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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtggggctatcaaaacccagatttttcattcagattgtcatgtcgtggtaacggcctaacgggttgttgtgaaccaaaccattgttcctgctgcagGGTCCAACAAGCAAGAACCCTCTTGCTTATAAGTGGTATAACAAGGAGGAAGTGATTCTCGGTAAGAAGATGAAG

Basic information

species Zea mays
transcript GRMZM2G081682_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G081682_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os07g47290.1 (Oryza sativa), 3'ss of exon 3
-gtggggctatcaaaacccagatttttcattcagattgtcatgtcgtggtaacggcctaacgggttgttgtgaaccaaaccattgttcc-------tgctgcagGGTCCAACAAGCAAGAACCCTCTTGCTTATAAGTGGTATAACAAGGAGGAAGTGATTCTCGGTAAGAAGATGAAG
 |      |   ||| |  |||  |||   | ||||||| || |  |||       ||   | |   |||||| | ||  | ||||| |         |||||||||||||  ||||||||||| |||||||| |||||||| ||    |||||||||||||| || ||||||||||||
agattacttgataaagcttagaaattt---ttagattgttatatattggactaaaactgctgtgac-ttgtgagctaagactttgttgcacaattgcactgcagGGTCCAAGCAGCAAGAACCCGCTTGCTTACAAGTGGTACAATGCTGAGGAAGTGATTCTTGGGAAGAAGATGAAG
















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|211316223|gb|FL334911.1|FL334911
EST:     ATGATTGGGAGGGGGAGTTCTTCCCCGGCGTCCCGAAAATCAAGTATGAG                         GGTCCAACAAGCAAGAACCCTCTTGCTTATAAGTGGTATAACAAGGAGGAA
genomic: ATGATTGGGAGGGGGAGTTCTTCCCCGGCGTCCCGAAAATCAAGTATGAGgtggggctat ... cctgctgcagGGTCCAACAAGCAAGAACCCTCTTGCTTATAAGTGGTATAACAAGGAGGAA
EST: gi|211075605|gb|FL344132.1|FL344132
EST:     ATGATTGGGAGGGGGAGTTCTTCCCCGGCGTCCCGAAAATCAAGTATGAG                         GGTCCAACAAGCAAGAACCCTCTTGCTTATAAGTGGTATAACAAGGAGGAA
genomic: ATGATTGGGAGGGGGAGTTCTTCCCCGGCGTCCCGAAAATCAAGTATGAGgtggggctat ... cctgctgcagGGTCCAACAAGCAAGAACCCTCTTGCTTATAAGTGGTATAACAAGGAGGAA
EST: gi|211288683|gb|FL312634.1|FL312634
EST:     ATGATTGGGAGGGGGAGTTCTTCCCCGGCGTCCCGAAAATCAAGTATGAG                         GGTCCAACAAGCAAGAACCCTCTTGCTTATAAGTGGTATAACAAGGAGGAA
genomic: ATGATTGGGAGGGGGAGTTCTTCCCCGGCGTCCCGAAAATCAAGTATGAGgtggggctat ... cctgctgcagGGTCCAACAAGCAAGAACCCTCTTGCTTATAAGTGGTATAACAAGGAGGAA
EST: gi|211328969|gb|FL341564.1|FL341564
EST:     ATGATTGGGAGGGGGAGTTCTTCCCCGGCGTCCCGAAAATCAAGTATGAG                         GGTCCAACAAGCAAGAACCCTCTTGCTTATAAGTGGTATAACAAGGAGGAA
genomic: ATGATTGGGAGGGGGAGTTCTTCCCCGGCGTCCCGAAAATCAAGTATGAGgtggggctat ... cctgctgcagGGTCCAACAAGCAAGAACCCTCTTGCTTATAAGTGGTATAACAAGGAGGAA
EST: gi|71426924|gb|DR807974.1|DR807974
EST:     ATGATTGGGAGGGGGAGTTCTTCCCCGGCGTCCCGAAAATCAAGTATGAG                         GGTCCAACAAGCAAGAACCCTCTTGCTTATAAGTGGTATAACAAGGAGGAA
genomic: ATGATTGGGAGGGGGAGTTCTTCCCCGGCGTCCCGAAAATCAAGTATGAGgtggggctat ... cctgctgcagGGTCCAACAAGCAAGAACCCTCTTGCTTATAAGTGGTATAACAAGGAGGAA
EST: gi|211416745|gb|FL321410.1|FL321410
EST:     ATGATTGGGAGGGGGAGTTCTTCCCCGGCGTCCCGAAAATCAAGTATGAG                         GGTCCAACAAGCAAGAACCCTCTTGCTTATAAGTGGTATAACAAGGAGGAA
genomic: ATGATTGGGAGGGGGAGTTCTTCCCCGGCGTCCCGAAAATCAAGTATGAGgtggggctat ... cctgctgcagGGTCCAACAAGCAAGAACCCTCTTGCTTATAAGTGGTATAACAAGGAGGAA
EST: gi|74245361|gb|DT653275.1|DT653275
EST:     ATGATTGGGAGGGGGAGTTCTTCCCCGGCGTCCCGAAAATCAAGTATGAG                         GGTCCAACAAGCAAGAACCCTCTTGCTTATAAGTGGTATAACAAGGAGGAA
genomic: ATGATTGGGAGGGGGAGTTCTTCCCCGGCGTCCCGAAAATCAAGTATGAGgtggggctat ... cctgctgcagGGTCCAACAAGCAAGAACCCTCTTGCTTATAAGTGGTATAACAAGGAGGAA
EST: gi|74232804|gb|DT640718.1|DT640718
EST:     ATGATTGGGAGGGGGAGTTCTTCCCCGGCGTCCCGAAAATCAAGTATGAG                         GGTCCAACAAGCAAGAACCCTCTTGCTTATAAGTGGTATAACAAGGAGGAA
genomic: ATGATTGGGAGGGGGAGTTCTTCCCCGGCGTCCCGAAAATCAAGTATGAGgtggggctat ... cctgctgcagGGTCCAACAAGCAAGAACCCTCTTGCTTATAAGTGGTATAACAAGGAGGAA
EST: gi|211420503|gb|FL364960.1|FL364960
EST:     ATGATTGGGAGGGGGAGTTCTTCCCCGGCGTCCCGAAAATCAAGTATGAG                         GGTCCAACAAGCAAGAACCCTCTTGCTTATAAGTGGTATAACAAGGAGGAA
genomic: ATGATTGGGAGGGGGAGTTCTTCCCCGGCGTCCCGAAAATCAAGTATGAGgtggggctat ... cctgctgcagGGTCCAACAAGCAAGAACCCTCTTGCTTATAAGTGGTATAACAAGGAGGAA
EST: gi|211457434|gb|FL331063.1|FL331063
EST:     ATGATTGGGAGGGGGAGTTCTTCCCCGGCGTCCCGAAAATCAAGTATGAG                         GGTCCAACAAGCAAGAACCCTCTTGCTTATAAGTGGTATAACAAGGAGGAA
genomic: ATGATTGGGAGGGGGAGTTCTTCCCCGGCGTCCCGAAAATCAAGTATGAGgtggggctat ... cctgctgcagGGTCCAACAAGCAAGAACCCTCTTGCTTATAAGTGGTATAACAAGGAGGAA
EST: gi|32866060|gb|CF005742.1|CF005742
EST:     ATGATTGGGAGGGGGAGTTCTTCCCCGGCGTCCCGAAAATCAAGTATGAG                         GGTCCAACAAGCAAGAACCCTCTTGCTTATAAGTGGTATAACAAGGAGGAA
genomic: ATGATTGGGAGGGGGAGTTCTTCCCCGGCGTCCCGAAAATCAAGTATGAGgtggggctat ... cctgctgcagGGTCCAACAAGCAAGAACCCTCTTGCTTATAAGTGGTATAACAAGGAGGAA
EST: gi|32909379|gb|CF014191.1|CF014191
EST:     ATGATTGGGAGGGGGAGTTCTTCCCCGGCGTCCCGAAAATCAAGTATGAG                         GGTCCAACAAGCAAGAACCCTCTTGCTTATAAGTGGTATAACAAGGAGGAA
genomic: ATGATTGGGAGGGGGAGTTCTTCCCCGGCGTCCCGAAAATCAAGTATGAGgtggggctat ... cctgctgcagGGTCCAACAAGCAAGAACCCTCTTGCTTATAAGTGGTATAACAAGGAGGAA
EST: gi|211310239|gb|FL338849.1|FL338849
EST:     TGNATTGGGAGGGGGAGTTCTTCCCCGGCGTCCCGAAAATCAAGTATGAG                         GGTCCAACAAGCAAGAACCCTCTTGCTTATAAGTGGTATAACAAGGAGGAA
genomic: TG-ATTGGGAGGGGGAGTTCTTCCCCGGCGTCCCGAAAATCAAGTATGAGgtggggctat ... cctgctgcagGGTCCAACAAGCAAGAACCCTCTTGCTTATAAGTGGTATAACAAGGAGGAA
EST: gi|211149448|gb|FL325049.1|FL325049
EST:     ATGATTGGGAGGGGGAGTTCTTCCC-GGCGTCCCGAAAATCAAGTATGAG                         GGTCCAACAAGCAAGAACC-TCTTGCTTAT
genomic: ATGATTGGGAGGGGGAGTTCTTCCCCGGCGTCCCGAAAATCAAGTATGAGgtggggctat ... cctgctgcagGGTCCAACAAGCAAGAACCCTCTTGCTTAT
EST: gi|211140891|gb|FL328471.1|FL328471
EST:     ATGATTGGGAGGGGGAGTTCTTCCCCGGCGTCCCGAAAATCAAGTATGAG                         GGTCCAACAAGCAAGAACCCTCTTGCTTATAAGTGGTATAACAAGGAGGAA
genomic: ATGATTGGGAGGGGGAGTTCTTCCCCGGCGTCCCGAAAATCAAGTATGAGgtggggctat ... cctgctgcagGGTCCAACAAGCAAGAACCCTCTTGCTTATAAGTGGTATAACAAGGAGGAA
EST: gi|211320715|gb|FL358326.1|FL358326
EST:     ATGATTGGGAGGGGGAGTTCTTCCCCGGCGTCCCGAAAATCAAGTATGAG                         GGTCCAACAAGCAAGAACCCTCTTGCTTATAAGTGGTATAACAAGGAGGAA
genomic: ATGATTGGGAGGGGGAGTTCTTCCCCGGCGTCCCGAAAATCAAGTATGAGgtggggctat ... cctgctgcagGGTCCAACAAGCAAGAACCCTCTTGCTTATAAGTGGTATAACAAGGAGGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtcgtggtaacggcctaacgggttgttgtgaaccaaaccattgttcctgctgcagGGTCCAACAAGCAAGAACCCTCTTGCTTATAAGTGGTATAACAAGGAGGAAGTGATTCTCGGTAAGAAGATGAAG
            gcctaac  putative branch site (score: 2)
                                        ttgttcct  putative PPT
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtggggctatcaaaacccagatttttcattcagattgtcatgtcgtggtaacggcctaacgggttgttgtgaaccaaaccattgttcctgctgcagGGTCCAACAAGCAAGAACCCTCTTGCTTATAAGTGGTATAACAAGGAGGAAGTGATTCTCGGTAAGAAGATGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG