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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGCAAAAAACAGGGGGGCAGGAACTTGTTGGAGGATTAGATTGTACAGTCCACCGAAACTTTTTTGGGAGTCAGgtaaatttggggatcatatggcatgtgatagtcatattattgaattttgcatcttcaaaggatttgtagttattattaaacacacaaatatgaacaccatgtttcattgcagactgtttctcttgcag

Basic information

species Zea mays
transcript GRMZM2G023528_T03
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G023528_T03 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os02g03740.1 (Oryza sativa), 5'ss of exon 4
GGCAAAAAACAGGGGGGCAGGAACTTGTTGGAGGATTAGATTGTACAGTCCACCGAAACTTTTTTGGGAGTCAGgtaaatttggggatcatatggcatgt--gatagtcatattattgaattttgcatcttcaaaggatttgtagttattattaaacacacaaatatgaacaccatgtttcattgcagactgtttctcttgcag
| |||||| | || || ||||| ||| |||||||| |||||||||| |||||||| |||||||||||||| ||||||| |||| ||||| | |    |||  ||| | |  |  | |      |     ||| |  |  |  |   | |||||  |      |  ||||| ||     |   ||||||                
GCCAAAAATCCGGAGGTCAGGAGCTTATTGGAGGACTAGATTGTACTGTCCACCGGAACTTTTTTGGGAGCCAGgtaactttgaggatcgtgttctctgtttgatggccggagcagttttcactatcatttctattgtctcttcaattttattttatttttgag-atgaatac---actctcttgcag----------------

upper sequence: GRMZM2G023528_T03 (Zea mays), 5'ss of exon 4
lower sequence: Vv06s0004g03000.t01 (Vitis vinifera), 5'ss of exon 4
GGCAAAAAACAGGGGGGCAGGAACTTGTTGGAGGATTAGATTGTACAGTCCACCGAAACTTTTTTGGGAGTCAGgtaaatttggggatcatatggcatgtgatagtcatattattgaattttgcatcttcaaaggatttgtagttattattaaacacacaaatatgaacaccatgtttcattgcagactgtttctcttgcag
| || |||||||| ||||||||||| ||||| ||  | ||||||||||| ||||| ||||| ||||| ||||||||||   |    ||  | || | | |||   || | ||| ||    |  ||     |||   || ||| ||   |  |  || | |||| | || | ||   |    ||                   
GACAGAAAACAGGTGGGCAGGAACTAGTTGGGGGCCTTGATTGTACAGTTCACCGGAACTTCTTTGGCAGTCAGgtaatgatatacattctgtgtcct-tgact-tcgtcttactg----tcacaaagataaaatgtt-gta-ttgaaaacatgcaaaaaaat-taaaaatcaaactgatatg-------------------
















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|6020368|gb|AW065296.1|AW065296
EST:     TTGTTGGAGGATTAGATTGTACAGTCCACCGAAACTTTTTTGGGAGTCAG                         CTTCAAAGCTTTGAGACAGAGCTTTCCGTGCCAAAGCTTTCGGAGAAGGAA
genomic: TTGTTGGAGGATTAGATTGTACAGTCCACCGAAACTTTTTTGGGAGTCAGgtaaatttgg ... tctcttgcagCTTCAAAGCTTTGAGACAGAGCTTTCCGTGCCAAAGCTTTCGGAGAAGGAA
EST: gi|71318383|gb|DR795955.1|DR795955
EST:     TTGTTGGAGGATTAGATTGTACAGTCCACCGAAACTTTTTTGGGAGTCAG                         CTTCAAAGCTTTGAGACAGAGCTTTCCGTGCCAAAGCTTTCGGAGAAGGAA
genomic: TTGTTGGAGGATTAGATTGTACAGTCCACCGAAACTTTTTTGGGAGTCAGgtaaatttgg ... tctcttgcagCTTCAAAGCTTTGAGACAGAGCTTTCCGTGCCAAAGCTTTCGGAGAAGGAA
EST: gi|91055149|gb|EB165567.1|EB165567
EST:     TTGTTGGAGGATTAGATTGTACAGTCCACCGAAACTTTTTTGGGAGTCAG                         CTTCAAAGCTTTGAGACAGAGCTTTCCGTGCCAAAGCTTTCGGAGAAGGAA
genomic: TTGTTGGAGGATTAGATTGTACAGTCCACCGAAACTTTTTTGGGAGTCAGgtaaatttgg ... tctcttgcagCTTCAAAGCTTTGAGACAGAGCTTTCCGTGCCAAAGCTTTCGGAGAAGGAA
EST: gi|5895630|gb|AW036876.1|AW036876
EST:     TTGTTGGAGGATTAGATTGTACAGTCCACCGAAACTTTTTTGGGAGTCAG                         CTTCAAAGCTTTGAGACAGAGCTTTCCGTGCCAAAGCTTTCGGAGAAGGAA
genomic: TTGTTGGAGGATTAGATTGTACAGTCCACCGAAACTTTTTTGGGAGTCAGgtaaatttgg ... tctcttgcagCTTCAAAGCTTTGAGACAGAGCTTTCCGTGCCAAAGCTTTCGGAGAAGGAA
EST: gi|78120474|gb|DV538858.1|DV538858
EST:     TTGTTGGAGGATTAGATTGTACAGTCCACCGAAACTTTTTTGGGAGTCAG                         CTTCAAAGCTTTGAGACAGAGCTTTCCGTGCCAAAGCTTTCGGAGAAGGAA
genomic: TTGTTGGAGGATTAGATTGTACAGTCCACCGAAACTTTTTTGGGAGTCAGgtaaatttgg ... tctcttgcagCTTCAAAGCTTTGAGACAGAGCTTTCCGTGCCAAAGCTTTCGGAGAAGGAA
EST: gi|32934367|gb|CF039179.1|CF039179
EST:     CAGTCCACCGAAACTTTTTTGGGAGTCAG                         CTTCAAAGCTTTGAGACAGAGCTTTCGGTGCCAAAGCTTTCGGAGAAGGAA
genomic: CAGTCCACCGAAACTTTTTTGGGAGTCAGgtaaatttgg ... tctcttgcagCTTCAAAGCTTTGAGACAGAGCTTTCCGTGCCAAAGCTTTCGGAGAAGGAA
EST: gi|33467208|gb|CF244257.1|CF244257
EST:     TTGTTGGAGGATTAGATTGTACAGTCCACCGAAACTTTTTTGGGAGTCAG                         CTTCAAAGCTTTGAGACAGAGCTTTCCGTGCCAAAGCTTTCGGAGAAGGAA
genomic: TTGTTGGAGGATTAGATTGTACAGTCCACCGAAACTTTTTTGGGAGTCAGgtaaatttgg ... tctcttgcagCTTCAAAGCTTTGAGACAGAGCTTTCCGTGCCAAAGCTTTCGGAGAAGGAA
EST: gi|37382875|gb|CF628406.1|CF628406
EST:     ACCGAAAC-TTTTTGGGAGTCAG                         CTTCAAAGCTTTGAGACAGAGCTTTCGGTGCCAAAGCTTTCGGAGAAGGAA
genomic: ACCGAAACTTTTTTGGGAGTCAGgtaaatttgg ... tctcttgcagCTTCAAAGCTTTGAGACAGAGCTTTCCGTGCCAAAGCTTTCGGAGAAGGAA
EST: gi|74233030|gb|DT640944.1|DT640944
EST:     TTGTTGGAGGATTAGATTGTACAGTCCACCGAAACTTTTTTGGGAGTCAG                         CTTCAAAGCTTTGAGACAGAGCTTTCCGTGCCAAAGCTTTCGGAGAAGGAA
genomic: TTGTTGGAGGATTAGATTGTACAGTCCACCGAAACTTTTTTGGGAGTCAGgtaaatttgg ... tctcttgcagCTTCAAAGCTTTGAGACAGAGCTTTCCGTGCCAAAGCTTTCGGAGAAGGAA
EST: gi|71437533|gb|DR818583.1|DR818583
EST:     TTGTTGGAGGATTAGATTGTACAGTCCACCGAAACTTTTTTGGGAGTCAG                         CTTCAAAGCTTTGAGACAGAGCTTTCCGTGCCAAAGCTTTCGGAGAAGGAA
genomic: TTGTTGGAGGATTAGATTGTACAGTCCACCGAAACTTTTTTGGGAGTCAGgtaaatttgg ... tctcttgcagCTTCAAAGCTTTGAGACAGAGCTTTCCGTGCCAAAGCTTTCGGAGAAGGAA
EST: gi|149073844|gb|EE162166.2|EE162166
EST:     TTGTTGGAGGATTAGATTGTACAGTCCACCGAAACTTTTTTGGGAGTCAG                         CTTCAAAGCTTTGAGACAGAGCTTTCCGTGCCAAAGCTTTCGGAGAAGGAA
genomic: TTGTTGGAGGATTAGATTGTACAGTCCACCGAAACTTTTTTGGGAGTCAGgtaaatttgg ... tctcttgcagCTTCAAAGCTTTGAGACAGAGCTTTCCGTGCCAAAGCTTTCGGAGAAGGAA
EST: gi|31359368|gb|CD443725.1|CD443725
EST:     TTGTTGGAGGATTAGATTGTACAGTCCACCGAAACTTTTTTGGGAGTCAG                         CTTCAAAGCTTTGAGACAGAGCTTTCCGTGCCAAAGCTTTCGGAGAAGGAA
genomic: TTGTTGGAGGATTAGATTGTACAGTCCACCGAAACTTTTTTGGGAGTCAGgtaaatttgg ... tctcttgcagCTTCAAAGCTTTGAGACAGAGCTTTCCGTGCCAAAGCTTTCGGAGAAGGAA
EST: gi|74233031|gb|DT640945.1|DT640945
EST:     TTGTTGGAGGATTAGATTGTACAGTCCACCGAAACTTTTTTGGGAGTCAG                         CTTTCAA-GCTTTGAGACAGAGCTTTCCGTGCCAAAGCTTTCCGAGAAGGA
genomic: TTGTTGGAGGATTAGATTGTACAGTCCACCGAAACTTTTTTGGGAGTCAGgtaaatttgg ... tctcttgcagCTT-CAAAGCTTTGAGACAGAGCTTTCCGTGCCAAAGCTTTCGGAGAAGGA
EST: gi|148986692|gb|EE030480.2|EE030480
EST:     TTGTTGGAGGATTAGATTGTACAGTCCACCGAAACTTTTTTGGGAGTCAG                         CTTCAAAGCTTTGAGACAGAGCTTTCCGTGCCAAAGCTTTCGGAGAAGGAA
genomic: TTGTTGGAGGATTAGATTGTACAGTCCACCGAAACTTTTTTGGGAGTCAGgtaaatttgg ... tctcttgcagCTTCAAAGCTTTGAGACAGAGCTTTCCGTGCCAAAGCTTTCGGAGAAGGAA
EST: gi|40303169|gb|CK347556.1|CK347556
EST:     TTGTTGGAGGATTAGATTGTACAGTCCACCGAAACTTTTTTGGGAGTCAG                         CTTCAAAGCTTTGAGACAGAGCTTTCGGTGCCAAAGCTTTCGGAGAAGGAA
genomic: TTGTTGGAGGATTAGATTGTACAGTCCACCGAAACTTTTTTGGGAGTCAGgtaaatttgg ... tctcttgcagCTTCAAAGCTTTGAGACAGAGCTTTCCGTGCCAAAGCTTTCGGAGAAGGAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGCAAAAAACAGGGGGGCAGGAACTTGTTGGAGGATTAGATTGTACAGTCCACCGAAACTTTTTTGGGAGTCAGgtaaatttggggatcatatggcatgtgatagtcatattattgaattttgcatcttcaaaggatttgtagttattattaaacacacaaatatgaacaccatgtttcattgcagactgtttctcttgcag

- - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - GAGGAT