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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagtggctgaggtgatcgatgaagctgatgagggtttgagagatttggaattagtttactatcttttaccttttgtccataattgtcctaggtagggtagtttttcttttcttttgtagtccttgaaaaactgtgacttctcttttcagGATCTTACTCCTGTCGGAAGAGATGCTTTGTCACGAATTAGGGGTCGAGACTTTGACTCAGCATGTGGTCTTACTGAGGATACTGGAGCCTTGATTGTAT

Basic information

species Zea mays
transcript GRMZM5G864001_T01
intron # 3
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|71311168|gb|DR791894.1|DR791894
EST:     AAGAAAGCACTGCACTGATACCTGCTGCTTCAGAAAGTAAGGCACAAAAG                         GATCTTACTCCTGTCGGAAGAGATGCTTTGTCACGAATTAGGGGTCGAGAC
genomic: AAGAAAGCACTGCACTGATACCTGCTGCTTCAGAAAGTAAGGCACAAAAGgtagtggctg ... ctcttttcagGATCTTACTCCTGTCGGAAGAGATGCTTTGTCACGAATTAGGGGTCGAGAC
EST: gi|76280638|gb|DV020206.1|DV020206
EST:     AAGAAAGCACTGCACTGATACCTGCTGCTTCAGAAAGTAAGGCACAAAAG                         GATCTTACTCCTGTCGGAAGAGATGCTTTGTCACGAATTAGGGGTCGAGAC
genomic: AAGAAAGCACTGCACTGATACCTGCTGCTTCAGAAAGTAAGGCACAAAAGgtagtggctg ... ctcttttcagGATCTTACTCCTGTCGGAAGAGATGCTTTGTCACGAATTAGGGGTCGAGAC
EST: gi|78117051|gb|DV535438.1|DV535438
EST:     AAGAAAGCACTGCACTGATACCTGCTGCTTCAGAAAGTAAGGCACAAAAG                         GATCTTACTCCTGTCGGAAGAGATGCTTTGTCACGAATTAGGGGTCGAGAC
genomic: AAGAAAGCACTGCACTGATACCTGCTGCTTCAGAAAGTAAGGCACAAAAGgtagtggctg ... ctcttttcagGATCTTACTCCTGTCGGAAGAGATGCTTTGTCACGAATTAGGGGTCGAGAC
EST: gi|78085722|gb|DV514115.1|DV514115
EST:     AAGAAAGCACTGCACTGATACCTGCTGCTTCAGAAAGTAAGGCACAAAAG                         GATCTTACTCCTGTCGGAAGAGATGCTTTGTCACGAATTAGGGGTCGAGAC
genomic: AAGAAAGCACTGCACTGATACCTGCTGCTTCAGAAAGTAAGGCACAAAAGgtagtggctg ... ctcttttcagGATCTTACTCCTGTCGGAAGAGATGCTTTGTCACGAATTAGGGGTCGAGAC
EST: gi|78114578|gb|DV532966.1|DV532966
EST:     AAGAAAGCACTGCACTGATACCTGCTGCTTCAGAAAGTAAGGCACAAAAG                         GATCTTACTCCTGTCGGAAGAGATGCTTTGTCACGAATTAGGGGTCGAGAC
genomic: AAGAAAGCACTGCACTGATACCTGCTGCTTCAGAAAGTAAGGCACAAAAGgtagtggctg ... ctcttttcagGATCTTACTCCTGTCGGAAGAGATGCTTTGTCACGAATTAGGGGTCGAGAC
EST: gi|71442324|gb|DR823374.1|DR823374
EST:     AAGAAAGCACTGCACTGATACCTGCTGCTTCAGAAAGTAAGGCACAAAAG                         GATCTTACTCCTGTCGGAAGAGATGCTTTGTCACGAATTAGGGGTCGAGAC
genomic: AAGAAAGCACTGCACTGATACCTGCTGCTTCAGAAAGTAAGGCACAAAAGgtagtggctg ... ctcttttcagGATCTTACTCCTGTCGGAAGAGATGCTTTGTCACGAATTAGGGGTCGAGAC
EST: gi|76020233|gb|DT947403.1|DT947403
EST:     AAGAAAGCACTGCACTGATACCTGCTGCTTCAGAAAGTAAGGCACAAAAG                         GATCTTACTCCTGTCGGAAGAGATGCTTTGTCACGAATTAGGGGTCGAGAC
genomic: AAGAAAGCACTGCACTGATACCTGCTGCTTCAGAAAGTAAGGCACAAAAGgtagtggctg ... ctcttttcagGATCTTACTCCTGTCGGAAGAGATGCTTTGTCACGAATTAGGGGTCGAGAC
EST: gi|76923784|gb|DV169660.1|DV169660
EST:     AAGAAAGCACTGCACTGATACCTGCTGCTTCAGAAAGTAAGGCACAAAAG                         GATCTTACTCCTGTCGGAAGAGATGCTTTGTCACGAATTAGGGGTCGAGAC
genomic: AAGAAAGCACTGCACTGATACCTGCTGCTTCAGAAAGTAAGGCACAAAAGgtagtggctg ... ctcttttcagGATCTTACTCCTGTCGGAAGAGATGCTTTGTCACGAATTAGGGGTCGAGAC
EST: gi|101382573|gb|EB813341.1|EB813341
EST:     AAGAAAGCACTGCACTGATACCTGCTGCTTCAGAAAGTAAGGCACAAAAG                         GATCTTACTCCTGTCGGAAGAGATGCTTTGTCACGAATTAGGGGTCGAGAC
genomic: AAGAAAGCACTGCACTGATACCTGCTGCTTCAGAAAGTAAGGCACAAAAGgtagtggctg ... ctcttttcagGATCTTACTCCTGTCGGAAGAGATGCTTTGTCACGAATTAGGGGTCGAGAC
EST: gi|71311170|gb|DR791895.1|DR791895
EST:     AAGAAAGCACTGCACTGATACCTGCTGCTTCAGAAAGTAAGGCACAAAAG                         GATCTTACTCCTGTCGGAAGAGATGCTTTGTCACGAATTAGGGGTCGAGAC
genomic: AAGAAAGCACTGCACTGATACCTGCTGCTTCAGAAAGTAAGGCACAAAAGgtagtggctg ... ctcttttcagGATCTTACTCCTGTCGGAAGAGATGCTTTGTCACGAATTAGGGGTCGAGAC
EST: gi|71437451|gb|DR818501.1|DR818501
EST:     AAGAAAGCACTGCACTGATACCTGCTGCTTCAGAAAGTAAGGCACAAAAG                         GATCTTACTCCTGTCGGAAGAGATGCTTTGTCACGAATTAGGGGTCGAGAC
genomic: AAGAAAGCACTGCACTGATACCTGCTGCTTCAGAAAGTAAGGCACAAAAGgtagtggctg ... ctcttttcagGATCTTACTCCTGTCGGAAGAGATGCTTTGTCACGAATTAGGGGTCGAGAC

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 11

AAGGGTGTCCTCTGAATCAACCCTTCCTTCAGTGGTGGGTACCACTGCAGAAGAAAGCACTGCACTGATACCTGCTGCTTCAGAAAGTAAGGCACAAAAGgtagtggctg ... ctcttttcagGATCTTACTCCTGTCGGAAGAGATGCTTTGTCACGAATTAGGGGTCGAGACTTTGACTCAGCATGTGGTCTTACTGAGGATACTGGAGCCTTGATTGTAT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gggtagtttttcttttcttttgtagtccttgaaaaactgtgacttctcttttcagGATCTTACTCCTGTCGGAAGAGATGCTTTGTCACGAATTAGGGGTCGAGACTTTGACTCAGCATGTGGTCTTACTGAGGATACTGGAGCCTTGATTGTAT
                                       tgacttctcttttc  CT-rich tract
      tttttcttttctttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagtggctgaggtgatcgatgaagctgatgagggtttgagagatttggaattagtttactatcttttaccttttgtccataattgtcctaggtagggtagtttttcttttcttttgtagtccttgaaaaactgtgacttctcttttcagGATCTTACTCCTGTCGGAAGAGATGCTTTGTCACGAATTAGGGGTCGAGACTTTGACTCAGCATGTGGTCTTACTGAGGATACTGGAGCCTTGATTGTAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT