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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atcatgtgtaaagtatactgtctgttagaccttggaatccatacttctgtctttcacgtttcattcacattttcacatatatgttctttacctttctcagTGGAGAGGATGCATTTGACTACTTCAAAAACGACCCTAATCTTTTTGATGTG

Basic information

species Zea mays
transcript GRMZM5G876003_T03
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G876003_T03 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os02g38060.2 (Oryza sativa), 3'ss of exon 2
--atcatgtgtaaagtatactgtctgttagaccttggaatccatacttctgtctttcacgtttcattcacattttcacatatatgttctttacctttctcagTGGAGAGGATGCATTTGACTACTTCAAAAACGACCCTAATCTTTTTGATGTG
   | |    |  |   |      |||   |      ||||    ||||  | || ||   ||||  |   |  ||| | || |||| |||    || |||||||| | ||||||||||||||||||| ||| || ||| ||||||||||||||
actttacccttggaaactggaaa-tgtagaaatcactaatcagagcttcatttttgcaatattcacacttttactcaaacat-tgtttttttttcttttcagTGGACAAGATGCATTTGACTACTTCACAAATGAGCCTGATCTTTTTGATGTG
















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|76923220|gb|DV169382.1|DV169382
EST:     TTATCTGGTGGCCATTTTAGAATGTTAAACGAGAAGCTATACACTTGCAG                         TGGAGAGGATGCATTTGACTACTTCAAAAACGACCCTAATCTTTTTGATGT
genomic: TTATCTGGTGGCCATTTTAGAATGTTAAACGAGAAGCTATACACTTGCAGgttcacattc ... cctttctcagTGGAGAGGATGCATTTGACTACTTCAAAAACGACCCTAATCTTTTTGATGT
EST: gi|211194090|gb|FL377673.1|FL377673
EST:     TTATCTGGTGGCCATTTTAGAATGTTAAACGAGAAGCTATACACTTGCAG                         TGGAGAGGATGCATTTGACTACTTCAAAAACGACCCTAATCTTTTTGATGT
genomic: TTATCTGGTGGCCATTTTAGAATGTTAAACGAGAAGCTATACACTTGCAGgttcacattc ... cctttctcagTGGAGAGGATGCATTTGACTACTTCAAAAACGACCCTAATCTTTTTGATGT
EST: gi|76281989|gb|DV021557.1|DV021557
EST:     TTATCTGGTGGCCATTTTAGAATGTTAAACGAGAAGCTATACACTTGCAG                         TGGAGAGGATGCATTTGACTACTTCAAAAACGACCCTAATCTTTTTGATGT
genomic: TTATCTGGTGGCCATTTTAGAATGTTAAACGAGAAGCTATACACTTGCAGgttcacattc ... cctttctcagTGGAGAGGATGCATTTGACTACTTCAAAAACGACCCTAATCTTTTTGATGT
EST: gi|74240435|gb|DT648349.1|DT648349
EST:     TTATCTGGTGGCCATTTTAGAATGTTAAACGAGAAGCTATACACTTGCAG                         TGGAGAGGATGCATTTGACTACTTCAAAAACGACCCTAATCTTTTTGATGT
genomic: TTATCTGGTGGCCATTTTAGAATGTTAAACGAGAAGCTATACACTTGCAGgttcacattc ... cctttctcagTGGAGAGGATGCATTTGACTACTTCAAAAACGACCCTAATCTTTTTGATGT
EST: gi|31354696|gb|CD439053.1|CD439053
EST:     TTATCTGGTGGCCATTTTAGAATGTTAAACGAGAAGCTATACACTTGCAG                         TGGAGAGGATGCATTTGACTACTTCAAAAACGACCCTAATCTTTTTGATGT
genomic: TTATCTGGTGGCCATTTTAGAATGTTAAACGAGAAGCTATACACTTGCAGgttcacattc ... cctttctcagTGGAGAGGATGCATTTGACTACTTCAAAAACGACCCTAATCTTTTTGATGT
EST: gi|71435218|gb|DR816268.1|DR816268
EST:     TTATCTGGTGGCCATTTTAGAATGTTAAACGAGAAGCTATACACTTGCAG                         TGGAGAGGATGCATTTGACTACTTCAAAAACGACCCTAATCTTTTTGATGT
genomic: TTATCTGGTGGCCATTTTAGAATGTTAAACGAGAAGCTATACACTTGCAGgttcacattc ... cctttctcagTGGAGAGGATGCATTTGACTACTTCAAAAACGACCCTAATCTTTTTGATGT
EST: gi|71429033|gb|DR810083.1|DR810083
EST:     TTATCTGGTGGCCATTTTAGAATGTTAAACGAGAAGCTATACACTTGCAG                         TGGAGAGGATGCATTTGACTACTTCAAAAACGACCCTAATCTTTTTGATGT
genomic: TTATCTGGTGGCCATTTTAGAATGTTAAACGAGAAGCTATACACTTGCAGgttcacattc ... cctttctcagTGGAGAGGATGCATTTGACTACTTCAAAAACGACCCTAATCTTTTTGATGT
EST: gi|71434799|gb|DR815849.1|DR815849
EST:     TTATCTGGGGGCCATTTTAGAATGTTAAACGAGAAGCTATACACTTGCAG                         TGGAGAGGATGCATTTGACTACTTCAAAAACGACCCTAATCTTTTTGATGT
genomic: TTATCTGGTGGCCATTTTAGAATGTTAAACGAGAAGCTATACACTTGCAGgttcacattc ... cctttctcagTGGAGAGGATGCATTTGACTACTTCAAAAACGACCCTAATCTTTTTGATGT
EST: gi|211163247|gb|FL415263.1|FL415263
EST:     TTATCTGGTGGCCATTTTAGAATGTTAAACGAGAAGCTATACACTTGCAG                         TGGAGAGGATGCATTTGACTACTTCAAAAACGACCCTAATCTTTTTGATGT
genomic: TTATCTGGTGGCCATTTTAGAATGTTAAACGAGAAGCTATACACTTGCAGgttcacattc ... cctttctcagTGGAGAGGATGCATTTGACTACTTCAAAAACGACCCTAATCTTTTTGATGT
EST: gi|78074350|gb|DV502784.1|DV502784
EST:     TTATCTGGTGGCCATTTTAGAATGTTAAACGAGAAGCTATACACTTGCAG                         TGGAGAGGATGCATTTGACTACTTCAAAAACGACCCTAATCTTTTTGATGT
genomic: TTATCTGGTGGCCATTTTAGAATGTTAAACGAGAAGCTATACACTTGCAGgttcacattc ... cctttctcagTGGAGAGGATGCATTTGACTACTTCAAAAACGACCCTAATCTTTTTGATGT
EST: gi|50329972|gb|CO525098.1|CO525098
EST:     TTATCTGGTGGCCATTTTAGAATGTTAAACGAGAAGCTATACACTTGCAG                         TGGAGAGGATGCATTTGACTACTTCAAAAACGACCCTAATCTTTTTGATGT
genomic: TTATCTGGTGGCCATTTTAGAATGTTAAACGAGAAGCTATACACTTGCAGgttcacattc ... cctttctcagTGGAGAGGATGCATTTGACTACTTCAAAAACGACCCTAATCTTTTTGATGT
EST: gi|211327567|gb|FL371066.1|FL371066
EST:     TTATCTGGTGGCCATTTTAGAATGTTAAACGAGAAGCTATACACTTGCAG                         TGGAGAGGATGCATTTGACTACTTCAAAAACGACCCTAATCTTTTTGATGT
genomic: TTATCTGGTGGCCATTTTAGAATGTTAAACGAGAAGCTATACACTTGCAGgttcacattc ... cctttctcagTGGAGAGGATGCATTTGACTACTTCAAAAACGACCCTAATCTTTTTGATGT
EST: gi|211025381|gb|FL421226.1|FL421226
EST:     TTATCTGGTGGCCATTTTAGAATGTTAAACGAGAAGCTATACACTTGCAG                         TGGAGAGGATGCATTTGACTACTTCAAAAACGACCCTAATCTTTTTGATGT
genomic: TTATCTGGTGGCCATTTTAGAATGTTAAACGAGAAGCTATACACTTGCAGgttcacattc ... cctttctcagTGGAGAGGATGCATTTGACTACTTCAAAAACGACCCTAATCTTTTTGATGT
EST: gi|76922748|gb|DV169154.1|DV169154
EST:     TTATCTGGTGGCCATTTTAGAATGTTAAACGAGAAGCTATACACTTGCAG                         TGGAGAGGATGCATTTGACTACTTCAAAAACGACCCTAATCTTTTTGATGT
genomic: TTATCTGGTGGCCATTTTAGAATGTTAAACGAGAAGCTATACACTTGCAGgttcacattc ... cctttctcagTGGAGAGGATGCATTTGACTACTTCAAAAACGACCCTAATCTTTTTGATGT
EST: gi|78108382|gb|DV526800.1|DV526800
EST:     TTATCTGGTGGCCATTTTAGAATGTTAAACGAGAAGCTATACACTTGCAG                         TGGAGAGGATGCATTTGACTACTTCAAAAACGACCCTAATCTTTTTGATGT
genomic: TTATCTGGTGGCCATTTTAGAATGTTAAACGAGAAGCTATACACTTGCAGgttcacattc ... cctttctcagTGGAGAGGATGCATTTGACTACTTCAAAAACGACCCTAATCTTTTTGATGT
EST: gi|74245743|gb|DT653657.1|DT653657
EST:     TTATCTGGTGGCCATTTTAGAATGTTAAACGAGAAGCTATACACTTGCAG                         TGGAGAGGATGCATTTGACTACTTCAAAAACGACCCTAATCTTTTTGATGT
genomic: TTATCTGGTGGCCATTTTAGAATGTTAAACGAGAAGCTATACACTTGCAGgttcacattc ... cctttctcagTGGAGAGGATGCATTTGACTACTTCAAAAACGACCCTAATCTTTTTGATGT
EST: gi|148948106|gb|EC893615.2|EC893615
EST:     TTATCTGGTGGCCATTTTAGAATGTTAAACGAGAAGCTATACACTTGCAG                         TGGAGAGGATGCATTTGACTACTTCAAAAACGACCCTAATCTTTTTGATGT
genomic: TTATCTGGTGGCCATTTTAGAATGTTAAACGAGAAGCTATACACTTGCAGgttcacattc ... cctttctcagTGGAGAGGATGCATTTGACTACTTCAAAAACGACCCTAATCTTTTTGATGT
EST: gi|149071083|gb|EE159484.2|EE159484
EST:     TTATCTGGTGGCCATTTTAGAATGTTAAACGAGAAGCTATACACTTGCAG                         TGGAGAGGATGCATTTGACTACTTCAAAAACGACCCTAATCTTTTTGATGT
genomic: TTATCTGGTGGCCATTTTAGAATGTTAAACGAGAAGCTATACACTTGCAGgttcacattc ... cctttctcagTGGAGAGGATGCATTTGACTACTTCAAAAACGACCCTAATCTTTTTGATGT
EST: gi|91055947|gb|EB166365.1|EB166365
EST:     TTATCTGGTGGCCATTTTAGAATGTTAAACGAGAAGCTATACACTTGCAG                         TGGAGAGGATGCATTTGACTACTTCAAAAACGACCCTAATCTTTTTGATGT
genomic: TTATCTGGTGGCCATTTTAGAATGTTAAACGAGAAGCTATACACTTGCAGgttcacattc ... cctttctcagTGGAGAGGATGCATTTGACTACTTCAAAAACGACCCTAATCTTTTTGATGT
EST: gi|149100899|gb|EE186995.2|EE186995
EST:     TTATCTGGTGGCCATTTTAGAATGTTAAACGAGAAGCTATACACTTGCAG                         TGGAGAGGATGCATTTGACTACTTCAAAAACGACCCTAATCTTTTTGATGT
genomic: TTATCTGGTGGCCATTTTAGAATGTTAAACGAGAAGCTATACACTTGCAGgttcacattc ... cctttctcagTGGAGAGGATGCATTTGACTACTTCAAAAACGACCCTAATCTTTTTGATGT
EST: gi|78080458|gb|DV508870.1|DV508870
EST:     TTATCTGGTGGCCATTTTAGAATGTTAAACGAGAAGCTATACACTTGCAG                         TGGAGAGGATGCATTTGACTACTTCAAAAACGACCCTAATCTTTTTGATGT
genomic: TTATCTGGTGGCCATTTTAGAATGTTAAACGAGAAGCTATACACTTGCAGgttcacattc ... cctttctcagTGGAGAGGATGCATTTGACTACTTCAAAAACGACCCTAATCTTTTTGATGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctgtctttcacgtttcattcacattttcacatatatgttctttacctttctcagTGGAGAGGATGCATTTGACTACTTCAAAAACGACCCTAATCTTTTTGATGTG
                                    tgttctttacctttct  CT-rich tract
                       attttcacatatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atcatgtgtaaagtatactgtctgttagaccttggaatccatacttctgtctttcacgtttcattcacattttcacatatatgttctttacctttctcagTGGAGAGGATGCATTTGACTACTTCAAAAACGACCCTAATCTTTTTGATGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG