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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cttagtgtgaagaaacatttggatcgtgatccattaccacccctaaatataccttgggcttatgtgaaactgcatttactaattttgtgtttcatctcagGTTGATGTTGCGCTCAAGCTCTCCAAGATGCAAGAGTACACTGGCCGCTCTGCCCCCACCGTTATCACATAAATTTTTGAAGAGTGATTTACAATGAGTT

Basic information

species Zea mays
transcript GRMZM2G023289_T01
intron # 17
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G023289_T03 (Zea mays), 3'ss of exon 17
lower sequence: LOC_Os03g50480.1 (Oryza sativa), 3'ss of exon 17
----------cttagtgtgaagaaacatttggatcgtgatccattaccacccctaaatataccttgggcttatgtgaaactgca-tttactaattttg------tgtttcatctcagGTTGATGTTGCGCTCAAGCTCTCCAAGATGCAAGAGTACACTGGCCGCTCTGCCCCCACCGTTATCACATAAATTTTTGAAGAGTGATT-TACAATGAGTT
          |    |||  |    | ||||  |  ||  || ||  | |    || | | |       ||   | | |||  | || |  || | ||      || || ||| |||||||||||||| || ||||| || ||||||||||||||||||||||| ||||| |||||||| |||||||||| |||| |||||  ||| || ||||  | 
gtaagacatccgcgctgtatattggc-tttgccttttggaccgttttc-cgagcaagtttgcggacctttttcttcagactttaattcagcaaatctgaccatctgctttatc-cagGTTGATGTTGCACTGAAGCTGTCAAAGATGCAAGAGTACACTGGCCGATCTGCTCCCACCGTCATCACATAAACTTTTCAAGAGCCATTCTAGAATGCTT-

upper sequence: GRMZM2G023289_T03 (Zea mays), 3'ss of exon 17
lower sequence: Vv01s0011g05370.t01 (Vitis vinifera), 3'ss of exon 18
cttagtgtgaagaaacatttggatcgtgatccattaccacccctaaatat-accttgggcttatgtgaaactgcatttactaattt-tgtgtttcatctcagGTTGATGTTGCGCTCAAGCTCTCCAAGATGCAAGAGTACACTGGCCGCTCTGCCCCCACCGTTATCACATAAATTTTTGAAGA-GTGATTTACAATGAGTT
           || |||| |   ||    ||  ||| ||   ||   ||| ||| ||  ||| ||   |  |   ||  || |  | ||  ||| ||| ||||| || ||||| |||||||| || |||||||| || | ||| ||||| ||||| ||||| ||||||||||| ||       |  |   |  ||||  |   
---------gtgagacatctctctc----tcttttatcaggactgtttatcaccctg--cttttgatcatatcttttggctgacctatgcatttgatcccagGTGGAGGTTGCTCTCAAGCTTTCTAAGATGCAGGAATTCACAGGCCGTTCTGCTCCCACTGTTATCACATAGATGCACACTGCTGCTGTACACAACAAAA-
















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|78108858|gb|DV527275.1|DV527275
EST:     AGGATTCCTCCAAGACCGGCAGGGATTCACAGGAGGCCCTTGCTCCACTG                         GTTGATGTTGCGCTCAAGCTCTCCAAGATGCAAGAGTACACTGGCCGCTCT
genomic: AGGATTCCTCCAAGACCGGCAGGGATTCACAGGAGGCCCTTGCTCCACTGgtaagataat ... ttcatctcagGTTGATGTTGCGCTCAAGCTCTCCAAGATGCAAGAGTACACTGGCCGCTCT
EST: gi|71426274|gb|DR807324.1|DR807324
EST:     AGGATTCCTCCAAGACCGGCAGGGATTCACAGGAGGCCCTTGCTCCACTG                         GTTGATGTTGCGCTCAAGCTCTCCAAGATGCAAGAGTACACTGGCCGCTCT
genomic: AGGATTCCTCCAAGACCGGCAGGGATTCACAGGAGGCCCTTGCTCCACTGgtaagataat ... ttcatctcagGTTGATGTTGCGCTCAAGCTCTCCAAGATGCAAGAGTACACTGGCCGCTCT
EST: gi|5296174|gb|AI782854.1|AI782854
EST:     AGGATTCCTCCAAGACCGGCAGGGATTCACAGGAGGCCCTTGCTCCACTG                         GTTGATGTTGCGCTCAAGCTCTCCAAGATGCAAGAGTACACTGGCCGCTCT
genomic: AGGATTCCTCCAAGACCGGCAGGGATTCACAGGAGGCCCTTGCTCCACTGgtaagataat ... ttcatctcagGTTGATGTTGCGCTCAAGCTCTCCAAGATGCAAGAGTACACTGGCCGCTCT
EST: gi|211541121|gb|FL006422.1|FL006422
EST:     AGGATTCCTCCAAGACCGGCAGGGATTCACAGGAGGCCCTTGCTCCACTG                         GTTGATGTTGCGCTCAAGCTCTCCAAGATGCAAGAGTACACTGGCCGCTCT
genomic: AGGATTCCTCCAAGACCGGCAGGGATTCACAGGAGGCCCTTGCTCCACTGgtaagataat ... ttcatctcagGTTGATGTTGCGCTCAAGCTCTCCAAGATGCAAGAGTACACTGGCCGCTCT
EST: gi|113799947|gb|DW921163.1|DW921163
EST:     AGGATTCCTCCAAGACCGGCAGGGATTCACAGGAGGCCCTTGCTCCACTG                         GTTGATGTTGCGCTCAAGCTCTCCAAGATGCAAGAG
genomic: AGGATTCCTCCAAGACCGGCAGGGATTCACAGGAGGCCCTTGCTCCACTGgtaagataat ... ttcatctcagGTTGATGTTGCGCTCAAGCTCTCCAAGATGCAAGAG
EST: gi|32906153|gb|CF010966.1|CF010966
EST:     AGGATTCCTCCAAGACCGGCAGGGATTCACAGGAGGCCCTTGCTCCACTG                         GTTGATGTTGCGCTCAAGCTCTCCAAGATGCAAGAGTACACTGGCCGCTCT
genomic: AGGATTCCTCCAAGACCGGCAGGGATTCACAGGAGGCCCTTGCTCCACTGgtaagataat ... ttcatctcagGTTGATGTTGCGCTCAAGCTCTCCAAGATGCAAGAGTACACTGGCCGCTCT
EST: gi|5895776|gb|AW037022.1|AW037022
EST:     AGGATTCCTCCAAGACCGGCAGGGATTCACAGGAGGCCCTTGCTCCACTG                         GTTGATGTTGCGCTCAAGCTCTCCAAGATGCAAGAGTACACTGGCCGCTCT
genomic: AGGATTCCTCCAAGACCGGCAGGGATTCACAGGAGGCCCTTGCTCCACTGgtaagataat ... ttcatctcagGTTGATGTTGCGCTCAAGCTCTCCAAGATGCAAGAGTACACTGGCCGCTCT
EST: gi|78024768|gb|DV493155.1|DV493155
EST:     AGGATTCCTCCAAGACCGGCAGGGATTCACAGGAGGCCCTTGCTCCACTG                         GTTGATGTTGCGCTCAAGCTCTCCAAGATGCAAGAGTACACTGGCCGCTCT
genomic: AGGATTCCTCCAAGACCGGCAGGGATTCACAGGAGGCCCTTGCTCCACTGgtaagataat ... ttcatctcagGTTGATGTTGCGCTCAAGCTCTCCAAGATGCAAGAGTACACTGGCCGCTCT
EST: gi|31357336|gb|CD441693.1|CD441693
EST:     AGGAAACATCCAAGACCGGCAGGGATTCACAGGAGGCCCTTGCTCCACTG                         GTTGATGTTGCGCTCAAGCTCTCCAAGATGCAAGAGTACACTGGCCGCTCT
genomic: AGGATTCCTCCAAGACCGGCAGGGATTCACAGGAGGCCCTTGCTCCACTGgtaagataat ... ttcatctcagGTTGATGTTGCGCTCAAGCTCTCCAAGATGCAAGAGTACACTGGCCGCTCT
EST: gi|67020139|gb|CO448888.1|CO448888
EST:     AGGATTCCTCCAAGACCGGCAGGGATTCACAGGAGGCCCTTGCTCCACTG                         GTTGATGTTGCGCTCAAGCTCTCCAAGATGCAAGAGTACACTGGCCGCTCT
genomic: AGGATTCCTCCAAGACCGGCAGGGATTCACAGGAGGCCCTTGCTCCACTGgtaagataat ... ttcatctcagGTTGATGTTGCGCTCAAGCTCTCCAAGATGCAAGAGTACACTGGCCGCTCT
EST: gi|32850278|gb|CD989959.1|CD989959
EST:     AGGATTCCTCCAAGACCGGCAGGGATTCACAGGAGGCCCTTGCTCCACTG                         GTTGATGTTGCGCTCAAGCTCTCCAAGATGCAAGAGT
genomic: AGGATTCCTCCAAGACCGGCAGGGATTCACAGGAGGCCCTTGCTCCACTGgtaagataat ... ttcatctcagGTTGATGTTGCGCTCAAGCTCTCCAAGATGCAAGAGT
EST: gi|211190026|gb|FL186116.1|FL186116
EST:     AGGATTCCTCCAAGACCGGCAGGGATTCACAGGAGGCCCTTGCTCCACTG                         GTTGATGTTGCGCTCAAGCTCTCCAAGATGCAAGAGTACACTGGCCGCTCT
genomic: AGGATTCCTCCAAGACCGGCAGGGATTCACAGGAGGCCCTTGCTCCACTGgtaagataat ... ttcatctcagGTTGATGTTGCGCTCAAGCTCTCCAAGATGCAAGAGTACACTGGCCGCTCT
EST: gi|149060808|gb|EE157260.2|EE157260
EST:     AGGATTCCTCCAAGACCGGCAGGGATTCACAGGAGGCCCTTGCTCCACTG                         GTTGATGTTGCGCTCAAGCTCTCCAAGATGCAAGAGTACACTGGCCGCTCT
genomic: AGGATTCCTCCAAGACCGGCAGGGATTCACAGGAGGCCCTTGCTCCACTGgtaagataat ... ttcatctcagGTTGATGTTGCGCTCAAGCTCTCCAAGATGCAAGAGTACACTGGCCGCTCT
EST: gi|5081034|gb|AI738296.1|AI738296
EST:     AGGATTCCTCCAAGACCGGCAGGGATTCACAGGAGGCCCTTGCTCCACTG                         GTTGATGTTGCGCTCAAGCTCTCCAAGATGCAAGAGTACACTGGCCGCTCT
genomic: AGGATTCCTCCAAGACCGGCAGGGATTCACAGGAGGCCCTTGCTCCACTGgtaagataat ... ttcatctcagGTTGATGTTGCGCTCAAGCTCTCCAAGATGCAAGAGTACACTGGCCGCTCT
EST: gi|78109659|gb|DV528075.1|DV528075
EST:     AGGATTCCTCCAAGACCGGCAGGGATTCACAGGAGGCCCTTGCTCCACTG                         GTTGATGTTGCGCTCAAGCTCTCCAAGATGCAAGAGTACACTGGCCGCTCT
genomic: AGGATTCCTCCAAGACCGGCAGGGATTCACAGGAGGCCCTTGCTCCACTGgtaagataat ... ttcatctcagGTTGATGTTGCGCTCAAGCTCTCCAAGATGCAAGAGTACACTGGCCGCTCT
EST: gi|44900765|gb|CK827310.1|CK827310
EST:     AGGATTCCTCCAAGACCGGCAGGGATTCACAGGAGGCCCTTGCTCCACTG                         GTTGATGTTGCGCTCAAGCTCTCCAAGATGCAAGAGTACACTGGCCGCTCT
genomic: AGGATTCCTCCAAGACCGGCAGGGATTCACAGGAGGCCCTTGCTCCACTGgtaagataat ... ttcatctcagGTTGATGTTGCGCTCAAGCTCTCCAAGATGCAAGAGTACACTGGCCGCTCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatataccttgggcttatgtgaaactgcatttactaattttgtgtttcatctcagGTTGATGTTGCGCTCAAGCTCTCCAAGATGCAAGAGTACACTGGCCGCTCTGCCCCCACCGTTATCACATAAATTTTTGAAGAGTGATTTACAATGAGTT
                               tactaat  putative branch site (score: 1)
                                            tttcatctc  putative PPT
                            atttactaattttgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cttagtgtgaagaaacatttggatcgtgatccattaccacccctaaatataccttgggcttatgtgaaactgcatttactaattttgtgtttcatctcagGTTGATGTTGCGCTCAAGCTCTCCAAGATGCAAGAGTACACTGGCCGCTCTGCCCCCACCGTTATCACATAAATTTTTGAAGAGTGATTTACAATGAGTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA