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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctgaaagtatagtatattttgtcttgaacaattaaattgggttttcttgcaaaggatgctacattttagcttacatttgctcttctttttgccaattcagGTTTTGCTTTATGCTGGTTCATTTGTCTACGGACAATGGACTAGTTGCTGCACTGTTTCTGTGATTCACCATGGGAAGCAGTGGAGCAGATACACCGTCT

Basic information

species Zea mays
transcript GRMZM2G088140_T02
intron # 1
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|71442579|gb|DR823629.1|DR823629
EST:     ACTAGACATCGTACCACCCAG                         GTTTTGCTTTATGCTGGTTCATTTGTCTACGGACAATGGACTAGTTGCTGC
genomic: ACTAGACATCGTACCACCCAGgtgatctcgc ... gccaattcagGTTTTGCTTTATGCTGGTTCATTTGTCTACGGACAATGGACTAGTTGCTGC
EST: gi|211355419|gb|FL036287.1|FL036287
EST:     CGCCCCGCCACCCGTCCTGCACACTCACAACTAGACATCGTACCACCCAG                         GTTTTGCTTTATGCTGGTTCATTTGTCTACGGACAATGGACTAGTTGCTGC
genomic: CGCCCCGCCACCCGTCCTGCACACTCACAACTAGACATCGTACCACCCAGgtgatctcgc ... gccaattcagGTTTTGCTTTATGCTGGTTCATTTGTCTACGGACAATGGACTAGTTGCTGC
EST: gi|211353027|gb|FL036283.1|FL036283
EST:     CGCCCCGCCACCCGTCCTGCACACTCACAACTAGACATCGTACCACCCAG                         GTTTTGCTTTATGCTGGTTCATTTGTCTACGGACAATGGACTAGTTGCTGC
genomic: CGCCCCGCCACCCGTCCTGCACACTCACAACTAGACATCGTACCACCCAGgtgatctcgc ... gccaattcagGTTTTGCTTTATGCTGGTTCATTTGTCTACGGACAATGGACTAGTTGCTGC
EST: gi|211353024|gb|FL036280.1|FL036280
EST:     CGCCCCGCCACCCGTCCTGCACACTCACAACTAGACATCGTACCACCCAG                         GTTTTGCTTTATGCTGGTTCATTTGTCTACGGACAATGGACTAGTTGCTGC
genomic: CGCCCCGCCACCCGTCCTGCACACTCACAACTAGACATCGTACCACCCAGgtgatctcgc ... gccaattcagGTTTTGCTTTATGCTGGTTCATTTGTCTACGGACAATGGACTAGTTGCTGC
EST: gi|211353025|gb|FL036281.1|FL036281
EST:     CGCCCCGCCACCCGTCCTGCACACTCACAACTAGACATCGTACCACCCAG                         GTTTTGCTTTATGCTGGTTCATTTGTCTACGGACAATGGACTAGTTGCTGC
genomic: CGCCCCGCCACCCGTCCTGCACACTCACAACTAGACATCGTACCACCCAGgtgatctcgc ... gccaattcagGTTTTGCTTTATGCTGGTTCATTTGTCTACGGACAATGGACTAGTTGCTGC
EST: gi|91056940|gb|EB167358.1|EB167358
EST:     CGCCCCGCCACCCGTCCTGCACACTCACAACTAGACATCGTACCACCCAG                         GTTTTGCTTTATGCTGGTTCATTTGTCTACGGACAATGGACTAGTTGCTGC
genomic: CGCCCCGCCACCCGTCCTGCACACTCACAACTAGACATCGTACCACCCAGgtgatctcgc ... gccaattcagGTTTTGCTTTATGCTGGTTCATTTGTCTACGGACAATGGACTAGTTGCTGC
EST: gi|91873165|gb|EB403122.1|EB403122
EST:     CGCCCCGCCACCCGTCCTGCACACTCACAACTAGACATCGTACCACCCAG                         GTTTTGCTTTATGCTGGTTCATTTGTCTACGGACAATGGACTAGTTGCTGC
genomic: CGCCCCGCCACCCGTCCTGCACACTCACAACTAGACATCGTACCACCCAGgtgatctcgc ... gccaattcagGTTTTGCTTTATGCTGGTTCATTTGTCTACGGACAATGGACTAGTTGCTGC
EST: gi|211353026|gb|FL036282.1|FL036282
EST:     CGCCCCGCCACCCGTCCTGCACACTCACAACTAGACATCGTACCACCCAG                         GTTTTGCTTTATGCTGGTTCATTTGTCTACGGACAATGGACTAGTTGCTGC
genomic: CGCCCCGCCACCCGTCCTGCACACTCACAACTAGACATCGTACCACCCAGgtgatctcgc ... gccaattcagGTTTTGCTTTATGCTGGTTCATTTGTCTACGGACAATGGACTAGTTGCTGC
EST: gi|211355416|gb|FL036284.1|FL036284
EST:     CGCCCCGCCACCCGTCATGCACACTCACAACTAGACATCGTACCACCCAG                         GTTTTGCTTTATGCTGGTTCATTTGTCTACGGACAATGGACTAGTTGCTGC
genomic: CGCCCCGCCACCCGTCCTGCACACTCACAACTAGACATCGTACCACCCAGgtgatctcgc ... gccaattcagGTTTTGCTTTATGCTGGTTCATTTGTCTACGGACAATGGACTAGTTGCTGC
EST: gi|211355418|gb|FL036286.1|FL036286
EST:     ACCCGTCCTGCACACTCACAACTAGACATCGTACCACCCAG                         GTTTTGCTTTATGCTGGTTCATTTGTCTACGGACAATGGACTAGTTGCTGC
genomic: ACCCGTCCTGCACACTCACAACTAGACATCGTACCACCCAGgtgatctcgc ... gccaattcagGTTTTGCTTTATGCTGGTTCATTTGTCTACGGACAATGGACTAGTTGCTGC
EST: gi|211353023|gb|FL036279.1|FL036279
EST:     CGCCCCGCCACCCGTCCTGCACACTCACAACTAGACATCGTACCACCCAG                         GTTTTGCTTTATGCTGGTTCATTTGTCTACGGACAATGGACTAGTTGCTGC
genomic: CGCCCCGCCACCCGTCCTGCACACTCACAACTAGACATCGTACCACCCAGgtgatctcgc ... gccaattcagGTTTTGCTTTATGCTGGTTCATTTGTCTACGGACAATGGACTAGTTGCTGC
EST: gi|211355417|gb|FL036285.1|FL036285
EST:     CGCCCCGCCACCCGTCCTGCACACTCACAACTAGACATCGTACCACCCAG                         GTTTTGCTTTATGCTGGTTCATTTGTCTACGGACAATGGACTAGTTGCTGC
genomic: CGCCCCGCCACCCGTCCTGCACACTCACAACTAGACATCGTACCACCCAGgtgatctcgc ... gccaattcagGTTTTGCTTTATGCTGGTTCATTTGTCTACGGACAATGGACTAGTTGCTGC
EST: gi|71772545|gb|DR970476.1|DR970476
EST:     CGCCCCGCCACCCGTCCTGCACACTCACAACTAGACATCGTACCACCCAG                         GTTTTGCTTTATGCTGGTTCATTTGTCTACGGACAATGGACTAGTTGCTGC
genomic: CGCCCCGCCACCCGTCCTGCACACTCACAACTAGACATCGTACCACCCAGgtgatctcgc ... gccaattcagGTTTTGCTTTATGCTGGTTCATTTGTCTACGGACAATGGACTAGTTGCTGC
EST: gi|211353577|gb|FL066645.1|FL066645
EST:     ACCCGTCCTGCACACTCACAACTAGGACATCGTACCACCCAG                         GTTTTGCTTTATGCTGGTTCATTTGTCTACGGACAATGGACTAGTTGCTGC
genomic: ACCCGTCCTGCACACTCACAACTA-GACATCGTACCACCCAGgtgatctcgc ... gccaattcagGTTTTGCTTTATGCTGGTTCATTTGTCTACGGACAATGGACTAGTTGCTGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttgcaaaggatgctacattttagcttacatttgctcttctttttgccaattcagGTTTTGCTTTATGCTGGTTCATTTGTCTACGGACAATGGACTAGTTGCTGCACTGTTTCTGTGATTCACCATGGGAAGCAGTGGAGCAGATACACCGTCT
                      agcttac  putative branch site (score: 3)
                              tttgctcttctttttg  CT-rich tract
              tacatttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctgaaagtatagtatattttgtcttgaacaattaaattgggttttcttgcaaaggatgctacattttagcttacatttgctcttctttttgccaattcagGTTTTGCTTTATGCTGGTTCATTTGTCTACGGACAATGGACTAGTTGCTGCACTGTTTCTGTGATTCACCATGGGAAGCAGTGGAGCAGATACACCGTCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT