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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agggcctatgtttcttttatgttttgatatattatatgttcaatcatgatgtcattcccctaatacagggcccatttctcttttctcctaatttttgcagCCTGACAAGACATCTGGTACAATCAAGGAGCAACTAGCAGCTATATCACCATCTTTAGAGACACTCCGCAGGAAAAAAGAGAGTAGGGTGAAAGAGTTTG

Basic information

species Zea mays
transcript GRMZM2G112337_T04
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G112337_T04 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os06g40840.1 (Oryza sativa), 3'ss of exon 3
---agggcctatgt---ttcttttatgt-tttgatatattatatgttcaatcatgatgt-cattcccctaatacagggcccatttctcttttctcctaatttttgcagCCTGACAAGACATCTGGTACAATCAAGGAGCAACTAGCAGCTATATCACCATCTTTAGAGACACTCCGCAGGAAAAAAGAGAGTAGGGTGAAAGAGTTTG
   ||   ||   |   |  ||| |||  | | ||   |||| |   | |  |  |    ||  ||   ||||    ||   |  ||| || || || | |||||||||||||||||||| | ||||| |||||||||||||||| ||| |||||||| |  || |||| |||| ||||| ||||||| |  ||||| | ||||||||
gtaagtatcttgataaatattttcatgaatataattccttattttccccaaaagtacacacacacctacaatatgctgcatctggctcattactgctgacttttgcagCCTGACAAGACAACCGGTACTATCAAGGAGCAACTAGAAGCAATATCACCTTTCTTGGAGAAACTCTGCAGGGAAAAAGATAAGAGGGTTAGAGAGTTTG
















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|71771990|gb|DR969927.1|DR969927
EST:     AACTGACTAGACTCCTTTCTGCATTAGGAGAGTCATCTATTTCTGGTGCT                         CCTGACAAGACATCTGGTACAATCAAGGAGCAACTAGCAGCTATATCACCA
genomic: AACTGACTAGACTCCTTTCTGCATTAGGAGAGTCATCTATTTCTGGTGCTgtaagtatct ... atttttgcagCCTGACAAGACATCTGGTACAATCAAGGAGCAACTAGCAGCTATATCACCA
EST: gi|148947544|gb|EC893017.2|EC893017
EST:     AACTGACTAGACTCCTTTCTGCATTAGGAGAGTCATCTATTTCTGGTGCT                         CCTGACAAGACATCTGGTACAATCAAGGAGCAACTAGCAGCTATATCACCA
genomic: AACTGACTAGACTCCTTTCTGCATTAGGAGAGTCATCTATTTCTGGTGCTgtaagtatct ... atttttgcagCCTGACAAGACATCTGGTACAATCAAGGAGCAACTAGCAGCTATATCACCA
EST: gi|149100805|gb|EE186899.2|EE186899
EST:     AACTGACTAGACTCCTTTCTGCATTAGGAGAGTCATCTATTTCTGGTGCT                         CCTGACAAGACATCTGGTACAATCAAGGAGCAACTAGCAGCTATATCACCA
genomic: AACTGACTAGACTCCTTTCTGCATTAGGAGAGTCATCTATTTCTGGTGCTgtaagtatct ... atttttgcagCCTGACAAGACATCTGGTACAATCAAGGAGCAACTAGCAGCTATATCACCA
EST: gi|88756751|gb|DY540892.1|DY540892
EST:     AACTGACTAGACTCCTTTCTGCATTAAGAGAGTCATCTATTTCTGGTGCT                         CCTGACAAGACATCTGGTACAATCAAGGAGCAACTAGCAGCTATATCACCA
genomic: AACTGACTAGACTCCTTTCTGCATTAGGAGAGTCATCTATTTCTGGTGCTgtaagtatct ... atttttgcagCCTGACAAGACATCTGGTACAATCAAGGAGCAACTAGCAGCTATATCACCA
EST: gi|149070598|gb|EE159003.2|EE159003
EST:     AACTGACTAGACTCCTTTCTGCATTAGGAGAGTCATCTATTTCTGGTGCT                         CCTGACAAGACATCTGGTACAATCAAGGAGCAACTAGCAGCTATATCACCA
genomic: AACTGACTAGACTCCTTTCTGCATTAGGAGAGTCATCTATTTCTGGTGCTgtaagtatct ... atttttgcagCCTGACAAGACATCTGGTACAATCAAGGAGCAACTAGCAGCTATATCACCA
EST: gi|71773222|gb|DR971131.1|DR971131
EST:     AACTGACTAGACTCCTTTCTGCATTAGGAGAGTCATCTATTTCTGGTGCT                         CCTGACAAGACATCTGGTACAATCAAGGAGCAACTAGCAGCTATATCACCA
genomic: AACTGACTAGACTCCTTTCTGCATTAGGAGAGTCATCTATTTCTGGTGCTgtaagtatct ... atttttgcagCCTGACAAGACATCTGGTACAATCAAGGAGCAACTAGCAGCTATATCACCA
EST: gi|71448830|gb|DR829880.1|DR829880
EST:     AACTGACTAGACTCCTTTCTGCATTAGGAGAGTCATCTATTTCTGGTGCT                         CCTGACAAGACATCTGGTACAATCAAGGAGCAACTAGCAGCTATATCACCA
genomic: AACTGACTAGACTCCTTTCTGCATTAGGAGAGTCATCTATTTCTGGTGCTgtaagtatct ... atttttgcagCCTGACAAGACATCTGGTACAATCAAGGAGCAACTAGCAGCTATATCACCA
EST: gi|76014764|gb|DT941934.1|DT941934
EST:     AACTGACTAGACTCCTTTCTGCATTAGGAGAGTCATCTATTTCTGGTGCT                         CCTGACAAGACATCTGGTACAATCAAGGAGCAACTAGCAGCTATATCACCA
genomic: AACTGACTAGACTCCTTTCTGCATTAGGAGAGTCATCTATTTCTGGTGCTgtaagtatct ... atttttgcagCCTGACAAGACATCTGGTACAATCAAGGAGCAACTAGCAGCTATATCACCA
EST: gi|149098530|gb|EE184516.2|EE184516
EST:     AACTGACTAGACTCCTTTCTGCATTAGGAGAGTCATCTATTTCTGGTGCT                         CCTGACAAGACATCTGGTACAATCAAGGAGCAACTAGCAGCTATATCACCA
genomic: AACTGACTAGACTCCTTTCTGCATTAGGAGAGTCATCTATTTCTGGTGCTgtaagtatct ... atttttgcagCCTGACAAGACATCTGGTACAATCAAGGAGCAACTAGCAGCTATATCACCA
EST: gi|89761743|gb|DY689636.1|DY689636
EST:     AACTGACTAGACTCCTTTCTGCATTAGGAGAGTCATCTATTTCTGGTGCT                         CCTGACAAGACATCTGGTACAATCAAGGAGCAACTAGCAGCTATATCACCA
genomic: AACTGACTAGACTCCTTTCTGCATTAGGAGAGTCATCTATTTCTGGTGCTgtaagtatct ... atttttgcagCCTGACAAGACATCTGGTACAATCAAGGAGCAACTAGCAGCTATATCACCA
EST: gi|89763679|gb|DY690773.1|DY690773
EST:     AACTGACTAGACTCCTTTCTGCATTAGGAGAGTCATCTATTTCTGGTGCT                         CCTGACAAGACATCTGGTACAATCAAGGAGCAACTAGCAGCTATATCACCA
genomic: AACTGACTAGACTCCTTTCTGCATTAGGAGAGTCATCTATTTCTGGTGCTgtaagtatct ... atttttgcagCCTGACAAGACATCTGGTACAATCAAGGAGCAACTAGCAGCTATATCACCA
EST: gi|76289491|gb|DV029059.1|DV029059
EST:     AACTGACTAGACTCCTTTCTGCATTAGGAGAGTCATCTATTTCTGGTGCT                         CCTGACAAGACATCTGGTACAATCAAGGAGCAACTAGCAGCTATATCACCA
genomic: AACTGACTAGACTCCTTTCTGCATTAGGAGAGTCATCTATTTCTGGTGCTgtaagtatct ... atttttgcagCCTGACAAGACATCTGGTACAATCAAGGAGCAACTAGCAGCTATATCACCA
EST: gi|148930867|gb|EC873288.2|EC873288
EST:     AACTGACTAGACTCCTTTCTGCATTAGGAGAGTCATCTATTTCTGGTGCT                         CCTGACAAGACATCTGGTACAATCAAGGAGCAACTAGCAGCTATATCACCA
genomic: AACTGACTAGACTCCTTTCTGCATTAGGAGAGTCATCTATTTCTGGTGCTgtaagtatct ... atttttgcagCCTGACAAGACATCTGGTACAATCAAGGAGCAACTAGCAGCTATATCACCA
EST: gi|149078382|gb|EE167157.2|EE167157
EST:     AACTGACTAGACTCCTTTCTGCATTAGGAGAGTCATCTATTTCTGGTGCT                         CCTGACAAGACATCTGGTACAATCAAGGAGCAACTAGCAGCTATATCACCA
genomic: AACTGACTAGACTCCTTTCTGCATTAGGAGAGTCATCTATTTCTGGTGCTgtaagtatct ... atttttgcagCCTGACAAGACATCTGGTACAATCAAGGAGCAACTAGCAGCTATATCACCA
EST: gi|148985938|gb|EE029851.2|EE029851
EST:     AACTGACTAAACTCCTTTCTGCATTAGGAGAGTCATCTATTTCTGGGGCT                         CCTGAAAAGAACATCTGGTACAAT
genomic: AACTGACTAGACTCCTTTCTGCATTAGGAGAGTCATCTATTTCTGGTGCTgtaagtatct ... atttttgcagCCTGACAAGA-CATCTGGTACAAT
EST: gi|148975390|gb|EE025689.2|EE025689
EST:     AACTGACTAGACTCCTTTCTGCATTAGGAGAGTCATCTATTTCTGGTGCT                         CCTGACAAGACATCTGGTACAATCAAGGAGCAACTAGCAGCTATATCACCA
genomic: AACTGACTAGACTCCTTTCTGCATTAGGAGAGTCATCTATTTCTGGTGCTgtaagtatct ... atttttgcagCCTGACAAGACATCTGGTACAATCAAGGAGCAACTAGCAGCTATATCACCA
EST: gi|148959723|gb|EC905625.2|EC905625
EST:     AACTGACTAGACTCCTTTCTGCATTAGGAGAGTCATCTATTTCTGGTGCT                         CCTGACAAGACATCTGGTACAATCAAGGAGCAACTAGCAGCTATATCACCA
genomic: AACTGACTAGACTCCTTTCTGCATTAGGAGAGTCATCTATTTCTGGTGCTgtaagtatct ... atttttgcagCCTGACAAGACATCTGGTACAATCAAGGAGCAACTAGCAGCTATATCACCA
EST: gi|148999825|gb|EE036849.2|EE036849
EST:     AACTGACTAGACTCCTTTCTGCATTAGGAGAGTCATCTATTTCTGGTGCT                         CCTGACAAGACATCTGGTACAATCAAGGAGCAACTAGCAGCTATATCACCA
genomic: AACTGACTAGACTCCTTTCTGCATTAGGAGAGTCATCTATTTCTGGTGCTgtaagtatct ... atttttgcagCCTGACAAGACATCTGGTACAATCAAGGAGCAACTAGCAGCTATATCACCA
EST: gi|149096273|gb|EE181983.2|EE181983
EST:     AACTGACTAGACTCCTTTCTGCATTAGGAGAGTCATCTATTTCTGGTGCT                         CCTGACAAGACATCTGGTACAATCAAGGAGCAACTAGCAGCTATATCACCA
genomic: AACTGACTAGACTCCTTTCTGCATTAGGAGAGTCATCTATTTCTGGTGCTgtaagtatct ... atttttgcagCCTGACAAGACATCTGGTACAATCAAGGAGCAACTAGCAGCTATATCACCA
EST: gi|148964767|gb|EC906024.2|EC906024
EST:     AACTGACTAGACTCCTTTCTGCATTAGGAGAGTCATCTATTTCTGGTGCT                         CCTGACAAGACATCTGGTACAATCAAGGAGCAACTAGCAGCTATATCACCA
genomic: AACTGACTAGACTCCTTTCTGCATTAGGAGAGTCATCTATTTCTGGTGCTgtaagtatct ... atttttgcagCCTGACAAGACATCTGGTACAATCAAGGAGCAACTAGCAGCTATATCACCA
EST: gi|149081898|gb|EE171059.2|EE171059
EST:     AACTGACTAGACTCCTTTCTGCATTAGGAGAGTCATCTATTTCTGGTGCT                         CCTGACAAGACATCTGGGACAATCAAGGAGCAACTAGCAACTATATCACCA
genomic: AACTGACTAGACTCCTTTCTGCATTAGGAGAGTCATCTATTTCTGGTGCTgtaagtatct ... atttttgcagCCTGACAAGACATCTGGTACAATCAAGGAGCAACTAGCAGCTATATCACCA
EST: gi|148995698|gb|EE034921.2|EE034921
EST:     AACTGACTAGACTCCTTTCTGCATTAGGAGAGTCATCTATTTCTGGTGCT                         CCTGACAAGACATCTGGTACAATCAAGGAGCAACTAGCAGCTATATCACCA
genomic: AACTGACTAGACTCCTTTCTGCATTAGGAGAGTCATCTATTTCTGGTGCTgtaagtatct ... atttttgcagCCTGACAAGACATCTGGTACAATCAAGGAGCAACTAGCAGCTATATCACCA
EST: gi|149015047|gb|EE044793.2|EE044793
EST:     AACTGACTAGACTCCTTTCTGCATTAGGAGAGTCATCTATTTCTGGTGCT                         CCTGACAAGACATCTGGTACAATCAAGGAGCAACTAGCAGCTATATCACCA
genomic: AACTGACTAGACTCCTTTCTGCATTAGGAGAGTCATCTATTTCTGGTGCTgtaagtatct ... atttttgcagCCTGACAAGACATCTGGTACAATCAAGGAGCAACTAGCAGCTATATCACCA
EST: gi|71324224|gb|DR798815.1|DR798815
EST:     AACTGACTAGACTCCTTTCTGCATTAGGAGAGTCATCTATTTCTGGTGCT                         CCTGACAAGACATCTGGTACAATCAAGGAGCAACTAGCAGCTATATCACCA
genomic: AACTGACTAGACTCCTTTCTGCATTAGGAGAGTCATCTATTTCTGGTGCTgtaagtatct ... atttttgcagCCTGACAAGACATCTGGTACAATCAAGGAGCAACTAGCAGCTATATCACCA
EST: gi|71306091|gb|DR789195.1|DR789195
EST:     AACTGACTAGACTCCTTTCTGCATTAGGAGAGTCATCTATTTCTGGTGCT                         CCTGACAAGACATCTGGTACAATCAAGGAGCAACTAGCAGCTATATCACCA
genomic: AACTGACTAGACTCCTTTCTGCATTAGGAGAGTCATCTATTTCTGGTGCTgtaagtatct ... atttttgcagCCTGACAAGACATCTGGTACAATCAAGGAGCAACTAGCAGCTATATCACCA
EST: gi|71438424|gb|DR819474.1|DR819474
EST:     AACTGACTAGACTCCTTTCTGCATTAGGAGAGTCATCTATTTCTGGTGCT                         CCTGACAAGACATCTGGTACAATCAAGGAGCAACTAGCAGCTATATCACCA
genomic: AACTGACTAGACTCCTTTCTGCATTAGGAGAGTCATCTATTTCTGGTGCTgtaagtatct ... atttttgcagCCTGACAAGACATCTGGTACAATCAAGGAGCAACTAGCAGCTATATCACCA
EST: gi|149088741|gb|EE177865.2|EE177865
EST:     AACTGACTAGACTCCTTTCTGCATTAGGAGAGTCATCTATTTCTGGTGCT                         CCTGACAAGACATCTGGTACAATCAAGGAGCAACTAGCAGCTATATCACCA
genomic: AACTGACTAGACTCCTTTCTGCATTAGGAGAGTCATCTATTTCTGGTGCTgtaagtatct ... atttttgcagCCTGACAAGACATCTGGTACAATCAAGGAGCAACTAGCAGCTATATCACCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgatgtcattcccctaatacagggcccatttctcttttctcctaatttttgcagCCTGACAAGACATCTGGTACAATCAAGGAGCAACTAGCAGCTATATCACCATCTTTAGAGACACTCCGCAGGAAAAAAGAGAGTAGGGTGAAAGAGTTTG
                                        tcctaat  putative branch site (score: 2)
                         cccatttctcttttct  CT-rich tract
                                           taattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agggcctatgtttcttttatgttttgatatattatatgttcaatcatgatgtcattcccctaatacagggcccatttctcttttctcctaatttttgcagCCTGACAAGACATCTGGTACAATCAAGGAGCAACTAGCAGCTATATCACCATCTTTAGAGACACTCCGCAGGAAAAAAGAGAGTAGGGTGAAAGAGTTTG

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