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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttcaaattttgacgacttactatagtcagcagtgaaagaaaaacaggacagtgtttccttttccttccatgaacttgaaatgttgactctggtttgcagGAATTTGCTGGATAAGCAGAATCTAGGTGACCAGTTCTCTGTATCCACTTCCATGGACTCCTTTGACTTCTCATCATCACATTCTTCCCCAAACCAAGCC

Basic information

species Zea mays
transcript GRMZM2G099862_T02
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|32855562|gb|CD995243.1|CD995243
EST:     AAAAGCTCAGCTGCTAATGTGACTGATCCATTCTCACTAGGGTCCAACAG                         GAATTTGCTGGATAAGCAGAATCTAGGTGACCAGTTCTCTGTATCCACTTC
genomic: AAAAGCTCAGCTGCTAATGTGACTGATCCATTCTCACTAGGGTCCAACAGgtgaagtcac ... tggtttgcagGAATTTGCTGGATAAGCAGAATCTAGGTGACCAGTTCTCTGTATCCACTTC
EST: gi|148970335|gb|EE021200.2|EE021200
EST:     AAAAGCTCAGCTGCTAATGTGACTGATCCATTCTCACTAGGGTCCAACAG                         GAATTTGCTGGATAAGCAGAATCTAGGTGACCAGTTCTCTGTATCCACTTC
genomic: AAAAGCTCAGCTGCTAATGTGACTGATCCATTCTCACTAGGGTCCAACAGgtgaagtcac ... tggtttgcagGAATTTGCTGGATAAGCAGAATCTAGGTGACCAGTTCTCTGTATCCACTTC
EST: gi|78077452|gb|DV505886.1|DV505886
EST:     AAAAGCTCAGCTGCTAATGTGACTGATCCATTCTCACTAGGGTCCAACAG                         GAATTTGCTGGATAAGCAGAATCTAGGTGACCAGTTCTCTGTATCCACTTC
genomic: AAAAGCTCAGCTGCTAATGTGACTGATCCATTCTCACTAGGGTCCAACAGgtgaagtcac ... tggtttgcagGAATTTGCTGGATAAGCAGAATCTAGGTGACCAGTTCTCTGTATCCACTTC
EST: gi|76017158|gb|DT944328.1|DT944328
EST:     AAAAGCTCAGCTGCTAATGTGACTGATCCATTCTCACTAGGGTCCAACAG                         GAATTTGCTGGATAAGCAGAATCTAGGTGACCAGTTCTCTGTATCCACTTC
genomic: AAAAGCTCAGCTGCTAATGTGACTGATCCATTCTCACTAGGGTCCAACAGgtgaagtcac ... tggtttgcagGAATTTGCTGGATAAGCAGAATCTAGGTGACCAGTTCTCTGTATCCACTTC
EST: gi|71437242|gb|DR818292.1|DR818292
EST:     AAAAGCTCAGCTGCTAATGTGACTGATCCATTCTCACTAGGGTCCAACAG                         GAATTTGCTGGATAAGCAGAATCTAGGTGACCAGTTCTCTGTATCCACTTC
genomic: AAAAGCTCAGCTGCTAATGTGACTGATCCATTCTCACTAGGGTCCAACAGgtgaagtcac ... tggtttgcagGAATTTGCTGGATAAGCAGAATCTAGGTGACCAGTTCTCTGTATCCACTTC
EST: gi|71444723|gb|DR825773.1|DR825773
EST:     AAAAGCTCAGCTGCTAATGTGACTGATCCATTCTCACTAGGGTCCAACAG                         GAATTTGCTGGATAAGCAGAATCTAGGTGACCAGTTCTCTGTATCCACTTC
genomic: AAAAGCTCAGCTGCTAATGTGACTGATCCATTCTCACTAGGGTCCAACAGgtgaagtcac ... tggtttgcagGAATTTGCTGGATAAGCAGAATCTAGGTGACCAGTTCTCTGTATCCACTTC
EST: gi|71320270|gb|DR796883.1|DR796883
EST:     AAAAGCTCAGCTGCTAATGTGACTGATCCATTCTCACTAGGGTCCAACAG                         GAATTTGCTGGATAAGCAGAATCTAGGTGACCAGTTCTCTGTATCCACTTC
genomic: AAAAGCTCAGCTGCTAATGTGACTGATCCATTCTCACTAGGGTCCAACAGgtgaagtcac ... tggtttgcagGAATTTGCTGGATAAGCAGAATCTAGGTGACCAGTTCTCTGTATCCACTTC
EST: gi|78077453|gb|DV505887.1|DV505887
EST:     AAAAGCTCAGCTGCTAATGTGACTGATCCATTCTCACTAGGGTCCAACAG                         GAATTTGCTGGATAAGCAGAATCTAGGTGACCAGTTCTCTGTATCCACTTC
genomic: AAAAGCTCAGCTGCTAATGTGACTGATCCATTCTCACTAGGGTCCAACAGgtgaagtcac ... tggtttgcagGAATTTGCTGGATAAGCAGAATCTAGGTGACCAGTTCTCTGTATCCACTTC
EST: gi|32798932|gb|CD951168.1|CD951168
EST:     AAAAGCTCAGCTGCTAATGTGACTGATCCATTCTCACTAGGGTCCAACAG                         GAATTTGCTGGATAAGCAGAATCTAGGTGACCAGTTCTCTGTATCCACTTC
genomic: AAAAGCTCAGCTGCTAATGTGACTGATCCATTCTCACTAGGGTCCAACAGgtgaagtcac ... tggtttgcagGAATTTGCTGGATAAGCAGAATCTAGGTGACCAGTTCTCTGTATCCACTTC
EST: gi|76911661|gb|DV164370.1|DV164370
EST:     AAAAGCTCAGCTGCTAATGTGACTGATCCATTCTCACTAGGGTCCAACAG                         GAATTTGCTGGATAAGCAGAATCTAGGTGACCAGTTCTCTGTATCCACTTC
genomic: AAAAGCTCAGCTGCTAATGTGACTGATCCATTCTCACTAGGGTCCAACAGgtgaagtcac ... tggtttgcagGAATTTGCTGGATAAGCAGAATCTAGGTGACCAGTTCTCTGTATCCACTTC

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: 49 (upstream exon), 49 (downstream exon)
Score: 99

CTGGTGGTTCATTGTTGCACAGCCATGCTGTTGCTTGGCAGCAGCAGGGCAAAAGCTCAGCTGCTAATGTGACTGATCCATTCTCACTAGGGTCCAACAGgtgaagtcac ... tggtttgcagGAATTTGCTGGATAAGCAGAATCTAGGTGACCAGTTCTCTGTATCCACTTCCATGGACTCCTTTGACTTCTCATCATCACATTCTTCCCCAAACCAAGCC


Block sizes: 43 (upstream exon), 18 (downstream exon)
Score: 3

CTGGTGGTTCATTGTTGCACAGCCATGCTGTTGCTTGGCAGCAGCAGGGCAAAAGCTCAGCTGCTAATGTGACTGATCCATTCTCACTAGGGTCCAACAGgtgaagtcac ... tggtttgcagGAATTTGCTGGATAAGCAGAATCTAGGTGACCAGTTCTCTGTATCCACTTCCATGGACTCCTTTGACTTCTCATCATCACATTCTTCCCCAAACCAAGCC


Block sizes: 39 (upstream exon), 44 (downstream exon)
Score: 4

CTGGTGGTTCATTGTTGCACAGCCATGCTGTTGCTTGGCAGCAGCAGGGCAAAAGCTCAGCTGCTAATGTGACTGATCCATTCTCACTAGGGTCCAACAGgtgaagtcac ... tggtttgcagGAATTTGCTGGATAAGCAGAATCTAGGTGACCAGTTCTCTGTATCCACTTCCATGGACTCCTTTGACTTCTCATCATCACATTCTTCCCCAAACCAAGCC


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 3

CTGGTGGTTCATTGTTGCACAGCCATGCTGTTGCTTGGCAGCAGCAGGGCAAAAGCTCAGCTGCTAATGTGACTGATCCATTCTCACTAGGGTCCAACAGgtgaagtcac ... tggtttgcagGAATTTGCTGGATAAGCAGAATCTAGGTGACCAGTTCTCTGTATCCACTTCCATGGACTCCTTTGACTTCTCATCATCACATTCTTCCCCAAACCAAGCC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aggacagtgtttccttttccttccatgaacttgaaatgttgactctggtttgcagGAATTTGCTGGATAAGCAGAATCTAGGTGACCAGTTCTCTGTATCCACTTCCATGGACTCCTTTGACTTCTCATCATCACATTCTTCCCCAAACCAAGCC
                                    tgttgac  putative branch site (score: 3)
                              ttgaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttcaaattttgacgacttactatagtcagcagtgaaagaaaaacaggacagtgtttccttttccttccatgaacttgaaatgttgactctggtttgcagGAATTTGCTGGATAAGCAGAATCTAGGTGACCAGTTCTCTGTATCCACTTCCATGGACTCCTTTGACTTCTCATCATCACATTCTTCCCCAAACCAAGCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA