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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaactgatataatctaaactagttccttccctaacaatgtctaacatttataaacaaaacaaatactttttttcactcgttgaatcatgctcgtttcccatttgcagGTAGATCTTTTCTTCTACAGAGACCCAGAGGAAGCGAAGCAGCTGGAGGAAGAAGAGGCTCTGGTTGCACCTGACTATGGCGCGGTTGCAGAATACACTG

Basic information

species Zea mays
transcript GRMZM2G159237_T03
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G159237_T03 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os07g42450.1 (Oryza sativa), 3'ss of exon 3
gtaaactgatataatctaaactagttccttccctaacaatgtctaacatttataaacaaaacaaatactttttttcactcgttgaatcatgctcgtttcccatttgcagGTAGATCTTTTCTTCTACAGAGACCCAGAGGAAGCGAAGCAGCTGGAGGAAGAAGAGG---CTCTGGTTGCACCTGACTATGGCGCGGTTGCAGAATACACTG
||| |||     |||||||||||||  | | |||   ||||| |   |||   ||| | ||             ||||| | || ||  || |  |||||  |||| |||| ||||| ||||||||||| |||||||||||||||||| |||  |||||||||||||   ||||||| || ||||| ||||| |||||||| |||||     
gtatact--cgcaatctaaactagtatcatgcctg-taatgtttgg-attctgaaatataa-------------tcact-gatgtatgttgtt--tttcctttttgtagGTTGATCTGTTCTTCTACAGGGACCCAGAGGAAGCGAAGGAGCAAGAGGAAGAAGAGGCGGCTCTGGTGGCTCCTGATTATGGTGCGGTTGCGGAATATG---
















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|78117854|gb|DV536241.1|DV536241
EST:     TCCTCCAGATGCGCGGTACAATTCTTCCAGGACACAAGTGGGACATCATG                         GTAGATCTTTTCTTCTACAGAGACCCAGAGGAAGCGAAGCAGCTGGAGGAA
genomic: TCCTCCAGATGCGCGGTACAATTCTTCCAGGACACAAGTGGGACATCATGgtaaactgat ... ccatttgcagGTAGATCTTTTCTTCTACAGAGACCCAGAGGAAGCGAAGCAGCTGGAGGAA
EST: gi|76908312|gb|DV162877.1|DV162877
EST:     TCCTCCAGATGCGCGGTACAATTCTTCCAGGACACAAGTGGGACATCATG                         GTAGATCTTTTCTTCTACAGAGACCCAGAGGAAGCGAAGCAGCTGGAGGAA
genomic: TCCTCCAGATGCGCGGTACAATTCTTCCAGGACACAAGTGGGACATCATGgtaaactgat ... ccatttgcagGTAGATCTTTTCTTCTACAGAGACCCAGAGGAAGCGAAGCAGCTGGAGGAA
EST: gi|22818897|gb|BU498987.1|BU498987
EST:     TCCTCCAGATGCGCGGTACAATTCTTCCAGGACACAAGTGGGACATCATG                         GTAGATCTTTTCTTCTACAGAGACCCAGAGGAAGCGAAGCAGCTGGAGGAA
genomic: TCCTCCAGATGCGCGGTACAATTCTTCCAGGACACAAGTGGGACATCATGgtaaactgat ... ccatttgcagGTAGATCTTTTCTTCTACAGAGACCCAGAGGAAGCGAAGCAGCTGGAGGAA
EST: gi|60396348|gb|DN229217.1|DN229217
EST:     TCCTCCAGATGCGCGGTACAATTCTTCCAGGACACAAGTGGGACATCATG                         GTAGATCTTTTCTTCTACAGAGACCCAGAGGAAGCGAAGCAGCTGGAGGAA
genomic: TCCTCCAGATGCGCGGTACAATTCTTCCAGGACACAAGTGGGACATCATGgtaaactgat ... ccatttgcagGTAGATCTTTTCTTCTACAGAGACCCAGAGGAAGCGAAGCAGCTGGAGGAA
EST: gi|29130009|gb|CB380713.1|CB380713
EST:     TCCTCCAGATGCGCGGTACAATTCTTCCAGGACACAAGTGGGACATCATG                         GTAGATCTTTTCTTCTACAGAGACCCAGAGGAAGCGAAGCAGCTGGAGGAA
genomic: TCCTCCAGATGCGCGGTACAATTCTTCCAGGACACAAGTGGGACATCATGgtaaactgat ... ccatttgcagGTAGATCTTTTCTTCTACAGAGACCCAGAGGAAGCGAAGCAGCTGGAGGAA
EST: gi|9742963|gb|BE519111.1|BE519111
EST:     TCCTCCAGATGCGCGGTACAATTCTTCCAGGACACAAGTGGGACATCATG                         GTAGATCTTTTCTTCTACAGAGACCCAGAGGAAGCGAAGCAGCTGGAGGAA
genomic: TCCTCCAGATGCGCGGTACAATTCTTCCAGGACACAAGTGGGACATCATGgtaaactgat ... ccatttgcagGTAGATCTTTTCTTCTACAGAGACCCAGAGGAAGCGAAGCAGCTGGAGGAA
EST: gi|76291477|gb|DV031045.1|DV031045
EST:     TCCTCCAGATGCGCGGTACAATTCTTCCAGGACACAAGTGGGACATCATG                         GTAGATCTTTTCTTCTACAGAGACCCAGAGGAAGCGAAGCAGCTGGAGGAA
genomic: TCCTCCAGATGCGCGGTACAATTCTTCCAGGACACAAGTGGGACATCATGgtaaactgat ... ccatttgcagGTAGATCTTTTCTTCTACAGAGACCCAGAGGAAGCGAAGCAGCTGGAGGAA
EST: gi|22541981|gb|BU092419.1|BU092419
EST:     AGATGCGCGGTACAATTCTTCCAGGACACAAGTGGGACATCATG                         GTAGATCTTTTCTTCTACAGAGACCCCGAGGAAGCGAAGCAGCTGGAGGAA
genomic: AGATGCGCGGTACAATTCTTCCAGGACACAAGTGGGACATCATGgtaaactgat ... ccatttgcagGTAGATCTTTTCTTCTACAGAGACCCAGAGGAAGCGAAGCAGCTGGAGGAA
EST: gi|22541961|gb|BU092399.1|BU092399
EST:     TCCTCCAGATGCGCGGTACAATTCTTCCAGGACACAAGTGGGACATCATG                         GTAGATCTTTTCTTCTACAGAGACCCAGAGGAAGCGAAGCAGCTGGAGGAA
genomic: TCCTCCAGATGCGCGGTACAATTCTTCCAGGACACAAGTGGGACATCATGgtaaactgat ... ccatttgcagGTAGATCTTTTCTTCTACAGAGACCCAGAGGAAGCGAAGCAGCTGGAGGAA
EST: gi|84980400|gb|DW530749.1|DW530749
EST:     TCCTCCAGATGCGCGGTACAATTCTTCCAGGACACAAGTGGGACATCATG                         GTAGATCTTTTCTTCTACAGAGACCCAGAGGAAGCGAAGCAGCTGGAGGAA
genomic: TCCTCCAGATGCGCGGTACAATTCTTCCAGGACACAAGTGGGACATCATGgtaaactgat ... ccatttgcagGTAGATCTTTTCTTCTACAGAGACCCAGAGGAAGCGAAGCAGCTGGAGGAA
EST: gi|87298795|gb|DY470798.1|DY470798
EST:     TCCTCCAGATGCGCGGTACAATTCTTCCAGGACACAAGTGGGACATCATG                         GTAGATCTTTTCTTCTACAGAGACCCAGAGGAAGCGAAGCAGCTGGAGGAA
genomic: TCCTCCAGATGCGCGGTACAATTCTTCCAGGACACAAGTGGGACATCATGgtaaactgat ... ccatttgcagGTAGATCTTTTCTTCTACAGAGACCCAGAGGAAGCGAAGCAGCTGGAGGAA
EST: gi|22472387|gb|BU036867.1|BU036867
EST:     TCCTCCAGATGCGCGGTACAATTCTTCCAGGACACAAGTGGGACATCATG                         GTAGATCTTTTCTTCTACAGAGACCCAGAGGAAGCGAAGCAGCTGGAGGAA
genomic: TCCTCCAGATGCGCGGTACAATTCTTCCAGGACACAAGTGGGACATCATGgtaaactgat ... ccatttgcagGTAGATCTTTTCTTCTACAGAGACCCAGAGGAAGCGAAGCAGCTGGAGGAA
EST: gi|30087470|gb|CB885676.1|CB885676
EST:     TCCTCCAGATGCGCGGTACAATTCTTCCAGGACACAAGTGGGACATCATG                         GTAGATCTTTTCTTCTACAGAGACCCAGAGGAAGCGAAGCAGCTGGAGGAA
genomic: TCCTCCAGATGCGCGGTACAATTCTTCCAGGACACAAGTGGGACATCATGgtaaactgat ... ccatttgcagGTAGATCTTTTCTTCTACAGAGACCCAGAGGAAGCGAAGCAGCTGGAGGAA
EST: gi|76280595|gb|DV020163.1|DV020163
EST:     TCCTCCAGATGCGCGGTACAATTCTTCCAGGACACAAGTGGGACATCATG                         GTAGATCTTTTCTTCTACAGAGACCCAGAGGAAGCGAAGCAGCTGGAGGAA
genomic: TCCTCCAGATGCGCGGTACAATTCTTCCAGGACACAAGTGGGACATCATGgtaaactgat ... ccatttgcagGTAGATCTTTTCTTCTACAGAGACCCAGAGGAAGCGAAGCAGCTGGAGGAA
EST: gi|149102131|gb|EE287570.2|EE287570
EST:     TCCTCCAGATGCGCGGTACAATTCTTCCAGGACACAAGTGGGACATCATG                         GTAGATCTTTTCTTCTACAGAGACCCAGAGGAAGCGAAGCAGCTGGAGGAA
genomic: TCCTCCAGATGCGCGGTACAATTCTTCCAGGACACAAGTGGGACATCATGgtaaactgat ... ccatttgcagGTAGATCTTTTCTTCTACAGAGACCCAGAGGAAGCGAAGCAGCTGGAGGAA
EST: gi|76287509|gb|DV027077.1|DV027077
EST:     TCCTCCAGATGCGCGGTACAATTCTTCCAGGACACAAGTGGGACATCATG                         GTAGATCTTTTCTTCTACAGAGACCCAGAGGAAGCGAAGCAGCTGGAGGAA
genomic: TCCTCCAGATGCGCGGTACAATTCTTCCAGGACACAAGTGGGACATCATGgtaaactgat ... ccatttgcagGTAGATCTTTTCTTCTACAGAGACCCAGAGGAAGCGAAGCAGCTGGAGGAA
EST: gi|211079787|gb|FK951931.1|FK951931
EST:     TCCTCCAGATGCGCGGTACAATTCTTCCAGGACACAAGTGGGACATCATG                         GTAGATCTTTTCTTCTACAGAGACCCAGAGGAAGCGAAGCAGCTGGAGGAA
genomic: TCCTCCAGATGCGCGGTACAATTCTTCCAGGACACAAGTGGGACATCATGgtaaactgat ... ccatttgcagGTAGATCTTTTCTTCTACAGAGACCCAGAGGAAGCGAAGCAGCTGGAGGAA
EST: gi|71311034|gb|DR791823.1|DR791823
EST:     TCCTCCAGATGCGCGGTACAATTCTTCCAGGACACAAGTGGGACATCATG                         GTAGATCTTTTCTTCTACAGAGACCCAGAGGAAGCGAAGCAGCTGGAGGAA
genomic: TCCTCCAGATGCGCGGTACAATTCTTCCAGGACACAAGTGGGACATCATGgtaaactgat ... ccatttgcagGTAGATCTTTTCTTCTACAGAGACCCAGAGGAAGCGAAGCAGCTGGAGGAA
EST: gi|60351426|gb|DN218399.1|DN218399
EST:     TCCTCCAGATGCGCGGTACAATTCTTCCAGGACACAAGTGGGACATCATG                         GTAGATCTTTTCTTCTACAGAGACCCAGAGGAAGCGAAGCAGCTGGAGGAA
genomic: TCCTCCAGATGCGCGGTACAATTCTTCCAGGACACAAGTGGGACATCATGgtaaactgat ... ccatttgcagGTAGATCTTTTCTTCTACAGAGACCCAGAGGAAGCGAAGCAGCTGGAGGAA
EST: gi|22472873|gb|BU037353.1|BU037353
EST:     TCCTCCAGATGCGCGGTACAATTCTTCCAGGACACAAGTGGGACATCATG                         GTAGATCTTTTCTTCTACAGAGACCCAGAGGAAGCGAAGCAGCTGGAGGAA
genomic: TCCTCCAGATGCGCGGTACAATTCTTCCAGGACACAAGTGGGACATCATGgtaaactgat ... ccatttgcagGTAGATCTTTTCTTCTACAGAGACCCAGAGGAAGCGAAGCAGCTGGAGGAA
EST: gi|22489242|gb|BU049165.1|BU049165
EST:     TCCTCCAGATGCGCGGTACAATTCTTCCAGGACACAAGTGGGACATCATG                         GTAGATCTTTTCTTCTACAGAGACCCAGAGGAAGCGAAGCAGCTGGAGGAA
genomic: TCCTCCAGATGCGCGGTACAATTCTTCCAGGACACAAGTGGGACATCATGgtaaactgat ... ccatttgcagGTAGATCTTTTCTTCTACAGAGACCCAGAGGAAGCGAAGCAGCTGGAGGAA
EST: gi|37382876|gb|CF628407.1|CF628407
EST:     TCCTCCAGATGCGCGGTACAATTCTTCCAGGACACAAGTGGGACATCATG                         GTAGATCTTTTCTTCTACAGAGACCCAGAGGAAGCGAAGCAGCTGGAGGAA
genomic: TCCTCCAGATGCGCGGTACAATTCTTCCAGGACACAAGTGGGACATCATGgtaaactgat ... ccatttgcagGTAGATCTTTTCTTCTACAGAGACCCAGAGGAAGCGAAGCAGCTGGAGGAA
EST: gi|211082513|gb|FK951932.1|FK951932
EST:     TCCTCCAGATGCGCGGTACAATTCTTCCAGGACACAAGTGGGACATCATG                         GTAGATCTTTTCTTCTACAGAGACCCAGAGGAAGCGAAGCAGCTGGAGGAA
genomic: TCCTCCAGATGCGCGGTACAATTCTTCCAGGACACAAGTGGGACATCATGgtaaactgat ... ccatttgcagGTAGATCTTTTCTTCTACAGAGACCCAGAGGAAGCGAAGCAGCTGGAGGAA
EST: gi|67030712|gb|CO459461.1|CO459461
EST:     TCCTCCAGATGCGCGGTACAATTCTTCCAGGACACAAGTGGGACATCATG                         GTAGATCTTTTCTTCTACAGAGACCCAGAGGAAGCGAAGCAGCTGGAGGAA
genomic: TCCTCCAGATGCGCGGTACAATTCTTCCAGGACACAAGTGGGACATCATGgtaaactgat ... ccatttgcagGTAGATCTTTTCTTCTACAGAGACCCAGAGGAAGCGAAGCAGCTGGAGGAA
EST: gi|60398004|gb|DN230820.1|DN230820
EST:     TCCTCCAGATGCGCGGTACAATTCTTCCAGGACACAAGTGGGACATCATG                         GTAGATCTTTTCTTCTACAGAGACCCAGAGGAAGCGAAGCAGCTGGAGGAA
genomic: TCCTCCAGATGCGCGGTACAATTCTTCCAGGACACAAGTGGGACATCATGgtaaactgat ... ccatttgcagGTAGATCTTTTCTTCTACAGAGACCCAGAGGAAGCGAAGCAGCTGGAGGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aacaaaacaaatactttttttcactcgttgaatcatgctcgtttcccatttgcagGTAGATCTTTTCTTCTACAGAGACCCAGAGGAAGCGAAGCAGCTGGAGGAAGAAGAGGCTCTGGTTGCACCTGACTATGGCGCGGTTGCAGAATACACTG
                                     ctcgtttcccattt  CT-rich tract
     aacaaatacttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaactgatataatctaaactagttccttccctaacaatgtctaacatttataaacaaaacaaatactttttttcactcgttgaatcatgctcgtttcccatttgcagGTAGATCTTTTCTTCTACAGAGACCCAGAGGAAGCGAAGCAGCTGGAGGAAGAAGAGGCTCTGGTTGCACCTGACTATGGCGCGGTTGCAGAATACACTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG