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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTTTCCCTGATGCATCACGTTGTCATGGGTGATGATCCAGAGGTGAAGGCTGGCAAACCATCCCCTGATATTTTTCTTGCTGCTATGAGGAGGTTTGAGgtattggattttgatcgtatggggcaacacttgcagctataatgtttttggatgctgtctgagaatctctactgatgcaactgcattgcatttcttttag

Basic information

species Zea mays
transcript GRMZM2G102231_T01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G102231_T03 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os08g14580.1 (Oryza sativa), 5'ss of exon 4
GTTTTCCCTGATGCATCACGTTGTCATGGGTGATGATCCAGAGGTGAAGGCTGGCAAACCATCCCCTGATATTTTTCTTGCTGCTATGAGGAGGTTTGAGgtattggattttgatcgtatggggcaacac-ttgcagctataatgttt-ttggatgctgtc---tgagaatctctactgatgcaactgcattgcatttcttttag
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GTTTACACTGATGCACCATGTTGTGATGGGGGATGATCCAGATGTGAAGACTGGCAAGCCATCTCCTGATATATTTCTTGCCGCTATGAGGAGGTTTGAGgtattg----ctg--tgtaagagctatttcctttcgagtgttctgtggattagacgtaataatgttataatgtcacctgatgaaatggcactgtgtattgttcag
















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|211004136|gb|FL435012.1|FL435012
EST:     TGGCAAACCATCCCCTGATATTTTTTCTTGCTGCTATGAGGAGGTTTGAG                         GGCGGCGTAGAACCTAGCAAGTGCTTGGTTTTTGAAGACGCTCCTTCGGGT
genomic: TGGCAAACCATCCCCTGATA-TTTTTCTTGCTGCTATGAGGAGGTTTGAGgtattggatt ... tttcttttagGGCGGCGTAGAACCTAGCAAGTGCTTGGTTTTTGAAGACGCTCCTTCGGGT
EST: gi|4572923|gb|AI586572.1|AI586572
EST:     CTGGCAAACCATCCCCTGATATTTTTCTTGCTGCTATGAGGAGGTTTGAG                         GGCGGCGTAGAACCTAGCAAGTGCTTGGTTTTTGAAGACGCTCCTTCGGGT
genomic: CTGGCAAACCATCCCCTGATATTTTTCTTGCTGCTATGAGGAGGTTTGAGgtattggatt ... tttcttttagGGCGGCGTAGAACCTAGCAAGTGCTTGGTTTTTGAAGACGCTCCTTCGGGT
EST: gi|5649952|gb|AI920312.1|AI920312
EST:     CTGGCAAACCATCCCCTGATATTTTTCTTGCTGCTATGAGGAGGTTTGAG                         GGCGGCGTAGAACCTAGCAAGTGCTTGGTTTTTGAAGACGCTCCTTCGGGT
genomic: CTGGCAAACCATCCCCTGATATTTTTCTTGCTGCTATGAGGAGGTTTGAGgtattggatt ... tttcttttagGGCGGCGTAGAACCTAGCAAGTGCTTGGTTTTTGAAGACGCTCCTTCGGGT
EST: gi|14245028|gb|BG842966.2|BG842966
EST:     CTGGCAAACCATCCCCTGATATTTTTCTTGCTGCTATGAGGAGGTTTGAG                         GGCGGCGTAGAACCTAGCAAGTGCTTGGTTTTTGAAGACGCTCCTTCGGGT
genomic: CTGGCAAACCATCCCCTGATATTTTTCTTGCTGCTATGAGGAGGTTTGAGgtattggatt ... tttcttttagGGCGGCGTAGAACCTAGCAAGTGCTTGGTTTTTGAAGACGCTCCTTCGGGT
EST: gi|4572860|gb|AI586509.1|AI586509
EST:     CTGGCAAACCATCCCCTGATATTTTTCTTGCTGCTATGAGGAGGTTTGAG                         GGCGGCGTAGAACCTAGCAAGTGCTTGGTTTTTGAAGACGCTCCTTCGGGT
genomic: CTGGCAAACCATCCCCTGATATTTTTCTTGCTGCTATGAGGAGGTTTGAGgtattggatt ... tttcttttagGGCGGCGTAGAACCTAGCAAGTGCTTGGTTTTTGAAGACGCTCCTTCGGGT
EST: gi|71438331|gb|DR819381.1|DR819381
EST:     TGGCAAACCATCCCCTGATATTTTTCTTGCTGCTATGAGGAGGTTTTGAG                         GGCGGCGTAGAACCTAGCAAGTGCTTGG
genomic: TGGCAAACCATCCCCTGATATTTTTCTTGCTGCTATGAGGAGGTTT-GAGgtattggatt ... tttcttttagGGCGGCGTAGAACCTAGCAAGTGCTTGG
EST: gi|50325634|gb|CO520760.1|CO520760
EST:     CTGGCAAACCATCCCCTGATATTTTTCTTGCTGCTATGAGGAGGTTTGAG                         GGCGGCGTAGAACCTAGCAAGTGCTTGGTTTTTGAAGACGCTCCTTCGGGT
genomic: CTGGCAAACCATCCCCTGATATTTTTCTTGCTGCTATGAGGAGGTTTGAGgtattggatt ... tttcttttagGGCGGCGTAGAACCTAGCAAGTGCTTGGTTTTTGAAGACGCTCCTTCGGGT
EST: gi|71759278|gb|DR957215.1|DR957215
EST:     CTGGCAAACCATCCCCTGATATTTTTCTTGCTGCTATGAGGAGGTTTGAG                         GGCGGCGTAGAACCTAGCAAGTGCTTGGTTTTTGAAGACGCTCCTTCGGGT
genomic: CTGGCAAACCATCCCCTGATATTTTTCTTGCTGCTATGAGGAGGTTTGAGgtattggatt ... tttcttttagGGCGGCGTAGAACCTAGCAAGTGCTTGGTTTTTGAAGACGCTCCTTCGGGT
EST: gi|50338089|gb|CO533215.1|CO533215
EST:     CTGGCAAACCATCCCCTGATATTTTTCTTGCTGCTATGAGGAGGTTTGAG                         GGCGGCGTAGAACCTAGCAAGTGCTTGGTTTTTGAAGACGCTCCTTCGGGT
genomic: CTGGCAAACCATCCCCTGATATTTTTCTTGCTGCTATGAGGAGGTTTGAGgtattggatt ... tttcttttagGGCGGCGTAGAACCTAGCAAGTGCTTGGTTTTTGAAGACGCTCCTTCGGGT
EST: gi|44901216|gb|CK827761.1|CK827761
EST:     CTGGCAAACCATCCCGTGATATTTTTCTTGCTGCTATGAGGAGGTTTGAG                         GGCGGCGTAGAACCTAGCAAGTGCTTGGTTTTTGAAGACGCTCCTTCGGGT
genomic: CTGGCAAACCATCCCCTGATATTTTTCTTGCTGCTATGAGGAGGTTTGAGgtattggatt ... tttcttttagGGCGGCGTAGAACCTAGCAAGTGCTTGGTTTTTGAAGACGCTCCTTCGGGT
EST: gi|24764320|gb|CA399485.1|CA399485
EST:     CTGGCAACCCATCCCCTGATATTTTTCTTGCTGCTATGAGGAGGTTTGAG                         GGCGGCGTAGAACCTAGCAAGTGCTTGGTTTTTGAAGACGCTCCTTCGGGT
genomic: CTGGCAAACCATCCCCTGATATTTTTCTTGCTGCTATGAGGAGGTTTGAGgtattggatt ... tttcttttagGGCGGCGTAGAACCTAGCAAGTGCTTGGTTTTTGAAGACGCTCCTTCGGGT
EST: gi|211035715|gb|FL440361.1|FL440361
EST:     CTGGCAAACCATCCCCTGATATTTTTCTTGCTGCTATGAGGAGGTTTGAG                         GGCGGCGTAGAMCCNTAGCAAGTGCTTGGTTTTTGAAGACGNCNTCYTTCG
genomic: CTGGCAAACCATCCCCTGATATTTTTCTTGCTGCTATGAGGAGGTTTGAGgtattggatt ... tttcttttagGGCGGCGTAGAACC-TAGCAAGTGCTTGGTTTTTGAAGACG-C-TCCTTCG
EST: gi|5649953|gb|AI920313.1|AI920313
EST:     CTGGCAAACCATCCCCTGATATTTTTCTTGCTGCTATGAGGAGGTTTGAG                         GGCGGCGTAGAACCTAGCAAGTGCTTGGTTTTTGAAGACGCTCCTTCGGGT
genomic: CTGGCAAACCATCCCCTGATATTTTTCTTGCTGCTATGAGGAGGTTTGAGgtattggatt ... tttcttttagGGCGGCGTAGAACCTAGCAAGTGCTTGGTTTTTGAAGACGCTCCTTCGGGT
EST: gi|149013686|gb|EE043136.2|EE043136
EST:     CTGGCAAACCATCCCCTGATATTTTTCTTGCTGCTATGAGGAGGTTTGAG                         GGCGGCGTAGAACCTAGCAAGTGCTTGGTTTTTGAAGACGCTCCTTCGGGT
genomic: CTGGCAAACCATCCCCTGATATTTTTCTTGCTGCTATGAGGAGGTTTGAGgtattggatt ... tttcttttagGGCGGCGTAGAACCTAGCAAGTGCTTGGTTTTTGAAGACGCTCCTTCGGGT
EST: gi|13558434|gb|BG549790.1|BG549790
EST:     CTGGCAAACCATCCCCTGATATTTTTCTTGCTGCTATGAGGAGGTTTGAG                         GGCGGCGTAGAACCTAGCAAGTGCTTGGTTTTTGAAGACGCTCCTTCGGGT
genomic: CTGGCAAACCATCCCCTGATATTTTTCTTGCTGCTATGAGGAGGTTTGAGgtattggatt ... tttcttttagGGCGGCGTAGAACCTAGCAAGTGCTTGGTTTTTGAAGACGCTCCTTCGGGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTTTCCCTGATGCATCACGTTGTCATGGGTGATGATCCAGAGGTGAAGGCTGGCAAACCATCCCCTGATATTTTTCTTGCTGCTATGAGGAGGTTTGAGgtattggattttgatcgtatggggcaacacttgcagctataatgtttttggatgctgtctgagaatctctactgatgcaactgcattgcatttcttttag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG