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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gttgaaaagtgtgatgaccttggtgtattacttgtgctacatttatgttgacattacgatatctgattgttgttaacacgtatgcatatcttattatcagGGAGCAACAACAAGGTGGACGCCCTAGATCAGAAGAGCCTCGGAGGGATGATCGTCGTGCCGATAG

Basic information

species Zea mays
transcript GRMZM2G113592_T01
intron # 8
splice site 3'
intron type U2

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|16137393|gb|BI894258.1|BI894258
EST:     GGATCAACCAGGATGGGTGGTACTGATACTGACAAANAGGATTCCACTAG                         GGAGCAACAACAAGGTGGACGCCCTAGATCAGAAGAGCCTCGGAGGGATGA
genomic: GGATCAAGCAGGATGGGTGGTACTGATACTGACAAAAAGGATTCCACTAGgtacatctgt ... ttattatcagGGAGCAACAACAAGGTGGACGCCCTAGATCAGAAGAGCCTCGGAGGGATGA
EST: gi|60338720|gb|DN205693.1|DN205693
EST:     GCAGGATGGGTGGTACTGATACTGACAAAAAGGATTCCACTAG                         GGAGCAACAACAAGGTGGACGCCCTAGATCAGAAGAGCCTCGGAGGGATGA
genomic: GCAGGATGGGTGGTACTGATACTGACAAAAAGGATTCCACTAGgtacatctgt ... ttattatcagGGAGCAACAACAAGGTGGACGCCCTAGATCAGAAGAGCCTCGGAGGGATGA
EST: gi|16137326|gb|BI894191.1|BI894191
EST:     GGATCAACCAGGATGGGTGGTACTGATACTGACAAAAAGGATTCCACTAG                         GGAGCAACAACAAGGTGGACGCCCTAGATCAGAAGAGCCTCGGAGGGATGA
genomic: GGATCAAGCAGGATGGGTGGTACTGATACTGACAAAAAGGATTCCACTAGgtacatctgt ... ttattatcagGGAGCAACAACAAGGTGGACGCCCTAGATCAGAAGAGCCTCGGAGGGATGA
EST: gi|15313685|gb|BI478905.1|BI478905
EST:     GGATCAACCAGGATGGGTGGTACTGATACTGACAAAAAGGATTCCACTAG                         GGAGCAACAACAAGGTGGACGCCCTAGATCAGAAGAGCCTCGGAGGGATGA
genomic: GGATCAAGCAGGATGGGTGGTACTGATACTGACAAAAAGGATTCCACTAGgtacatctgt ... ttattatcagGGAGCAACAACAAGGTGGACGCCCTAGATCAGAAGAGCCTCGGAGGGATGA
EST: gi|16137392|gb|BI894257.1|BI894257
EST:     GGATCAACCAGGATGGGTGGTACTGATACTGACAAAAAGGATTCCACTAG                         GGAGCAACAACAAGGTGGACGCCCTAGATCAGAAGAGCCTCGGAGGGATGA
genomic: GGATCAAGCAGGATGGGTGGTACTGATACTGACAAAAAGGATTCCACTAGgtacatctgt ... ttattatcagGGAGCAACAACAAGGTGGACGCCCTAGATCAGAAGAGCCTCGGAGGGATGA
EST: gi|15323613|gb|BI478906.1|BI478906
EST:     GGATCAACCAGGATGGGTGGTACTGATACTGACAAAAAGGATTCCACTAG                         GGAGCAACAACAAGGTGGACGCCCTAGATCAGAAGAGCCTCGGAGGGATGA
genomic: GGATCAAGCAGGATGGGTGGTACTGATACTGACAAAAAGGATTCCACTAGgtacatctgt ... ttattatcagGGAGCAACAACAAGGTGGACGCCCTAGATCAGAAGAGCCTCGGAGGGATGA
EST: gi|60342767|gb|DN209740.1|DN209740
EST:     GGATCAAGCAGGATGGGTGGTACTGATACTGACAAAAAGGATTCCACTAG                         GGAGCAACAACAAGGTGGACGCCCTAGATCAGAAGAGCCTCGGAGGGATGA
genomic: GGATCAAGCAGGATGGGTGGTACTGATACTGACAAAAAGGATTCCACTAGgtacatctgt ... ttattatcagGGAGCAACAACAAGGTGGACGCCCTAGATCAGAAGAGCCTCGGAGGGATGA
EST: gi|16137327|gb|BI894192.1|BI894192
EST:     GGATCAACCAGGATGGGTGGTACTGATACTGACAAAAAGGATTCCACTAG                         GGAGCAACAACAAGGTGGACGCCCTAGATCAGAAGAGCCTCGGAGGGATGA
genomic: GGATCAAGCAGGATGGGTGGTACTGATACTGACAAAAAGGATTCCACTAGgtacatctgt ... ttattatcagGGAGCAACAACAAGGTGGACGCCCTAGATCAGAAGAGCCTCGGAGGGATGA
EST: gi|60342884|gb|DN209857.1|DN209857
EST:     GGATCAAGCAGGATGGGTGGTACTGATACTGACAAAAAGGATTCCACTAG                         GGAGCAACAACAAGGTGGACGCCCTAGATCAGAAGAGCCTCGGAGGGATGA
genomic: GGATCAAGCAGGATGGGTGGTACTGATACTGACAAAAAGGATTCCACTAGgtacatctgt ... ttattatcagGGAGCAACAACAAGGTGGACGCCCTAGATCAGAAGAGCCTCGGAGGGATGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttgacattacgatatctgattgttgttaacacgtatgcatatcttattatcagGGAGCAACAACAAGGTGGACGCCCTAGATCAGAAGAGCCTCGGAGGGATGATCGTCGTGCCGATAG
                         tgttaac  putative branch site (score: 2)
                                           tcttatt  putative PPT
                                        atatcttattatca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttgaaaagtgtgatgaccttggtgtattacttgtgctacatttatgttgacattacgatatctgattgttgttaacacgtatgcatatcttattatcagGGAGCAACAACAAGGTGGACGCCCTAGATCAGAAGAGCCTCGGAGGGATGATCGTCGTGCCGATAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA