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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aacccacatcgttccgaaaccaaacacatgcttggagtccaaagaaaagtttgcgcttaccattgttgctagtactttattgattaacctatctttccagGTTGGTGCAAAACGGCTGGATGCGGCCGCAAAGAAAGGGAACACGTATAGTTGGAGTCTCATTTTCAGCAGCAAGAAGTCAGCATGACCAAATTGCTCGT

Basic information

species Zea mays
transcript GRMZM2G003692_T02
intron # 9
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|12968787|gb|BG265824.1|BG265824
EST:     TGTACTTGGTGCAATACATGCCAACAATTGGTTATTGGCTAATGGACAAG                         GTTGGTGCAAAACGGCTGGATGCGGCCGCAAAGAAAGGGAACACGTATAGT
genomic: TGTACTTGGTGCAATACATGCCAACAATTGGTTATTGGCTAATGGACAAGgtatttcttc ... atctttccagGTTGGTGCAAAACGGCTGGATGCGGCCGCAAAGAAAGGGAACACGTATAGT
EST: gi|32919173|gb|CF023985.1|CF023985
EST:     TGTACTTGGTGCAATACATGCCAACAATTGGTTATTGGCTAATGGACAAG                         GTTGGTGCAAAACGGCTGGATGCGGCCGCAAAGAAAGGGAACACGTATAGT
genomic: TGTACTTGGTGCAATACATGCCAACAATTGGTTATTGGCTAATGGACAAGgtatttcttc ... atctttccagGTTGGTGCAAAACGGCTGGATGCGGCCGCAAAGAAAGGGAACACGTATAGT
EST: gi|166410271|gb|EG044485.1|EG044485
EST:     CAATTGGTTATTGGCTAATGGACAAG                         GTTGGTGCAAAACGGCTGGATGCGGCCGCAAAGAAAGGGAACACGTATAGT
genomic: CAATTGGTTATTGGCTAATGGACAAGgtatttcttc ... atctttccagGTTGGTGCAAAACGGCTGGATGCGGCCGCAAAGAAAGGGAACACGTATAGT
EST: gi|91875090|gb|EB405047.1|EB405047
EST:     TGTACTTGGTGCAATACATGCCAACAATTGGTTATTGGCTAATGGACAAG                         GTTGGTGCAAAACGGCTGGAT
genomic: TGTACTTGGTGCAATACATGCCAACAATTGGTTATTGGCTAATGGACAAGgtatttcttc ... atctttccagGTTGGTGCAAAACGGCTGGAT
EST: gi|32919094|gb|CF023906.1|CF023906
EST:     TGTACTTGGTGCAATACATGCCAACAATTGGTTATTGGCTAATGGACAAG                         GTTGGTGCAAAACGGCTGGATGCGGCCGCAAAGAAAGGGAACACGTATAGT
genomic: TGTACTTGGTGCAATACATGCCAACAATTGGTTATTGGCTAATGGACAAGgtatttcttc ... atctttccagGTTGGTGCAAAACGGCTGGATGCGGCCGCAAAGAAAGGGAACACGTATAGT
EST: gi|113703640|gb|EE681144.1|EE681144
EST:     TGTACTTGGTGCAATACATGCCAACAATTGGTTATTGGCTAATGGACAAG                         GTTGGTGCAAAACGGCTGGATGCGGCCGC
genomic: TGTACTTGGTGCAATACATGCCAACAATTGGTTATTGGCTAATGGACAAGgtatttcttc ... atctttccagGTTGGTGCAAAACGGCTGGATGCGGCCGC
EST: gi|88757473|gb|DY541614.1|DY541614
EST:     TGTACTTGGTGCAATACATGCCAACAATTGGTTATTGGCTAATGGACAAG                         GTTGGTGCAAAACGGCTGGAT
genomic: TGTACTTGGTGCAATACATGCCAACAATTGGTTATTGGCTAATGGACAAGgtatttcttc ... atctttccagGTTGGTGCAAAACGGCTGGAT
EST: gi|32909212|gb|CF014024.1|CF014024
EST:     TGTACTTGGTGCAATACATGCCAACAATTGGTTATTGGCTAATGGACAAG                         GTTGGTGCAAAACGGCTGGATGCGGCCGCAAAGAAAGGGAACACGTATAGT
genomic: TGTACTTGGTGCAATACATGCCAACAATTGGTTATTGGCTAATGGACAAGgtatttcttc ... atctttccagGTTGGTGCAAAACGGCTGGATGCGGCCGCAAAGAAAGGGAACACGTATAGT
EST: gi|88757474|gb|DY541615.1|DY541615
EST:     TGTACTTGGTGCAATACATGCCAACAATTGGTTATTGGCTAATGGACAAG                         GTTGGTGCAAAACGGCTGGAT
genomic: TGTACTTGGTGCAATACATGCCAACAATTGGTTATTGGCTAATGGACAAGgtatttcttc ... atctttccagGTTGGTGCAAAACGGCTGGAT
EST: gi|6101980|gb|AW126450.1|AW126450
EST:     TGTACTTGGTGCAATACATGCCAACAATTGGTTATTGGCTAATGGACAAG                         GTTGGTGCAAAACGGCTGGATGCGGCCGCAAAGAAAGGGAACACGTATAGT
genomic: TGTACTTGGTGCAATACATGCCAACAATTGGTTATTGGCTAATGGACAAGgtatttcttc ... atctttccagGTTGGTGCAAAACGGCTGGATGCGGCCGCAAAGAAAGGGAACACGTATAGT
EST: gi|32940945|gb|CF045764.1|CF045764
EST:     ACTTGGTGCAATACATGCCAACAATTGGTTATTGGCTAATGGACAAG                         GTTGGTGCAAAACGGCTGGATGCGGCCGCAAAGAAAGGGAACACGTATAGT
genomic: ACTTGGTGCAATACATGCCAACAATTGGTTATTGGCTAATGGACAAGgtatttcttc ... atctttccagGTTGGTGCAAAACGGCTGGATGCGGCCGCAAAGAAAGGGAACACGTATAGT
EST: gi|37390564|gb|CF632514.1|CF632514
EST:     TGTACTTGGTGCAATACATGCCAACAATTGGTTATTGGCTAATGGACAAG                         GTTGGTGCAAAACGGCTGGATGCGGCCGC
genomic: TGTACTTGGTGCAATACATGCCAACAATTGGTTATTGGCTAATGGACAAGgtatttcttc ... atctttccagGTTGGTGCAAAACGGCTGGATGCGGCCGC
EST: gi|31362808|gb|CD447165.1|CD447165
EST:     TGTACTTGGTGCAATACATGCCAACAATTGGTTATTGGCTAATGGACAAG                         GTTGGTGCAAAACGGCTGGATGCGGCCGCAAAGAAAGGGAACACGTATAGT
genomic: TGTACTTGGTGCAATACATGCCAACAATTGGTTATTGGCTAATGGACAAGgtatttcttc ... atctttccagGTTGGTGCAAAACGGCTGGATGCGGCCGCAAAGAAAGGGAACACGTATAGT
EST: gi|32864068|gb|CF003750.1|CF003750
EST:     TGTACTTGGTGCAATACATGCCAACAATTGGTTATTGGCTAATGGACAAG                         GTTGGTGCAAAACGGCTGGATGCGGCCGCAAAGAAAGGGAACACGTATAGT
genomic: TGTACTTGGTGCAATACATGCCAACAATTGGTTATTGGCTAATGGACAAGgtatttcttc ... atctttccagGTTGGTGCAAAACGGCTGGATGCGGCCGCAAAGAAAGGGAACACGTATAGT
EST: gi|31363218|gb|CD447575.1|CD447575
EST:     TGTACTTGGTGCAATACATGCCAACAATTGGTTATTGGCTAATGGACAAG                         GTTGGTGCAAAACGGCTGGATGCGGCCGCAAAGAAAGGGAACACGTATAGT
genomic: TGTACTTGGTGCAATACATGCCAACAATTGGTTATTGGCTAATGGACAAGgtatttcttc ... atctttccagGTTGGTGCAAAACGGCTGGATGCGGCCGCAAAGAAAGGGAACACGTATAGT
EST: gi|7227555|gb|AW566196.1|AW566196
EST:     TGTACTTGGTGCAATACATGCCAACAATTGGTTATTGGCTAATGGACAAG                         GTTGGTGCAAAACGGCTGGATGCGGCCGCAAAGAAAGGGAACACGTATAGT
genomic: TGTACTTGGTGCAATACATGCCAACAATTGGTTATTGGCTAATGGACAAGgtatttcttc ... atctttccagGTTGGTGCAAAACGGCTGGATGCGGCCGCAAAGAAAGGGAACACGTATAGT
EST: gi|6022668|gb|AW067596.1|AW067596
EST:     TGTACTTGGTGCAATACATGCCAACAATTGGTTATTGGCTAATGGACAAG                         GTTGGTGCAAAACGGCTGGATGCGGCCGCAAAGAAAGGGAACACGTATAGT
genomic: TGTACTTGGTGCAATACATGCCAACAATTGGTTATTGGCTAATGGACAAGgtatttcttc ... atctttccagGTTGGTGCAAAACGGCTGGATGCGGCCGCAAAGAAAGGGAACACGTATAGT
EST: gi|211078663|gb|FL128724.1|FL128724
EST:     TGTACTTGGTGCAATACATGCCAACAATTGGTTATTGGCTAATGGACAAG                         GTTGGTGCAAAACGGCTGGATGCGGCCGCAAAGAAAGGGAACACGTATAGT
genomic: TGTACTTGGTGCAATACATGCCAACAATTGGTTATTGGCTAATGGACAAGgtatttcttc ... atctttccagGTTGGTGCAAAACGGCTGGATGCGGCCGCAAAGAAAGGGAACACGTATAGT
EST: gi|78021266|gb|DV489653.1|DV489653
EST:     TGTACTTGGTGCAATACATGCCAACAATTGGTTATTGGCTAATGGACAAG                         GTTGGTGCAAAACGGCTGGATGCGGCCGCAAAGAAAGGGAACACGTATAGT
genomic: TGTACTTGGTGCAATACATGCCAACAATTGGTTATTGGCTAATGGACAAGgtatttcttc ... atctttccagGTTGGTGCAAAACGGCTGGATGCGGCCGCAAAGAAAGGGAACACGTATAGT
EST: gi|211495955|gb|FL480154.1|FL480154
EST:     TGTACTTGGTGCAATACATGCCAACAATTGGTTATTGGCTAATGGACAAG                         GTTGGTGCAAAACGGCTGGATGCGGCCGCAAAGAAAGGGAACACGTATAGT
genomic: TGTACTTGGTGCAATACATGCCAACAATTGGTTATTGGCTAATGGACAAGgtatttcttc ... atctttccagGTTGGTGCAAAACGGCTGGATGCGGCCGCAAAGAAAGGGAACACGTATAGT
EST: gi|22935891|gb|BU572166.1|BU572166
EST:     TGTACTTGGTGCAATACATGCCCACAATTGGTTATTGGCTAATGGACAAG                         GTTGGTGCAAAACGGCTGGATGCGGCCGCAAAGAAAGGGAACACGTATAGT
genomic: TGTACTTGGTGCAATACATGCCAACAATTGGTTATTGGCTAATGGACAAGgtatttcttc ... atctttccagGTTGGTGCAAAACGGCTGGATGCGGCCGCAAAGAAAGGGAACACGTATAGT
EST: gi|32856553|gb|CD996234.1|CD996234
EST:     TGTACTTGGTGCAATACATGCCAACAATTGGTTATTGGCTAATGGACAAG                         GTTGGTGCAAAACGGCTGGATGCGGCCGCAAAGAAAGGGAACACGTATAGT
genomic: TGTACTTGGTGCAATACATGCCAACAATTGGTTATTGGCTAATGGACAAGgtatttcttc ... atctttccagGTTGGTGCAAAACGGCTGGATGCGGCCGCAAAGAAAGGGAACACGTATAGT
EST: gi|5915523|gb|AW053164.1|AW053164
EST:     TGTACTTGGTGCAATACATGCCAACAATTGGTTATTGGCTAATGGACAAG                         GTTGGTGCAAAACGGCTGGATGCGGCCGCAAAGAAAGGGAACACGTATAGT
genomic: TGTACTTGGTGCAATACATGCCAACAATTGGTTATTGGCTAATGGACAAGgtatttcttc ... atctttccagGTTGGTGCAAAACGGCTGGATGCGGCCGCAAAGAAAGGGAACACGTATAGT
EST: gi|211078661|gb|FL128722.1|FL128722
EST:     TGTACTTGGTGCAATACATGCCAACAATTGGTTATTGGCTAATGGACAAG                         GTTGGTGCAAAACGGCTGGATGCGGCCGCAAAGAAAGGGAACACGTATAGT
genomic: TGTACTTGGTGCAATACATGCCAACAATTGGTTATTGGCTAATGGACAAGgtatttcttc ... atctttccagGTTGGTGCAAAACGGCTGGATGCGGCCGCAAAGAAAGGGAACACGTATAGT
EST: gi|71767908|gb|DR965845.1|DR965845
EST:     TGTACTTGGTGCAATACATGCCAACAATTGGTTATTGGCTAATGGACAAG                         GTTGGTGCAAAACGGCTGGAT
genomic: TGTACTTGGTGCAATACATGCCAACAATTGGTTATTGGCTAATGGACAAGgtatttcttc ... atctttccagGTTGGTGCAAAACGGCTGGAT
EST: gi|60353742|gb|DN220715.1|DN220715
EST:     TGTACTTGGTGCAATACATGCCAACAATTGGTTATTGGCTAATGGACAAG                         GTTGGTGCAAAACGGCTGGATGCGGCCGCAAAGAAAGGGAACACGTATAGT
genomic: TGTACTTGGTGCAATACATGCCAACAATTGGTTATTGGCTAATGGACAAGgtatttcttc ... atctttccagGTTGGTGCAAAACGGCTGGATGCGGCCGCAAAGAAAGGGAACACGTATAGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaagtttgcgcttaccattgttgctagtactttattgattaacctatctttccagGTTGGTGCAAAACGGCTGGATGCGGCCGCAAAGAAAGGGAACACGTATAGTTGGAGTCTCATTTTCAGCAGCAAGAAGTCAGCATGACCAAATTGCTCGT
                                    gattaac  putative branch site (score: 2)
                                          cctatctttcc  CT-rich tract
                           tactttattgattaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aacccacatcgttccgaaaccaaacacatgcttggagtccaaagaaaagtttgcgcttaccattgttgctagtactttattgattaacctatctttccagGTTGGTGCAAAACGGCTGGATGCGGCCGCAAAGAAAGGGAACACGTATAGTTGGAGTCTCATTTTCAGCAGCAAGAAGTCAGCATGACCAAATTGCTCGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT