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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aacagcgaaagtgctagttggcaatcttgtaacgcttaattccgtattctgaatggggcctgcttatcctctgttgactgacgagaatatatactttcagGAAGAAGAGTATTCAAAAGATCGGGTAATTGTTGCAGTGCGGCAAGGGAACATCCTCGCAACTGCTTTCCACCCAGAATTGACATCAGACTCCAGATG

Basic information

species Zea mays
transcript GRMZM2G023528_T03
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G023528_T03 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os02g03740.1 (Oryza sativa), 3'ss of exon 5
aacagcgaaagtgctagttggcaatcttgtaacgcttaattccgtattctgaatgggg--cctgcttatcctctgttgactgacgag-aatata-tacttt--cagGAAGAAGAGTATTCAAAAGATCGGGTAATTGTTGCAGTGCGGCAAGGGAACATCCTCGCAACTGCTTTCCACCCAGAATTGACATCAGACTCCAGATG
      |||||| || |  |       |||   ||  |    | || ||| | ||      ||| ||||| |||||  ||||| |   |||| | ||||||  |||||||||| ||| || |||||||||||||||||||| ||  ||||||||||||||||||| |||||||| ||||||||||||||||||||||| |||||
----ttgaaagttct-gccgattgatgtgttgtgcgaagaatc-tagtctaattgaaagttctgtttatcttctgtgcactgatgttcaatacaatactttggcagGAAGAAGTGTACTCGAAAGATCGGGTAATTGTTGCTGTAAGGCAAGGGAACATCCTCGCTACTGCTTTTCACCCAGAATTGACATCAGACTCTAGATG
















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:     TTCCTGTTGACAGACCCAGCATTACAATATCATTTGGGGAGGGTACTGAG                         GAAGAAGAGTATTCAAAAGATCGGGTAATTGTTGCAGTGCGGCAAGGGAAC
genomic: TTCCTGTTGACAGACCCAGCATTACAATATCATTTGGGGAGGGTACTGAGgtttgtatgt ... atactttcagGAAGAAGAGTATTCAAAAGATCGGGTAATTGTTGCAGTGCGGCAAGGGAAC
EST: gi|71318383|gb|DR795955.1|DR795955
EST:     TTCCTGTTGACAGACCCAGCATTACAATATCATTTGGGGAGGGTACTGAG                         GAAGAAGAGTATTCAAAAGATCGGGTAATTGTTGCAGTGCGGCAAGGGAAC
genomic: TTCCTGTTGACAGACCCAGCATTACAATATCATTTGGGGAGGGTACTGAGgtttgtatgt ... atactttcagGAAGAAGAGTATTCAAAAGATCGGGTAATTGTTGCAGTGCGGCAAGGGAAC
EST: gi|5714344|gb|AI944329.1|AI944329
EST:     AATATCATTTGGGGAGGGTACTGAG                         GAAGAAGAGTATTCAAAAGATCGGGTAATTGTTGCAGTGCGGCAAGGGAAC
genomic: AATATCATTTGGGGAGGGTACTGAGgtttgtatgt ... atactttcagGAAGAAGAGTATTCAAAAGATCGGGTAATTGTTGCAGTGCGGCAAGGGAAC
EST: gi|5895630|gb|AW036876.1|AW036876
EST:     TTCCTGTTGACAGACCCAGCATTACAATATCATTTGGGGAGGGTACTGAG                         GAAGAAGAGTATTCAAAAGATCGGGTAATTGTTGCAGTGCGGCAAGGGAAC
genomic: TTCCTGTTGACAGACCCAGCATTACAATATCATTTGGGGAGGGTACTGAGgtttgtatgt ... atactttcagGAAGAAGAGTATTCAAAAGATCGGGTAATTGTTGCAGTGCGGCAAGGGAAC
EST: gi|78120474|gb|DV538858.1|DV538858
EST:     TTCCTGTTGACAGACCCAGCATTACAATATCATTTGGGGAGGGTACTGAG                         GAAGAAGAGTATTCAAAAGATCGGGTAATTGTTGCAGTGCG
genomic: TTCCTGTTGACAGACCCAGCATTACAATATCATTTGGGGAGGGTACTGAGgtttgtatgt ... atactttcagGAAGAAGAGTATTCAAAAGATCGGGTAATTGTTGCAGTGCG
EST: gi|32934367|gb|CF039179.1|CF039179
EST:     TCCTGTTGACAGACCCAGCATTACAATATCATTTGGGGAGGGTACCTGAG                         GAAGAAGAGTATTCAAAAGATCGGGTAATTGTTGCAGTGCGGCAAGGGAA
genomic: TCCTGTTGACAGACCCAGCATTACAATATCATTTGGGGAGGGTAC-TGAGgtttgtatgt ... atactttcagGAAGAAGAGTATTCAAAAGATCGGGTAATTGTTGCAGTGCGGCAAGGGAA
EST: gi|33467208|gb|CF244257.1|CF244257
EST:     TTCCTGTTGACAGACCCAGCATTACAATATCATTTGGGGAGGGTACTGAG                         GAAGAAGAGTATTCAAAAGATCGGGTAATTGTTGCAGTGCGGCAAGGGAAC
genomic: TTCCTGTTGACAGACCCAGCATTACAATATCATTTGGGGAGGGTACTGAGgtttgtatgt ... atactttcagGAAGAAGAGTATTCAAAAGATCGGGTAATTGTTGCAGTGCGGCAAGGGAAC
EST: gi|37382875|gb|CF628406.1|CF628406
EST:     TTCCTGTTGACAGACCCAGCATTACAATATCATTTGGGGAGGGTACTGAG                         GAAGAAGAGTATTCAAAAGATCGGGTAATTGTTGCAGTGCGGCAAGGGAAC
genomic: TTCCTGTTGACAGACCCAGCATTACAATATCATTTGGGGAGGGTACTGAGgtttgtatgt ... atactttcagGAAGAAGAGTATTCAAAAGATCGGGTAATTGTTGCAGTGCGGCAAGGGAAC
EST: gi|74233030|gb|DT640944.1|DT640944
EST:     TTCCTGTTGACAGACCCAGCATTACAATATCATTTGGGGAGGGTACTGAG                         GAAGAAGAGTATTCAAAAGATCGGGTAATTGTTGCAGTGCGGCAAGGGAAC
genomic: TTCCTGTTGACAGACCCAGCATTACAATATCATTTGGGGAGGGTACTGAGgtttgtatgt ... atactttcagGAAGAAGAGTATTCAAAAGATCGGGTAATTGTTGCAGTGCGGCAAGGGAAC
EST: gi|71437533|gb|DR818583.1|DR818583
EST:     TTCCTGTTGACAGACCCAGCATTACAATATCATTTGGGGAGGGTACTGAG                         GAAGAAGAGTATTCAAAAGATCGGGTAATTGTTGCAGTGCGGCAAGGGAAC
genomic: TTCCTGTTGACAGACCCAGCATTACAATATCATTTGGGGAGGGTACTGAGgtttgtatgt ... atactttcagGAAGAAGAGTATTCAAAAGATCGGGTAATTGTTGCAGTGCGGCAAGGGAAC
EST: gi|91055148|gb|EB165566.1|EB165566
EST:     TTCCTGTTGACAGACCCAGCATTACAATATCATTTGGGGAGGGTACTGAG                         GAAGAAGAGTATTCAAAAGATCGGGTAATTGTTGCAGTGCGGCAAGGGAAC
genomic: TTCCTGTTGACAGACCCAGCATTACAATATCATTTGGGGAGGGTACTGAGgtttgtatgt ... atactttcagGAAGAAGAGTATTCAAAAGATCGGGTAATTGTTGCAGTGCGGCAAGGGAAC
EST: gi|149073844|gb|EE162166.2|EE162166
EST:     TTCCTGTTGACAGACCCAGCATTACAATATCATTTGGGGAGGGTACTGAG                         GAAGAAGAGTATTCAAAAGATCGGGTAATTGTTGCA
genomic: TTCCTGTTGACAGACCCAGCATTACAATATCATTTGGGGAGGGTACTGAGgtttgtatgt ... atactttcagGAAGAAGAGTATTCAAAAGATCGGGTAATTGTTGCA
EST: gi|31359368|gb|CD443725.1|CD443725
EST:     TTCCTGCTGACAGACCCAGCATTACAATATCATTTGGGGAGGGTACTGAG                         GAAGAAGAGTATTCAAAAGATCGGGTAATTGTTGCAGTGCGGCAAGGGAAC
genomic: TTCCTGTTGACAGACCCAGCATTACAATATCATTTGGGGAGGGTACTGAGgtttgtatgt ... atactttcagGAAGAAGAGTATTCAAAAGATCGGGTAATTGTTGCAGTGCGGCAAGGGAAC
EST: gi|78021493|gb|DV489880.1|DV489880
EST:     TTCCTGTTGACAGACCCAGCATTACAATATCATTTGGGGAGGGTACTGAG                         GAAGAAGAGTATTCAAAAGATCGGGTAATTGTTGCAGTGCGGCAAGGGAAC
genomic: TTCCTGTTGACAGACCCAGCATTACAATATCATTTGGGGAGGGTACTGAGgtttgtatgt ... atactttcagGAAGAAGAGTATTCAAAAGATCGGGTAATTGTTGCAGTGCGGCAAGGGAAC
EST: gi|60340407|gb|DN207380.1|DN207380
EST:     TTCCTGTTGACAGACCCAGCATTACAATATCATTTGGGGAGGGTACTGAG                         GAAGAAGAGTATTCAAAAGATCGGGTAATTGTTGCAGTGCGGCAAGGGAAC
genomic: TTCCTGTTGACAGACCCAGCATTACAATATCATTTGGGGAGGGTACTGAGgtttgtatgt ... atactttcagGAAGAAGAGTATTCAAAAGATCGGGTAATTGTTGCAGTGCGGCAAGGGAAC
EST: gi|5804728|gb|AI979698.1|AI979698
EST:     TTCCTGTTGCCAGACCCAGCATTACAATATCATTTGGGGAGGGTACTGAG                         GAAGAAGAGTATTCAAAAGATCGGGTAATTGTTGCAGTGCGGCAAGGGAAC
genomic: TTCCTGTTGACAGACCCAGCATTACAATATCATTTGGGGAGGGTACTGAGgtttgtatgt ... atactttcagGAAGAAGAGTATTCAAAAGATCGGGTAATTGTTGCAGTGCGGCAAGGGAAC
EST: gi|148986692|gb|EE030480.2|EE030480
EST:     TTCCTGTTGACAGACCCAGCATTACAATATCATTTGGGGAGGGTACTGAG                         GAAGAAGAGTATTCAAAAGATCCGGTAATTGTTGCAGTGCGGCAAGG
genomic: TTCCTGTTGACAGACCCAGCATTACAATATCATTTGGGGAGGGTACTGAGgtttgtatgt ... atactttcagGAAGAAGAGTATTCAAAAGATCGGGTAATTGTTGCAGTGCGGCAAGG
EST: gi|40303169|gb|CK347556.1|CK347556
EST:     TTCCTGTTGACAGACCCAGCATTACAATATCATTTGGGGAGGGTACTGAG                         GAAGAAGAGTATTCAAAAGATCGGGTAATTGTTGCAGTGCGGCAAGGGAAC
genomic: TTCCTGTTGACAGACCCAGCATTACAATATCATTTGGGGAGGGTACTGAGgtttgtatgt ... atactttcagGAAGAAGAGTATTCAAAAGATCGGGTAATTGTTGCAGTGCGGCAAGGGAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attctgaatggggcctgcttatcctctgttgactgacgagaatatatactttcagGAAGAAGAGTATTCAAAAGATCGGGTAATTGTTGCAGTGCGGCAAGGGAACATCCTCGCAACTGCTTTCCACCCAGAATTGACATCAGACTCCAGATG
                              gactgac  putative branch site (score: 2)
                                              tactttc  putative PPT
                                      agaatatatacttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aacagcgaaagtgctagttggcaatcttgtaacgcttaattccgtattctgaatggggcctgcttatcctctgttgactgacgagaatatatactttcagGAAGAAGAGTATTCAAAAGATCGGGTAATTGTTGCAGTGCGGCAAGGGAACATCCTCGCAACTGCTTTCCACCCAGAATTGACATCAGACTCCAGATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - gtgctag
- - - - - - - - - - - - - - - - - - - - - - - - ctgaatg