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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctgcacctgattcttgcacgtgctggggcggggtggcggcggatcgatgatagattcgtgcgatccttttggctcatgttgaggtgtatatgtcgtgcagGAACATCCGGGGATGTCGACTCCTGCGAGGAAGAGGCTGATGAGGGATTTCAAGCGGTTGATGCAGGACCCTCCGGCCGGCATAAGTGGCGCCCCGCAGG

Basic information

species Zea mays
transcript GRMZM2G110983_T03
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G110983_T03 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os05g08960.1 (Oryza sativa), 3'ss of exon 1
ctgcacctgattcttgcacgtgctggggcggggtggcggcggatcgatgatagatt--cgtgcgatccttttggctcatgttgaggtgtatatgtcgtgcagGAACATCCGGGGATGTCGACTCCTGCGAGGAAGAGGCTGATGAGGGATTTCAAGCGGTTGATGCAGGACCCTCCGGCCGGCATAAGTGGCGCCCCGCAGG-----
 |    |||   || | | |||    ||          |    ||  ||   | ||  | | |  ||  ||| ||| || | | |   |          ||||       |   |||||||| || || ||||||||| |||||||||||||||| ||  |||||||||| ||||| || ||||||||||| ||||| ||||     
attggtctgg--ctagtaggtgtcatgggtaaactaaagaatctcagtgtaggtttcccattccttctatttagcttatttggtgacttggtatctacacagGG-----TGAATATGTCGACGCCAGCAAGGAAGAGGTTGATGAGGGATTTCAAACGACTGATGCAGGATCCTCCAGCTGGCATAAGTGGGGCCCCACAGGACAAC

upper sequence: GRMZM2G110983_T03 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA04G34170.2 (Glycine max), 3'ss of exon 1
ctgcacctgattcttgcacgtgctggggcggggtggcggcggatcgatgatagattcgtgcgatcct-tttggctcatgttgaggtgtatatgtcgtgcagGAACATCCGGGGATGTCGACTCCTGCGAGGAAGAGGCTGATGAGGGATTTCAAGCGGTTGATGCAGGACCCTCCGGCCGGCATAAGTGGCGCCCCGCAGG---
    |  || |  |   | ||    ||      || |  |  |   |   | ||||  | | |  || ||    || |  |   | || |  ||  | || |      ||   |||||||||||||| ||||||||||||||||| || |||||| || ||   || ||||| || || || || || || ||||| ||||   
--ttatgtggtgttgctatgttggaggcttttttgcccccttaaatacactcgattgattcaagtctattcttttccttattgtgagtgttggtttttcaagGTGG--CGACAATGTCGACTCCTGCTAGGAAGAGGCTGATGAGAGACTTCAAGAGGCTGCAACAAGACCCGCCTGCAGGGATCAGCGGTGCCCCCCAGGATA

upper sequence: GRMZM2G110983_T03 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA08G40860.1 (Glycine max), 3'ss of exon 1
ctgcacctgattcttgcacgtgctggggcggggtggcggcggatcgatgatagattcgtgcgatccttttggctcatgttgaggtgtatatg-tcgtgcagGAACATCCGGGGATGTCGACTCCTGCGAGGAAGAGGCTGATGAGGGATTTCAAGCGGTTGATGCAGGACCCTCCGGCCGGCATAAGTGGCGCCCCGCAGG---
      ||  ||    |||   ||    |    |  |      |   | ||   | |    || |   ||        ||||  ||||  || | | |    |  |   |  |||||||||||| || |||||||| |||||||||||||| ||  | |||   || || ||||| || ||||| ||||| || || || |   
----ttcttgtttactcactcactctccctttctatctcaattttttttatccgtgcacatgagctgattactattgtttgaattgtacttgattgggataaagGAGGTGAAGATGTCGACTCCGGCTAGGAAGAGACTGATGAGGGATTTTAAAAGATTGCAACAAGATCCTCCTGCTGGCATCAGTGGGGCTCCCCAAGACA

upper sequence: GRMZM2G110983_T03 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA17G10640.1 (Glycine max), 3'ss of exon 1
---------ctgcacctgat---tcttgcacgtgctggggcggggtggcggcggatcgatgatagattcgtgcgatccttttggctcatgttgaggtgtatatgtcgtgcagGAACATCCGGGGATGTCGACTCCTGCGAGGAAGAGGCTGATGAGGGATTTCAAGCGGTTGATGCAGGACCCTCCGGCCGGCATAAGTGGCGCCCCGCAGG
          ||  ||| |    |||  | |    |    |    ||  |  |  | ||  | | | | |   | |  ||     |  | ||| ||    ||  |  |  |||     |  |  |||||||||||||| ||||||||||| ||||| ||||||||| || ||   || |||||||| || || || ||||||||||      
tctcttctcttgttccttaaccatctaactcaccttatatctccttgttgttg--ttgaaaagaaaattg-aagttatttccattttttcttgtggctgttagTTTTTCTAGGTG---CTAGCAATGTCGACTCCTGCTAGGAAGAGGCTCATGAGAGATTTCAAGAGGCTGCAACAAGACCCTCCTGCAGGAATCAGTGGCGCCC------

upper sequence: GRMZM2G110983_T03 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA05G01270.1 (Glycine max), 3'ss of exon 1
-ctgcacctgattcttgcacgtgctggggcggggtggcggcggatcgatgatagattcgtgcgatccttttggctcatgttgaggtgtatatgtcgtgcagGAACATCCGGGGATGTCGACTCCTGCGAGGAAGAGGCTGATGAGGGATTTCAAGCGGTTGATGCAGGACCCTCCGGCCGGCATAAGTGGCGCCCCGCAGG---
   | | |||| |    |   || |   ||    |    |    |  ||   | |||   |  ||     |      | |   | |||   | |      |  | |||     |||||||||||||| ||||||||||| ||||| ||||||||| || ||   || ||||| || || || || || || || || ||||   
ttggaatctgaattgacctgttggttatgcttcttaatagttttttaatagaaaattgaagttatttccgttttctctttgtggctgttggtttttctagGTGATATC----AATGTCGACTCCTGCTAGGAAGAGGCTCATGAGAGATTTCAAGAGGCTGCAACAAGACCCGCCTGCAGGAATCAGCGGGGCACCTCAGGATA

upper sequence: GRMZM2G110983_T03 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA17G10640.2 (Glycine max), 3'ss of exon 1
ctgcacctgat---tcttgcacgtgctggggcggggtggcggcggatcgatgatagattcgtgcgatccttttggctcatgttgaggtgtatatgtcgtgcagGAACATCCGGGGATGTCGACTCCTGCGAGGAAGAGGCTGATGAGGGATTTCAAGCGGTTGATGCAGGACCCTCCGGCCGGCATAAGTGGCGCCCCGCAGG---
 ||  ||| |    |||  | |    |    |    ||  |  |  | ||  | | | | |   | |  ||     |  | ||| ||    ||  |  |  |||     |  |  |||||||||||||| ||||||||||| ||||| ||||||||| || ||   || |||||||| || || || ||||||||||| ||||   
ttgttccttaaccatctaactcaccttatatctccttgttgttg--ttgaaaagaaaattg-aagttatttccattttttcttgtggctgttagtttttctagGTG---CTAGCAATGTCGACTCCTGCTAGGAAGAGGCTCATGAGAGATTTCAAGAGGCTGCAACAAGACCCTCCTGCAGGAATCAGTGGCGCCCCTCAGGATA

upper sequence: GRMZM2G110983_T03 (Zea mays), 3'ss of exon 1
lower sequence: AT1G14400.1 (Arabidopsis thaliana), 3'ss of exon 1
ctgcacctgattcttgcacgtgctggggcggggtggcggcggatcgat-gatagattcgtgcgatccttttggctcatg----ttgaggtgtatatgtcgtgcagGAACATCCGGGGATGTCGACTCCTGCGAGGAAGAGGCTGATGAGGGATTTCAAGCGGTTGATGCAGGACCCTCCGGCCGGCATAAGTGGCGCCCCGCAGG
         | | | |||   |          || |       | ||| ||||||     | || | |    | | |||    ||  |  |  | |||     || || |   | |||||||||| || || ||||||||| | ||||||||||||||| |||||  ||| ||||| || || || || ||||| || || ||||
-----agcaactttagcatacgtaaatcgttagtagtaatttctagattgatagaggttcgagaccttaaaaggtgatgaatatttggtgggttttgtttattagAAAGAAAGGAGGATGTCGACGCCAGCAAGGAAGAGGTTAATGAGGGATTTCAAGAGGTTGCAGCAAGACCCACCTGCGGGTATTAGTGGTGCTCCACAGG

upper sequence: GRMZM2G110983_T03 (Zea mays), 3'ss of exon 1
lower sequence: AT1G14400.2 (Arabidopsis thaliana), 3'ss of exon 1
ctgcacctgattcttgcacgtgctggggcggggtggcggcggatcgat-gatagattcgtgcgatccttttggctcatg----ttgaggtgtatatgtcgtgcagGAACATCCGGGGATGTCGACTCCTGCGAGGAAGAGGCTGATGAGGGATTTCAAGCGGTTGATGCAGGACCCTCCGGCCGGCATAAGTGGCGCCCCGCAGG----
         | | | |||   |          || |       | ||| ||||||     | || | |    | | |||    ||  |  |  | |||     || || |   | |||||||||| || || ||||||||| | ||||||||||||||| |||||  ||| ||||| || || || || ||||| || || ||||    
---------actttagcatacgtaaatcgttagtagtaatttctagattgatagaggttcgagaccttaaaaggtgatgaatatttggtgggttttgtttattagaaagAAAGGAGGATGTCGACGCCAGCAAGGAAGAGGTTAATGAGGGATTTCAAGAGGTTGCAGCAAGACCCACCTGCGGGTATTAGTGGTGCTCCACAGGACAA

upper sequence: GRMZM2G110983_T03 (Zea mays), 3'ss of exon 1
lower sequence: AT2G02760.1 (Arabidopsis thaliana), 3'ss of exon 1
ctgcacctgattcttgcacgtgctggggcggggtggcggcggatcgatgatagattcgtgcgatccttttggctcatgttgaggtgtatatgtcgtgcagGAACATCCGGGGATGTCGACTCCTGCGAGGAAGAGGCTGATGAGGGATTTCAAGCGGTTGATGCAGGACCCTCCGGCCGGCATAAGTGGCGCCCCGCAGG
 |||     |   |   | |   || |            |  | |  ||| | | | |     |    |    | ||| |  | |       |     ||    |     ||||||||||||| |||||||||||  ||||||||||||||||| |||||  ||| ||||| || || || || ||||| || || || |
ttgcttggcagattcaaatggtttgagataattgcatatccaagctctgagatagttggtttttgaaatactgtaatggttggttactgggatttgatagAGTAAGAGAAGGATGTCGACTCCAGCGAGGAAGAGATTGATGAGGGATTTCAAGAGGTTGCAGCAAGACCCACCTGCAGGAATTAGTGGTGCTCCACAAG

upper sequence: GRMZM2G110983_T03 (Zea mays), 3'ss of exon 1
lower sequence: Vv01s0026g01770.t01 (Vitis vinifera), 3'ss of exon 2
ctgcacctgattcttgcacgtgctggggcggggtggcggcggatcgatg-atagattcgtgcgatccttttggctcatgttgaggtgtata-tgtcgtgcagGAACATCCGG---GGATGTCGACTCCTGCGAGGAAGAGGCTGATGAGGGATTTCAAGCGGTTGATGCAGGACCCTCCGGCCGGCATAAGTGGCGCCCCGCAGG---
       ||| |  |  || |||          ||     |  ||  || || | ||     |||  |        ||||||   ||  |    ||     |||| |  |||   ||||||||||||| || ||||||||||| ||||||||||||||| |||||   ||||| || || || ||||| ||||| || || || |   
------ttgagtgataaacatgcattatactattgtaattgactcactgcattgtttaagatgat--taccaagcaatgttgttttggttggcttctctttggaatagGCGGTGAGGATGTCGACTCCAGCCAGGAAGAGGCTCATGAGGGATTTCAAGAGGTTGCAACAGGATCCACCTGCAGGCATCAGTGGTGCTCCTCAAGACA

upper sequence: GRMZM2G110983_T03 (Zea mays), 3'ss of exon 1
lower sequence: Vv14s0108g00140.t01 (Vitis vinifera), 3'ss of exon 1
-------ctgcacctgattcttgcacgtgctggggcggggtggcggcggatcgatgatagattcgtgcgatccttttggctcatgttgaggtgtatatgtcgtgcagGAACATCCGGGGATGTCGACTCCTGCGAGGAAGAGGCTGATGAGGGATTTCAAGCGGTTGATGCAGGACCCTCCGGCCGGCATAAGTGGCGCCCCGCAGG---
        || |  | | | |      ||  |          |         |  ||  ||    |   |||   |||  |   | ||      || | |   || |        | |||||||||| ||  | ||||||||||||||||||||||||||| || |   ||| || ||||| || || || ||||| || || || |   
ctaatgaatgaaatttagtttcttgtttgtggatttttatatgttattagctggagaaggaccaatcgaatctgattgattttggctggaa---attttttagGCGG-------TGAGGATGTCGACCCCATCAAGGAAGAGGCTGATGAGGGATTTCAAGAGGCTTCAGCAAGATCCTCCTGCTGGTATCAGTGGGGCACCCCATGACA

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|15005418|gb|BI325485.1|BI325485
EST:     CATCTGCTGGACCTCGATTGGTTTCTTCTTACCTAG                         GAACATCCGGGGATGTCGACTCCTGCGAGGAAGAGGCTGATGAGGGATTTC
genomic: CATCTGCTGGACCTCGATTGGTTTCTTCTTACCTAGgtaaagctct ... tgtcgtgcagGAACATCCGGGGATGTCGACTCCTGCGAGGAAGAGGCTGATGAGGGATTTC
EST: gi|74244314|gb|DT652228.1|DT652228
EST:     CCACCAGTCCGGTCCATCTGCTGGACCTCGATTGGTTTCTTCTTACCTAG                         GAACATCCGGGGATGTCGACTCCTGCGAGGAAGAGGCTGATGAGGGATTTC
genomic: CCACCAGTCCGGTCCATCTGCTGGACCTCGATTGGTTTCTTCTTACCTAGgtaaagctct ... tgtcgtgcagGAACATCCGGGGATGTCGACTCCTGCGAGGAAGAGGCTGATGAGGGATTTC
EST: gi|211206903|gb|FL385656.1|FL385656
EST:     CCACCAKTCCGGTCCATCTGCTGGACCTCGATTGGTTTCTTCTTACCTAG                         GAACATCCGGGGATGTCGACTCCTGCSAGGAAGAGGCTGATGAGGGATTTC
genomic: CCACCAGTCCGGTCCATCTGCTGGACCTCGATTGGTTTCTTCTTACCTAGgtaaagctct ... tgtcgtgcagGAACATCCGGGGATGTCGACTCCTGCGAGGAAGAGGCTGATGAGGGATTTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatgatagattcgtgcgatccttttggctcatgttgaggtgtatatgtcgtgcagGAACATCCGGGGATGTCGACTCCTGCGAGGAAGAGGCTGATGAGGGATTTCAAGCGGTTGATGCAGGACCCTCCGGCCGGCATAAGTGGCGCCCCGCAGG
                                       tgtatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctgcacctgattcttgcacgtgctggggcggggtggcggcggatcgatgatagattcgtgcgatccttttggctcatgttgaggtgtatatgtcgtgcagGAACATCCGGGGATGTCGACTCCTGCGAGGAAGAGGCTGATGAGGGATTTCAAGCGGTTGATGCAGGACCCTCCGGCCGGCATAAGTGGCGCCCCGCAGG

ctgcacc
- - - - - ttcttgc
- - - - - - - - - cgtgctg
- - - - - - - - - - - - - - - - - -gcggcgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -atgttga