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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaggctttgaatattctacttactacgtccccgaaaaacaaatctacttacatatcccatctatggtttacttcttctggctctgttttgcatcagatggtgtcactattaacgttacatgcatgcctatgattcactcttatctgcaatataagctcttgtttaatcaatgatgatgtattcgtgaattcagGAACATTTCAAGAAAAACAAGATGACCATTAATCTGAAGTACATAG

Basic information

species Zea mays
transcript GRMZM2G443985_T01
intron # 11
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|32938375|gb|CF043194.1|CF043194
EST:     GCAACGAGCTGCTTCTTGATGTTGGCCTTTGGTTATCTCAGAAGATAAAT                         GAACATTTCAAGAAAAACAAGATGACCATTAATCTGAAGT
genomic: GCAACGAGCTGCTTCTTGATGTTGGCCTTTGGTTATCTCAGAAGATAAATgtgaggcttt ... gtgaattcagGAACATTTCAAGAAAAACAAGATGACCATTAATCTGAAGT
EST: gi|5846823|gb|AI999906.1|AI999906
EST:     GCAACGAGCTGCTTCTTGATGTTGGCCTTTGGTTATCTCAGAAGATAAAT                         GAACATTTCAAGAAAAACAAGATGACCATTAATCTGAAGTACATAG
genomic: GCAACGAGCTGCTTCTTGATGTTGGCCTTTGGTTATCTCAGAAGATAAATgtgaggcttt ... gtgaattcagGAACATTTCAAGAAAAACAAGATGACCATTAATCTGAAGTACATAG
EST: gi|6095550|gb|AW120217.1|AW120217
EST:     GCAACGAGCTGCTTCTTGATGTTGGCCTTTGGTTATCTCAGAAGATAAAT                         GAACATTTCAAGAAAAACAAGATGACCATTAATCTGAAGTACATAG
genomic: GCAACGAGCTGCTTCTTGATGTTGGCCTTTGGTTATCTCAGAAGATAAATgtgaggcttt ... gtgaattcagGAACATTTCAAGAAAAACAAGATGACCATTAATCTGAAGTACATAG
EST: gi|32938968|gb|CF043787.1|CF043787
EST:     GCAACGAGCTGCTTCTTGATGTTGGCCTTTGGTTATCTCAGAAGATAAAT                         GAACATTTCAAGAAAAACAAGATGACCATTAATCTGAAGT
genomic: GCAACGAGCTGCTTCTTGATGTTGGCCTTTGGTTATCTCAGAAGATAAATgtgaggcttt ... gtgaattcagGAACATTTCAAGAAAAACAAGATGACCATTAATCTGAAGT
EST: gi|32857486|gb|CD997167.1|CD997167
EST:     GCAACGAGCTGCTTCTTGATGTTGGCCTTTGGTTATCTCAGAAGATAAAT                         GAACATTTCAAGAAAAACAAGATGACCATTAATCTGAAGTACATAG
genomic: GCAACGAGCTGCTTCTTGATGTTGGCCTTTGGTTATCTCAGAAGATAAATgtgaggcttt ... gtgaattcagGAACATTTCAAGAAAAACAAGATGACCATTAATCTGAAGTACATAG
EST: gi|91872759|gb|EB402716.1|EB402716
EST:     GCAACGAGCTGCTTCTTGATGTTGGCCTTTGGTTATCTCAGAAGATAAAT                         GAACATTTCAAGAAAAACAAGATGACCATTAATCTGAAGTACATAG
genomic: GCAACGAGCTGCTTCTTGATGTTGGCCTTTGGTTATCTCAGAAGATAAATgtgaggcttt ... gtgaattcagGAACATTTCAAGAAAAACAAGATGACCATTAATCTGAAGTACATAG
EST: gi|32939806|gb|CF044625.1|CF044625
EST:     GCAACGAGCTGCTTCTTGATGTTGGCCTTTGGTTATCTCAGAAGATAAAT                         GAACATTTCAAGAAAAACAAGATGACCATTAATCTGAAGTAC
genomic: GCAACGAGCTGCTTCTTGATGTTGGCCTTTGGTTATCTCAGAAGATAAATgtgaggcttt ... gtgaattcagGAACATTTCAAGAAAAACAAGATGACCATTAATCTGAAGTAC
EST: gi|148972519|gb|EE023480.2|EE023480
EST:     GCAACGAGCTGCTTCTTGATGTTGGCCTTTGGTTATCTCAGAAGATAAAT                         GAACATTTCAAGAAAAACAAGATGACCATTAATCTGAAGTACATAG
genomic: GCAACGAGCTGCTTCTTGATGTTGGCCTTTGGTTATCTCAGAAGATAAATgtgaggcttt ... gtgaattcagGAACATTTCAAGAAAAACAAGATGACCATTAATCTGAAGTACATAG
EST: gi|33285656|gb|CF075451.1|CF075451
EST:     GCAACGAGCTGCTTCTTGATGTTGGCCTTTGGTTATCTCAGAAGATAAAT                         GAACATTTCAAGAAAAACAAGATGACCATTAATCTGAAGTACATAG
genomic: GCAACGAGCTGCTTCTTGATGTTGGCCTTTGGTTATCTCAGAAGATAAATgtgaggcttt ... gtgaattcagGAACATTTCAAGAAAAACAAGATGACCATTAATCTGAAGTACATAG
EST: gi|32939493|gb|CF044312.1|CF044312
EST:     GCAACGAGCTGCTTCTTGATGTTGGCCTTTGGTTATCTCAGAAGATAAAT                         GAACATTTCAAGAAAAACAAGATGACCATTAATCTGAAGTAC
genomic: GCAACGAGCTGCTTCTTGATGTTGGCCTTTGGTTATCTCAGAAGATAAATgtgaggcttt ... gtgaattcagGAACATTTCAAGAAAAACAAGATGACCATTAATCTGAAGTAC
EST: gi|5895959|gb|AW037205.1|AW037205
EST:     GCAACGAGCTGCTTCTTGATGTTGGCCTTTGGTTATCTCAGAAGATAAAT                         GAACATTTCAAGAAAAACAAGATGACCATTAATCTGAAGTACATAG
genomic: GCAACGAGCTGCTTCTTGATGTTGGCCTTTGGTTATCTCAGAAGATAAATgtgaggcttt ... gtgaattcagGAACATTTCAAGAAAAACAAGATGACCATTAATCTGAAGTACATAG
EST: gi|148982504|gb|EE028349.2|EE028349
EST:     GCAACGAGCTGCTTCTTGATGTTGGCCTTTGGTTATCTCAGAAGATAAAT                         GAACATTTCAAGAAAAACAAGATGACCATTAATCTGAAGTACATAG
genomic: GCAACGAGCTGCTTCTTGATGTTGGCCTTTGGTTATCTCAGAAGATAAATgtgaggcttt ... gtgaattcagGAACATTTCAAGAAAAACAAGATGACCATTAATCTGAAGTACATAG
EST: gi|76016085|gb|DT943255.1|DT943255
EST:     GCAACGAGCTGCTTCTTGATGTTGGCCTTTGGTTATCTCAGAAGATAAAT                         GAACATTTCAAGAAAAACAAGATGACCATTAATGTGAAGTACATAG
genomic: GCAACGAGCTGCTTCTTGATGTTGGCCTTTGGTTATCTCAGAAGATAAATgtgaggcttt ... gtgaattcagGAACATTTCAAGAAAAACAAGATGACCATTAATCTGAAGTACATAG
EST: gi|6020683|gb|AW065491.1|AW065491
EST:     GCAACGAGCTGCTTCTTGATGTTGGCCTTTGGTTATCTCAGAAGATAAAT                         GAACATTTCAAGAAAAACAAGATGACCATTAATCTGAAGTACATAG
genomic: GCAACGAGCTGCTTCTTGATGTTGGCCTTTGGTTATCTCAGAAGATAAATgtgaggcttt ... gtgaattcagGAACATTTCAAGAAAAACAAGATGACCATTAATCTGAAGTACATAG
EST: gi|76921243|gb|DV168509.1|DV168509
EST:     GCAACGAGCTGCTTCTTGATGTTGGCCTTTGGTTATCTCAGAAGATAAAT                         GAACATTTCAAGAAAAACAAGATGACCATTAATCTGAAGTACATAG
genomic: GCAACGAGCTGCTTCTTGATGTTGGCCTTTGGTTATCTCAGAAGATAAATgtgaggcttt ... gtgaattcagGAACATTTCAAGAAAAACAAGATGACCATTAATCTGAAGTACATAG
EST: gi|78022684|gb|DV491071.1|DV491071
EST:     CAGAAGATAAAT                         GAACATTTCAAGAAAAACAAGATGACCATTAATCTGAAGTACATAG
genomic: CAGAAGATAAATgtgaggcttt ... gtgaattcagGAACATTTCAAGAAAAACAAGATGACCATTAATCTGAAGTACATAG
EST: gi|5325011|gb|AI783202.1|AI783202
EST:     GCAACGAGCTGCTTCTTGATGTTGGCCTTTGGTTATCTCAGAAGATAAAT                         GAACATTTCAAGAAAAACAAGATGACCATTAATCTGAAGTACATAG
genomic: GCAACGAGCTGCTTCTTGATGTTGGCCTTTGGTTATCTCAGAAGATAAATgtgaggcttt ... gtgaattcagGAACATTTCAAGAAAAACAAGATGACCATTAATCTGAAGTACATAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttatctgcaatataagctcttgtttaatcaatgatgatgtattcgtgaattcagGAACATTTCAAGAAAAACAAGATGACCATTAATCTGAAGTACATAG
                      gtttaat  putative branch site (score: 4)
                       tttaatcaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgaggctttgaatattctacttactacgtccccgaaaaacaaatctacttacatatcccatctatggtttacttcttctggctctgttttgcatcagatggtgtcactattaacgttacatgcatgcctatgattcactcttatctgcaatataagctcttgtttaatcaatgatgatgtattcgtgaattcagGAACATTTCAAGAAAAACAAGATGACCATTAATCTGAAGTACATAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG