Skip to another splice site:
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 5'  3'   		2  
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 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtgtttgtatgaccgttgttaccgagatatttttcagttatccagccttactggctatccttgatggatcatggtttgttaattttgtgattaattgcagGTATGTTGTGGACGCTGCTGACCGAGATAGTGTCCCAATCGCGAAAAGTGAGTTGCATGATCTGCTGACGAAACAGTCTTTGGCTGGGATTCCCTTGCTT

Basic information

species Zea mays
transcript GRMZM2G171060_T02
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G171060_T02 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os02g49980.2 (Oryza sativa), 3'ss of exon 4
--gtgtttgtatgaccgttgttaccgagatatttttcagttatccagccttactggcta-tccttgatggatcatggtttgttaattttgtgattaattgcagGTATGTTGTGGACGCTGCTGACCGAGATAGTGTCCCAATCGCGAAAAGTGAGTTGCATGATCTGCTGACGAAACAGTCTTTGGCTGGGATTCCCTTGCTT
   |   || ||||   ||||| |     | | | |    |||||||||| |||  ||| |  | ||    | | |  |  |||| |      | |||||||| ||||| ||||| ||||||||||| |||||  | || || || |||||||| |||||||| |||||||| ||||| ||||| ||||||||||| || || 
tactagctgcatgatgcttgtttcttgcttctgtgtt--ctatccagcctaactacctaatggtggaattgttaagaataattaactg-acattcaattgcagATATGTGGTGGATGCTGCTGACCGGGATAGCATTCCGATAGCTAAAAGTGAATTGCATGACCTGCTGACAAAACAATCTTTAGCTGGGATTCCTTTACTA
















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|211076135|gb|FL255305.1|FL255305
EST:     AGATTCCGCACTATGTGGGAGCGCTATTGCCGTGGAGTTTCTGCTATTCT                         ATATGTTGTGGACGCTGCTGACCGAGATAGTGTCCCAATCGCGAAAAGTGA
genomic: AGATTCCGCACTATGTGGGAGCGCTATTGCCGTGGAGTTTCTGCTATTCTgtaattcctg ... ttaattgcagGTATGTTGTGGACGCTGCTGACCGAGATAGTGTCCCAATCGCGAAAAGTGA
EST: gi|211078875|gb|FL255314.1|FL255314
EST:     AGATTCCGCACTATGTGGGAGCGCTATTGCCGTGGAGTTTCTGCTATTCT                         ATATGTTGTGGACGCTGCTGACCGAGATAGTGTCC-AATCGCGAAAAGTGA
genomic: AGATTCCGCACTATGTGGGAGCGCTATTGCCGTGGAGTTTCTGCTATTCTgtaattcctg ... ttaattgcagGTATGTTGTGGACGCTGCTGACCGAGATAGTGTCCCAATCGCGAAAAGTGA
EST: gi|211076132|gb|FL255302.1|FL255302
EST:     AGATTCCGCACTATGTGGGAGCGCTATTGCCGTGGAGTTTCTGCTATTCT                         ATATGTTGTGGACGC
genomic: AGATTCCGCACTATGTGGGAGCGCTATTGCCGTGGAGTTTCTGCTATTCTgtaattcctg ... ttaattgcagGTATGTTGTGGACGC
EST: gi|76286949|gb|DV026517.1|DV026517
EST:     AGATTCCGCACTATGTGGGAGCGCTATTGCCGTGGAGTTTCTGCTATTCT                         GTATGTTGTGGACGCTGCTGACCGAGATAGTGTCCCAATCGCGAAAAGTGA
genomic: AGATTCCGCACTATGTGGGAGCGCTATTGCCGTGGAGTTTCTGCTATTCTgtaattcctg ... ttaattgcagGTATGTTGTGGACGCTGCTGACCGAGATAGTGTCCCAATCGCGAAAAGTGA
EST: gi|211076136|gb|FL255306.1|FL255306
EST:     AGATTCCGCACTATGTGGGAGCGCTATTGCCGTGGAGTTTCTGCTATTCT                         GTATGTTGTGGACGCTGCTGACCGAGATAGTGTCCCAATCGCGAAAAGTGA
genomic: AGATTCCGCACTATGTGGGAGCGCTATTGCCGTGGAGTTTCTGCTATTCTgtaattcctg ... ttaattgcagGTATGTTGTGGACGCTGCTGACCGAGATAGTGTCCCAATCGCGAAAAGTGA
EST: gi|211076137|gb|FL255307.1|FL255307
EST:     AGATTCCGCACTATGTGGGAGCGCTATTGCCGTGGAGTTTCTGCTATTCT                         ATATGTTGTGGACGCTGCTGACCGAGATAGTGTCCCAATCGCGAAAAGTGA
genomic: AGATTCCGCACTATGTGGGAGCGCTATTGCCGTGGAGTTTCTGCTATTCTgtaattcctg ... ttaattgcagGTATGTTGTGGACGCTGCTGACCGAGATAGTGTCCCAATCGCGAAAAGTGA
EST: gi|113702664|gb|EE680168.1|EE680168
EST:     GCTATTGCCGTGGAGTTTTTGCTATTCT                         GTATGTTGTGGACGCTGCTGACCGAGATAGTGTCCCAATCGCGAAAAGTGA
genomic: GCTATTGCCGTGGAGTTTCTGCTATTCTgtaattcctg ... ttaattgcagGTATGTTGTGGACGCTGCTGACCGAGATAGTGTCCCAATCGCGAAAAGTGA
EST: gi|211076142|gb|FL255312.1|FL255312
EST:     AGATTCCGCACTATGTGGGAGCGCTATTGCCGTGGAGTTTCTGCTATTCT                         GTATGTTGTGGACGCTGCTGACCGAGATAGTGTCCCAATCGCGAAAAGTGA
genomic: AGATTCCGCACTATGTGGGAGCGCTATTGCCGTGGAGTTTCTGCTATTCTgtaattcctg ... ttaattgcagGTATGTTGTGGACGCTGCTGACCGAGATAGTGTCCCAATCGCGAAAAGTGA
EST: gi|34391306|gb|CF384534.1|CF384534
EST:     AGATTCCGCACTATGTGGGAGCGCTATTGCCGTGGAGTTTCTGCTATTCT                         GTATGTTGTGGACGCTGCTGACCGAGATAGTGTCCCAATCGCGAAAAGTGA
genomic: AGATTCCGCACTATGTGGGAGCGCTATTGCCGTGGAGTTTCTGCTATTCTgtaattcctg ... ttaattgcagGTATGTTGTGGACGCTGCTGACCGAGATAGTGTCCCAATCGCGAAAAGTGA
EST: gi|32806604|gb|CD958838.1|CD958838
EST:     AGATTCCGCACTATGTGGGAGCGCTATTGCCGTGGAGTTTCTGCTATTCT                         GTATGTTGTGGACGCTGCTGACCGAGATAGTGTCCCAATCGCGGAAAGTGA
genomic: AGATTCCGCACTATGTGGGAGCGCTATTGCCGTGGAGTTTCTGCTATTCTgtaattcctg ... ttaattgcagGTATGTTGTGGACGCTGCTGACCGAGATAGTGTCCCAATCGCGAAAAGTGA
EST: gi|211078883|gb|FL255322.1|FL255322
EST:     AGATTCCGCACTATGTGGGAGCGCTATTGCCGTGGAGTTTCTGCTATTCT                         ATATGTTGTGGACGCTGCTGACCGAGATAGTTGTCC
genomic: AGATTCCGCACTATGTGGGAGCGCTATTGCCGTGGAGTTTCTGCTATTCTgtaattcctg ... ttaattgcagGTATGTTGTGGACGCTGCTGACCGAGATAGT-GTCC
EST: gi|211076141|gb|FL255311.1|FL255311
EST:     AGATTCCGCACTATGTGGGAGCGCTATTGCCGTGGAGTTTCTGCTATTCT                         GTATGTTGTGGACGCTGCTGACCGAGATAGTGTCCCAATCGCGAAAAGTGA
genomic: AGATTCCGCACTATGTGGGAGCGCTATTGCCGTGGAGTTTCTGCTATTCTgtaattcctg ... ttaattgcagGTATGTTGTGGACGCTGCTGACCGAGATAGTGTCCCAATCGCGAAAAGTGA
EST: gi|211076129|gb|FL255299.1|FL255299
EST:     AGATTCCGCACTATGTGGGAGCGCTATTGCCGTGGAGTTTCTGCTATTCT                         ATATGTTGTGGACGCTGCTGACCGAGATAGTGTCCCAATCGCGAAAAGTGA
genomic: AGATTCCGCACTATGTGGGAGCGCTATTGCCGTGGAGTTTCTGCTATTCTgtaattcctg ... ttaattgcagGTATGTTGTGGACGCTGCTGACCGAGATAGTGTCCCAATCGCGAAAAGTGA
EST: gi|76286861|gb|DV026429.1|DV026429
EST:     AGATTCCGCACTATGTGGGAGCGCTATTGCCGTGGAGTTTCTGCTATTCT                         GTATGTTGTGGACGCTGCTGACCGAGATAGTGTCCCAATCGCGAAAAGTGA
genomic: AGATTCCGCACTATGTGGGAGCGCTATTGCCGTGGAGTTTCTGCTATTCTgtaattcctg ... ttaattgcagGTATGTTGTGGACGCTGCTGACCGAGATAGTGTCCCAATCGCGAAAAGTGA
EST: gi|28566462|gb|CB278110.1|CB278110
EST:     AGATTCCGCACTATGTGGGAGCGCTATTGCCGTGGAGTTTCTGCTATTCT                         GTATGTTGTGGACGCTGCTGACCGAGATAGTGTCCCAATCGCGAAAAGTGA
genomic: AGATTCCGCACTATGTGGGAGCGCTATTGCCGTGGAGTTTCTGCTATTCTgtaattcctg ... ttaattgcagGTATGTTGTGGACGCTGCTGACCGAGATAGTGTCCCAATCGCGAAAAGTGA
EST: gi|149077255|gb|EE165928.2|EE165928
EST:     AGATTCCGCACTATGTGGGAGCGCTATTGCCGTGGAGTTTCTGCTATTCT                         GTATGTTGTGGACGCTGCTGACCGAGATAGTGTCCCAATCGCGAAAAGTGA
genomic: AGATTCCGCACTATGTGGGAGCGCTATTGCCGTGGAGTTTCTGCTATTCTgtaattcctg ... ttaattgcagGTATGTTGTGGACGCTGCTGACCGAGATAGTGTCCCAATCGCGAAAAGTGA
EST: gi|8103003|gb|AW927671.1|AW927671
EST:     TATGTGGGAGCGCTATTGCCGTGGAGTTTCTGCTATTCT                         GTATGTTGTGGACGCTGCTGACCGAGATAGTGTCCCAATCGCGAAAAGTGA
genomic: TATGTGGGAGCGCTATTGCCGTGGAGTTTCTGCTATTCTgtaattcctg ... ttaattgcagGTATGTTGTGGACGCTGCTGACCGAGATAGTGTCCCAATCGCGAAAAGTGA
EST: gi|211076140|gb|FL255310.1|FL255310
EST:     AGATTCCGCACTATGTGGGAGCGCTATTGCCGTGGAGTTTCTGCTATTCT                         ATATGTTGTGGACGCTGCTGACCGAGATAGTGTCCCAATCGCGAAAAGTGA
genomic: AGATTCCGCACTATGTGGGAGCGCTATTGCCGTGGAGTTTCTGCTATTCTgtaattcctg ... ttaattgcagGTATGTTGTGGACGCTGCTGACCGAGATAGTGTCCCAATCGCGAAAAGTGA
EST: gi|32809543|gb|CD961777.1|CD961777
EST:     AGATTCCGCACTATGTGGGAGCGCTATTGCCGTGGAGTTTCTGCTATTCT                         GTATGTTGTGGACGCTGCTGACCGAGATAGTGTCCCAATCGCGAAAAGTGA
genomic: AGATTCCGCACTATGTGGGAGCGCTATTGCCGTGGAGTTTCTGCTATTCTgtaattcctg ... ttaattgcagGTATGTTGTGGACGCTGCTGACCGAGATAGTGTCCCAATCGCGAAAAGTGA
EST: gi|211078880|gb|FL255319.1|FL255319
EST:     AGATTCCGCACTATGTGGGAGCGCTATTGCCGTGGAGTTTCTGCTATTCT                         ATATGTTGTGGACGCTGCTGACCGAGATAGTGTCC-AATCGCGAAAAGTGA
genomic: AGATTCCGCACTATGTGGGAGCGCTATTGCCGTGGAGTTTCTGCTATTCTgtaattcctg ... ttaattgcagGTATGTTGTGGACGCTGCTGACCGAGATAGTGTCCCAATCGCGAAAAGTGA
EST: gi|40287223|gb|CK327615.1|CK327615
EST:     AGATTCCGCACTATGTGGGAGCGCTATTGCCGTGGAGTTTCTGCTATTCT                         GTATGTTGTGGACGCTGCTGACCGAGATAGTGTCCCAATCGCGAAAAGTGA
genomic: AGATTCCGCACTATGTGGGAGCGCTATTGCCGTGGAGTTTCTGCTATTCTgtaattcctg ... ttaattgcagGTATGTTGTGGACGCTGCTGACCGAGATAGTGTCCCAATCGCGAAAAGTGA
EST: gi|78086343|gb|DV514736.1|DV514736
EST:     AGATTCCGCACTATGTGGGAGCGCTATTGCCGTGGAGTTTCTGCTATTCT                         GTATGTTGTGGACGCTGCTGACCGAGATAGTGTCCCAATCGCGAAAAGTGA
genomic: AGATTCCGCACTATGTGGGAGCGCTATTGCCGTGGAGTTTCTGCTATTCTgtaattcctg ... ttaattgcagGTATGTTGTGGACGCTGCTGACCGAGATAGTGTCCCAATCGCGAAAAGTGA
EST: gi|78113799|gb|DV532188.1|DV532188
EST:     AGATTCCGCACTATGTGGGAGCGCTATTGCCGTGGAGTTTCTGCTATTCT                         GTATGTTGTGGACGCTGCTGACCGAGATAGTGTCCCAATCGCGAAAAGTGA
genomic: AGATTCCGCACTATGTGGGAGCGCTATTGCCGTGGAGTTTCTGCTATTCTgtaattcctg ... ttaattgcagGTATGTTGTGGACGCTGCTGACCGAGATAGTGTCCCAATCGCGAAAAGTGA
EST: gi|211078879|gb|FL255318.1|FL255318
EST:     AGATTCCGCACTATGTGGGAGCGCTATTGCCGTGGAGTTTCTGCTATTCT                         GTATGTTGTGGACGCTGCTGACCGAGATAGTGTCCCAATCGCGAAAAGTGA
genomic: AGATTCCGCACTATGTGGGAGCGCTATTGCCGTGGAGTTTCTGCTATTCTgtaattcctg ... ttaattgcagGTATGTTGTGGACGCTGCTGACCGAGATAGTGTCCCAATCGCGAAAAGTGA
EST: gi|211078882|gb|FL255321.1|FL255321
EST:     AGATTCCGCACTATGTGGGAGCGCTATTGCCGTGGAGTTTCTGCTATTCT                         GTATGTTGTGGACGCTGCTGACCGAGATAGTGTCCCAATCGCGAAAAGTGA
genomic: AGATTCCGCACTATGTGGGAGCGCTATTGCCGTGGAGTTTCTGCTATTCTgtaattcctg ... ttaattgcagGTATGTTGTGGACGCTGCTGACCGAGATAGTGTCCCAATCGCGAAAAGTGA
EST: gi|78086342|gb|DV514735.1|DV514735
EST:     AGATTCCGCACTATGTGGGAGCGCTATTGCCGTGGAGTTTTTGCTATTCT                         GTATGTTGTGGACGCTGCTGACCGAGATAGTGTCCCAATCGCGAAAAGTGA
genomic: AGATTCCGCACTATGTGGGAGCGCTATTGCCGTGGAGTTTCTGCTATTCTgtaattcctg ... ttaattgcagGTATGTTGTGGACGCTGCTGACCGAGATAGTGTCCCAATCGCGAAAAGTGA
EST: gi|148953854|gb|EC899230.2|EC899230
EST:     AGATTCCGCACTATGTGGGAGCGCTATTGCCGTGGAGTTTCTGCTATTCT                         GTATGTTGTGGACGCTGCTGACCGAGATAGTGTCCCAATCGCGAAAAGTGA
genomic: AGATTCCGCACTATGTGGGAGCGCTATTGCCGTGGAGTTTCTGCTATTCTgtaattcctg ... ttaattgcagGTATGTTGTGGACGCTGCTGACCGAGATAGTGTCCCAATCGCGAAAAGTGA
EST: gi|78113800|gb|DV532189.1|DV532189
EST:     AGATTCCGCACTATGTGGGAGCGCTATTGCCGTGGAGTTTCTGCTATTCT                         GTATGTTGTGGACGCTGCTGACCGAGATAGTGTCCCAATCGCGAAAAGTGA
genomic: AGATTCCGCACTATGTGGGAGCGCTATTGCCGTGGAGTTTCTGCTATTCTgtaattcctg ... ttaattgcagGTATGTTGTGGACGCTGCTGACCGAGATAGTGTCCCAATCGCGAAAAGTGA
EST: gi|85152988|gb|DW587926.1|DW587926
EST:     AAATTCCGCACTATGTGGGAGCGCTATTGCCGTGGAGTTTCTGCTATTCT                         GTATGTTGTGGACGCTGCTGACCGAGATAGTGTCCCAATCGCGAAAAGTGA
genomic: AGATTCCGCACTATGTGGGAGCGCTATTGCCGTGGAGTTTCTGCTATTCTgtaattcctg ... ttaattgcagGTATGTTGTGGACGCTGCTGACCGAGATAGTGTCCCAATCGCGAAAAGTGA
EST: gi|211076139|gb|FL255309.1|FL255309
EST:     AGATTCCGCACTATGTGGGAGCGCTATTGCCGTGGAGTTTCTGCTATTCT                         GTATGTTGTGGACGCTGCTGACCGAGATAGTGTCCCAATCGCGAAAAGTGA
genomic: AGATTCCGCACTATGTGGGAGCGCTATTGCCGTGGAGTTTCTGCTATTCTgtaattcctg ... ttaattgcagGTATGTTGTGGACGCTGCTGACCGAGATAGTGTCCCAATCGCGAAAAGTGA
EST: gi|110945770|gb|EE165927.1|EE165927
EST:     AGATTCCGCACTATGTGGGAGCGCTATTGCCGTGGAGTTTTTGCTATTCT                         GTATGTTGTGGACGCTGCTGACCGAGATAGTGTCCCAATCGCGAAAAGTGA
genomic: AGATTCCGCACTATGTGGGAGCGCTATTGCCGTGGAGTTTCTGCTATTCTgtaattcctg ... ttaattgcagGTATGTTGTGGACGCTGCTGACCGAGATAGTGTCCCAATCGCGAAAAGTGA
EST: gi|211078874|gb|FL255313.1|FL255313
EST:     AGATTCCGCACTATGTGGGAGCGCTATTGCCGTGGAGTTTCTGCTATTCT                         ATATGTTGTGGACGCTGCTGACCGAGATAGTGTCCCAATCGCGAAAAGTGA
genomic: AGATTCCGCACTATGTGGGAGCGCTATTGCCGTGGAGTTTCTGCTATTCTgtaattcctg ... ttaattgcagGTATGTTGTGGACGCTGCTGACCGAGATAGTGTCCCAATCGCGAAAAGTGA
EST: gi|89760881|gb|DY689115.1|DY689115
EST:     AGATTCCGCACTATGTGGGAGCGCTATTGCCGTGGAGTTTCTGCTATTCT                         GTATGTTGTGGACGCTGCTGACCGAGATAGTGTCCCAATCGCGAAAAGTGA
genomic: AGATTCCGCACTATGTGGGAGCGCTATTGCCGTGGAGTTTCTGCTATTCTgtaattcctg ... ttaattgcagGTATGTTGTGGACGCTGCTGACCGAGATAGTGTCCCAATCGCGAAAAGTGA
EST: gi|12046965|gb|BF729104.1|BF729104
EST:     AGATTCCGCCCTATGTGGGAGCGCTATTGCCGTGGAGTTTCTGCTATTCT                         GTATGTTGTGGACGCTGCTGACCGAGATAGTGTCCCAATCGCGAAAAGTGA
genomic: AGATTCCGCACTATGTGGGAGCGCTATTGCCGTGGAGTTTCTGCTATTCTgtaattcctg ... ttaattgcagGTATGTTGTGGACGCTGCTGACCGAGATAGTGTCCCAATCGCGAAAAGTGA
EST: gi|38229789|gb|CF920102.1|CF920102
EST:     AGATTCCGCACTATGTGGGAGCGCTATTGCCGTGGAGTTTCTGCTATTCT                         GTATGTTGGCGGACGCTGCTGACCGAGATAGTGTCCCAATCGCGAAAAGTG
genomic: AGATTCCGCACTATGTGGGAGCGCTATTGCCGTGGAGTTTCTGCTATTCTgtaattcctg ... ttaattgcagGTATGTTGT-GGACGCTGCTGACCGAGATAGTGTCCCAATCGCGAAAAGTG
EST: gi|32793765|gb|CD946001.1|CD946001
EST:     AGATTCCGCACTATGTGGGAGCGCTATTGCCGTGGAGTTTCTGCTATTCT                         GTATGTTGTGGACGCTGCTGACCGAGATAGTGTCCCAATCGCGAAAAGTGA
genomic: AGATTCCGCACTATGTGGGAGCGCTATTGCCGTGGAGTTTCTGCTATTCTgtaattcctg ... ttaattgcagGTATGTTGTGGACGCTGCTGACCGAGATAGTGTCCCAATCGCGAAAAGTGA
EST: gi|211076133|gb|FL255303.1|FL255303
EST:     AGATTCCGCACTATGTGGGAGCGCTATTGCCGTGGAGTTTCTGCTATTCT                         ATATGTTGTGGACGCTGCTGACCGAGATAGTGTCCCAATCGCGAAAAGTGA
genomic: AGATTCCGCACTATGTGGGAGCGCTATTGCCGTGGAGTTTCTGCTATTCTgtaattcctg ... ttaattgcagGTATGTTGTGGACGCTGCTGACCGAGATAGTGTCCCAATCGCGAAAAGTGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccttactggctatccttgatggatcatggtttgttaattttgtgattaattgcagGTATGTTGTGGACGCTGCTGACCGAGATAGTGTCCCAATCGCGAAAAGTGAGTTGCATGATCTGCTGACGAAACAGTCTTTGGCTGGGATTCCCTTGCTT
                                           gattaat  putative branch site (score: 3)
                             tttgttaattttgtga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgtttgtatgaccgttgttaccgagatatttttcagttatccagccttactggctatccttgatggatcatggtttgttaattttgtgattaattgcagGTATGTTGTGGACGCTGCTGACCGAGATAGTGTCCCAATCGCGAAAAGTGAGTTGCATGATCTGCTGACGAAACAGTCTTTGGCTGGGATTCCCTTGCTT

-tgtttgt
- - - - - - - - - - - - - - - - - - - - - - - cttactg