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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctgtttgaatatccacaactgcttgcacccatgaatctcgagtacatggataccatttcactccattatcgtaactgctcttcctacttgatttcttcagAACTCCATAAGAAGGAAACTTGTGAGGCTGTTACCATCATTGAAACCCCTCCTCTTGTCATTGTTGGGCTCGTGGCATATGTGAAGACTCCTCGTGGCCT

Basic information

species Zea mays
transcript GRMZM2G135727_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G135727_T03 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os11g06750.1 (Oryza sativa), 3'ss of exon 3
ctgtttgaatatccacaactgcttgcac-ccatgaatctcgagtacat--ggatac-catttcactccattatcgtaac-tgctcttcctacttgatttcttcagAACTCCATAAGAAGGAAACTTGTGAGGCTGTTACCATCATTGAAACCCCTCCTCTTGTCATTGTTGGGCTCGTGGCATATGTGAAGACTCCTCGTGGCCT
     ||    |   | |   |||  |  | | || | | |  | |||  | |||  |||   |||  |      |||| |  || |  | ||     | |||||||||||| |||||||| || ||||||||||||||||| ||||| || |||||| ||||| ||||||| || ||||| |||||||||||||| |||||| |
-----tggcctttagccaagactttaatactaagactttagtattcatctgaatatgcatactactgaagagatttaaccttgtcatttttctaatgcttttcagAACTCCACAAGAAGGAGACCTGTGAGGCTGTTACCATTATTGAGACACCTCCTATTGTCGTTGTTGGACTTGTGGCCTATGTGAAGACTCCACGTGGCTT

upper sequence: GRMZM2G135727_T03 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA20G30810.1 (Glycine max), 3'ss of exon 3
---------ctgtttgaatatccacaactgcttgcacccatgaatctcgagtacatggataccatttcactccattatcgtaactgctcttcctacttgatttcttcagAACTCCATAAGAAGGAAACTTGTGAGGCTGTTACCATCATTGAAACCCCTCCTCTTGTCATTGTTGGGCTCGTGGCATATGTGAAGACTCCTCGTGGCCT
          ||| |     ||   ||||| || ||   |    ||||   |   |  |||| ||    ||  ||     |||||        |  |  ||    ||||| || || ||||||||||| |||||| ||||||| || ||||| ||||||||  | || ||||||||  | ||||  |||||||| ||||| ||||| ||
aagctaatgatgtattgcattctttaactgtttacatgtaacgttctcttat---tatatactatc---ctttatctatctaactatataatattttctata---tcagAGCTTCACAAGAAGGAAACATGTGAGCCTGTTACAATTATTGAGACCCCTCCAATGGTTATTGTTGGTGTTGTGGGTTATGTGAAAACTCCCCGTGGTCT

upper sequence: GRMZM2G135727_T03 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA10G36780.1 (Glycine max), 3'ss of exon 3
---------ctgtttgaatatccacaactgcttgcacccatgaatctcgagtacatggataccatttcactccattatcgtaactgctcttcctacttgatttcttcagAACTCCATAAGAAGGAAACTTGTGAGGCTGTTACCATCATTGAAACCCCTCCTCTTGTCATTGTTGGGCTCGTGGCATATGTGAAGACTCCTCGTGGCCT
           || |  |  ||   ||||  |   ||     | | ||   ||| ||  ||     ||| |  |||||| |||||    ||| |  ||       ||||| || || |||||||||||||||||| ||||||| || ||||| ||||||||  | || ||||||||  | ||||  |||||||| ||||| ||||| ||
tgaagctaatagtattgaattctttaactatt---acatgaaactttctcttacttgt-tatagcatcatttaattatc-taactatatttctttttta----tatcagAGCTTCACAAGAAGGAAACTTGTGAGCCTGTTACAATTATTGAGACCCCTCCAATGGTTATTGTTGGTGTTGTGGGTTATGTGAAAACTCCACGTGGTCT

upper sequence: GRMZM2G135727_T03 (Zea mays), 3'ss of exon 3
lower sequence: AT1G43170.7 (Arabidopsis thaliana), 3'ss of exon 3
ctgtttgaatatccacaactgcttgcacccatgaatctcgagtacatggataccatttcactccattatcgt-aactgctcttcctacttgatttcttcagAACTCCATAAGAAGGAAACTTGTGAGGCTGTTACCATCATTGAAACCCCTCCTCTTGTCATTGTTGGGCTCGTGGCATATGTGAAGACTCCTCGTGGCCT
      | |  |  ||   || ||     |||     |    |   ||||     || |  |  |   |||| ||||     |  |  |||  || |  ||| || || |||||||| || ||||||||||||||||||||||| || ||| || | ||  |||||||  | || || ||||||||||||||| | ||  |
------gtaagtgaacttgtgttt-ttttcattctgatttgttttgtggaggtttttgcgatttaaagtcgtcaactttgtgtttttattg--ttgtgtagAGCTTCACAAGAAGGAGACATGTGAGGCTGTTACCATCATTGAGACACCTGCTATGGTGGTTGTTGGAGTTGTTGCCTATGTGAAGACTCCTAGAGGTTT

upper sequence: GRMZM2G135727_T03 (Zea mays), 3'ss of exon 3
lower sequence: AT1G43170.4 (Arabidopsis thaliana), 3'ss of exon 1
ctgtttgaatatccacaactgcttgcacccatgaatctcgagtacatggataccatttcactccattatcgtaactgctcttcctacttgatttcttcagAACTCCATAAGAAGGAAACTTGTGAGGCTGTTACCATCATTGAAACCCCTCCTCTTGTCATTGTTGGGCTCGTGGCATATGTGAAGACTCCTCGTGGCCT-----------
     ||||  |       |  |    |  ||   | | | | |  |   | | |||| |   | | | | |   || | ||  |       || |  ||| || || |||||||| || ||||||||||||||||||||||| || ||| || | ||  |||||||  | || || ||||||||||||||| | ||  |           
---agtgaacttgtgtt-tttttcattctgatttgttttgtggaggtttttgcgatttaaagtcgtcaactttg-tgtttttattg------ttgtgtagagcttcacaagAAGGAGACATGTGAGGCTGTTACCATCATTGAGACACCTGCTATGGTGGTTGTTGGAGTTGTTGCCTATGTGAAGACTCCTAGAGGTTTGAGGTCTTTGA

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|211090378|gb|FL409094.1|FL409094
EST:     CAA-GCTGGCATGACTCACATTGTCCGTGAGGTTGAGAAGCCAGGATCCA                         AACTCCATAAGAAGGAAACTTGTGAGGCTGTTACCATCATTGAAACCCCTC
genomic: CAAGGCTGGCATGACTCACATTGTCCGTGAGGTTGAGAAGCCAGGATCCAgtatgtccac ... atttcttcagAACTCCATAAGAAGGAAACTTGTGAGGCTGTTACCATCATTGAAACCCCTC
EST: gi|211310954|gb|FL375976.1|FL375976
EST:     CAA-GCTGGCATGACTCACATTGTCCGTGA-GTTGAGAAGCCAGGATCCA                         AACTCCATAAGAAGGAAACTTGTGAGGCTGTTACCATCATTGAAACCCCTC
genomic: CAAGGCTGGCATGACTCACATTGTCCGTGAGGTTGAGAAGCCAGGATCCAgtatgtccac ... atttcttcagAACTCCATAAGAAGGAAACTTGTGAGGCTGTTACCATCATTGAAACCCCTC
EST: gi|211090116|gb|FL396349.1|FL396349
EST:     CAA-GCTGGCATGACTCACATTGTCCGTGA-GTTGAGAAGCCAGGATCCA                         AACTCCATAAGAAGGAAACTTGTGANSCTGTTACCATCATTGAAACCCCTC
genomic: CAAGGCTGGCATGACTCACATTGTCCGTGAGGTTGAGAAGCCAGGATCCAgtatgtccac ... atttcttcagAACTCCATAAGAAGGAAACTTGTGAGGCTGTTACCATCATTGAAACCCCTC
EST: gi|211275659|gb|FL423577.1|FL423577
EST:     CAAG-CTGGCATGACTCACATTGTCCGTGAG-TTGAGAAGCCAGGATCCA                         AACTCCATAAGAAGGAAACTTGTGAGGCTGTTACCATCATTGAAACCCCTC
genomic: CAAGGCTGGCATGACTCACATTGTCCGTGAGGTTGAGAAGCCAGGATCCAgtatgtccac ... atttcttcagAACTCCATAAGAAGGAAACTTGTGAGGCTGTTACCATCATTGAAACCCCTC
EST: gi|211449441|gb|FL371193.1|FL371193
EST:     CAA-GCTGGCATGACTCACATTGTCCGTGAGGTTGAGAAGCCAGGATCCA                         AACTCCATAAGAAGGAAACTTGTGAGGCTGTTACCATCATTGAAACCCCTC
genomic: CAAGGCTGGCATGACTCACATTGTCCGTGAGGTTGAGAAGCCAGGATCCAgtatgtccac ... atttcttcagAACTCCATAAGAAGGAAACTTGTGAGGCTGTTACCATCATTGAAACCCCTC
EST: gi|211143441|gb|FL420875.1|FL420875
EST:     CAAG-CTGGCATGACTCACATTGTCCGTGAGGTTTAGAAGCCAGGATCCA                         AACTCCATAAGAAGGAAACTTGTGAGGCTGTTACCATCATTGAAAACCCTC
genomic: CAAGGCTGGCATGACTCACATTGTCCGTGAGGTTGAGAAGCCAGGATCCAgtatgtccac ... atttcttcagAACTCCATAAGAAGGAAACTTGTGAGGCTGTTACCATCATTGAAACCCCTC
EST: gi|211390616|gb|FL418025.1|FL418025
EST:     CAA-GCTGGCATGACTCACATTGTCCGTGA-GTTGAGAAGCCAGGATCCA                         AACTCCATAAGAAGGAAACTTGTGAGGCTGTTACCATCATTGAAACCCCTC
genomic: CAAGGCTGGCATGACTCACATTGTCCGTGAGGTTGAGAAGCCAGGATCCAgtatgtccac ... atttcttcagAACTCCATAAGAAGGAAACTTGTGAGGCTGTTACCATCATTGAAACCCCTC
EST: gi|211512093|gb|FL429019.1|FL429019
EST:     CAA-GCTGGCATGACTCACATTGTCCGTGAGGTTGAGAAGCCAGGATCCA                         AACTCCATAAGAAGGAAACTTGTGAGGCTGTTACCATCATTGAAACCCCTC
genomic: CAAGGCTGGCATGACTCACATTGTCCGTGAGGTTGAGAAGCCAGGATCCAgtatgtccac ... atttcttcagAACTCCATAAGAAGGAAACTTGTGAGGCTGTTACCATCATTGAAACCCCTC
EST: gi|211054045|gb|FL387661.1|FL387661
EST:     CAAGGCTGGCATGACTCACATTGTCCGTGAGGTTGAGAAGCCAGGATCCA                         AACTCCATAAGAAGGAAACTTGTGAGGCTGTTACCATCATTGAAACCCCTC
genomic: CAAGGCTGGCATGACTCACATTGTCCGTGAGGTTGAGAAGCCAGGATCCAgtatgtccac ... atttcttcagAACTCCATAAGAAGGAAACTTGTGAGGCTGTTACCATCATTGAAACCCCTC
EST: gi|78122260|gb|DV540644.1|DV540644
EST:     CAAGGGTGGCATGACTCACATTGTCCGTGAGGTTGAAAAGCCAGGATCCA                         AACTCCATAAAAAGGAAACTTGTGAGGGTGTTACCATCATTGAAACCCCTC
genomic: CAAGGCTGGCATGACTCACATTGTCCGTGAGGTTGAGAAGCCAGGATCCAgtatgtccac ... atttcttcagAACTCCATAAGAAGGAAACTTGTGAGGCTGTTACCATCATTGAAACCCCTC
EST: gi|211332072|gb|FL381804.1|FL381804
EST:     CAA-GCTGGCATGACTCACATTGTCCGTGAGGTTGAGAAGCCAGGATCCA                         AACTCCATAAGAAGGAAACTTGTGAGGCTGTTACCATCATTGAAACCCCTC
genomic: CAAGGCTGGCATGACTCACATTGTCCGTGAGGTTGAGAAGCCAGGATCCAgtatgtccac ... atttcttcagAACTCCATAAGAAGGAAACTTGTGAGGCTGTTACCATCATTGAAACCCCTC
EST: gi|211522091|gb|FL426849.1|FL426849
EST:     CAA-GCTGGCATGACTCACATTGTCCGTGA-GTTGAGAAGCCAGGATCCA                         AACTCCATAAGAAGGAAACTTGTGAGGCTGTTACCATCATTGAAACCCCTC
genomic: CAAGGCTGGCATGACTCACATTGTCCGTGAGGTTGAGAAGCCAGGATCCAgtatgtccac ... atttcttcagAACTCCATAAGAAGGAAACTTGTGAGGCTGTTACCATCATTGAAACCCCTC
EST: gi|211158132|gb|FL392760.1|FL392760
EST:     CAAGGCTGGCATGACTCACATTGTCCGTGA-GTTGAGAAGCCAGGATCCA                         AACTCCATAAGAAGGAAACTTGTGAGGCTGTTACCATCATTGAAACCCCTC
genomic: CAAGGCTGGCATGACTCACATTGTCCGTGAGGTTGAGAAGCCAGGATCCAgtatgtccac ... atttcttcagAACTCCATAAGAAGGAAACTTGTGAGGCTGTTACCATCATTGAAACCCCTC
EST: gi|211221704|gb|FL402207.1|FL402207
EST:     CAA-GCTGGCATGACTCACATTGTCCGTGAGGTTGAGAAGCCAGGATCCA                         AACTCCATAAGAAGGAAACTTGTGAGGCTGTTACCATCATTGAAACCCCTC
genomic: CAAGGCTGGCATGACTCACATTGTCCGTGAGGTTGAGAAGCCAGGATCCAgtatgtccac ... atttcttcagAACTCCATAAGAAGGAAACTTGTGAGGCTGTTACCATCATTGAAACCCCTC
EST: gi|211080224|gb|FL420002.1|FL420002
EST:     CAAG-CTGGCATGACTCACATTGTCCGTGAG-TTGAGAAGCCAGGATCCA                         AACTCCATAAGAAGGAAACTTGTGAGGCTGTTACCATCATTGAAACCCCT
genomic: CAAGGCTGGCATGACTCACATTGTCCGTGAGGTTGAGAAGCCAGGATCCAgtatgtccac ... atttcttcagAACTCCATAAGAAGGAAACTTGTGAGGCTGTTACCATCATTGAAACCCCT
EST: gi|211209612|gb|FL397447.1|FL397447
EST:     CAA-GCTGGCATGACTCACATTGTCCGTGAGGTTGAGAAGCCAGGATCCA                         AACTCCATAAGAAGGAAACTTGTGAGGCTGTTACCATCATTGAAACCCCTC
genomic: CAAGGCTGGCATGACTCACATTGTCCGTGAGGTTGAGAAGCCAGGATCCAgtatgtccac ... atttcttcagAACTCCATAAGAAGGAAACTTGTGAGGCTGTTACCATCATTGAAACCCCTC
EST: gi|211390088|gb|FL395682.1|FL395682
EST:     CAAGGCTGGCATGACTCACATTGTCCGTGAGGTTGAGAAGCCAGGATCCA                         AACTCCATAAGAAGGAAACTTGTGAGGCTGTTACCATCATTGAAACCCCTC
genomic: CAAGGCTGGCATGACTCACATTGTCCGTGAGGTTGAGAAGCCAGGATCCAgtatgtccac ... atttcttcagAACTCCATAAGAAGGAAACTTGTGAGGCTGTTACCATCATTGAAACCCCTC
EST: gi|211013857|gb|FL374962.1|FL374962
EST:     CAA-GCTGGCATGACTCACATTGTCCGTGA-GTTGAGAAGCCAGGATCCA                         AACTCCATAAGAAGGAAACTTGTGAGGCTGTTACCATCATTGAAACCCCTC
genomic: CAAGGCTGGCATGACTCACATTGTCCGTGAGGTTGAGAAGCCAGGATCCAgtatgtccac ... atttcttcagAACTCCATAAGAAGGAAACTTGTGAGGCTGTTACCATCATTGAAACCCCTC
EST: gi|211045469|gb|FL401139.1|FL401139
EST:     AAGGCTGGCATGACTCACATTGTCCGTGAGGTTGAGAAGCCAGGATCCGA                         AACTCCATAAGAAGGAAACTTGTGAGGCTGTTACCATCATTGAAACCCCT
genomic: AAGGCTGGCATGACTCACATTGTCCGTGAGGTTGAGAAGCCAGGATCC-Agtatgtccac ... atttcttcagAACTCCATAAGAAGGAAACTTGTGAGGCTGTTACCATCATTGAAACCCCT
EST: gi|211290580|gb|FL410149.1|FL410149
EST:     CAAGGCTGGCATGACTCACATTGTCCGTGAG-TTGAGAAGCCAGGATCCA                         AACTCCATAAGAAGGAAACTTGTGAGGCT-TTACCATCATTGAAACCCCTC
genomic: CAAGGCTGGCATGACTCACATTGTCCGTGAGGTTGAGAAGCCAGGATCCAgtatgtccac ... atttcttcagAACTCCATAAGAAGGAAACTTGTGAGGCTGTTACCATCATTGAAACCCCTC
EST: gi|211045111|gb|FL385036.1|FL385036
EST:     CAA-GCTGGCATGACTCACATTGTCCGTGA-GTTGAGAAGCCAGGATCCA                         AACTCCATAAGAAGGAAACTTGTGAGGCTGTTACCATCATTGAAACCCCTC
genomic: CAAGGCTGGCATGACTCACATTGTCCGTGAGGTTGAGAAGCCAGGATCCAgtatgtccac ... atttcttcagAACTCCATAAGAAGGAAACTTGTGAGGCTGTTACCATCATTGAAACCCCTC
EST: gi|211143439|gb|FL420873.1|FL420873
EST:     CAA-GCTGGCATGACTCACATTGTCCGTGA-GTTGAGAAGCCAGGATCCA                         AACTCCATAAGAAGGAAACTTGTGAGGCTGTTACCATCATTGAAACCCCTC
genomic: CAAGGCTGGCATGACTCACATTGTCCGTGAGGTTGAGAAGCCAGGATCCAgtatgtccac ... atttcttcagAACTCCATAAGAAGGAAACTTGTGAGGCTGTTACCATCATTGAAACCCCTC
EST: gi|211490707|gb|FL394879.1|FL394879
EST:     CAAGGCTGGCATGACTCACATTGTCCGTGAGGTTGAGAAGCCAGGATCCA                         AACTCCATAAGAAGGAAACTTGTGAGGCTGTTACCATCATTGAWACCCCTC
genomic: CAAGGCTGGCATGACTCACATTGTCCGTGAGGTTGAGAAGCCAGGATCCAgtatgtccac ... atttcttcagAACTCCATAAGAAGGAAACTTGTGAGGCTGTTACCATCATTGAAACCCCTC
EST: gi|211209607|gb|FL397442.1|FL397442
EST:     CAA-GCTGGCATGACTCACATTGTCCGTGA-GTTGAGAAGCCAGGATCCA                         AACTCCATAAGAWRGGAAACTTGTGAGGCTGTTACCATCATTGAAACCCCT
genomic: CAAGGCTGGCATGACTCACATTGTCCGTGAGGTTGAGAAGCCAGGATCCAgtatgtccac ... atttcttcagAACTCCATAAGA-AGGAAACTTGTGAGGCTGTTACCATCATTGAAACCCCT
EST: gi|211118724|gb|FL427527.1|FL427527
EST:     CAAGGCTGGCATGACTCACATTGTCCGTGAG-TTGAGAAGCCAGGATCCA                         AACTCCATAAGAAGGAAACTTGTGAGG
genomic: CAAGGCTGGCATGACTCACATTGTCCGTGAGGTTGAGAAGCCAGGATCCAgtatgtccac ... atttcttcagAACTCCATAAGAAGGAAACTTGTGAGG
EST: gi|211045112|gb|FL385037.1|FL385037
EST:     CAAGGCTGGCATGACTCACATTGTCCGTGAGGTTGAGAAGCCAGGATCCA                         AACTCCATAAGAAGGAAACTTGTGAGGCTGTTACCATCATTGAAACCCCTC
genomic: CAAGGCTGGCATGACTCACATTGTCCGTGAGGTTGAGAAGCCAGGATCCAgtatgtccac ... atttcttcagAACTCCATAAGAAGGAAACTTGTGAGGCTGTTACCATCATTGAAACCCCTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atggataccatttcactccattatcgtaactgctcttcctacttgatttcttcagAACTCCATAAGAAGGAAACTTGTGAGGCTGTTACCATCATTGAAACCCCTCCTCTTGTCATTGTTGGGCTCGTGGCATATGTGAAGACTCCTCGTGGCCT
                                ctcttcctacttgatt  CT-rich tract
                                          ttgattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctgtttgaatatccacaactgcttgcacccatgaatctcgagtacatggataccatttcactccattatcgtaactgctcttcctacttgatttcttcagAACTCCATAAGAAGGAAACTTGTGAGGCTGTTACCATCATTGAAACCCCTCCTCTTGTCATTGTTGGGCTCGTGGCATATGTGAAGACTCCTCGTGGCCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC