACATCCGACCTAAAATGGTGTCAGTGCTTCGTGAAAAGTTTGCA
genomic: GAAGAAACTGTAGCCAAGAAGAACGGGATGAATTTGAGAAGTACGATAAGgtataaattg ... tttcctgcagGTGCATAACATCCGACCTAAAATGGTGTCAGTGCTTCGTGAAAAGTTTGCA
EST: gi|148947872|gb|EC893365.2|EC893365
EST:     GAAGAAACTGTAGCCAAGAAGAACGGGATGAATTTGAGAAGTACGATAAG                         GTGCATAACATCCGACCTAAAATGGTGTCAGTGCTTCGTGAAAAGTTTGCA
genomic: GAAGAAACTGTAGCCAAGAAGAACGGGATGAATTTGAGAAGTACGATAAGgtataaattg ... tttcctgcagGTGCATAACATCCGACCTAAAATGGTGTCAGTGCTTCGTGAAAAGTTTGCA
EST: gi|71299718|gb|DR785869.1|DR785869
EST:     GAAGAAACTGTAGCCAAGAAGAACGGGATGAATTTGAGAAGTACGATAAG                         GTGCATAACATCCGACCTAAAATGGTGTCAGTGCTTCGTGAAAAGTTTGCA
genomic: GAAGAAACTGTAGCCAAGAAGAACGGGATGAATTTGAGAAGTACGATAAGgtataaattg ... tttcctgcagGTGCATAACATCCGACCTAAAATGGTGTCAGTGCTTCGTGAAAAGTTTGCA
EST: gi|32909183|gb|CF013995.1|CF013995
EST:     GAAGAAACTGTAGCCAAGAAGAACGTGATGAATTTGAGAAGTACGATAAG                         GTGCATAACATCCGACCTAAAATGGTGTCAGTGCTTCGTGAAAAGTTTGCA
genomic: GAAGAAACTGTAGCCAAGAAGAACGGGATGAATTTGAGAAGTACGATAAGgtataaattg ... tttcctgcagGTGCATAACATCCGACCTAAAATGGTGTCAGTGCTTCGTGAAAAGTTTGCA
EST: gi|76280414|gb|DV019982.1|DV019982
EST:     GAAGAAACTGTAGCCAAGAAGAACGGGATGAATTTGAGAAGTACGATAAG                         GTGCATAACATCCGACCTAAAATGGTGTCAGTGCTTCGTGAAAAGTTTGCA
genomic: GAAGAAACTGTAGCCAAGAAGAACGGGATGAATTTGAGAAGTACGATAAGgtataaattg ... tttcctgcagGTGCATAACATCCGACCTAAAATGGTGTCAGTGCTTCGTGAAAAGTTTGCA
EST: gi|32909184|gb|CF013996.1|CF013996
EST:     GAAGAAACTGTAGCCAAGAAGAACGTGATGAATTTGAGAAGTACGATAAG                         GTGCATAACATCCGACCTAAAATGGTGTCAGTGCTTCGTGAAAAGTTTGCA
genomic: GAAGAAACTGTAGCCAAGAAGAACGGGATGAATTTGAGAAGTACGATAAGgtataaattg ... tttcctgcagGTGCATAACATCCGACCTAAAATGGTGTCAGTGCTTCGTGAAAAGTTTGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagtaggagaggatggaataaaatctatgggactgaaacagttgatttcctgcagGTGCATAACATCCGACCTAAAATGGTGTCAGTGCTTCGTGAAAAGTTTGCACACATGAACTTGACATTTTCTATCGGAGGGCAGATTAGTTTTGAT
                                       agttgat  putative branch site (score: 5)
                                             tttcctgc  CT-rich tract
                aataaaatctat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtataaattgtgtactaaaagtcagtaccttttcttagtaggagaggatggaataaaatctatgggactgaaacagttgatttcctgcagGTGCATAACATCCGACCTAAAATGGTGTCAGTGCTTCGTGAAAAGTTTGCACACATGAACTTGACATTTTCTATCGGAGGGCAGATTAGTTTTGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT