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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGAAAAGAGAAACCAGAACTTGACTTATATACTGAACACCCATCATCACTATGATCATACTGGTGGAAACTTGGAATTGAAGGCAAAATATGGTGCAAAGgtatagctttgggctattttatttgttctttctttttctgtatcgttcagtgactctgatacagtatgtgacaatgacacaatcaaaatgggtttttgtt...

Basic information

species Zea mays
transcript GRMZM2G120300_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G120300_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os09g34100.1 (Oryza sativa), 5'ss of exon 3
GGAAAAGAGAAACCAGAACTTGACTTATATACTGAACACCCATCATCACTATGATCATACTGGTGGAAACTTGGAATTGAAGGCAAAATATGGTGCAAAGgtatagctttgggctattttatttgttctttctttttctgtatcgttcagtgactctgatacagtatgtgacaatga---cacaatcaaaatgggtt-tttgtt
 ||||| ||||||||||||||||| || |||||||||||||||||||||||||| ||||||||||| ||||||||| |||||||||||||||||||||||||||     | || |   |   || || |   || |||   || |||  ||  | || | |  || | |    ||||   |  |   | |||| ||  | || |
AGAAAAAAGAAACCAGAACTTGACCTACATACTGAACACCCATCATCACTATGACCATACTGGTGGCAACTTGGAACTGAAGGCAAAATATGGTGCAAAGgtatgcacataggttgcctctcttattttcgtttgttcc--attgttt-gtagcactaa-attgtgtattgttatgagttcttatggacaatgagtaatatggt
















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|5325053|gb|AI783244.1|AI783244
EST:     ATGATCATACTGGTGGAAACTTGGAATTGAAGGCAAAATATGGTGCAAAG                         GTAATTGGTTCTGAGAAGGATAAGGACAGAATACCTGGCATTGACATCACT
genomic: ATGATCATACTGGTGGAAACTTGGAATTGAAGGCAAAATATGGTGCAAAGgtatagcttt ... tgcattttagGTAATTGGTTCTGAGAAGGATAAGGACAGAATACCTGGCATTGACATCACG
EST: gi|111991062|gb|EE331971.1|EE331971
EST:     ATGATCATACTGGTGGAAACTTGGAATTGAAGGCAAAATATGGTGCAAAG                         GTAATTGGTTCTGAGAAGGATAAGGACAGAATACCTGGCATTGACATCACG
genomic: ATGATCATACTGGTGGAAACTTGGAATTGAAGGCAAAATATGGTGCAAAGgtatagcttt ... tgcattttagGTAATTGGTTCTGAGAAGGATAAGGACAGAATACCTGGCATTGACATCACG
EST: gi|78086882|gb|DV515275.1|DV515275
EST:     ATGATCATACTGGTGGAAACTTGGAATTGAAGGCAAAATATGGTGCAAAG                         GTAATTGGTTCTGAGAAGGATAAGGACAGAATACCTGGCATTGACATCACG
genomic: ATGATCATACTGGTGGAAACTTGGAATTGAAGGCAAAATATGGTGCAAAGgtatagcttt ... tgcattttagGTAATTGGTTCTGAGAAGGATAAGGACAGAATACCTGGCATTGACATCACG
EST: gi|149112938|gb|EE295731.2|EE295731
EST:     ATGATCATACTGGTGGAAACTTGGAATTGAAGGCAAAATATGGTGCAAAG                         GTAATTGGTTCTGAGAAGGATAAGGACAGAATACCTGGCATTGACATCACG
genomic: ATGATCATACTGGTGGAAACTTGGAATTGAAGGCAAAATATGGTGCAAAGgtatagcttt ... tgcattttagGTAATTGGTTCTGAGAAGGATAAGGACAGAATACCTGGCATTGACATCACG
EST: gi|74238485|gb|DT646399.1|DT646399
EST:     ATGATCATACTGGTGGAAACTTGGAATTGAAGGCAAAATATGGTGCAAAG                         GTAATTGGTTCTGAGAAGGATAAGGACAGAATACCTGGCATTGACATCACG
genomic: ATGATCATACTGGTGGAAACTTGGAATTGAAGGCAAAATATGGTGCAAAGgtatagcttt ... tgcattttagGTAATTGGTTCTGAGAAGGATAAGGACAGAATACCTGGCATTGACATCACG
EST: gi|78113025|gb|DV531419.1|DV531419
EST:     ATGATCATACTGGTGGAAACTTGGAATTGAAGGCAAAATATGGTGCAAAG                         GTAATTGGTTCTGAGAAGGATAAGGACAGAATACCTGGCATTGACATCACG
genomic: ATGATCATACTGGTGGAAACTTGGAATTGAAGGCAAAATATGGTGCAAAGgtatagcttt ... tgcattttagGTAATTGGTTCTGAGAAGGATAAGGACAGAATACCTGGCATTGACATCACG
EST: gi|148939665|gb|EC884322.2|EC884322
EST:     ATGATCATACTGGTGGAAACTTGGAATTGAAGGCAAAATATGGTGCAAAG                         GTAATTGGTTCTGAGAAGGATAAGGACAGAATACCTGGCATTGACATCACG
genomic: ATGATCATACTGGTGGAAACTTGGAATTGAAGGCAAAATATGGTGCAAAGgtatagcttt ... tgcattttagGTAATTGGTTCTGAGAAGGATAAGGACAGAATACCTGGCATTGACATCACG
EST: gi|148957405|gb|EC903461.2|EC903461
EST:     ATGATCATACTGGTGGAAACTTGGAATTGAAGGCAAAATATGGTGCAAAG                         GTAATTGGTTCTGAGAAGGATAAGGACAGAATACCTGGCATTGACATCACG
genomic: ATGATCATACTGGTGGAAACTTGGAATTGAAGGCAAAATATGGTGCAAAGgtatagcttt ... tgcattttagGTAATTGGTTCTGAGAAGGATAAGGACAGAATACCTGGCATTGACATCACG
EST: gi|211007084|gb|FL215830.1|FL215830
EST:     ACGATCATACTGGTGGAAACTTGGAATTGAAGGCAAAATATGGTGCAAAG                         GTAATTGGTTCTGAGAAGGATAAGGACAGAATACCTGGCATTGACATCACT
genomic: ATGATCATACTGGTGGAAACTTGGAATTGAAGGCAAAATATGGTGCAAAGgtatagcttt ... tgcattttagGTAATTGGTTCTGAGAAGGATAAGGACAGAATACCTGGCATTGACATCACG
EST: gi|149075909|gb|EE164468.2|EE164468
EST:     ATGATCATACTGGTGGAAACTTGGAATTGAAGGCAAAATATGGTGCAAAG                         GTAATTGGTTCTGAGAAGGATAAGGACAGAATACCTGGCATTGACATCACG
genomic: ATGATCATACTGGTGGAAACTTGGAATTGAAGGCAAAATATGGTGCAAAGgtatagcttt ... tgcattttagGTAATTGGTTCTGAGAAGGATAAGGACAGAATACCTGGCATTGACATCACG
EST: gi|5846865|gb|AI999948.1|AI999948
EST:     ATGATCATACTGGTGGAAACTTGGAATTGAAGGCAAAATATGGTGCAAAG                         GTAATTGGTTCTGAGAAGGATAAGGACAGAATACCTGGCATTGACATCACT
genomic: ATGATCATACTGGTGGAAACTTGGAATTGAAGGCAAAATATGGTGCAAAGgtatagcttt ... tgcattttagGTAATTGGTTCTGAGAAGGATAAGGACAGAATACCTGGCATTGACATCACG
EST: gi|27522113|gb|CA989219.1|CA989219
EST:     ATGATCATACTGGTGGAAACTTGGAATTGAAGGCAAAATATGGTGCAAAG                         GTAATTGGTTCTGAGAAAGATAAGGACAGAATACCTGGCATTGACAT
genomic: ATGATCATACTGGTGGAAACTTGGAATTGAAGGCAAAATATGGTGCAAAGgtatagcttt ... tgcattttagGTAATTGGTTCTGAGAAGGATAAGGACAGAATACCTGGCATTGACAT
EST: gi|60400379|gb|DN233186.1|DN233186
EST:     ATGATCATACTGGTGGAAACTTGGAATTGAAGGCAAAATATGGTGCAAAG                         GTAATTGGTTCTGAGAAGGATAAGGACAGAATACCTGGCATTGACATCACG
genomic: ATGATCATACTGGTGGAAACTTGGAATTGAAGGCAAAATATGGTGCAAAGgtatagcttt ... tgcattttagGTAATTGGTTCTGAGAAGGATAAGGACAGAATACCTGGCATTGACATCACG
EST: gi|76286961|gb|DV026529.1|DV026529
EST:     ATGATCATACTGGTGGAAACTTGGAATTGAAGGCAAAATATGGTGCAAAG                         GTAATTGGTTCTGAGAAGGATAAGGACAGAATACCTGGCATTGACATCACG
genomic: ATGATCATACTGGTGGAAACTTGGAATTGAAGGCAAAATATGGTGCAAAGgtatagcttt ... tgcattttagGTAATTGGTTCTGAGAAGGATAAGGACAGAATACCTGGCATTGACATCACG
EST: gi|89758697|gb|DY687784.1|DY687784
EST:     ATGATCATACTGGTGGAAACTTGGAATTGAAGGCAAAATATGGTGCAAAG                         GTAATTGGTTCTGAGAAGGATAAGGACAGAATACCTGGCATTGACATCACG
genomic: ATGATCATACTGGTGGAAACTTGGAATTGAAGGCAAAATATGGTGCAAAGgtatagcttt ... tgcattttagGTAATTGGTTCTGAGAAGGATAAGGACAGAATACCTGGCATTGACATCACG
EST: gi|78125192|gb|DV543576.1|DV543576
EST:     ATGATCATACTGGTGGAAACTTGGAATTGAAGGCAAAATATGGTGCAAAG                         GTAATTGGTTCTGAGAAGGATAAGGACAGAATACCTGGCATTGACATCACG
genomic: ATGATCATACTGGTGGAAACTTGGAATTGAAGGCAAAATATGGTGCAAAGgtatagcttt ... tgcattttagGTAATTGGTTCTGAGAAGGATAAGGACAGAATACCTGGCATTGACATCACG
EST: gi|89755748|gb|DY686053.1|DY686053
EST:     ATGATCATACTGGTGGAAACTTGGAATTGAAGGCAAAATATGGTGCAAAG                         GTATTTGGTTCTGAGAAGGATAAGGACAGAATACCTGGCATTGACATCACG
genomic: ATGATCATACTGGTGGAAACTTGGAATTGAAGGCAAAATATGGTGCAAAGgtatagcttt ... tgcattttagGTAATTGGTTCTGAGAAGGATAAGGACAGAATACCTGGCATTGACATCACG
EST: gi|76912679|gb|DV164844.1|DV164844
EST:     ATGATCATACTGGTGGAAACTTGGAATTGAAGGCAAAATATGGTGCAAAG                         GTAATTGGTTCTGAGAAGGATAAGGACAGAATACCTGGCATTGACATCACG
genomic: ATGATCATACTGGTGGAAACTTGGAATTGAAGGCAAAATATGGTGCAAAGgtatagcttt ... tgcattttagGTAATTGGTTCTGAGAAGGATAAGGACAGAATACCTGGCATTGACATCACG
EST: gi|6194731|gb|AW146835.1|AW146835
EST:     ATGATCATACTGGTGGAAACTTGGAATTGAAGGCAAAATATGGTGCAAAG                         GTAATTGGTTCTGAGAAGGATAAGGACAGAATACCTGGCATTGACATCACT
genomic: ATGATCATACTGGTGGAAACTTGGAATTGAAGGCAAAATATGGTGCAAAGgtatagcttt ... tgcattttagGTAATTGGTTCTGAGAAGGATAAGGACAGAATACCTGGCATTGACATCACG
EST: gi|93282109|gb|EB674373.1|EB674373
EST:     ATGATCATACTGGTGGAAACTTGGAATTGAAGGCAAAATATGGTGCAAAG                         GTAATTGGTTCTGAGAAGGATAAGGACAGAATACCTGGCATTGACATCACG
genomic: ATGATCATACTGGTGGAAACTTGGAATTGAAGGCAAAATATGGTGCAAAGgtatagcttt ... tgcattttagGTAATTGGTTCTGAGAAGGATAAGGACAGAATACCTGGCATTGACATCACG
EST: gi|211480476|gb|FL101272.1|FL101272
EST:     ATGATCATACTGGTGGAAACTTGGAATTGAAGGCAAAATATGGTGCAAAG                         GTAATTGGTTCTGAGAAGGATAAGGACAGAATACCTGGCATTGACATCACG
genomic: ATGATCATACTGGTGGAAACTTGGAATTGAAGGCAAAATATGGTGCAAAGgtatagcttt ... tgcattttagGTAATTGGTTCTGAGAAGGATAAGGACAGAATACCTGGCATTGACATCACG
EST: gi|6445407|gb|AW179475.1|AW179475
EST:     ATGATCATACTGGTGGAAACTTGGAATTGAAGGCAAAATATGGTGCAAAG                         GTAATTGGTTCTGAGAAGGATAAGGACAGAATACCTGGCATTGACATCACG
genomic: ATGATCATACTGGTGGAAACTTGGAATTGAAGGCAAAATATGGTGCAAAGgtatagcttt ... tgcattttagGTAATTGGTTCTGAGAAGGATAAGGACAGAATACCTGGCATTGACATCACG
EST: gi|149103112|gb|EE288479.2|EE288479
EST:     ATGATCATACTGGTGGAAACTTGGAATTGAAGGCAAAATATGGTGCAAAG                         GTAATTGGTTCTGAGAAGGATAAGGACAGAATACCTGGCATTGACATCACG
genomic: ATGATCATACTGGTGGAAACTTGGAATTGAAGGCAAAATATGGTGCAAAGgtatagcttt ... tgcattttagGTAATTGGTTCTGAGAAGGATAAGGACAGAATACCTGGCATTGACATCACG
EST: gi|149026716|gb|EE046118.2|EE046118
EST:     ATGATCATACTGGTGGAAACTTGGAATTGAAGGCAAAATATGGTGCAAAG                         GTAATTGGTTCTGAGAAGGATAAGGACAGAATACCTGGCATTGACATCACG
genomic: ATGATCATACTGGTGGAAACTTGGAATTGAAGGCAAAATATGGTGCAAAGgtatagcttt ... tgcattttagGTAATTGGTTCTGAGAAGGATAAGGACAGAATACCTGGCATTGACATCACG
EST: gi|76929251|gb|DV171925.1|DV171925
EST:     ATGATCATACTGGTGGAAACTTGGAATTGAAGGCAAAATATGGTGCAAAG                         GTAATTGGTTCTGAGAAGGATAAGGACAGAATACCTGGCATTGACATCACG
genomic: ATGATCATACTGGTGGAAACTTGGAATTGAAGGCAAAATATGGTGCAAAGgtatagcttt ... tgcattttagGTAATTGGTTCTGAGAAGGATAAGGACAGAATACCTGGCATTGACATCACG
EST: gi|91048227|gb|EB158645.1|EB158645
EST:     ATGATCATACTGGTGGAAACTTGGAATTGAAGGCAAAATATGGTGCAAAG                         GTAATTGGTTCTGAGAAGGATAAGGACAGAATACCTGGCATTGACATCACG
genomic: ATGATCATACTGGTGGAAACTTGGAATTGAAGGCAAAATATGGTGCAAAGgtatagcttt ... tgcattttagGTAATTGGTTCTGAGAAGGATAAGGACAGAATACCTGGCATTGACATCACG
EST: gi|67017612|gb|CO446361.1|CO446361
EST:     ATGATCATACTGGTGGAAACTTGGAATTGAAGGCAAAATATGGTGCAAAG                         GTAATTGGTTCTGAGAAGGATAAGGACAGAATACCTGGCATTGACATCACG
genomic: ATGATCATACTGGTGGAAACTTGGAATTGAAGGCAAAATATGGTGCAAAGgtatagcttt ... tgcattttagGTAATTGGTTCTGAGAAGGATAAGGACAGAATACCTGGCATTGACATCACG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGAAAAGAGAAACCAGAACTTGACTTATATACTGAACACCCATCATCACTATGATCATACTGGTGGAAACTTGGAATTGAAGGCAAAATATGGTGCAAAGgtatagctttgggctattttatttgttctttctttttctgtatcgttcagtgactctgatacagtatgtgacaatgacacaatcaaaatgggtttttgtt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG