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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgggttatacacatattcccttttattttagcaactggtttcttaatatttggtctaacaagatcgggttttctccagGTTTGGTAAAAAGAGACTAGAGGATGATCTTGATCTAATGTCAAGTAAAGCTAATTCTCTAAGAGAGAAGACAGATAATTCAGCAGTTCTTCAGAAACTT

Basic information

species Zea mays
transcript GRMZM2G162184_T01
intron # 19
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|22521204|gb|BU080015.1|BU080015
EST:     AGCAATCGGCTGGAAATTGCTGAGCTGCTTATAGAACTAGAGAATGAGAG                         GTTTGGTAAAAAGAGACTAGAGGATGATCTTGATCTAATGTCAAGTAAAGC
genomic: AGCAATCGGCTGGAAATTGCTGAGCTGCTTATAGAACTAGAGAATGAGAGgtgggttata ... ttttctccagGTTTGGTAAAAAGAGACTAGAGGATGATCTTGATCTAATGTCAAGTAAAGC
EST: gi|5325153|gb|AI783344.1|AI783344
EST:     AGCAATCGGCTGGAAATTGCTGAGCTGCTTATAGAACTAGAGAATGAGAG                         GTTTGGTAAAAAGAGACTAGAGGATGATCTTGATCTAATGTC
genomic: AGCAATCGGCTGGAAATTGCTGAGCTGCTTATAGAACTAGAGAATGAGAGgtgggttata ... ttttctccagGTTTGGTAAAAAGAGACTAGAGGATGATCTTGATCTAATGTC
EST: gi|113701917|gb|EE679421.1|EE679421
EST:     TCGGCTGGAAATTGCTGAGCTGCTTATAGAACTAGAGAATGAGAG                         GTTTGGAAAAAAGAGACTAGAGGATGATCTTGATCTAATGTCAAGTAAAGC
genomic: TCGGCTGGAAATTGCTGAGCTGCTTATAGAACTAGAGAATGAGAGgtgggttata ... ttttctccagGTTTGGTAAAAAGAGACTAGAGGATGATCTTGATCTAATGTCAAGTAAAGC
EST: gi|60351698|gb|DN218671.1|DN218671
EST:     AGCAATCGGCTGGAAATTGCTGAGCTGCTTATAGAACTAGAGAATGAGAG                         GTTTGGTAAAAAGAGACTAGAGGATGATCTTGATCTAATGTCAAGTAAAGC
genomic: AGCAATCGGCTGGAAATTGCTGAGCTGCTTATAGAACTAGAGAATGAGAGgtgggttata ... ttttctccagGTTTGGTAAAAAGAGACTAGAGGATGATCTTGATCTAATGTCAAGTAAAGC
EST: gi|47961592|gb|CN844301.1|CN844301
EST:     GCAATCGGCTGGAAATTGCTGAGCTGCTTATAGAAACTAGAGAATGAGAG                         GTTTGGTAAAA-GAGACTAGAGGATGATCTTGATCTAATGTCAAGTAAAGC
genomic: GCAATCGGCTGGAAATTGCTGAGCTGCTTATAGAA-CTAGAGAATGAGAGgtgggttata ... ttttctccagGTTTGGTAAAAAGAGACTAGAGGATGATCTTGATCTAATGTCAAGTAAAGC
EST: gi|5847246|gb|AW000325.1|AW000325
EST:     AGCAATCGGCTGGAAATTGCTGAGCTGCTTATAGAACTAGAGAATGAGAG                         GTTTGGTAAAAAGAGACTAGAGGATGATCTTGATCTAATGTCAAGTAAAGC
genomic: AGCAATCGGCTGGAAATTGCTGAGCTGCTTATAGAACTAGAGAATGAGAGgtgggttata ... ttttctccagGTTTGGTAAAAAGAGACTAGAGGATGATCTTGATCTAATGTCAAGTAAAGC
EST: gi|6022486|gb|AW067519.1|AW067519
EST:     AGCAATCGGCTGGAAATTGCTGAGCTGCTTATAGAACTAGAGAATGAGAG                         GTTTGGTAAAAAGAGACTAGAGGATGATCTTGATCTAATGTCAAGTAAAGC
genomic: AGCAATCGGCTGGAAATTGCTGAGCTGCTTATAGAACTAGAGAATGAGAGgtgggttata ... ttttctccagGTTTGGTAAAAAGAGACTAGAGGATGATCTTGATCTAATGTCAAGTAAAGC

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 4 RNA-Seq libraries.


Block sizes: 45 (upstream exon), 43 (downstream exon)
Score: 99

AAGCTCCAAAGCTCAGGCAGTCAATGGATGTTCTACAAGCGAAGGCTGGGAGCAATCGGCTGGAAATTGCTGAGCTGCTTATAGAACTAGAGAATGAGAGgtgggttata ... ttttctccagGTTTGGTAAAAAGAGACTAGAGGATGATCTTGATCTAATGTCAAGTAAAGCTAATTCTCTAAGAGAGAAGACAGATAATTCAGCAGTTCTTCAGAAACTT


Block sizes: 49 (upstream exon), 44 (downstream exon)
Score: 42

AAGCTCCAAAGCTCAGGCAGTCAATGGATGTTCTACAAGCGAAGGCTGGGAGCAATCGGCTGGAAATTGCTGAGCTGCTTATAGAACTAGAGAATGAGAGgtgggttata ... ttttctccagGTTTGGTAAAAAGAGACTAGAGGATGATCTTGATCTAATGTCAAGTAAAGCTAATTCTCTAAGAGAGAAGACAGATAATTCAGCAGTTCTTCAGAAACTT


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 94

AAGCTCCAAAGCTCAGGCAGTCAATGGATGTTCTACAAGCGAAGGCTGGGAGCAATCGGCTGGAAATTGCTGAGCTGCTTATAGAACTAGAGAATGAGAGgtgggttata ... ttttctccagGTTTGGTAAAAAGAGACTAGAGGATGATCTTGATCTAATGTCAAGTAAAGCTAATTCTCTAAGAGAGAAGACAGATAATTCAGCAGTTCTTCAGAAACTT


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 94

AAGCTCCAAAGCTCAGGCAGTCAATGGATGTTCTACAAGCGAAGGCTGGGAGCAATCGGCTGGAAATTGCTGAGCTGCTTATAGAACTAGAGAATGAGAGgtgggttata ... ttttctccagGTTTGGTAAAAAGAGACTAGAGGATGATCTTGATCTAATGTCAAGTAAAGCTAATTCTCTAAGAGAGAAGACAGATAATTCAGCAGTTCTTCAGAAACTT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattttagcaactggtttcttaatatttggtctaacaagatcgggttttctccagGTTTGGTAAAAAGAGACTAGAGGATGATCTTGATCTAATGTCAAGTAAAGCTAATTCTCTAAGAGAGAAGACAGATAATTCAGCAGTTCTTCAGAAACTT
                             gtctaac  putative branch site (score: 94)
                                             ttttctcc  putative PPT
               tttcttaatattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgggttatacacatattcccttttattttagcaactggtttcttaatatttggtctaacaagatcgggttttctccagGTTTGGTAAAAAGAGACTAGAGGATGATCTTGATCTAATGTCAAGTAAAGCTAATTCTCTAAGAGAGAAGACAGATAATTCAGCAGTTCTTCAGAAACTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA