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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gacctgaggagtgctactcagaccacctaaccaactcagctagaggccctttcgcgagtaccagttttatcatatttctctaattctctttatgtttcagGAATGGTGGCAGCTTTAACAAACGAGAGTGCAACAAGCAAATCTGTATATTTTGCTCATTGCACGTCAGAGATGATATTCATTACTCATTTGCTGACAGA

Basic information

species Zea mays
transcript GRMZM2G155348_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G155348_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os01g71280.1 (Oryza sativa), 3'ss of exon 3
-gacctgag-gagtgctactcagaccacctaaccaactcagctagaggccctttcgcgagtaccagttttatcatatttctctaattctctttatgtttcagGAATGGTGGCAGCTTTAACAAACGAGAGTGCAACAAGCAAATCTGTATATTTTGCTCATTGCACGTCAGAGATGATATTCATTACTCATTTGCTGACAGA
 |  |||   ||   ||  | | |     ||      ||       |  |         || |  |||||   || |     |||  | |||| |||| |||||||||| ||||||||||| || ||||||||||||||||| || || ||||||||||||||||||||||||||||||||||||||||||||||| |||||
agttctgtttgaagactgtttacaagttatagttttttctctctctgttcaaggtatatgt-catgttttgagat-taataataacccactttctgttccagGAATGGTTGCAGCTTTAACTAATGAGAGTGCAACAAGCAAGTCGGTGTATTTTGCTCATTGCACGTCAGAGATGATATTCATTACTCATTTGCTCACAGA

upper sequence: GRMZM2G155348_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA10G15900.1 (Glycine max), 3'ss of exon 2
----gacctgaggagtg-ctactcagaccacctaaccaactcagctagaggccctttcgcgagtaccagttttatcatatttctcta-attctctttatgtttcagGAATGGTGGCAGCTTTAACAAACGAGAGTGCAACAAGCAAATCTGTATATTTTGCTCATTGCACGTCAGAGATGATATTCATTACTCATTTGCTGACAGA
        | |  |||| | | |  ||  |  | ||     ||    ||  |    |         || ||  |  |  |   | || |||||  |||| | ||||||||||| |||||  | || || |||||||| || ||||||||||| || ||||| || ||||| |||||||||||||| || ||||||||| || | ||
gtttagtattacaagtggcaaatgggaaaatttgactgcgacaataggaacctgccttat-----tcatttccacaacttacatttacattcttattat-tgtcagGAATGGTAGCAGCCCTTACCAATGAGAGTGCTACTAGCAAATCTGTCTACTTTGCACACTGCACATCAGAGATGATATTTATCACTCATTTGTTGGCTGA

upper sequence: GRMZM2G155348_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA03G28970.1 (Glycine max), 3'ss of exon 2
gacctgaggagtgctactcagaccacctaaccaactcagctagaggccctttcgcgagtaccagttt-tatcatat---ttctctaattctcttta-tgtt-tcagGAATGGTGGCAGCTTTAACAAACGAGAGTGCAACAAGCAAATCTGTATATTTTGCTCATTGCACGTCAGAGATGATATTCATTACTCATTTGCTGACAGA
     |   |      |||  |     | |    |    | |  | |     |  || | |   |||  |   |||   | || |  |||  |||| |||| ||||||||||| || ||  | || || |||||||| |||||||||||||| || ||||| || |||||||| || |||||||| || ||||||||| || | ||
-----gtttaacatacctctaattttatgagaggcattcccat-gtcttacacttgatttctgatttacaatctataaatcctgtttttcattttaatgttgtcagGAATGGTAGCTGCCCTTACCAATGAGAGTGCTACAAGCAAATCTGTGTACTTTGCACACTGCACGTCGGAAATGATATTTATCACTCATTTGTTGGCTGA

upper sequence: GRMZM2G155348_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA19G31730.1 (Glycine max), 3'ss of exon 2
gacctgaggagtgctactcagaccacctaaccaactcagctagaggccctttcgcg----agtaccagttttatcatattt---ctctaattctcttt---atgtt-tcagGAATGGTGGCAGCTTTAACAAACGAGAGTGCAACAAGCAAATCTGTATATTTTGCTCATTGCACGTCAGAGATGATATTCATTACTCATTTGCTGACAGA
      | ||  |    |||    ||||   | |||    |||||||  |  |  |      |  | | ||||| |||| |     ||  || || ||   ||| | ||||||||||| |||||  | ||||| |||||||| ||||||||||| || || ||||| || |||||||| || |||||||| || ||||| ||| || | ||
------aagaaaggggttcaacatacct---ctactt--ttagaggcattcccatgtcttgctttctgatttataatatataaatcctgtttttcattttaatgctgtcagGAATGGTAGCAGCCCTTACAAATGAGAGTGCCACAAGCAAATCCGTGTACTTTGCACACTGCACGTCGGAAATGATATTTATCACTCACTTGTTGGCTGA

upper sequence: GRMZM2G155348_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA12G01380.1 (Glycine max), 3'ss of exon 2
gacctgaggagtgctactcagaccacctaaccaactcagctagag-gccctttcgcgagtaccagtt-ttatcatatttctctaattctctttatgtttcagGAATGGTGGCAGCTTTAACAAACGAGAGTGCAACAAGCAAATCTGTATATTTTGCTCATTGCACGTCAGAGATGATATTCATTACTCATTTGCTGACAGA
   ||   |||   |           ||| |  ||     || |  || || |    | |  || || || | || | |    |   |  |  || |  |||||||||| || ||||||||||| |||||||| || ||||| || || || |||||||| ||||| || |||||||| || || |||||| |  || ||||
--tctattgagctttgaattccttttctatctcaccatagtatattgcactcttaatattttcaattcttgtaatttgtactcacgaccttcaatttaacagGAATGGTAGCCGCTTTAACAAATGAGAGTGCCACCAGCAAGTCAGTGTACTTTGCTCACTGCACATCTGAGATGATTTTTATAACTCATCTATTGGCAGA

upper sequence: GRMZM2G155348_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA02G33340.1 (Glycine max), 3'ss of exon 3
----------------------gacctgaggagtgctactcagaccacctaaccaactcagctagaggccct------ttcgcgagtaccagttttatcatatttctctaattctctttatgtt-tcagGAATGGTGGCAGCTTTAACAAACGAGAGTGCAACAAGCAAATCTGTATATTTTGCTCATTGCACGTCAGAGATGATATTCATTACTCATTTGCTGACAGA
                          ||   |||  ||||     ||  |    || |  |   | | |  |       |  |  ||  || ||  | ||  || | || ||| ||||  | || ||||||||||| |||||  | || || |||||||| || |||||||||||||| ||||| || ||||| |||||||                            
aatgctaattcttgttctcttccttttgtttagtattactagtggcaaatgggaaagtttgactgtgacaataggaacctgccttgtttcatttcca-cagCTTACACTTATTTTCTTATTATTGTCAGGAATGGTAGCAGCCCTTACCAATGAGAGTGCTACCAGCAAATCTGTATACTTTGCACACTGCACATCAGAGA----------------------------

upper sequence: GRMZM2G155348_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA11G20840.1 (Glycine max), 3'ss of exon 2
--gacctgaggagtgctactcagaccacctaaccaactcagctagaggccctttcgcgagtaccagtttta--tcatatttctctaattctctttatgtttcagGAATGGTGGCAGCTTTAACAAACGAGAGTGCAACAAGCAAATCTGTATATTTTGCTCATTGCACGTCAGAGATGATATTCATTACTCATTTGCTGACAGA
  ||  |   |     |      |        |||  |||   ||    | |||        | ||| |||     ||||| | |||||   |  || |  |||||||||| || ||||||||||| || ||||| || |||||||||||||| |||||||| || || ||||||||||| || || |||||| |  || ||||
ttgatgttttggactttttgattatttttctgccagttca-tgagtcctctttttatatcgtcaagtcttaaactgtatttatttaatt---tcaatttaacagGAATGGTAGCTGCTTTAACAAATGAAAGTGCCACCAGCAAATCTGTATACTTTGCTCACTGTACTTCAGAGATGATTTTTATCACTCATCTATTGGCAGA

upper sequence: GRMZM2G155348_T01 (Zea mays), 3'ss of exon 3
lower sequence: AT2G41540.2 (Arabidopsis thaliana), 3'ss of exon 3
gacctgaggagtgctactcagaccacctaaccaactcagctagaggccctttcg-cgagtaccagttttatcatatttctctaattctctttatgtttcagGAATGGTGGCAGCTTTAACAAACGAGAGTGCAACAAGCAAATCTGTATATTTTGCTCATTGCACGTCAGAGATGATATTCATTACTCATTTGCTGACAGA
                        |  |     |   ||  |  |        |   | || ||  ||| ||| | ||   |  ||||  || |||| |||| ||||| || ||  | || |||||||| || |||||||| || || |||||||||||||| || || ||||||||||| || |||||||| ||  ||||
---------------------gtaagtttctgtatgtagacacggatttgagtgataattatcaagttt-tcacactttgatccttcttgttgtgtt-cagGTATGGTAGCGGCGCTCACTAACGAGAGCGCTACAAGCAAGTCGGTGTATTTTGCTCATTGTACATCTGAGATGATATTTATAACTCATTTACTAGCAGA

upper sequence: GRMZM2G155348_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv13s0158g00340.t01 (Vitis vinifera), 3'ss of exon 2
---gacctgaggagtgctactcagacc-acctaaccaactcagctagaggccctttcgcgagtaccagttttatcatatttctctaattctctttatgtttcagGAATGGTGGCAGCTTTAACAAACGAGAGTGCAACAAGCAAATCTGTATATTTTGCTCATTGCACGTCAGAGATGATATTCATTACTCATTTGCTGACAGA
     | || |   | ||  ||  |   |  |  ||   | |   | |     ||||  |  |   | || ||   | || || | |     |||   |  |||||||||| |||||| |||| || |||||||| || |||||||| || || ||||| ||||| || ||||||||||| || ||||| ||| |  |  ||||
gcattcttgtgtgatcctgttctaatttatatttccttttgaagaatattgagtttctgggttggaatttgtaagttcttactttga----atttgcataacagGAATGGTAGCAGCTCTAACCAATGAGAGTGCCACCAGCAAATCAGTGTACTTTGCACATTGTACATCAGAGATGATTTTTATTACCCATCTTTTATCAGA

upper sequence: GRMZM2G155348_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv08s0007g09000.t01 (Vitis vinifera), 3'ss of exon 2
------------------------------------------------------------------------------------gacctgaggagtgctactcagaccacct-aaccaactcagctagaggccct----ttcgcgagtacca-------gttttatcatatttctctaattctc---tttatgtttcagGAATGGTGGCAGCTTTAACAAACGAGAGTGCAACAAGCAAATCTGTATATTTTGCTCATTGCACGTCAGAGATGATATTCATTACTCATTTGCTGACAGA
                                                                                     || | || | || |        ||  |  ||| |||  |  |      |     ||    | |            ||| ||||    ||||  ||| ||   || || || |||||||||| |||||  | || || |||||||| || |||||||||||||| ||||| ||||| || ||||||||||| ||||||||||||||| || | ||
gtaagttgttatttctttatgatggtaatataatagagggatcattgtgcttgaagtttcatatatgagcatccttgtcagataaacttcagcaatgatctggttctcattttgacctactaggagaagaaaaccaaaatttaaaaatgttgttattggatttaatcaagagtctcacattttcactttgattttccagGAATGGTAGCAGCCCTGACCAATGAGAGTGCTACCAGCAAATCTGTATACTTTGCACATTGTACATCAGAGATGATCTTCATTACTCATTTGTTGGCTGA

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|148948103|gb|EC893612.2|EC893612
EST:     CAATCGGTGCTG                         GAATGGTGGCAGCTTTAACAAACGAGAGTGCAACAAGCAAATCTGTATATT
genomic: CAATCGGTGCTGgtaatactaa ... tatgtttcagGAATGGTGGCAGCTTTAACAAACGAGAGTGCAACAAGCAAATCTGTATATT
EST: gi|32789125|gb|CD941361.1|CD941361
EST:     CACCCATGAGGTGATGGGTGGCCTGAAGAATGTCTATGCAATCGGTGCTG                         GAATGGTGGCAGC
genomic: CACCCATGAGGTGATGGGTGGCCTGAAGAATGTCTATGCAATCGGTGCTGgtaatactaa ... tatgtttcagGAATGGTGGCAGC
EST: gi|74237292|gb|DT645206.1|DT645206
EST:     CACCCATGAGGTGATGGGTGGCCTGAAGAATGTCTATGCAATCGGTGCTG                         GAATGGTGGCAGCTTTAACAAACGAGAGTGCAACAAGCAAATCTGTATATT
genomic: CACCCATGAGGTGATGGGTGGCCTGAAGAATGTCTATGCAATCGGTGCTGgtaatactaa ... tatgtttcagGAATGGTGGCAGCTTTAACAAACGAGAGTGCAACAAGCAAATCTGTATATT
EST: gi|74245777|gb|DT653691.1|DT653691
EST:     CACCCATGAGGTGATGGGTGGCCTGAAGAATGTCTATGCAATCGGTGCTG                         GAATGGTGGCAGCTTTAACAAACGAGAGTGCAACAAGCAAATCTGTATATT
genomic: CACCCATGAGGTGATGGGTGGCCTGAAGAATGTCTATGCAATCGGTGCTGgtaatactaa ... tatgtttcagGAATGGTGGCAGCTTTAACAAACGAGAGTGCAACAAGCAAATCTGTATATT
EST: gi|32808682|gb|CD960916.1|CD960916
EST:     CACCCATGAGGTGATGGGTGGCCTGAAGAATGTCTATGCAATCGGTGCTG                         GAATGGTGGCAGCTTTA
genomic: CACCCATGAGGTGATGGGTGGCCTGAAGAATGTCTATGCAATCGGTGCTGgtaatactaa ... tatgtttcagGAATGGTGGCAGCTTTA
EST: gi|32798272|gb|CD950508.1|CD950508
EST:     CACCCATGAGGTGATGGGTGGCCTGAAGAATGTCTATGCAATCGGTGCTG                         GAATGGTGGCAGCTTTA
genomic: CACCCATGAGGTGATGGGTGGCCTGAAGAATGTCTATGCAATCGGTGCTGgtaatactaa ... tatgtttcagGAATGGTGGCAGCTTTA
EST: gi|32798448|gb|CD950684.1|CD950684
EST:     CACCCATGAGGTGATGGGTGGCCTGAAGAATGTCTATGCAATCGGTGCTG                         GAATGGTGGCAGCTTTA
genomic: CACCCATGAGGTGATGGGTGGCCTGAAGAATGTCTATGCAATCGGTGCTGgtaatactaa ... tatgtttcagGAATGGTGGCAGCTTTA
EST: gi|32798637|gb|CD950873.1|CD950873
EST:     CACCCATGAGGTGATGGGTGGCCTGAAGAATGTCTATGCAATCGGTGCTG                         GAATGGTGGCAGCTTTA
genomic: CACCCATGAGGTGATGGGTGGCCTGAAGAATGTCTATGCAATCGGTGCTGgtaatactaa ... tatgtttcagGAATGGTGGCAGCTTTA
EST: gi|60359720|gb|DN226693.1|DN226693
EST:     TACCCATGAGGTGATGGGTGGCCTGAAGAATGTCTATGCAATCGGTGCTG                         GAATGGTGGCAGCTTTAACAAACGAGAGTGCAACAAGCAAATCTGTATATT
genomic: CACCCATGAGGTGATGGGTGGCCTGAAGAATGTCTATGCAATCGGTGCTGgtaatactaa ... tatgtttcagGAATGGTGGCAGCTTTAACAAACGAGAGTGCAACAAGCAAATCTGTATATT
EST: gi|78111933|gb|DV530329.1|DV530329
EST:     AATCGGTGCTG                         GAAAGGTGGCAGCTTTTACAAACGAGAGTGCAACAAGCAAATCTGTATATT
genomic: AATCGGTGCTGgtaatactaa ... tatgtttcagGAATGGTGGCAGCTTTAACAAACGAGAGTGCAACAAGCAAATCTGTATATT
EST: gi|74245778|gb|DT653692.1|DT653692
EST:     CACCCATGAGGTGATGGGTGGCCTGAAGAATGTCTATGCAATCGGTGCTG                         GAATGGTGGCAGCTTTAACAAACGAGAGTGCAACAAGCAAATCTGTATATT
genomic: CACCCATGAGGTGATGGGTGGCCTGAAGAATGTCTATGCAATCGGTGCTGgtaatactaa ... tatgtttcagGAATGGTGGCAGCTTTAACAAACGAGAGTGCAACAAGCAAATCTGTATATT
EST: gi|32790350|gb|CD942586.1|CD942586
EST:     CACCCATGAGGTGATGGGTGGCCTGAAGAATGTCTATGCAATCGGTGCTG                         GAATGGTGGCAGCTTTA
genomic: CACCCATGAGGTGATGGGTGGCCTGAAGAATGTCTATGCAATCGGTGCTGgtaatactaa ... tatgtttcagGAATGGTGGCAGCTTTA
EST: gi|74237291|gb|DT645205.1|DT645205
EST:     CACCCATGAGGTGATGGGTGGCCTGAAGAATGTCTATGCAATCGGTGCTG                         GAATGGTGGCAGCTTTAACAAACGAGAGTGCAACAAGCAAATCTGTATATT
genomic: CACCCATGAGGTGATGGGTGGCCTGAAGAATGTCTATGCAATCGGTGCTGgtaatactaa ... tatgtttcagGAATGGTGGCAGCTTTAACAAACGAGAGTGCAACAAGCAAATCTGTATATT
EST: gi|76908350|gb|DV162896.1|DV162896
EST:     CACCCATGAGGTGATGGGTGGCCTGAAGAATGTCTATGCAATCGGTGCTG                         GAATGGTGGCAGCTTTAACAAACGAGAGTGCAACAAGCAAATCTGTATATT
genomic: CACCCATGAGGTGATGGGTGGCCTGAAGAATGTCTATGCAATCGGTGCTGgtaatactaa ... tatgtttcagGAATGGTGGCAGCTTTAACAAACGAGAGTGCAACAAGCAAATCTGTATATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gccctttcgcgagtaccagttttatcatatttctctaattctctttatgtttcagGAATGGTGGCAGCTTTAACAAACGAGAGTGCAACAAGCAAATCTGTATATTTTGCTCATTGCACGTCAGAGATGATATTCATTACTCATTTGCTGACAGA
                                ctctaat  putative branch site (score: 3)
                             tttctctaattctctt  CT-rich tract
                   ttttatcatatttctc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gacctgaggagtgctactcagaccacctaaccaactcagctagaggccctttcgcgagtaccagttttatcatatttctctaattctctttatgtttcagGAATGGTGGCAGCTTTAACAAACGAGAGTGCAACAAGCAAATCTGTATATTTTGCTCATTGCACGTCAGAGATGATATTCATTACTCATTTGCTGACAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG