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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtatgacatcatgcaattgttagtacactatccatcgagtgccctgatgtccgaaagtgacacattcaagctatttctacctcagatatactgatattatagaatatatgaatttgaaatcatcatgtatctcgtaatagccacacttgtgcatgctaacctttttttttcatatttttggtgcagCGGAGGAAATTTTGTACATAATACACTTACCTGCAGTGTACAGAAACAAGAAAAGATGGCGATTTACTAATGTCTGCTGCCTGGCAGAGAATTGAACTAC

Basic information

species Zea mays
transcript GRMZM2G452580_T01
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G452580_T01 (Zea mays), 3'ss of exon 14
lower sequence: LOC_Os02g48990.1 (Oryza sativa), 3'ss of exon 14
gtaagtatgacatcatgcaattgttagtacactatccatcgagtgccctgatgtccgaaagtgacacattcaagctatttctacctcaga-tatactgatattatagaatatatgaatttgaaatcatcatgtatctcgtaatagccacacttgtgcatgctaacctttttttttcatatttttggtgcagCGGAGGAAATTTTGTACATAATACACTTACCTGCAGTGTACAGAAACAAGAAAAGA-----TGGCGATTTACTAATGTCTGCTGCCTGGCAGAGAATTGAACTAC
                                                                               | || | |||| |||| |  ||||    | | |     ||| |  || |  |||   |   |   || | | |  |  ||       ||| |||||| | | | |  ||||| | || ||||||||||||||||| ||||| | ||| ||||||| ||||||||||||      | ||| ||||||||| | ||   |   || | || | |     
-------------------------------------------------------------------------------tgtagcacagactatatttgtattt---attctgcagcttttatttcttggtgttcttgtcagacgctaaattcctttat-------tttatttttcttgtctgt--tgcagAGAAGAAAATTTTGTACATAATAAACTTAGCAGCAATGTACAGGAACAAGAAAAGAAGAGTCGACGACTTACTAATGCCGGCATTCCAACATAAAACTAA-----
















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|113702853|gb|EE680357.1|EE680357
EST:     AAATGCAGATGGCAGAAACCTTGGAAGCTGTAACGGAGCCTGATCTTAGG                         CGGAGGAAATTTTGTACATAATACACTTACCTGCAGTGTACAGAAACAAGA
genomic: AAATGCAGATGGCAGAAACCTTGGAAGCTGTAACGGAGCCGGATCTTAGGgtaagtatga ... tttggtgcagCGGAGGAAATTTTGTACATAATACACTTACCTGCAGTGTACAGAAACAAGA
EST: gi|5919382|gb|AW054479.1|AW054479
EST:     AAATGCAGATGGCAGAAACCTTGGAAGCTGTAACGGAGCCTGATCTTAGG                         CGGAGGAAATTTTGTACATAATACACTTACCTGCAGTGTACAGAAACAAGA
genomic: AAATGCAGATGGCAGAAACCTTGGAAGCTGTAACGGAGCCGGATCTTAGGgtaagtatga ... tttggtgcagCGGAGGAAATTTTGTACATAATACACTTACCTGCAGTGTACAGAAACAAGA
EST: gi|67015738|gb|CO444487.1|CO444487
EST:     AAATGCAGATGGCAGAAACCTTGGAAGCTGTAACGGAGCCGGATCTTAGG                         CGGAGGAAATTTTGTACATAATACACTTACCTGCAGTGTACAGAAACAAGA
genomic: AAATGCAGATGGCAGAAACCTTGGAAGCTGTAACGGAGCCGGATCTTAGGgtaagtatga ... tttggtgcagCGGAGGAAATTTTGTACATAATACACTTACCTGCAGTGTACAGAAACAAGA
EST: gi|4624363|gb|AI615196.1|AI615196
EST:     AAATGCAGATGGCAGAAACCTTGGAAGCTGTAACGGAGCCGGATCTTAGG                         CGGAGGAAATTTTGTACATAATACACTTACCTGCAGTGTACAGAAACAAGA
genomic: AAATGCAGATGGCAGAAACCTTGGAAGCTGTAACGGAGCCGGATCTTAGGgtaagtatga ... tttggtgcagCGGAGGAAATTTTGTACATAATACACTTACCTGCAGTGTACAGAAACAAGA
EST: gi|211320220|gb|FL223755.1|FL223755
EST:     AAATGCAGATGGCAGAAACCTTGGAAGCTGTAACGGAGCCTGATCTTAGG                         CGGAGAAAATTTTGTACATAATACACTTACCTGCAGTGTAC
genomic: AAATGCAGATGGCAGAAACCTTGGAAGCTGTAACGGAGCCGGATCTTAGGgtaagtatga ... tttggtgcagCGGAGGAAATTTTGTACATAATACACTTACCTGCAGTGTAC
EST: gi|86470348|gb|DY236718.1|DY236718
EST:     AAATGCAGATGGCAGAAACCTTGGAAGCTGTAACGGAGCCGGATTTTAGG                         CGGAGGAAATTTTGTACATAATACACTTACCTGCAGTGTACAGAAACAAGA
genomic: AAATGCAGATGGCAGAAACCTTGGAAGCTGTAACGGAGCCGGATCTTAGGgtaagtatga ... tttggtgcagCGGAGGAAATTTTGTACATAATACACTTACCTGCAGTGTACAGAAACAAGA
EST: gi|31356668|gb|CD441025.1|CD441025
EST:     AAATGCAGATGGCAGAAACCTTGGAAGCTGTAACGGAGCCGGATCTTAGG                         CGGAGGAAATTTTGTACATAATACACTTACCTGCAGTGTACAGAAACAAGA
genomic: AAATGCAGATGGCAGAAACCTTGGAAGCTGTAACGGAGCCGGATCTTAGGgtaagtatga ... tttggtgcagCGGAGGAAATTTTGTACATAATACACTTACCTGCAGTGTACAGAAACAAGA
EST: gi|4776546|gb|AI665549.1|AI665549
EST:     AAATGCAGATGGCAGAAACCTTGGAAGCTGTAACGGAGCCTGATCTTAGG                         CGGAGGAAATTTTGTACATAATACACTTACCTGCAGTGTACAGAAACAAGA
genomic: AAATGCAGATGGCAGAAACCTTGGAAGCTGTAACGGAGCCGGATCTTAGGgtaagtatga ... tttggtgcagCGGAGGAAATTTTGTACATAATACACTTACCTGCAGTGTACAGAAACAAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcgtaatagccacacttgtgcatgctaacctttttttttcatatttttggtgcagCGGAGGAAATTTTGTACATAATACACTTACCTGCAGTGTACAGAAACAAGAAAAGATGGCGATTTACTAATGTCTGCTGCCTGGCAGAGAATTGAACTAC
                      tgctaac  putative branch site (score: 1)
                            cctttttttttcatat  CT-rich tract
                         taacctttttttttca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtatgacatcatgcaattgttagtacactatccatcgagtgccctgatgtccgaaagtgacacattcaagctatttctacctcagatatactgatattatagaatatatgaatttgaaatcatcatgtatctcgtaatagccacacttgtgcatgctaacctttttttttcatatttttggtgcagCGGAGGAAATTTTGTACATAATACACTTACCTGCAGTGTACAGAAACAAGAAAAGATGGCGATTTACTAATGTCTGCTGCCTGGCAGAGAATTGAACTAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC