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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gagaataatccactgttctaccttttcttgtattgccctgcaacatatggctgctctatgtctttcctggcaaattcaataaactcttgctgttgtccagGTGATGGCAGATTATGGTTACAGCATTGAGCACATTCTCATGGTTGATATCATCCCTGACGCTGCTGTTCGTAAGGCAATGAACGACATAAATGCAG

Basic information

species Zea mays
transcript GRMZM2G173858_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G026884_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os06g04460.1 (Oryza sativa), 3'ss of exon 3
-------gagaataatccactgttctaccttttcttgtattgccctgcaacatatggctgctctatgtctttcctggcaaattcaataaactcttgctgttgtccagGTGATGGCAGATTATGGTTACAGCATTGAGCACATTCTCATGGTTGATATCATCCCTGACGCTGCTGTTCGTAAGGCAATGAACGACATAAATGCAG
        |     ||   ||||||  | |||||||  || | | |    | ||  |  | |   |||| |  || |||| ||  |||||  || | || | |||||||||||| ||||||||||||||||||||||||||||||||||||||| ||||||||||| |||||||| || |  |||||||| || ||||||||||
gaatcacaatgtccatggtctgttcatctttttcttcgatggtcttct--cgtactgtagtttc-tgtcgt--cttgcaa-tttgataaatcctagatgct-tccagGTGATGGGAGATTATGGTTACAGCATTGAGCACATTCTCATGGTTGACATCATCCCTGATGCTGCTGTACGCAGAGCAATGAATGAAATAAATGCAG

upper sequence: GRMZM2G026884_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA09G28170.1 (Glycine max), 3'ss of exon 3
gagaataatccactgttctaccttttcttgtattgccctgcaacatatg-gctgctctatgtctttcctggcaaat-tcaataaactcttgctgttgt---ccagGTGATGGCAGATTATGGTTACAGCATTGAGCACATTCTCATGGTTGATATCATCCCTGACGCTGCTGTTCGTAAGGCAATGAACGACATAAATGCAG
      |||  |||    ||  |    ||||  ||  ||    ||| |  |||    ||| | | | |   | ||| || |||    |||  | |  |    |||||||||| ||| ||||| || || || |||||||| |||||||||||||| || |||||  ||||||| |||||||||||||| || || ||||| |
----gaaatatactaagttaa-taagattgtgctgtgcttgttcatttatgctctattatttatctgcataccaatgtctatatctccttcatttcatgtatcagGTGATGGGAGAGTATGGCTATAGTATAGAGCACATACTCATGGTTGATATTATACCTGATCCTGCTGTGCGTAAGGCAATGAATGAGATCAATGCCG

upper sequence: GRMZM2G026884_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA16G32990.1 (Glycine max), 3'ss of exon 3
gagaataatccactgttctaccttttcttgtattgccctgcaacatatggctgctctatgtctttcctggcaaattcaataaa----ctcttg---ctgttgt-ccagGTGATGGCAGATTATGGTTACAGCATTGAGCACATTCTCATGGTTGATATCATCCCTGACGCTGCTGTTCGTAAGGCAATGAACGACATAAATGCAG
             |||| ||  || | ||| | |    ||      | |  |||  | ||  | | |    |   |  || |     ||| ||    |  |||  |||||||||| ||| ||||| || || || |||||||| |||||||||||||| || |||||  ||||||| |||||||||||||| || || |||||||
-------tattgttgttgtat-ttgttttgaaatatgatgatgagcaagattgccttgtgcttgttcatttatgcttgattatttatctcctgaatttcatgtatcagGTGATGGGAGAATATGGATATAGTATAGAGCACATACTCATGGTTGATATTATACCTGATCCTGCTGTGCGTAAGGCAATGAATGAGATCAATGCAG

upper sequence: GRMZM2G026884_T01 (Zea mays), 3'ss of exon 2
lower sequence: AT5G51570.1 (Arabidopsis thaliana), 3'ss of exon 3
gagaataatccactgttctaccttttcttgta--ttgccct-gcaacatatggctgctct-atgtctttcctggcaaattcaataaactcttgctgttgtccagGTGATGGCAGATTATGGTTACAGCATTGAGCACATTCTCATGGTTGATATCATCCCTGACGCTGCTGTTCGTAAGGCAATGAACGACATAAATGCAG
 |||| | |  | |    ||  ||     |||   |||  | |  ||   ||    || |  |     || || |  ||  | |  | |  |    || | ||||||||||  | |||||| |||||||||||||||||||| |||||||| || || |||||  |  |||| || |||||||||||||| || |||||||
-agaaaagt--aataacatatattcgagggtagcctgctttcgagactggtgaagacttttgtaatggtcatgactcatg-attggagttgtttgtttcttcagGTGATGGGTGCTTATGGATACAGCATTGAGCACATTCTAATGGTTGACATTATTCCTGATCCCTCTGTACGCAAGGCAATGAACGAAATCAATGCAG

upper sequence: GRMZM2G026884_T01 (Zea mays), 3'ss of exon 2
lower sequence: Vv16s0022g01690.t01 (Vitis vinifera), 3'ss of exon 3
--gagaataatccactgttctaccttttcttgtattgccctgcaacatatggctgctctatgtctttcctggcaaattcaataaactcttgc--tgttgtccagGTGATGGCAGATTATGGTTACAGCATTGAGCACATTCTCATGGTTGATATCATCCCTGACGCTGCTGTTCGTAAGGCAATGAACGACATAAATGCAG
      ||  ||  |  ||  |    |      | |    ||||  | |  ||  || |||   ||| ||   | ||  | || |   |       | |  |||||||||| || ||| || || | ||| |||||||| || ||||||||||| || ||||| ||| |||| || ||||||||||| || ||||||||||
ctttctatcttctgccattgcataactgaacaaaattttgtgcactaaa-agcaactttat---ttttctaaaatatctattatatgttgaaaacatggatcagGTGATGGGAGCTTACGGATATAACATAGAGCACATACTGATGGTTGATATTATACCTGATGCTTCTGTACGCAAGGCAATGAATGAGATAAATGCAG

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|78115187|gb|DV533575.1|DV533575
EST:     TTGAGCAGAAGAACGATGTGGCCAAAGCTGTATTGGAGGAGCTTGAAAAG                         GTGATGGCAGATTATGGTTACAGCATTGAGCACATTCTCATGGTTGATATC
genomic: TTGAGCAGAAGAACGATGTGGCCAAAGCTGTATTGGAGGAGCTTGAAAAGgtatttctaa ... tgttgtccagGTGATGGCAGATTATGGTTACAGCATTGAGCACATTCTCATGGTTGATATC
EST: gi|78092689|gb|DV521063.1|DV521063
EST:     ACGATGTGGCCAAAGCTGTATTGGAGGAGCTTGAAAAG                         GTGATGGCAGATTATGGTTACAGCATGGAGCACATTCTCATGGTTGATATC
genomic: ACGATGTGGCCAAAGCTGTATTGGAGGAGCTTGAAAAGgtatttctaa ... tgttgtccagGTGATGGCAGATTATGGTTACAGCATTGAGCACATTCTCATGGTTGATATC
EST: gi|50337496|gb|CO532622.1|CO532622
EST:     AGGAGCTTGAAAAG                         GTGATGGCAGATTATGGTTACAGCATTGAGCACATTCTCATGGTTGATATC
genomic: AGGAGCTTGAAAAGgtatttctaa ... tgttgtccagGTGATGGCAGATTATGGTTACAGCATTGAGCACATTCTCATGGTTGATATC
EST: gi|67017254|gb|CO446003.1|CO446003
EST:     TTGAGCAGAAGAACGATGTGGCCAAAGCTGTATTGGAGGAGCTTGAAAAG                         GTGATGGCAGATTATGGTTACAGCATTGAGCACATTCTCATGGTTGATATC
genomic: TTGAGCAGAAGAACGATGTGGCCAAAGCTGTATTGGAGGAGCTTGAAAAGgtatttctaa ... tgttgtccagGTGATGGCAGATTATGGTTACAGCATTGAGCACATTCTCATGGTTGATATC
EST: gi|149076480|gb|EE165106.2|EE165106
EST:     GCCAAAGCTGTATTGGAGGAGCTTGAAAAG                         GTGATGGCAGATTATGGTTACAGCATTGAGCACATTCTCATGGTTGATATC
genomic: GCCAAAGCTGTATTGGAGGAGCTTGAAAAGgtatttctaa ... tgttgtccagGTGATGGCAGATTATGGTTACAGCATTGAGCACATTCTCATGGTTGATATC
EST: gi|71419996|gb|DR804971.1|DR804971
EST:     TTGAGCAGAAGAACGATGTGGCCAAAGCTGTATTGGAGGAGCTTGAAAAG                         GTGATGGCAGATTATGGTTACAGCATTGAGCACATTCTCATGGTTGATATC
genomic: TTGAGCAGAAGAACGATGTGGCCAAAGCTGTATTGGAGGAGCTTGAAAAGgtatttctaa ... tgttgtccagGTGATGGCAGATTATGGTTACAGCATTGAGCACATTCTCATGGTTGATATC
EST: gi|89251645|gb|DY623431.1|DY623431
EST:     TTGAGCAGAAGAACGATGTGGCCAAAGCTGTATTGGAGGAGCTTGAAAAG                         GTGATGGCAGATTATGGTTACAGCATTGAGCACATTCTCATGGTTGATATC
genomic: TTGAGCAGAAGAACGATGTGGCCAAAGCTGTATTGGAGGAGCTTGAAAAGgtatttctaa ... tgttgtccagGTGATGGCAGATTATGGTTACAGCATTGAGCACATTCTCATGGTTGATATC
EST: gi|149064912|gb|EE286584.2|EE286584
EST:     GAGCAGAAGAACGATGTGGCCAAAGCTGTATTGGAGGAGCTTGAAAAG                         GTGATGGCAGATTATGGTTACAGCATTGAGCACATTCTCATGGTTGATATC
genomic: GAGCAGAAGAACGATGTGGCCAAAGCTGTATTGGAGGAGCTTGAAAAGgtatttctaa ... tgttgtccagGTGATGGCAGATTATGGTTACAGCATTGAGCACATTCTCATGGTTGATATC
EST: gi|93011732|gb|EB637252.1|EB637252
EST:     TTGAGCAGAAGAACGATGTGGCCAAAGCTGTATTGGAGGAGCTTGAAAAG                         GTGATGGCAGATTATGGTTACAGCATTGAGCACATTCTCATGGTTGATATC
genomic: TTGAGCAGAAGAACGATGTGGCCAAAGCTGTATTGGAGGAGCTTGAAAAGgtatttctaa ... tgttgtccagGTGATGGCAGATTATGGTTACAGCATTGAGCACATTCTCATGGTTGATATC
EST: gi|71762921|gb|DR960858.1|DR960858
EST:     TTGAGCAGAAGAACGATGTGGCCAAAGCTGTATTGGAGGAGCTTGAAAAG                         GTGATGGCAGATTATGGTTACAGCATTGAGCACATTCTCATGGTTGATATC
genomic: TTGAGCAGAAGAACGATGTGGCCAAAGCTGTATTGGAGGAGCTTGAAAAGgtatttctaa ... tgttgtccagGTGATGGCAGATTATGGTTACAGCATTGAGCACATTCTCATGGTTGATATC
EST: gi|101385178|gb|EB814635.1|EB814635
EST:     TTGAGCAGAAGAACGATGTGGCCAAAGCTGTATTGGAGGAGCTTGAAAAG                         GTGATGGCAGATTATGGTTACAGCATTGAGCACATTCTCATGGTTGATATC
genomic: TTGAGCAGAAGAACGATGTGGCCAAAGCTGTATTGGAGGAGCTTGAAAAGgtatttctaa ... tgttgtccagGTGATGGCAGATTATGGTTACAGCATTGAGCACATTCTCATGGTTGATATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatggctgctctatgtctttcctggcaaattcaataaactcttgctgttgtccagGTGATGGCAGATTATGGTTACAGCATTGAGCACATTCTCATGGTTGATATCATCCCTGACGCTGCTGTTCGTAAGGCAATGAACGACATAAATGCAG
                                      ctcttgct  CT-rich tract
                          aaattcaataaact  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gagaataatccactgttctaccttttcttgtattgccctgcaacatatggctgctctatgtctttcctggcaaattcaataaactcttgctgttgtccagGTGATGGCAGATTATGGTTACAGCATTGAGCACATTCTCATGGTTGATATCATCCCTGACGCTGCTGTTCGTAAGGCAATGAACGACATAAATGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT
gagaataa
- - - - -ccactgt
- - - - - - - - - - - - - - tgtattg
- - - - - - - - - - - - - - - - - - -ctgcaac
- - - - - - - - - - - - - - - - - - - - - - - atggctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caataaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctcttgc