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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtaaatccatatggctggttcagtatatttgttgtagacatgtctttatgcgtttattaaacatatattgcagaaaacgtgcaacaaagattcgtgattctggactaatgctaaattttggacgagctataaagatgtcacttgttttttgtgaaagcttgaaataacactaatgtcaaaattcttggggcacagGTTTGTGATTTCACTGGTGATGCTTTTCAAAGGGAAGAACGGGAACGATGGCTGCCATTGGTGCCACTACCTGAACTGCGTGCCAACATCCAAGTGGAAG

Basic information

species Zea mays
transcript GRMZM2G116514_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G116514_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os09g35730.1 (Oryza sativa), 3'ss of exon 4
gtaagtaaatccatatggctggttcagtatatttgttgtaga-catgtct-ttatgcgtttattaaacatatattgcagaaaacgt-gcaacaaagattcgtgattctggactaatgctaaattttggacgagctataaagatgtcacttgttttttgtgaaagcttgaaataacactaatgtcaaaattcttggggcacagGTTTGTGATTTCACTGGTGATGCTTTTCAAAGGGAAGAACGGGAACGATGGCTGCCATTGGTGCCACTACCTGAACTGCGTGCCAACATCCAAGTGGAAG
|||||| |||         |   |   || |  | |||  || ||   || ||||| |  |||| |   |  |    |  | |  | | || |    ||| || |  ||   || | |   |||   |  |    ||  |||||     |  ||| ||| ||| |||||||| |  || ||  ||| | | |||     |||||||||| ||||||| |||||||| ||||| || ||||| || || || || ||||| ||||||||||||||||||||||| || ||||| |||||||||
gtaagttaattggctacaatatatggttagaaatattggggaacaccactgttatgtgcatattcatagtccaaaatatgatatatagaaatatgcgttcatgctggtgatttatttccttattagtgg-gcatcatccagatggtgtat-ctttatgtcaaa-cttgaaatgatcctgataccaagaat-ttgcaatgcagGTTTGTGGTTTCACTAGTGATGCTCTTCAAGGGTAAGAATGGAAATGACGGATGCCACTGGTGCCACTACCTGAACTGCGTACCCACATCGAAGTGGAAG
















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|211195218|gb|FL318595.1|FL318595
EST:     GCATACCAGTATATTTTGTGGGTTGTGGCACTCGTCTTGCTGTTAGTTGG                         GTTTGTGATTTCACTGGTGATGCTTTTCAAAGGGAAGAACGGGAACGATGG
genomic: GCATACCAGTATATTTTGTGGGTTGTGGCACTCGTCTTGCTGTTAGTTGGgtaagtaaat ... tggggcacagGTTTGTGATTTCACTGGTGATGCTTTTCAAAGGGAAGAACGGGAACGATGG
EST: gi|32916798|gb|CF021610.1|CF021610
EST:     GCATACCAGTATATTTTGTGGGTTGTGGCACTCGTCTTGCTGTTAGTTGG                         GTTTGTGATTTCACTGGTGACGCTTTTCAAAGGGAAGAACGGGAACGATGG
genomic: GCATACCAGTATATTTTGTGGGTTGTGGCACTCGTCTTGCTGTTAGTTGGgtaagtaaat ... tggggcacagGTTTGTGATTTCACTGGTGATGCTTTTCAAAGGGAAGAACGGGAACGATGG
EST: gi|76286368|gb|DV025936.1|DV025936
EST:     GCATACCAGTATATTTTGTGGGTTGTGGCACTCGTCTTGCTGTTAGTTGG                         GTTTGTGATTTCACTGGTGATGCTTTTCAAAGGGAAGAACGGGAACGATGG
genomic: GCATACCAGTATATTTTGTGGGTTGTGGCACTCGTCTTGCTGTTAGTTGGgtaagtaaat ... tggggcacagGTTTGTGATTTCACTGGTGATGCTTTTCAAAGGGAAGAACGGGAACGATGG
EST: gi|78075432|gb|DV503866.1|DV503866
EST:     GCATACCAGTATATTTTGTGGGTTGTGGCACTCGTCTTGCTGTTAGTTGG                         GTTTGTGATTTCACTGGTGATGCTTTTCAAAGGGAAGAACGGGAACGATGG
genomic: GCATACCAGTATATTTTGTGGGTTGTGGCACTCGTCTTGCTGTTAGTTGGgtaagtaaat ... tggggcacagGTTTGTGATTTCACTGGTGATGCTTTTCAAAGGGAAGAACGGGAACGATGG
EST: gi|32862952|gb|CF002634.1|CF002634
EST:     GCATACCAGTATATTTTGTGGGTTGTGGCACTCGTCTTGCTGTTAGTTGG                         GTTTGTGATTTCACTGGTGATGCTTTTCAAAGGGAAGAACGGGAACGATGG
genomic: GCATACCAGTATATTTTGTGGGTTGTGGCACTCGTCTTGCTGTTAGTTGGgtaagtaaat ... tggggcacagGTTTGTGATTTCACTGGTGATGCTTTTCAAAGGGAAGAACGGGAACGATGG
EST: gi|67024823|gb|CO453572.1|CO453572
EST:     GCATACCAGTATATTTTGTGGGTTGTGGCACTCGTCTTGCTGTTAGTTGG                         GTTTGTGATTTCACTGGTGATGCTTTTCAAAGGGAAGAACGGGAACGATGG
genomic: GCATACCAGTATATTTTGTGGGTTGTGGCACTCGTCTTGCTGTTAGTTGGgtaagtaaat ... tggggcacagGTTTGTGATTTCACTGGTGATGCTTTTCAAAGGGAAGAACGGGAACGATGG
EST: gi|88749438|gb|DY533579.1|DY533579
EST:     GCATACCAGTATATTTTGTGGGTTGTGGCACTCGTCTTGCTGTTAGTTGG                         GTTTGTGATTTCACTGGTGATGCTTTTCAAAGGGAAGAACGGGAACGATGG
genomic: GCATACCAGTATATTTTGTGGGTTGTGGCACTCGTCTTGCTGTTAGTTGGgtaagtaaat ... tggggcacagGTTTGTGATTTCACTGGTGATGCTTTTCAAAGGGAAGAACGGGAACGATGG
EST: gi|148967077|gb|EE018244.2|EE018244
EST:     GCATACCAGTATATTTTGTGGGTTGTGGCACTCGTCTTGCTGTTAGTTGG                         GTTTGTGATTTCACTGGTGATGCTTTTCAAAGGGAAGAACGGGAACGATGG
genomic: GCATACCAGTATATTTTGTGGGTTGTGGCACTCGTCTTGCTGTTAGTTGGgtaagtaaat ... tggggcacagGTTTGTGATTTCACTGGTGATGCTTTTCAAAGGGAAGAACGGGAACGATGG
EST: gi|32795657|gb|CD947893.1|CD947893
EST:     GCATACCAGTATATTTTGTGGGTTGTGGCACTCGTCTTGCTGTTAGTTAG                         GTTTGTGATTTCACTGGTGATGCTTTTCAAAGGGAAGAACGGGAACGATGG
genomic: GCATACCAGTATATTTTGTGGGTTGTGGCACTCGTCTTGCTGTTAGTTGGgtaagtaaat ... tggggcacagGTTTGTGATTTCACTGGTGATGCTTTTCAAAGGGAAGAACGGGAACGATGG
EST: gi|116821652|gb|EC864979.1|EC864979
EST:     GCATACCAGTATATTTTGTGGGTTGTGGCACTCGTCTTGCTGTTAGTTGG                         GTTTGTGATTTCACTGGTGATGCTTTTCAAAGGGAAGAACGGGAACGATGG
genomic: GCATACCAGTATATTTTGTGGGTTGTGGCACTCGTCTTGCTGTTAGTTGGgtaagtaaat ... tggggcacagGTTTGTGATTTCACTGGTGATGCTTTTCAAAGGGAAGAACGGGAACGATGG
EST: gi|211018463|gb|FL453055.1|FL453055
EST:     GCATHCCAGTATATTTTGTGGGTTGTGGCACTCGTCTTGCTGTTAGTTGG                         GTTTGTGATTTCMCTGGTGATGCTTTTCAAAGGGAAGAMCGGGAACGATGG
genomic: GCATACCAGTATATTTTGTGGGTTGTGGCACTCGTCTTGCTGTTAGTTGGgtaagtaaat ... tggggcacagGTTTGTGATTTCACTGGTGATGCTTTTCAAAGGGAAGAACGGGAACGATGG
EST: gi|7555088|gb|AW681272.1|AW681272
EST:     GCATACCAGTATATTTTGTGGGTTGTGGCACTCGTCTTGCTGTTAGTTGG                         GTTTGTGATTTCACTGGTGATGCTTTTCAAAGGGAAGAACGGGAACGATGG
genomic: GCATACCAGTATATTTTGTGGGTTGTGGCACTCGTCTTGCTGTTAGTTGGgtaagtaaat ... tggggcacagGTTTGTGATTTCACTGGTGATGCTTTTCAAAGGGAAGAACGGGAACGATGG
EST: gi|32865051|gb|CF004733.1|CF004733
EST:     GCATACCAGTATATTTTGTGGGTTGTGGCACTCGTCTTGCTGTTAGTTGG                         GTTTGTGATTTCACTGGTGATGCTTTTCAAAGGGAAGAACGGGAACGATGG
genomic: GCATACCAGTATATTTTGTGGGTTGTGGCACTCGTCTTGCTGTTAGTTGGgtaagtaaat ... tggggcacagGTTTGTGATTTCACTGGTGATGCTTTTCAAAGGGAAGAACGGGAACGATGG
EST: gi|32865213|gb|CF004895.1|CF004895
EST:     GCATACCAGTATATTTTGTGGGTTGTGGCACTCGTCTTGCTGTTAGTTGG                         GTTTGTGATTTCACTGGTGATGCTTTTCAAAGGGAAGAACGGGAACGATGG
genomic: GCATACCAGTATATTTTGTGGGTTGTGGCACTCGTCTTGCTGTTAGTTGGgtaagtaaat ... tggggcacagGTTTGTGATTTCACTGGTGATGCTTTTCAAAGGGAAGAACGGGAACGATGG
EST: gi|18180175|gb|BM381385.1|BM381385
EST:     GCATACCAGTATATTTTGTGGGTTGTGGCACTCGTCTTGCTGTTAGTTGG                         GTTTGTGATTTCACTGGTGATGCTTTTCAAAGGGAAGAACGGGAACGATGG
genomic: GCATACCAGTATATTTTGTGGGTTGTGGCACTCGTCTTGCTGTTAGTTGGgtaagtaaat ... tggggcacagGTTTGTGATTTCACTGGTGATGCTTTTCAAAGGGAAGAACGGGAACGATGG
EST: gi|7262338|gb|AW585281.1|AW585281
EST:     GCATACCAGTATATTTTGTGGGTTGTGGCACTCGTCTTGCTGTTAGTTGG                         GTTTGTGATTTCACTGGTGATGCTTTTCAAAGGGAAGAACGGGAACGATGG
genomic: GCATACCAGTATATTTTGTGGGTTGTGGCACTCGTCTTGCTGTTAGTTGGgtaagtaaat ... tggggcacagGTTTGTGATTTCACTGGTGATGCTTTTCAAAGGGAAGAACGGGAACGATGG
EST: gi|88748281|gb|DY532422.1|DY532422
EST:     GCATACCAGTATATTTTGTGGGTTGTGGCACTCGTCTTGCTGTTAGTTGG                         GTTTGTGATTTCACTGGTGATGCTTTTCAAAGGGAAGAACGGGAACGATGG
genomic: GCATACCAGTATATTTTGTGGGTTGTGGCACTCGTCTTGCTGTTAGTTGGgtaagtaaat ... tggggcacagGTTTGTGATTTCACTGGTGATGCTTTTCAAAGGGAAGAACGGGAACGATGG
EST: gi|71764175|gb|DR962112.1|DR962112
EST:     GCATACCAGTATATTTTGTGGGTTGTGGCACTCGTCTTGCTGTTAGTTGG                         GTTTGTGATTTCACTGGTGATGCTTTTCAAAGGGAAGAACGGGAACGATGG
genomic: GCATACCAGTATATTTTGTGGGTTGTGGCACTCGTCTTGCTGTTAGTTGGgtaagtaaat ... tggggcacagGTTTGTGATTTCACTGGTGATGCTTTTCAAAGGGAAGAACGGGAACGATGG
EST: gi|76020120|gb|DT947290.1|DT947290
EST:     GCATACCAGTATATTTTGTGGGTTGTGGCACTCGTCTTGCTGTTAGTTGG                         GTTTGTGATTTCACTGGTGATGCTTTTCAAAGGGAAGAACGGGAACGATGG
genomic: GCATACCAGTATATTTTGTGGGTTGTGGCACTCGTCTTGCTGTTAGTTGGgtaagtaaat ... tggggcacagGTTTGTGATTTCACTGGTGATGCTTTTCAAAGGGAAGAACGGGAACGATGG
EST: gi|71309283|gb|DR790928.1|DR790928
EST:     GCATACCAGTATATTTTGTGGGTTGTGGCACTCGTCTTGCTGTTAGTTGG                         GTTTGTGATTTCACTGGTGATGCTTTTCAAAGGGAAGAACGGGAACGATGG
genomic: GCATACCAGTATATTTTGTGGGTTGTGGCACTCGTCTTGCTGTTAGTTGGgtaagtaaat ... tggggcacagGTTTGTGATTTCACTGGTGATGCTTTTCAAAGGGAAGAACGGGAACGATGG
EST: gi|88753239|gb|DY537380.1|DY537380
EST:     GCATACCAGTATATTTTGTGGGTTGTGGCACTCGTCTTGCTGTTAGTTGG                         GTTTGTGATTTCACTGGTGATGCTTTTCAAAGGGAAGAACGGGAACGATGG
genomic: GCATACCAGTATATTTTGTGGGTTGTGGCACTCGTCTTGCTGTTAGTTGGgtaagtaaat ... tggggcacagGTTTGTGATTTCACTGGTGATGCTTTTCAAAGGGAAGAACGGGAACGATGG
EST: gi|149048393|gb|EE048303.2|EE048303
EST:     GCATACCAGTATATTTTGTGGGTTGTGGCATTCGTCTTGCTGTTAGTGGG                         GTTTGTGATTTCACTGGTGATGCTTTTCAAAGGGAAGAACGGGAACGATGG
genomic: GCATACCAGTATATTTTGTGGGTTGTGGCACTCGTCTTGCTGTTAGTTGGgtaagtaaat ... tggggcacagGTTTGTGATTTCACTGGTGATGCTTTTCAAAGGGAAGAACGGGAACGATGG
EST: gi|5006174|gb|AI712236.1|AI712236
EST:     GCATACCAGTATATTTTGTGGGTTGTGGCACTCGTCTTGCTGTTAGTTGG                         GTTTGTGATTTCACTGGTGATGCTTTTCAAAGGGAAGAACGGGAACGATGG
genomic: GCATACCAGTATATTTTGTGGGTTGTGGCACTCGTCTTGCTGTTAGTTGGgtaagtaaat ... tggggcacagGTTTGTGATTTCACTGGTGATGCTTTTCAAAGGGAAGAACGGGAACGATGG
EST: gi|78027476|gb|DV495863.1|DV495863
EST:     GCATACCAGTATATTTTGTGGGTTGTGGCACTCGTCTTGCTGTTAGTTGG                         GTTTGTGATTTCACTGGTGATGCTTTTCAAAGGGAAGAACGGGAACGATGG
genomic: GCATACCAGTATATTTTGTGGGTTGTGGCACTCGTCTTGCTGTTAGTTGGgtaagtaaat ... tggggcacagGTTTGTGATTTCACTGGTGATGCTTTTCAAAGGGAAGAACGGGAACGATGG
EST: gi|101386350|gb|EB815194.1|EB815194
EST:     GCATACCAGTATATTTTGTGGGTTGTGGCACTCGTCTTGCTGTTAGTTGG                         GTTTGTGATTTCACTGGTGATGCTTTTCAAAGGGAAGAACGGGAACGATGG
genomic: GCATACCAGTATATTTTGTGGGTTGTGGCACTCGTCTTGCTGTTAGTTGGgtaagtaaat ... tggggcacagGTTTGTGATTTCACTGGTGATGCTTTTCAAAGGGAAGAACGGGAACGATGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttgttttttgtgaaagcttgaaataacactaatgtcaaaattcttggggcacagGTTTGTGATTTCACTGGTGATGCTTTTCAAAGGGAAGAACGGGAACGATGGCTGCCATTGGTGCCACTACCTGAACTGCGTGCCAACATCCAAGTGGAAG
                           cactaat  putative branch site (score: 2)
                                         ttctt  putative PPT
                  ttgaaataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtaaatccatatggctggttcagtatatttgttgtagacatgtctttatgcgtttattaaacatatattgcagaaaacgtgcaacaaagattcgtgattctggactaatgctaaattttggacgagctataaagatgtcacttgttttttgtgaaagcttgaaataacactaatgtcaaaattcttggggcacagGTTTGTGATTTCACTGGTGATGCTTTTCAAAGGGAAGAACGGGAACGATGGCTGCCATTGGTGCCACTACCTGAACTGCGTGCCAACATCCAAGTGGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG