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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ccacctattagcgggacacaccaaactggcaatttgcctgctgtgtgtgatatcgatacaaaataacaggattcttttcgctgtttgcatgtggtcccagGATATCAAGACAGCTGACTGGTCGGAGAACGTGGCCCCGTTTTGGCCCGCCGTGATAAAATCAGCGCTAACATGGAAGGGCTTCACCTCTCTGCTGACGA

Basic information

species Zea mays
transcript GRMZM2G035213_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G035213_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os02g47310.1 (Oryza sativa), 3'ss of exon 4
----------------------ccacctattagcggg---acacaccaaactggca--atttgcctgc-----tgtgtgtgatatcgatacaaaata----acaggattcttttcgctgtttg-catgtg----gtcccagGATATCAAGACAGCTGACTGGTCGGAGAACGTGGCCCCGTTTTGGCCCGCCGTGATAAAATCAGCGCTAACATGGAAGGGCTTCACCTCTCTGCTGACGA
                        ||   | || |     |     |||  ||  |   |||||         || ||   ||  ||||    | |     |   |||||||     ||| || ||||||    || ||||||||| | ||||||||| ||||| |||||||| ||||| || ||||| || || |||||||||||  | |||||||| || || || |||||||| |  |
gtaaaaaaacttttcatgctctgaactcgtaagtgaatttaagttacaacttgatatggtttgcacatcaacttgcgtaccatgccgatttgcattctcgcaagagattcttgcatgtgtgtgacatgtgaaatgtgccagGATATAAGGACAGCTGATTGGTCAGAGAACGTCGCCCCATTCTGGCCTGCGGTTATAAAATCAGCATTGACATGGAAAGGTTTAACTTCTCTGCTAAGAA
















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|50339074|gb|CO534200.1|CO534200
EST:     CACCTTCAGACTATGTGAACATTGCCAAGTCACTGTCTCTCGAG                         GATATCAAGACAGCTGACTGGTCGGAGAACGTGGCCCCGTTTTGGCCCGCC
genomic: CACCTTCAGACTATGTGAACATTGCCAAGTCACTGTCTCTCGAGgtaaatagct ... gtggtcccagGATATCAAGACAGCTGACTGGTCGGAGAACGTGGCCCCGTTTTGGCCCGCC
EST: gi|211523613|gb|FL478748.1|FL478748
EST:     GGTGCTCACCTTCAGACTATGTGAACATTGCCAAGTCACTGTCTCTCGAG                         GATATCAAGACAGCTGACTGGTCGGAGAACGTGGCCCCGTTTTGGCCC-CC
genomic: GGTGCTCACCTTCAGACTATGTGAACATTGCCAAGTCACTGTCTCTCGAGgtaaatagct ... gtggtcccagGATATCAAGACAGCTGACTGGTCGGAGAACGTGGCCCCGTTTTGGCCCGCC
EST: gi|211427825|gb|FL005434.1|FL005434
EST:     GGTGCTCACCTTCAGACTATGTGAACATTGCCAAGTCACTGTCTCTCGAG                         GATATCAAGACAGCTGACTGGTCGGAGAACGTGGCCCCGTTTTGGCCCGCC
genomic: GGTGCTCACCTTCAGACTATGTGAACATTGCCAAGTCACTGTCTCTCGAGgtaaatagct ... gtggtcccagGATATCAAGACAGCTGACTGGTCGGAGAACGTGGCCCCGTTTTGGCCCGCC
EST: gi|60354019|gb|DN220992.1|DN220992
EST:     GGTGCTCACCTTCAGACTATGTGAACATTGCCAAGTCACTGTCTCTCGAG                         GATATCAAGACAGCTGACTGGTCGGAGAACGTGGCCCCGTTTTGGCCCGCC
genomic: GGTGCTCACCTTCAGACTATGTGAACATTGCCAAGTCACTGTCTCTCGAGgtaaatagct ... gtggtcccagGATATCAAGACAGCTGACTGGTCGGAGAACGTGGCCCCGTTTTGGCCCGCC
EST: gi|4730548|gb|AI649714.1|AI649714
EST:     GGTGCTCACCTTCAGACTATGTGAACATTGCCAAGTCACTGTCTCTCGAG                         GATATCAAGACAGCTGACTGGTCGGAGAACGTGGCCCCGTTTTGGCCCGCC
genomic: GGTGCTCACCTTCAGACTATGTGAACATTGCCAAGTCACTGTCTCTCGAGgtaaatagct ... gtggtcccagGATATCAAGACAGCTGACTGGTCGGAGAACGTGGCCCCGTTTTGGCCCGCC
EST: gi|71429488|gb|DR810538.1|DR810538
EST:     GGTGCTCACCTTCAGACTATGTGAACATTGCCAAGTCACTGTCTCTCGAG                         GATATCAAGACAGCTGACTGGTCGGAGAACGTGGCCCCGTTTTGGCCCGCC
genomic: GGTGCTCACCTTCAGACTATGTGAACATTGCCAAGTCACTGTCTCTCGAGgtaaatagct ... gtggtcccagGATATCAAGACAGCTGACTGGTCGGAGAACGTGGCCCCGTTTTGGCCCGCC
EST: gi|32845749|gb|CD985430.1|CD985430
EST:     GGTGCTCACCTTCAGACTATGTGAACATTGCCAAGTCACTGTCTCTCGAG                         GATATCAAGACAGCTGACTGGTCGGAGAACGTGGCCCCGTTTTGGCCCGCC
genomic: GGTGCTCACCTTCAGACTATGTGAACATTGCCAAGTCACTGTCTCTCGAGgtaaatagct ... gtggtcccagGATATCAAGACAGCTGACTGGTCGGAGAACGTGGCCCCGTTTTGGCCCGCC
EST: gi|211297442|gb|FL323860.1|FL323860
EST:     GGTGCTCACCTTCAGACTATGTGAACATTGCCAAGTCACTGTCTCTCGAG                         GATATCAAGACAGCTGACTGGTCGGAGAACGTGGCCCCGTTTTGGCCCGCC
genomic: GGTGCTCACCTTCAGACTATGTGAACATTGCCAAGTCACTGTCTCTCGAGgtaaatagct ... gtggtcccagGATATCAAGACAGCTGACTGGTCGGAGAACGTGGCCCCGTTTTGGCCCGCC
EST: gi|71450247|gb|DR831297.1|DR831297
EST:     GGTGCTCACCTTCAGACTATGTGAACATTGCCAAGTCACTGTCTCTCGAG                         GATATCAAGACAGCTGACTGGTCGGAGAACGTGGCCCCGTTTTGGCCCGCC
genomic: GGTGCTCACCTTCAGACTATGTGAACATTGCCAAGTCACTGTCTCTCGAGgtaaatagct ... gtggtcccagGATATCAAGACAGCTGACTGGTCGGAGAACGTGGCCCCGTTTTGGCCCGCC
EST: gi|71432949|gb|DR813999.1|DR813999
EST:     GGTGCTCACCTTCAGACTATGTGAACATTGCCAAGTCACTGTCTCTCGAG                         GATATCAAGACAGCTGACTGGTCGGAGAACGTGGCCCCGTTTTGGCCCGCC
genomic: GGTGCTCACCTTCAGACTATGTGAACATTGCCAAGTCACTGTCTCTCGAGgtaaatagct ... gtggtcccagGATATCAAGACAGCTGACTGGTCGGAGAACGTGGCCCCGTTTTGGCCCGCC
EST: gi|211423160|gb|FL478625.1|FL478625
EST:     GAACATTGCCAAGTCACTGTCTCTCGAG                         GATATCAAGACAGCTGACTGGTCGGAGAACGTGGCCCCGTTTTGGCCCGCC
genomic: GAACATTGCCAAGTCACTGTCTCTCGAGgtaaatagct ... gtggtcccagGATATCAAGACAGCTGACTGGTCGGAGAACGTGGCCCCGTTTTGGCCCGCC
EST: gi|76012355|gb|DT939525.1|DT939525
EST:     GTGCTCACCTTCAGACTATGTGAACATTGCCAAGTCACCTGTCTCTCGAG                         GATATCAAGACAGCTGACTGGTCGGAGAACGTGGCCCCGTTTT
genomic: GTGCTCACCTTCAGACTATGTGAACATTGCCAAGTCAC-TGTCTCTCGAGgtaaatagct ... gtggtcccagGATATCAAGACAGCTGACTGGTCGGAGAACGTGGCCCCGTTTT
EST: gi|71324812|gb|DR799112.1|DR799112
EST:     GGTGCTCACCTTCAGACTATGTGAACATTGCCTAGTCACTGTCTCTCGAG                         GATATCAAGACAGCTGACTGGTCGGGAGA-CGTGGCC
genomic: GGTGCTCACCTTCAGACTATGTGAACATTGCCAAGTCACTGTCTCTCGAGgtaaatagct ... gtggtcccagGATATCAAGACAGCTGACTGGTCGG-AGAACGTGGCC
EST: gi|32925586|gb|CF030398.1|CF030398
EST:     GGTGCTCACCTTCAGACTATGTGAACATTGCCAAGTCACTGTCTCTCGAG                         GATATCAAGACAGCTGACTGGTCGGAGAACGTGGCCCCGTTTTGGCCCGCC
genomic: GGTGCTCACCTTCAGACTATGTGAACATTGCCAAGTCACTGTCTCTCGAGgtaaatagct ... gtggtcccagGATATCAAGACAGCTGACTGGTCGGAGAACGTGGCCCCGTTTTGGCCCGCC
EST: gi|71760345|gb|DR958282.1|DR958282
EST:     GGTGCTCACCTTCAGACTATGTGAACATTGCCAAGTCACTGTCTCTCGAG                         GATATCAAGACAGCTGACTGGTCGGAGAACGGGGCCCCGTTTTGGCCCGCC
genomic: GGTGCTCACCTTCAGACTATGTGAACATTGCCAAGTCACTGTCTCTCGAGgtaaatagct ... gtggtcccagGATATCAAGACAGCTGACTGGTCGGAGAACGTGGCCCCGTTTTGGCCCGCC
EST: gi|116813618|gb|EC856075.1|EC856075
EST:     GGTGCTCACCTTCAGACTATGTGAACATTGCCAAGTCACTGTCTCTCGAG                         GATATCAAGACAGCTGACTGGTCGGAGAACGTGGCCCCGTTTTGGCCCGCC
genomic: GGTGCTCACCTTCAGACTATGTGAACATTGCCAAGTCACTGTCTCTCGAGgtaaatagct ... gtggtcccagGATATCAAGACAGCTGACTGGTCGGAGAACGTGGCCCCGTTTTGGCCCGCC
EST: gi|89754665|gb|DY685373.1|DY685373
EST:     GTGCTCACCCTTCAGACTATGTGAACATTGCCAAGTCACTGTCTCTCGAG                         GATATCAAGACAGCTGACTGGTCGGAGAACGTGGCCCCGTTTTGGCCCGCC
genomic: GTGCTCA-CCTTCAGACTATGTGAACATTGCCAAGTCACTGTCTCTCGAGgtaaatagct ... gtggtcccagGATATCAAGACAGCTGACTGGTCGGAGAACGTGGCCCCGTTTTGGCCCGCC
EST: gi|71450246|gb|DR831296.1|DR831296
EST:     GGTGCTCACCTTCAGACTATGTGAACATTGCCAAGTCACTGTCTCTCGAG                         GATATCAAGACAGCTGACTGGTCGGAGAACGTGGCCCCGTTTTGGCCCGCC
genomic: GGTGCTCACCTTCAGACTATGTGAACATTGCCAAGTCACTGTCTCTCGAGgtaaatagct ... gtggtcccagGATATCAAGACAGCTGACTGGTCGGAGAACGTGGCCCCGTTTTGGCCCGCC
EST: gi|91052239|gb|EB162657.1|EB162657
EST:     GGTGCTCACCTTCAGACTATGTGAACATTGCCAAGTCACTGTCTCTCGAG                         GATATCAAGACAGCTGACTGGTCGGAGAACGTGGCCCCGTTTTGGCCCGCC
genomic: GGTGCTCACCTTCAGACTATGTGAACATTGCCAAGTCACTGTCTCTCGAGgtaaatagct ... gtggtcccagGATATCAAGACAGCTGACTGGTCGGAGAACGTGGCCCCGTTTTGGCCCGCC
EST: gi|71429489|gb|DR810539.1|DR810539
EST:     GGTGCTCACCTTCAGACTATGTGAACATTGCCAAGTCACTGTCTCTCGAG                         GATATCAAGACAGCTGACTGTTCGGAGAACGTGGCCCCGTTTTGGGCGGCC
genomic: GGTGCTCACCTTCAGACTATGTGAACATTGCCAAGTCACTGTCTCTCGAGgtaaatagct ... gtggtcccagGATATCAAGACAGCTGACTGGTCGGAGAACGTGGCCCCGTTTTGGCCCGCC
EST: gi|32925978|gb|CF030790.1|CF030790
EST:     GGTGCTCACCTTCAGACTATGTGAACATTGCCAAGTCACTGTCTCTCGAG                         GATATCAAGACAGCTGACTGGTCGGAGAACGTGGCCCCGTTTTGGCCCGCC
genomic: GGTGCTCACCTTCAGACTATGTGAACATTGCCAAGTCACTGTCTCTCGAGgtaaatagct ... gtggtcccagGATATCAAGACAGCTGACTGGTCGGAGAACGTGGCCCCGTTTTGGCCCGCC
EST: gi|13149776|gb|BG320098.1|BG320098
EST:     GGTGCTCACCTTCAGACTATGTGAACATTGCCAAGTCACTGTCTCTCGAG                         GATATCAAGACAGCTGACTGGTCGGAGAACGTGGCCCCGTTTTGGCCCGCC
genomic: GGTGCTCACCTTCAGACTATGTGAACATTGCCAAGTCACTGTCTCTCGAGgtaaatagct ... gtggtcccagGATATCAAGACAGCTGACTGGTCGGAGAACGTGGCCCCGTTTTGGCCCGCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtgatatcgatacaaaataacaggattcttttcgctgtttgcatgtggtcccagGATATCAAGACAGCTGACTGGTCGGAGAACGTGGCCCCGTTTTGGCCCGCCGTGATAAAATCAGCGCTAACATGGAAGGGCTTCACCTCTCTGCTGACGA
               aaataac  putative branch site (score: 2)
          atacaaaataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ccacctattagcgggacacaccaaactggcaatttgcctgctgtgtgtgatatcgatacaaaataacaggattcttttcgctgtttgcatgtggtcccagGATATCAAGACAGCTGACTGGTCGGAGAACGTGGCCCCGTTTTGGCCCGCCGTGATAAAATCAGCGCTAACATGGAAGGGCTTCACCTCTCTGCTGACGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG