Skip to another splice site:
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 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctgtttgaatatccacaactgcttgcacccatgaatctcgagtatatggataccatttcactccattatcgtaactgctctgcctacttgatttctacagAACTCCATAAGAAGGAAACTTGTGAGGCTGTTACCATCATTGAAACCCCTCCTCTTGTCATTGTTGGGCTCGTGGCATATGTGAAGACTCCTCGTGGCCT

Basic information

species Zea mays
transcript GRMZM2G109677_T03
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G109677_T03 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os11g06750.1 (Oryza sativa), 3'ss of exon 3
ctgtttgaatatccacaactgcttgcac-ccatgaatctcgagt--atatggatac-catttcactccattatcgtaactgctctgcctacttgat-ttctacagAACTCCATAAGAAGGAAACTTGTGAGGCTGTTACCATCATTGAAACCCCTCCTCTTGTCATTGTTGGGCTCGTGGCATATGTGAAGACTCCTCGTGGCCT
     ||    |   | |   |||  |  | | || | | |  |  || || |||  |||   |||  |      ||||         |   | ||  | | |||||||||| |||||||| || ||||||||||||||||| ||||| || |||||| ||||| ||||||| || ||||| |||||||||||||| |||||| |
-----tggcctttagccaagactttaatactaagactttagtattcatctgaatatgcatactactgaagagatttaaccttgtcatttttctaatgcttttcagAACTCCACAAGAAGGAGACCTGTGAGGCTGTTACCATTATTGAGACACCTCCTATTGTCGTTGTTGGACTTGTGGCCTATGTGAAGACTCCACGTGGCTT

upper sequence: GRMZM2G109677_T03 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA20G30810.1 (Glycine max), 3'ss of exon 3
---------ctgtttgaatatccacaactgcttgcacccatgaatctcgagtatatggataccatttcactccattatcgtaactgctctgcctacttgatttctacagAACTCCATAAGAAGGAAACTTGTGAGGCTGTTACCATCATTGAAACCCCTCCTCTTGTCATTGTTGGGCTCGTGGCATATGTGAAGACTCCTCGTGGCCT
          ||| |     ||   ||||| || ||   |    ||||   |   |  |||| ||    ||  ||     |||||        |  |  || ||   ||| || || ||||||||||| |||||| ||||||| || ||||| ||||||||  | || ||||||||  | ||||  |||||||| ||||| ||||| ||
aagctaatgatgtattgcattctttaactgtttacatgtaacgttctcttat---tatatactatc---ctttatctatctaactatataatattttctatatc---agAGCTTCACAAGAAGGAAACATGTGAGCCTGTTACAATTATTGAGACCCCTCCAATGGTTATTGTTGGTGTTGTGGGTTATGTGAAAACTCCCCGTGGTCT

upper sequence: GRMZM2G109677_T03 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA10G36780.1 (Glycine max), 3'ss of exon 3
ctgtttgaatatccacaactgcttgcacc----catgaatctcgagtata-tggataccatttcactccattatcgtaactgctctgcctacttgatttctacagAACTCCATAAGAAGGAAACTTGTGAGGCTGTTACCATCATTGAAACCCCTCCTCTTGTCATTGTTGGGCTCGTGGCATATGTGAAGACTCCTCGTGGCCT
       ||||      | | |||  ||     |||||| ||      || | | ||     ||| |  |||||| |||||    | | |  ||   |    |||| || || |||||||||||||||||| ||||||| || ||||| ||||||||  | || ||||||||  | ||||  |||||||| ||||| ||||| ||
tgaagctaatagtattgaattctttaactattacatgaaactttctcttacttgttatagcatcatttaattatc-taactatatttcttttttatat----cagAGCTTCACAAGAAGGAAACTTGTGAGCCTGTTACAATTATTGAGACCCCTCCAATGGTTATTGTTGGTGTTGTGGGTTATGTGAAAACTCCACGTGGTCT

upper sequence: GRMZM2G109677_T03 (Zea mays), 3'ss of exon 5
lower sequence: AT1G43170.7 (Arabidopsis thaliana), 3'ss of exon 3
ctgtttgaatatccacaactgcttgcacccatgaatctcgagtatatggataccatttcactccattatcgtaactgctctgcctacttgat-ttctacagAACTCCATAAGAAGGAAACTTGTGAGGCTGTTACCATCATTGAAACCCCTCCTCTTGTCATTGTTGGGCTCGTGGCATATGTGAAGACTCCTCGTGGCCT
      | |  |  ||   || ||     |||     |    | | ||||     || |  |  |   ||||  |  || ||  |  ||  | || |  ||| || || |||||||| || ||||||||||||||||||||||| || ||| || | ||  |||||||  | || || ||||||||||||||| | ||  |
------gtaagtgaacttgtgttt-ttttcattctgatttgttttgtggaggtttttgcgatttaaagtcgt--caactttgtgtttttattgttgtgtagAGCTTCACAAGAAGGAGACATGTGAGGCTGTTACCATCATTGAGACACCTGCTATGGTGGTTGTTGGAGTTGTTGCCTATGTGAAGACTCCTAGAGGTTT

upper sequence: GRMZM2G109677_T03 (Zea mays), 3'ss of exon 5
lower sequence: AT1G43170.4 (Arabidopsis thaliana), 3'ss of exon 1
ctgtttgaatatccacaactgcttgcacccatgaatctcgagtatatggataccatttcactccattatcgtaactgctctgcctacttgat-ttctacagAACTCCATAAGAAGGAAACTTGTGAGGCTGTTACCATCATTGAAACCCCTCCTCTTGTCATTGTTGGGCTCGTGGCATATGTGAAGACTCCTCGTGGCCT-----------
           |  ||   || ||     |||     |    | | ||||     || |  |  |   ||||  |  || ||  |  ||  | || |  ||| || || |||||||| || ||||||||||||||||||||||| || ||| || | ||  |||||||  | || || ||||||||||||||| | ||  |           
---------agtgaacttgtgttt-ttttcattctgatttgttttgtggaggtttttgcgatttaaagtcgt--caactttgtgtttttattgttgtgtagagcttcacaagAAGGAGACATGTGAGGCTGTTACCATCATTGAGACACCTGCTATGGTGGTTGTTGGAGTTGTTGCCTATGTGAAGACTCCTAGAGGTTTGAGGTCTTTGA

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|24764081|gb|CA399250.1|CA399250
EST:     CAAGGCTGGCATGACTCACATTGTCCGTGAGGTTGAGAAGCCAGGATCCA                         AACTCCATAAGAAGGAAACTTGTGAGGCTGTTACCATCATTGAAACCCCTC
genomic: CAAGGCTGGCATGACTCACATTGTCCGTGAGGTTGAGAAGCCAGGATCCAgtatgtccac ... atttctacagAACTCCATAAGAAGGAAACTTGTGAGGCTGTTACCATCATTGAAACCCCTC
EST: gi|33101639|gb|CF061599.1|CF061599
EST:     CAAGGCTGGCATGACTCACATTGTCCGTGAGGTTGAGAAGCCAGGATCCA                         AACTCCATAAGAAGGAAACTTGTGAGGCTGTTACCATCATTGAAACCCCTC
genomic: CAAGGCTGGCATGACTCACATTGTCCGTGAGGTTGAGAAGCCAGGATCCAgtatgtccac ... atttctacagAACTCCATAAGAAGGAAACTTGTGAGGCTGTTACCATCATTGAAACCCCTC
EST: gi|67023430|gb|CO452179.1|CO452179
EST:     CAAGGGTGGCGTGACTCACATTGTCCGTGAGGTTGAGAAGCCAGGATCCA                         AACTCCATAAGAAGGAAACTTGTGAGGCTGTTACCATCATTGAAACCCCTC
genomic: CAAGGCTGGCATGACTCACATTGTCCGTGAGGTTGAGAAGCCAGGATCCAgtatgtccac ... atttctacagAACTCCATAAGAAGGAAACTTGTGAGGCTGTTACCATCATTGAAACCCCTC
EST: gi|32928358|gb|CF033170.1|CF033170
EST:     CAAGGCTGGCATGACTCACATTGTCCGTGAGGTTGAGAAGCCAGGATCCA                         AACTCCATAAGAAGGAAACTTGTGAGGCTGTTACCATCATTGAAACCCCTC
genomic: CAAGGCTGGCATGACTCACATTGTCCGTGAGGTTGAGAAGCCAGGATCCAgtatgtccac ... atttctacagAACTCCATAAGAAGGAAACTTGTGAGGCTGTTACCATCATTGAAACCCCTC
EST: gi|32912719|gb|CF017531.1|CF017531
EST:     GAGAAGCCAGGATCCA                         AACTCCATAAGAAGGAAACTTGTGAGGCTGTTACCATCATTGAAACCCCTC
genomic: GAGAAGCCAGGATCCAgtatgtccac ... atttctacagAACTCCATAAGAAGGAAACTTGTGAGGCTGTTACCATCATTGAAACCCCTC
EST: gi|33095113|gb|CF055107.1|CF055107
EST:     CAAGGCTGGCATGACTCACATTGTCCGTGAGGTTGAGAAGCCAGGATCCA                         AACTCCATAAGAAGGAAGCTTGTGAGGCTGTTACCATCATTGAAACCCCTC
genomic: CAAGGCTGGCATGACTCACATTGTCCGTGAGGTTGAGAAGCCAGGATCCAgtatgtccac ... atttctacagAACTCCATAAGAAGGAAACTTGTGAGGCTGTTACCATCATTGAAACCCCTC
EST: gi|15590218|gb|BI674834.1|BI674834
EST:     CAAGGCTGGCATGACTCACATTGTCCGTGAGGTTGAGAAGCCAGGATCCA                         AACTCCATAAGAAGGAAACTTGTGAGGCTGTTACCATCATTGAAACCCCTC
genomic: CAAGGCTGGCATGACTCACATTGTCCGTGAGGTTGAGAAGCCAGGATCCAgtatgtccac ... atttctacagAACTCCATAAGAAGGAAACTTGTGAGGCTGTTACCATCATTGAAACCCCTC
EST: gi|32943001|gb|CF047820.1|CF047820
EST:     CAAGGCTGGCATGACTCACATTGTCCGTGAGGTTGAGAAGCCAGGATCCA                         AACTCCATAAGAAGGAAACTTGTGAGGCTGTTACCATCATTGAAACCCCTC
genomic: CAAGGCTGGCATGACTCACATTGTCCGTGAGGTTGAGAAGCCAGGATCCAgtatgtccac ... atttctacagAACTCCATAAGAAGGAAACTTGTGAGGCTGTTACCATCATTGAAACCCCTC
EST: gi|31353364|gb|CD437721.1|CD437721
EST:     CAAGGCTGGCATGACTCACATTGTCCGTGAGGTTGAGAAGCCAGGATCCA                         AACTCCATAAGAAGGAAACTTGTGAGGCTGTTACCATCATTGAAACCCCTC
genomic: CAAGGCTGGCATGACTCACATTGTCCGTGAGGTTGAGAAGCCAGGATCCAgtatgtccac ... atttctacagAACTCCATAAGAAGGAAACTTGTGAGGCTGTTACCATCATTGAAACCCCTC
EST: gi|60345996|gb|DN212969.1|DN212969
EST:     CAAGGCTGGCATGACTCACATTGTCCGTGAGGTTGAGAAGCCAGGATCCA                         AACTCCATAAGAAGGAAACTTGTGAGGCTGTTACCATCATTGAAACCCCTC
genomic: CAAGGCTGGCATGACTCACATTGTCCGTGAGGTTGAGAAGCCAGGATCCAgtatgtccac ... atttctacagAACTCCATAAGAAGGAAACTTGTGAGGCTGTTACCATCATTGAAACCCCTC
EST: gi|15590112|gb|BI674728.1|BI674728
EST:     CAAGGCTGGCATGACTCACATTGTCCGTGAGGTTGAGAAGCCAGGATCCA                         AACTCCATAAGAAGGAAACTTGTGAGGCTGTTACCATCATTGAAACCCCTC
genomic: CAAGGCTGGCATGACTCACATTGTCCGTGAGGTTGAGAAGCCAGGATCCAgtatgtccac ... atttctacagAACTCCATAAGAAGGAAACTTGTGAGGCTGTTACCATCATTGAAACCCCTC
EST: gi|26557715|gb|CA829950.1|CA829950
EST:     TTGTCCGTGAGGTTGAGAAGCCAGGATCCA                         AACTCCATAAGAAGGAAACTTGTGAGGCTGTTACCATCATTGAAACCCCTC
genomic: TTGTCCGTGAGGTTGAGAAGCCAGGATCCAgtatgtccac ... atttctacagAACTCCATAAGAAGGAAACTTGTGAGGCTGTTACCATCATTGAAACCCCTC
EST: gi|33093228|gb|CF053222.1|CF053222
EST:     CAAGGCTGGCATGACTCACATTGTCCGTGAGGTTGAGAAGCCAGGATCCA                         AACTCCATAAGAAGGAAACTTGTGAGGCTGTTACCATCATTGAAACCCCTC
genomic: CAAGGCTGGCATGACTCACATTGTCCGTGAGGTTGAGAAGCCAGGATCCAgtatgtccac ... atttctacagAACTCCATAAGAAGGAAACTTGTGAGGCTGTTACCATCATTGAAACCCCTC
EST: gi|13126327|gb|BG316897.1|BG316897
EST:     CAAGGCTGGCATGACTCACATTGTCCGTGAGGTTGAGAAGCCAGGATCCA                         AACTCCATAAGAAGGAAACTTGTGAGGCTGTTACCATCATTGAAACCCCTC
genomic: CAAGGCTGGCATGACTCACATTGTCCGTGAGGTTGAGAAGCCAGGATCCAgtatgtccac ... atttctacagAACTCCATAAGAAGGAAACTTGTGAGGCTGTTACCATCATTGAAACCCCTC
EST: gi|32908163|gb|CF012976.1|CF012976
EST:     CAAGGCTGGCATGACTCACATTGTCCGTGAGGTTGAGAAGCCAGGATCCA                         AACTCCATAAGAAGGAAACTTGTGAGGCTGTTACCATCATTGAAACCCCTC
genomic: CAAGGCTGGCATGACTCACATTGTCCGTGAGGTTGAGAAGCCAGGATCCAgtatgtccac ... atttctacagAACTCCATAAGAAGGAAACTTGTGAGGCTGTTACCATCATTGAAACCCCTC
EST: gi|32944723|gb|CF049542.1|CF049542
EST:     CAAGGCTGGCATGACTCACATTGTCCGTGAGGTTGAGAAGCCAGGATCCA                         AACTCCATAAGAAGGAAACTTGTGAGGCTGTTACCATCATTGAAACCCCTC
genomic: CAAGGCTGGCATGACTCACATTGTCCGTGAGGTTGAGAAGCCAGGATCCAgtatgtccac ... atttctacagAACTCCATAAGAAGGAAACTTGTGAGGCTGTTACCATCATTGAAACCCCTC
EST: gi|32943644|gb|CF048463.1|CF048463
EST:     CAAGGCTGGCATGACTCACATTGTCCGTGAGGTTGAGAAGCCAGGATCCA                         AACTCCATAAGAAGGAAACTTGTGAGGCTGTTACCATCATTGAAACCCCTC
genomic: CAAGGCTGGCATGACTCACATTGTCCGTGAGGTTGAGAAGCCAGGATCCAgtatgtccac ... atttctacagAACTCCATAAGAAGGAAACTTGTGAGGCTGTTACCATCATTGAAACCCCTC
EST: gi|32912720|gb|CF017532.1|CF017532
EST:     GAGAAGCCAGGATCCA                         AACTCCATAAGAAGGAAACTTGTGAGGCTGTTACCATCATTGAAACCCCTC
genomic: GAGAAGCCAGGATCCAgtatgtccac ... atttctacagAACTCCATAAGAAGGAAACTTGTGAGGCTGTTACCATCATTGAAACCCCTC
EST: gi|29544483|gb|CB604863.1|CB604863
EST:     CAAGGCTGGCATGACTCACATTGTCCGTGAGGTTGAGAAGCCAGGATCCA                         AACTCCATAAGAAGGAAACTTGTGAGGCTGTTACCATCATTGAAACCCCTC
genomic: CAAGGCTGGCATGACTCACATTGTCCGTGAGGTTGAGAAGCCAGGATCCAgtatgtccac ... atttctacagAACTCCATAAGAAGGAAACTTGTGAGGCTGTTACCATCATTGAAACCCCTC
EST: gi|76925171|gb|DV170310.1|DV170310
EST:     CAAGGCTGGCATGACTCACATTGTCCGTGAGGTTGAGAAGCCAGGATCCA                         AACTCCATAAGAAGGAAACTTGTGAGGCTGTTACCATCATTGAAACCCCTC
genomic: CAAGGCTGGCATGACTCACATTGTCCGTGAGGTTGAGAAGCCAGGATCCAgtatgtccac ... atttctacagAACTCCATAAGAAGGAAACTTGTGAGGCTGTTACCATCATTGAAACCCCTC
EST: gi|31353630|gb|CD437987.1|CD437987
EST:     CAAGGCTGGCATGACTCACATTGTCCGTGAGGTTGAGAAGCCAGGATCCA                         AACTCCATAAGAAGGAAACTTGTGAGGCTGTTACCATCATTGAAACCCCTC
genomic: CAAGGCTGGCATGACTCACATTGTCCGTGAGGTTGAGAAGCCAGGATCCAgtatgtccac ... atttctacagAACTCCATAAGAAGGAAACTTGTGAGGCTGTTACCATCATTGAAACCCCTC
EST: gi|33095136|gb|CF055130.1|CF055130
EST:     CAAGGCTGGCATGACTCACATTGTCCGTGAGGTTGAGAAGCCAGGATCCA                         AACTCCATAAGAAGGAAACTTGTGAGGCTGTTACCATCATTGAAACCCCTC
genomic: CAAGGCTGGCATGACTCACATTGTCCGTGAGGTTGAGAAGCCAGGATCCAgtatgtccac ... atttctacagAACTCCATAAGAAGGAAACTTGTGAGGCTGTTACCATCATTGAAACCCCTC
EST: gi|32944255|gb|CF049074.1|CF049074
EST:     CAAGGCTGGCATGACTCACATTGTCCGTGAGGTTGAGAAGCCAGGATCCA                         AACTCCATAAGAAGGAAACTTGTGAGGCTGTTACCATCATTGAAACCCCTC
genomic: CAAGGCTGGCATGACTCACATTGTCCGTGAGGTTGAGAAGCCAGGATCCAgtatgtccac ... atttctacagAACTCCATAAGAAGGAAACTTGTGAGGCTGTTACCATCATTGAAACCCCTC
EST: gi|9953363|gb|BE639946.1|BE639946
EST:     CGTGAGGTTGAGAAGCCAGGATCCA                         AACTCCATAAGAAGGAAACTTGTGAGGCTGTTACCATCATTGAAACCCCTC
genomic: CGTGAGGTTGAGAAGCCAGGATCCAgtatgtccac ... atttctacagAACTCCATAAGAAGGAAACTTGTGAGGCTGTTACCATCATTGAAACCCCTC
EST: gi|31353612|gb|CD437969.1|CD437969
EST:     CAAGGCTGGCATGACTCACATTGTCCGTGAGGTTGAGAAGCCAGGATCCA                         AACTCCATAAGAAGGAAACTTGTGAGGCTGTTACCATCATTGAAACCCCTC
genomic: CAAGGCTGGCATGACTCACATTGTCCGTGAGGTTGAGAAGCCAGGATCCAgtatgtccac ... atttctacagAACTCCATAAGAAGGAAACTTGTGAGGCTGTTACCATCATTGAAACCCCTC
EST: gi|15177507|gb|BI398446.1|BI398446
EST:     CAAGGCTGGCATGACTCACATTGTCCGTGAGGTTGAGAAGCCAGGATCCA                         AACTCCATAAGAAGGAAACTTGTGAGGCTGTTACCATCATTGAAACCCCTC
genomic: CAAGGCTGGCATGACTCACATTGTCCGTGAGGTTGAGAAGCCAGGATCCAgtatgtccac ... atttctacagAACTCCATAAGAAGGAAACTTGTGAGGCTGTTACCATCATTGAAACCCCTC
EST: gi|13126729|gb|BG317299.1|BG317299
EST:     CAAGGCTGGCATGACTCACATTGTCCGTGAGGTTGAGAAGCCAGGATCCA                         AACTCCATAAGAAGGAAACTTGTGAGGCTGTTACCATCATTGAAACCCCTC
genomic: CAAGGCTGGCATGACTCACATTGTCCGTGAGGTTGAGAAGCCAGGATCCAgtatgtccac ... atttctacagAACTCCATAAGAAGGAAACTTGTGAGGCTGTTACCATCATTGAAACCCCTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atggataccatttcactccattatcgtaactgctctgcctacttgatttctacagAACTCCATAAGAAGGAAACTTGTGAGGCTGTTACCATCATTGAAACCCCTCCTCTTGTCATTGTTGGGCTCGTGGCATATGTGAAGACTCCTCGTGGCCT
                                              tttctac  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctgtttgaatatccacaactgcttgcacccatgaatctcgagtatatggataccatttcactccattatcgtaactgctctgcctacttgatttctacagAACTCCATAAGAAGGAAACTTGTGAGGCTGTTACCATCATTGAAACCCCTCCTCTTGTCATTGTTGGGCTCGTGGCATATGTGAAGACTCCTCGTGGCCT

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