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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...catacgatgtgttctcctttactaattaacttgtgagcacaattgctttttgtgagtgcaagagtctcctaatatttttctttgtttcattttactacagTGAAGTTAGTGGTGATAGAGAAGTGCAAAGGACAATGTTGGAATTGCTGAACCAGCTTGATGGATTTAGCAGCGATGAGAGGATAAAG

Basic information

species Zea mays
transcript GRMZM2G027282_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G027282_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os02g56000.1 (Oryza sativa), 3'ss of exon 6
-catacgatgtgttctcctttactaattaacttgtgagcacaattgctttttgtgagtgcaagagtctcctaatatttttctttgtttcattttactacagTGAAGTTAGTGGTGATAGAGAAGTGCAAAGGACAATGTTGGAATTGCTGAACCAGCTTGATGGATTTAGCAGCGATGAGAGGATAAAG
  | |    |  || || ||||  |||  |         |||  |  || ||   |||  || |  ||  |||| |||| ||             ||||||||||||||||||||| |||||||||||  | ||||||||||| |||||||| ||||| |||||||| || || || ||||||||||||
gtacatttagcattgtc-tttatcaatgcatgcaactagacatattattgttcacagtataataaactg-taattttttcct------------gctacagTGAAGTTAGTGGTGACAGAGAAGTGCAGCGCACAATGTTGGAGTTGCTGAATCAGCTAGATGGATTCAGTAGTGACGAGAGGATAAAG

upper sequence: GRMZM2G027282_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA20G38030.1 (Glycine max), 3'ss of exon 6
-----------catacgatgtgttctcctttactaattaacttgtgagcacaattgct-------ttttgtgagtgcaagagtctcctaatatttttctttgtttcattttactacagTGAAGTTAGTGGTGATAGAGAAGTGCAAAGGACAATGTTGGAATTGCTGAACCAGCTTGATGGATTTAGCAGCGATGAGAGGATAAAG
           || |  ||  | | | | ||   |||| |||| |     |     ||        |  |  |    |      | | ||  ||  | | | ||     | | | ||||||||| ||||| || ||||| || ||| |||||||||| |||||||| || ||||||||||| |||||||| |||||  |||| |||
gtattagctggcaaaaaattagatatacatttgcaattgacttttttttcccccctctagagagactcaggtaaaatatagtggttccaaccttgatgtatcttgtggctgattgcagTGAAGTAAGTGGAGACAGAGAGGTCCAACGGACAATGTTAGAATTGCTTAATCAGCTTGATGGTTTTAGCAGTGATGACCGGATTAAG

upper sequence: GRMZM2G027282_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA10G29250.1 (Glycine max), 3'ss of exon 6
-----------------------------catacgat--gtgttctcctttactaattaacttgtgagcacaattgctttttgtgagtgcaagagtctc----ctaatatttttctttgtttcattttactacagTGAAGTTAGTGGTGATAGAGAAGTGCAAAGGACAATGTTGGAATTGCTGAACCAGCTTGATGGATTTAGCAGCGATGAGAGGATAAAG
                               | | ||     || | ||||  |  || |  |      |  |  | | ||  | |||  ||  |||||    ||||  ||  | | | ||     | | | ||||||||| ||||| || ||||| || ||| | || ||||| |||||||| || ||||||||||| |||||||| |||||  |||| |||
gtattagctggcagtaatttagatatacatttgcaattgacttttttctttcttttttgaggtagagagatcagag-tgttacttagttaaattgtctcggttctaactttgatgtatcttgtggctaattgcagTGAAGTAAGTGGAGACAGAGAGGTACAACGAACTATGTTAGAATTGCTTAATCAGCTTGATGGTTTTAGCAGTGATGACCGGATCAAG

upper sequence: GRMZM2G027282_T01 (Zea mays), 3'ss of exon 6
lower sequence: AT1G09100.1 (Arabidopsis thaliana), 3'ss of exon 6
catacgatgtgttctcctttactaattaacttgtgagcacaattgctttttgtgagtgcaagagtctcctaatatttttctttgtttcattttactacagTGAAGTTAGTGGTGATAGAGAAGTGCAAAGGACAATGTTGGAATTGCTGAACCAGCTTGATGGATTTAGCAGCGATGAGAGGATAAAG
              | || ||   |    | ||| |  || |||   |||| |   || | ||     |||||  |    |||  ||   ||    |||| ||||||||||| ||  | || || |||||||||||||||||  |||| ||||||||||||||||| |||||||||||  | || |||
-------------gtactctatctagagtcatgtcataactattttattttctttctg-atga-----ctaatgctgacttttaattggctt----acagCGAAGTTAGTGGAGACCGTGAGGTACAAAGGACAATGTTGGAGCTGCTCAACCAGCTTGATGGATTCAGCAGCGATGATCGCATTAAG

upper sequence: GRMZM2G027282_T01 (Zea mays), 3'ss of exon 6
lower sequence: AT3G05530.1 (Arabidopsis thaliana), 3'ss of exon 6
catacgatgtgttctcctttactaattaacttgtgagcacaattgctttttgtgagtgcaagagtctcctaatatttttctttgtttcattttactacagTGAAGTTAGTGGTGATAGAGAAGTGCAAAGGACAATGTTGGAATTGCTGAACCAGCTTGATGGATTTAGCAGCGATGAGAGGATAAAG
  ||| |    || ||   | | |||| |       | |    |||  ||| | ||        |   | |||    ||||||| || |    | ||||||||||| || || || || |||||||| ||||| |||||||| ||||| || || ||||| ||||| || ||||||||  | || |||
-gtacaaatctttttctgattccaattcat------gtatttctgcactttctcagct---atttgctcaaatcacattctttggttgag---agtacagTGAAGTCAGCGGAGACAGGGAAGTGCAGAGGACTATGTTGGAGTTGCTCAATCAACTTGACGGATTCAGTAGCGATGAACGTATTAAG

upper sequence: GRMZM2G027282_T01 (Zea mays), 3'ss of exon 6
lower sequence: Vv14s0060g02260.t01 (Vitis vinifera), 3'ss of exon 6
-------------------------catacgatgtgttctcctttactaattaacttgtgagcacaattgctttttgtgagtgcaagagt----ctcctaatatttttctttgtttcattttactacagTGAAGTTAGTGGTGATAGAGAAGTGCAAAGGACAATGTTGGAATTGCTGAACCAGCTTGATGGATTTAGCAGCGATGAGAGGATAAAG
                         |||      || | |  ||  | || |   ||  ||    ||||  |    ||||   || |||       | | |   |   ||||  | | ||||| | ||||||||| ||||| ||||| || |||||  ||||||||||||| ||  |||| ||||||||||| |||||||| |||||  | ||||||
gtaaaccattattggtttagcactacatctttcatgatatttttatcaaaatggatttggattgaaatta-tcaaggtgaactcatgagcagcctccttgactatagacttttctgccttttattgcagTGAAGTGAGTGGAGATAGGGAGGTGCAGCGGACAATGTTGGAGTTATTGAATCAGCTTGATGGCTTTAGCAGTGATGATCGCATAAAG

upper sequence: GRMZM2G027282_T01 (Zea mays), 3'ss of exon 6
lower sequence: Vv05s0020g01180.t01 (Vitis vinifera), 3'ss of exon 7
----------------catacgatgt-gttctcctttactaattaacttgtga---------gcacaattgct------ttttgtgagtgcaagagtctcc--taatatttttctttgtttcattttactacagTGAAGTTAGTGGTGATAGAGAAGTGCAAAGGACAATGTTGGAATTGCTGAACCAGCTTGATGGATTTAGCAGCGATGAGAGGATAAAG
                | | | |  | |||   |||||| ||||     | ||         | ||||    |      |  |||   |  || ||| | |  | ||  || |  |||| | ||||||||||||||| || ||||| ||||||||||||||  | ||||||||||||||||| || ||||||||||| ||||| || |||||  | ||||||
gtatctcgtgttctatcttgcaaattagttgctctttacaaatttgacggagatgcattacggtacaaccaatggggagtgctgtttattaaaaagtgttcagtgattgttgttattgtgttattttactacagTGAGGTGAGTGGAGATAGAGAAGTGCAGCGAACAATGTTGGAATTGCTCAATCAGCTTGATGGTTTTAGTAGTGATGACCGTATAAAG

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|67022292|gb|CO451041.1|CO451041
EST:     ATCATCTTTATTGATGAAATTGATGCCATTGGAACAAAGCGTTTTGACAG                         TGAAGTTAGTGGCGATAGAGAAGTGCAAAGGACAATGTTGGAATTGCTGAA
genomic: ATCATCTTTATTGATGAAATTGATGCCATTGGAACAAAGCGTTTTGACAGgtacattttt ... tttactacagTGAAGTTAGTGGTGATAGAGAAGTGCAAAGGACAATGTTGGAATTGCTGAA
EST: gi|211381567|gb|FL475794.1|FL475794
EST:     ATCATCTTTATTGATGAAATTGATGCCATTGGAACAAAGCGTTTTGACAG                         TGAAGTTAGTGGCGATAGAGAAGTGCAAAGGACAATGTTGGAATTGCTGAA
genomic: ATCATCTTTATTGATGAAATTGATGCCATTGGAACAAAGCGTTTTGACAGgtacattttt ... tttactacagTGAAGTTAGTGGTGATAGAGAAGTGCAAAGGACAATGTTGGAATTGCTGAA
EST: gi|20802484|gb|BQ293534.1|BQ293534
EST:     ATCATCTTTATTGATGAAATTGATGCCATTGGAACAAAGCGTTTTGACAG                         TGAAGTTAGTGGCGATAGAGAAGTGCAAAGGACAATGTTGGAATTGCTGAA
genomic: ATCATCTTTATTGATGAAATTGATGCCATTGGAACAAAGCGTTTTGACAGgtacattttt ... tttactacagTGAAGTTAGTGGTGATAGAGAAGTGCAAAGGACAATGTTGGAATTGCTGAA
EST: gi|211086754|gb|FL006906.1|FL006906
EST:     ATCATCTTTATTGATGAAATTGATGCCATTGGAACAAAGCGTTTTGACAG                         TGAAGTTAGTGGCGATAGAGAAGTGCAAAGGACAATGTTGGAATTGCTGAA
genomic: ATCATCTTTATTGATGAAATTGATGCCATTGGAACAAAGCGTTTTGACAGgtacattttt ... tttactacagTGAAGTTAGTGGTGATAGAGAAGTGCAAAGGACAATGTTGGAATTGCTGAA
EST: gi|61118362|gb|DN559323.1|DN559323
EST:     ATCATCTTTATTGATGAAATTGATGCCATTGGAACAAAGCGTTTTGACAG                         TGAAGTTAGTGGCGATAGAGAAGTGCAAAGGACAATGTTGGAATTGCTGAA
genomic: ATCATCTTTATTGATGAAATTGATGCCATTGGAACAAAGCGTTTTGACAGgtacattttt ... tttactacagTGAAGTTAGTGGTGATAGAGAAGTGCAAAGGACAATGTTGGAATTGCTGAA
EST: gi|60397914|gb|DN230730.1|DN230730
EST:     ATCATCTTTATTGATGAAATTGATGCCATTGGAACAAAGCGTTTTGACAG                         TGAAGTTAGTGGCGATAGAGAAGTGCAAAGGACAATGTTGGAATTGCTGAA
genomic: ATCATCTTTATTGATGAAATTGATGCCATTGGAACAAAGCGTTTTGACAGgtacattttt ... tttactacagTGAAGTTAGTGGTGATAGAGAAGTGCAAAGGACAATGTTGGAATTGCTGAA
EST: gi|32851366|gb|CD991047.1|CD991047
EST:     ATCATCTTTATTGATGAAATTGATGCCATTGGAACAAAGCGTTTTGACAG                         TGAAGTTAGTGGCGATAGAGAAGTGCAAAGGACAATGTTGGAATTGCTGAA
genomic: ATCATCTTTATTGATGAAATTGATGCCATTGGAACAAAGCGTTTTGACAGgtacattttt ... tttactacagTGAAGTTAGTGGTGATAGAGAAGTGCAAAGGACAATGTTGGAATTGCTGAA
EST: gi|37400681|gb|CF637697.1|CF637697
EST:     ATCATCTTTATTGATGAAATTGATGCCATTGGAACAAAGCGTTTTGACAG                         TGAAGTTAGTGGCGATAGAGAAGTGCAAAGGACAATGTTGGAATTGCTGAA
genomic: ATCATCTTTATTGATGAAATTGATGCCATTGGAACAAAGCGTTTTGACAGgtacattttt ... tttactacagTGAAGTTAGTGGTGATAGAGAAGTGCAAAGGACAATGTTGGAATTGCTGAA
EST: gi|61118361|gb|DN559322.1|DN559322
EST:     ATCATCTTTATTGATGAAATTGATGCCATTGGAACAAAGCGTTTTGACAG                         TGAAGTTAGTGGCGATAGAGAAGTGCAAAGGACAATGTTGGAATTGCTGAA
genomic: ATCATCTTTATTGATGAAATTGATGCCATTGGAACAAAGCGTTTTGACAGgtacattttt ... tttactacagTGAAGTTAGTGGTGATAGAGAAGTGCAAAGGACAATGTTGGAATTGCTGAA
EST: gi|31357355|gb|CD441712.1|CD441712
EST:     ATCATCTTTATTGATGAAATTGATGCCATTGGAACAAAGCGTTTTGACAG                         TGAAGTTAGTGGCGATAGAGAAGTGCAAAGGACAATGTTGGAATTGCTGAA
genomic: ATCATCTTTATTGATGAAATTGATGCCATTGGAACAAAGCGTTTTGACAGgtacattttt ... tttactacagTGAAGTTAGTGGTGATAGAGAAGTGCAAAGGACAATGTTGGAATTGCTGAA
EST: gi|31356703|gb|CD441060.1|CD441060
EST:     ATCATCTTTATTGATGAAATTGATGCCATTGGAACAAAGCGTTTTGACAG                         TGAAGTTAGTGGCGATAGAGAAGTGCAAAGGACAATGTTGGAATTGCTGAA
genomic: ATCATCTTTATTGATGAAATTGATGCCATTGGAACAAAGCGTTTTGACAGgtacattttt ... tttactacagTGAAGTTAGTGGTGATAGAGAAGTGCAAAGGACAATGTTGGAATTGCTGAA
EST: gi|109637342|gb|EC590887.1|EC590887
EST:     ATCATCTTTATTGATGAAATTGATGCCATTGGAACAAAGCGTTTTGACAG                         TGAAGTTAGTGGCGATAGAGAAGTGCAAAGGACAATGTTGGAATTGCTGAA
genomic: ATCATCTTTATTGATGAAATTGATGCCATTGGAACAAAGCGTTTTGACAGgtacattttt ... tttactacagTGAAGTTAGTGGTGATAGAGAAGTGCAAAGGACAATGTTGGAATTGCTGAA
EST: gi|88758537|gb|DY542906.1|DY542906
EST:     GCGTTTTGACAG                         TGAAGTTAGTGGTGATAGAGAAGTGCAAAGGACAATGTTGGAATTGCTGAA
genomic: GCGTTTTGACAGgtacattttt ... tttactacagTGAAGTTAGTGGTGATAGAGAAGTGCAAAGGACAATGTTGGAATTGCTGAA
EST: gi|5456459|gb|AI834149.1|AI834149
EST:     GCGTTTTGACAG                         TGAAGTTAGTGGCGATAGAGAAGTGCAAAGGNCAATGTTGGAATTGCTGAA
genomic: GCGTTTTGACAGgtacattttt ... tttactacagTGAAGTTAGTGGTGATAGAGAAGTGCAAAGGACAATGTTGGAATTGCTGAA
EST: gi|78543926|gb|DV621424.1|DV621424
EST:     ATCATCTTTATTGATGAAATTGATGCCATTGGAACAAAGCGTTTTGACAG                         TGAAGTTAGTGGCGATAGAGAAGTGCAAAGGACAATGTTGGAATTGCTGAA
genomic: ATCATCTTTATTGATGAAATTGATGCCATTGGAACAAAGCGTTTTGACAGgtacattttt ... tttactacagTGAAGTTAGTGGTGATAGAGAAGTGCAAAGGACAATGTTGGAATTGCTGAA
EST: gi|78544181|gb|DV621679.1|DV621679
EST:     ATCATCTTTATTGATGAAATTGATGCCATTGGAACAAAGCGTTTTGACAG                         TGAAGTTAGTGGCGATAGAGAAGTGCAAAGGACAATGTTGGAATTGCTGAA
genomic: ATCATCTTTATTGATGAAATTGATGCCATTGGAACAAAGCGTTTTGACAGgtacattttt ... tttactacagTGAAGTTAGTGGTGATAGAGAAGTGCAAAGGACAATGTTGGAATTGCTGAA
EST: gi|6827952|gb|AW331595.1|AW331595
EST:     ATCATCTTTATTGATGAAATTGATGCCATTGGAACAAAGCGTTTTGACAG                         TGAAGTTAGTGGCGATAGAGAAGTGCAAAGGACAATGTTGGAATTGCTGAA
genomic: ATCATCTTTATTGATGAAATTGATGCCATTGGAACAAAGCGTTTTGACAGgtacattttt ... tttactacagTGAAGTTAGTGGTGATAGAGAAGTGCAAAGGACAATGTTGGAATTGCTGAA
EST: gi|32851382|gb|CD991063.1|CD991063
EST:     ATCATCTTTATTGATGAAATTGATGCCATTGGAACAAAGCGTTTTGACAG                         TGAAGTTAGTGGCGATAGAGAAGTGCAAAGGACAATGTTGGAATTGCTGAA
genomic: ATCATCTTTATTGATGAAATTGATGCCATTGGAACAAAGCGTTTTGACAGgtacattttt ... tttactacagTGAAGTTAGTGGTGATAGAGAAGTGCAAAGGACAATGTTGGAATTGCTGAA
EST: gi|211086756|gb|FL006908.1|FL006908
EST:     ATCATCTTTATTGATGAAATTGATGCCATTGGAACAAAGCGTTTTGACAG                         TGAAGTTAGTGGCGATAGAGAAGTGCAAAGGACAATGTTGGAATTGCTGAA
genomic: ATCATCTTTATTGATGAAATTGATGCCATTGGAACAAAGCGTTTTGACAGgtacattttt ... tttactacagTGAAGTTAGTGGTGATAGAGAAGTGCAAAGGACAATGTTGGAATTGCTGAA
EST: gi|4885759|gb|AI676879.1|AI676879
EST:     ATCATCTTTATTGATGAAATTGATGCCATTGGAACAAAGCGTTTTGACAG                         TGAAGTTAGTGGCGATAGAGAAGTGCAAAGGACAATGTTGGAATTGCTGAA
genomic: ATCATCTTTATTGATGAAATTGATGCCATTGGAACAAAGCGTTTTGACAGgtacattttt ... tttactacagTGAAGTTAGTGGTGATAGAGAAGTGCAAAGGACAATGTTGGAATTGCTGAA
EST: gi|6563657|gb|AW231384.1|AW231384
EST:     ATCATCTTTATTGATGAAATTGATGCCATTGGANCAAAGCGTTTTGACAG                         TGAAGTTAGTGGCGATAGAGAAGTGCAAAGGACAATGTTGGAATTGCTGAA
genomic: ATCATCTTTATTGATGAAATTGATGCCATTGGAACAAAGCGTTTTGACAGgtacattttt ... tttactacagTGAAGTTAGTGGTGATAGAGAAGTGCAAAGGACAATGTTGGAATTGCTGAA
EST: gi|37401285|gb|CF638005.1|CF638005
EST:     ATCATCTTTATTGATGAAATTGATGCCATTGGAACAAAGCGTTTTGACAG                         TGAAGTTAGTGGCGATAGAGAAGTGCAAAGGACAATGTTGGAATTGCTGAA
genomic: ATCATCTTTATTGATGAAATTGATGCCATTGGAACAAAGCGTTTTGACAGgtacattttt ... tttactacagTGAAGTTAGTGGTGATAGAGAAGTGCAAAGGACAATGTTGGAATTGCTGAA
EST: gi|31355810|gb|CD440167.1|CD440167
EST:     ATCATCTTTATTGATGAAATTGATGCCATTGGAACAAAGCGTTTTGACAG                         TGAAGTTAGTGGCGATAGAGAAGTGCAAAGGACAATGTTGGAATTGCTGAA
genomic: ATCATCTTTATTGATGAAATTGATGCCATTGGAACAAAGCGTTTTGACAGgtacattttt ... tttactacagTGAAGTTAGTGGTGATAGAGAAGTGCAAAGGACAATGTTGGAATTGCTGAA
EST: gi|83278765|gb|DV942773.1|DV942773
EST:     ATCATCTTTATTGATGAAATTGATGCCATTGGAACAAAGCGTTTTGACAG                         TGAAGTTAGTGGCGATAGAGAAGTGCAAAGGACAATGTTGGAATTGCTGAA
genomic: ATCATCTTTATTGATGAAATTGATGCCATTGGAACAAAGCGTTTTGACAGgtacattttt ... tttactacagTGAAGTTAGTGGTGATAGAGAAGTGCAAAGGACAATGTTGGAATTGCTGAA
EST: gi|60352075|gb|DN219048.1|DN219048
EST:     ATCATCTTTATTGATGAAATTGATGCCATTGGAACAAAGCGTTTTGACAG                         TGAAGTTAGTGGCGATAGAGAAGTGCAAAGGACAATGTTGGAATTGCTGAA
genomic: ATCATCTTTATTGATGAAATTGATGCCATTGGAACAAAGCGTTTTGACAGgtacattttt ... tttactacagTGAAGTTAGTGGTGATAGAGAAGTGCAAAGGACAATGTTGGAATTGCTGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctttttgtgagtgcaagagtctcctaatatttttctttgtttcattttactacagTGAAGTTAGTGGTGATAGAGAAGTGCAAAGGACAATGTTGGAATTGCTGAACCAGCTTGATGGATTTAGCAGCGATGAGAGGATAAAG
                     tcctaat  putative branch site (score: 2)
                             tttttctttgtttcat  CT-rich tract
                        taatatttttctttgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
catacgatgtgttctcctttactaattaacttgtgagcacaattgctttttgtgagtgcaagagtctcctaatatttttctttgtttcattttactacagTGAAGTTAGTGGTGATAGAGAAGTGCAAAGGACAATGTTGGAATTGCTGAACCAGCTTGATGGATTTAGCAGCGATGAGAGGATAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT