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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGAGGACGCACGCCGTTCGGACCGCGCACGAGAACATCGACCGCACGCTGCGCTCCGCGGATGTGATCCTCACCCAGTTCGACAGGACCCGAGAGgtgcttcctcctaacttcactcctcccatgctcgtcgattgagtttcacgctatgtgcatccccgcgtacttgcaagtcggacctgcagtttaatctagc...

Basic information

species Zea mays
transcript GRMZM2G046590_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G046590_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os04g58880.1 (Oryza sativa), 5'ss of exon 2
GTGAGGACGCACGCCGTTCGGACCGCGCACGAGAACATCGACCGCACGCTGCGCTCCGCGGATGTGATCCTCACCCAGTTCGACAGGACCCGAGAGgtgcttcctc---ctaacttcactcctcccatgctcgtcgattgagtttcacgctatgtgcatccccgcgtacttgcaagtcggacctgcagtttaatctagc-
||||||||||||||||| ||||| || ||||||||||||||||| |||||||||||||| ||||| |||||||| ||||||||  | || ||||||||||| | ||     |||  ||    |||| | ||  |   | |   | ||   ||||    |  |    |   |||    |   | ||  |||   |  | | 
GTGAGGACGCACGCCGTGCGGACGGCCCACGAGAACATCGACCGGACGCTGCGCTCCGCCGATGTCATCCTCACGCAGTTCGATCGAACTCGAGAGgtgctccatcgcttcaaccccagatttccc-tacttcttactagtactaca---tatgctattaacaatatgtgtgccccgcccgcttgtggttggttggaact
















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|211425858|gb|FL143031.1|FL143031
EST:     CGCTGCGCTCCGCGGATGTGATCCTCACCCAGTTCGACAGGACCCGAGAG                         GCAGAGCGTGAAATACAGAAGGGACCGCATGAGAACCTTCAAGGTTTCCTA
genomic: CGCTGCGCTCCGCGGATGTGATCCTCACCCAGTTCGACAGGACCCGAGAGgtgcttcctc ... atatgtacagGCAGAGCGTGAAATACAGAAGGGGCCGCATGAGAACCTTCAAGGTTTCCTA
EST: gi|71438744|gb|DR819794.1|DR819794
EST:     CGCTGCGCTCCGCGGATGTGATCCTCACCCAGTTCGACAGGACCCGAGAG                         GCAGAGCGTGAAATACAGAAGGGGCCGCATGAGAACCTTCAAGGTTTCCTA
genomic: CGCTGCGCTCCGCGGATGTGATCCTCACCCAGTTCGACAGGACCCGAGAGgtgcttcctc ... atatgtacagGCAGAGCGTGAAATACAGAAGGGGCCGCATGAGAACCTTCAAGGTTTCCTA
EST: gi|211425857|gb|FL143030.1|FL143030
EST:     CGCTGCGCTCCGCGGATGTGATCCTCACCCAGTTCGACAGGACCCGAGAG                         GCAGAGCGTGAAATACAGAAGGGACCGCATGAGAACCTTCAAGGTTTCCTA
genomic: CGCTGCGCTCCGCGGATGTGATCCTCACCCAGTTCGACAGGACCCGAGAGgtgcttcctc ... atatgtacagGCAGAGCGTGAAATACAGAAGGGGCCGCATGAGAACCTTCAAGGTTTCCTA
EST: gi|211425849|gb|FL143022.1|FL143022
EST:     CGCTGCGCTCCGCGGATGTGATCCTCACCCAGTTCGACAGGACCCGAGAG                         G-AGAGCGTGAAATACAGAAGGGACCGCATGAGAACCTTCAAGGTTTCCTA
genomic: CGCTGCGCTCCGCGGATGTGATCCTCACCCAGTTCGACAGGACCCGAGAGgtgcttcctc ... atatgtacagGCAGAGCGTGAAATACAGAAGGGGCCGCATGAGAACCTTCAAGGTTTCCTA
EST: gi|211428442|gb|FL143033.1|FL143033
EST:     CGCTGCGCTCCGCGGATGTGATCCTCACCCAGTTCGACAGGACCCGAGAG                         GCAGAGCGTGAAATACAGAAGGGACCGCATGAGAACCTTCAAGGTTTCCTA
genomic: CGCTGCGCTCCGCGGATGTGATCCTCACCCAGTTCGACAGGACCCGAGAGgtgcttcctc ... atatgtacagGCAGAGCGTGAAATACAGAAGGGGCCGCATGAGAACCTTCAAGGTTTCCTA
EST: gi|160481670|gb|EY254240.1|EY254240
EST:     CGCTGCGCTCCGCGGATGTGATCCTCACCCAGTTCGACAGGACCCGAGAG                         GCAGAGCGTGAAATACAGAAGGGGCCGCATGAGAACCTTCAAGGTTTCCTA
genomic: CGCTGCGCTCCGCGGATGTGATCCTCACCCAGTTCGACAGGACCCGAGAGgtgcttcctc ... atatgtacagGCAGAGCGTGAAATACAGAAGGGGCCGCATGAGAACCTTCAAGGTTTCCTA
EST: gi|211425850|gb|FL143023.1|FL143023
EST:     CGCTGCGCTCCGCGGATGTGATCCTCACCCAGTTCGACAGGACCCGAGAG                         GCAGAGCGTGAAATACAGAAGGGACCGCATGAGAACCTTCAAGGTTTCCTA
genomic: CGCTGCGCTCCGCGGATGTGATCCTCACCCAGTTCGACAGGACCCGAGAGgtgcttcctc ... atatgtacagGCAGAGCGTGAAATACAGAAGGGGCCGCATGAGAACCTTCAAGGTTTCCTA
EST: gi|211425855|gb|FL143028.1|FL143028
EST:     CGCTGCGCTCCGCGGATGTGATCCTCACCCAGTTCGACAGGACCCGAGAG                         GCAGAGCGTGAAATACAGAAGGGACCGCATGAGAACCTTCAAGGTTTCCTA
genomic: CGCTGCGCTCCGCGGATGTGATCCTCACCCAGTTCGACAGGACCCGAGAGgtgcttcctc ... atatgtacagGCAGAGCGTGAAATACAGAAGGGGCCGCATGAGAACCTTCAAGGTTTCCTA
EST: gi|60358995|gb|DN225968.1|DN225968
EST:     CGCTGCGCTCCGCGGATGTGATCCTCACCCAGTTCGACAGGACCCGAGAG                         GCAGAGCGTGAAATACAGAAGGGGCCGCATGAGAACCTTCAAGGTTTCCTA
genomic: CGCTGCGCTCCGCGGATGTGATCCTCACCCAGTTCGACAGGACCCGAGAGgtgcttcctc ... atatgtacagGCAGAGCGTGAAATACAGAAGGGGCCGCATGAGAACCTTCAAGGTTTCCTA
EST: gi|149098030|gb|EE183977.2|EE183977
EST:     CGCTGCGCTCCGCGGATGTGATCCTCACCCAGTTCGACAGGACCCGAGAG                         GCAGAGCGTGAAATACAGAAGGCGCCGCATGAGAACCTTCAAGGTTTCCTA
genomic: CGCTGCGCTCCGCGGATGTGATCCTCACCCAGTTCGACAGGACCCGAGAGgtgcttcctc ... atatgtacagGCAGAGCGTGAAATACAGAAGGGGCCGCATGAGAACCTTCAAGGTTTCCTA
EST: gi|148983420|gb|EE029420.2|EE029420
EST:     CGCTGCGCTCCGCGGATGTGATCCTCACCCAGTTCGACAGGACCCGAGAG                         GCAGAGCGTGAAATACAGAAGGGGCCGCATGAGAACCTTCAAGGTTTCCTA
genomic: CGCTGCGCTCCGCGGATGTGATCCTCACCCAGTTCGACAGGACCCGAGAGgtgcttcctc ... atatgtacagGCAGAGCGTGAAATACAGAAGGGGCCGCATGAGAACCTTCAAGGTTTCCTA
EST: gi|211425851|gb|FL143024.1|FL143024
EST:     CGCTGCGCTCCGCGGATGTGATCCTCACCCAGTTCGACAGGACCCGAGAG                         GCAGAGCGTGAAATACAGAAGGGGCCGCATGAGAACCTTCAAGGTTTCCTA
genomic: CGCTGCGCTCCGCGGATGTGATCCTCACCCAGTTCGACAGGACCCGAGAGgtgcttcctc ... atatgtacagGCAGAGCGTGAAATACAGAAGGGGCCGCATGAGAACCTTCAAGGTTTCCTA
EST: gi|149103987|gb|EE289410.2|EE289410
EST:     CGCTGCGCTCCGCGGATGTGATCCTCACCCAGTTCGACAGGACCCGAGAG                         GCAGAGCGTGAAATACAGAAGGGGCCGCATGAGAACCTTCAAGGTTTCCTA
genomic: CGCTGCGCTCCGCGGATGTGATCCTCACCCAGTTCGACAGGACCCGAGAGgtgcttcctc ... atatgtacagGCAGAGCGTGAAATACAGAAGGGGCCGCATGAGAACCTTCAAGGTTTCCTA
EST: gi|211425859|gb|FL143032.1|FL143032
EST:     CGCTGCGCTCCGCGGATGTGATCCTCACCCAGTTCGACAGGACCCGAGAG                         GCAGAGCGTGAAATACAGAAGGGGCCGCATGAGAACCTTCAAGGTTTCCTA
genomic: CGCTGCGCTCCGCGGATGTGATCCTCACCCAGTTCGACAGGACCCGAGAGgtgcttcctc ... atatgtacagGCAGAGCGTGAAATACAGAAGGGGCCGCATGAGAACCTTCAAGGTTTCCTA
EST: gi|78117266|gb|DV535653.1|DV535653
EST:     CGCTGCGCTCCGCGGATGTGATCCTCACCCAGTTCGACAGGACCCGAGAG                         GCAGAGCGTGAAATACAGAAGGGGCCGCATGAGAACCTTCAAGGTTTCCTA
genomic: CGCTGCGCTCCGCGGATGTGATCCTCACCCAGTTCGACAGGACCCGAGAGgtgcttcctc ... atatgtacagGCAGAGCGTGAAATACAGAAGGGGCCGCATGAGAACCTTCAAGGTTTCCTA
EST: gi|211425854|gb|FL143027.1|FL143027
EST:     CGCTGCGCTCCGCGGATGTGATCCTCACCCAGTTCGACAGGACCCGAGAG                         GCAGAGCGTGAAATACAGAAGGGACCGCATGAGAACCTTCAAGGTTTCCTA
genomic: CGCTGCGCTCCGCGGATGTGATCCTCACCCAGTTCGACAGGACCCGAGAGgtgcttcctc ... atatgtacagGCAGAGCGTGAAATACAGAAGGGGCCGCATGAGAACCTTCAAGGTTTCCTA
EST: gi|211428443|gb|FL143034.1|FL143034
EST:     CGCTGCGCTCCGCGGATGTGATCCTCACCCAGTTCGACAGGACCCGAGAG                         GCAGAGCGTGAAATACAGAAGGGACCGCATGAGAACCTTCAAGGTTTCCTA
genomic: CGCTGCGCTCCGCGGATGTGATCCTCACCCAGTTCGACAGGACCCGAGAGgtgcttcctc ... atatgtacagGCAGAGCGTGAAATACAGAAGGGGCCGCATGAGAACCTTCAAGGTTTCCTA
EST: gi|211425856|gb|FL143029.1|FL143029
EST:     CGCTGCGCTCCGCGGATGTGATCCTCACCCAGTTCGACAGGACCCGAGAG                         GCAGAGCGTGAAATACAGAAGGGACCGCATGAGAACCTTCAAGGTTTCCTA
genomic: CGCTGCGCTCCGCGGATGTGATCCTCACCCAGTTCGACAGGACCCGAGAGgtgcttcctc ... atatgtacagGCAGAGCGTGAAATACAGAAGGGGCCGCATGAGAACCTTCAAGGTTTCCTA
EST: gi|211425853|gb|FL143026.1|FL143026
EST:     CGCTGCGCTCCGCGGATGTGATCCTCACCCAGTTCGACAGGACCCGAGAG                         GCAGAGCGTGAAATACAGAAGGGACCGCATGAGAACCTTCAAGGTTTCCTA
genomic: CGCTGCGCTCCGCGGATGTGATCCTCACCCAGTTCGACAGGACCCGAGAGgtgcttcctc ... atatgtacagGCAGAGCGTGAAATACAGAAGGGGCCGCATGAGAACCTTCAAGGTTTCCTA
EST: gi|211425852|gb|FL143025.1|FL143025
EST:     CGCTGCGCTCCGCGGATGTGATCCTCACCCAGTTCGACAGGACCCGAGAG                         GCAGAGCGTGAAATACAGAAGGGACCGCATGAGAACCTTCAAGGTTTCCTA
genomic: CGCTGCGCTCCGCGGATGTGATCCTCACCCAGTTCGACAGGACCCGAGAGgtgcttcctc ... atatgtacagGCAGAGCGTGAAATACAGAAGGGGCCGCATGAGAACCTTCAAGGTTTCCTA
EST: gi|149089875|gb|EE179160.2|EE179160
EST:     CGCTGCGCTCCGCGGATGTGATCCTCACCCAGTTCGACAGGACCCGAGAG                         GCAGAGCGTGAAATACAGAAGGGGCCGCATGAGAACCTTCAAGGTTTCCTA
genomic: CGCTGCGCTCCGCGGATGTGATCCTCACCCAGTTCGACAGGACCCGAGAGgtgcttcctc ... atatgtacagGCAGAGCGTGAAATACAGAAGGGGCCGCATGAGAACCTTCAAGGTTTCCTA
EST: gi|149088666|gb|EE177784.2|EE177784
EST:     CGCTGCGCTCCGCGGATGTGATCCTCACCCAGTTCGACAGGACCCGAGAG                         GCAGAGCGTGAAATACAGAAGGGGCCGCATGAGAACCTTCAAGGTTTCCTA
genomic: CGCTGCGCTCCGCGGATGTGATCCTCACCCAGTTCGACAGGACCCGAGAGgtgcttcctc ... atatgtacagGCAGAGCGTGAAATACAGAAGGGGCCGCATGAGAACCTTCAAGGTTTCCTA
EST: gi|149090520|gb|EE179830.2|EE179830
EST:     CGCTGCGCTCCGCGGATGTGATCCTCACCCAGTTCGACAGGACCCGAGAG                         GCAGAGCGTGAAATACAGAAGGGGCCGCATGAGAACCTTCAAGGTTTCCTA
genomic: CGCTGCGCTCCGCGGATGTGATCCTCACCCAGTTCGACAGGACCCGAGAGgtgcttcctc ... atatgtacagGCAGAGCGTGAAATACAGAAGGGGCCGCATGAGAACCTTCAAGGTTTCCTA

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 94

GTGAGGACGCACGCCGTTCGGACCGCGCACGAGAACATCGACCGCACGCTGCGCTCCGCGGATGTGATCCTCACCCAGTTCGACAGGACCCGAGAGgtgcttcctc ... atatgtacagGCAGAGCGTGAAATACAGAAGGGGCCGCATGAGAACCTTCAAGGTTTCCTAGATGCAGTTGATCGCTTGAGAAGTATTGAGCGTTTCTTTAGTTCAAATC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 139

GTGAGGACGCACGCCGTTCGGACCGCGCACGAGAACATCGACCGCACGCTGCGCTCCGCGGATGTGATCCTCACCCAGTTCGACAGGACCCGAGAGgtgcttcctc ... atatgtacagGCAGAGCGTGAAATACAGAAGGGGCCGCATGAGAACCTTCAAGGTTTCCTAGATGCAGTTGATCGCTTGAGAAGTATTGAGCGTTTCTTTAGTTCAAATC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 132

GTGAGGACGCACGCCGTTCGGACCGCGCACGAGAACATCGACCGCACGCTGCGCTCCGCGGATGTGATCCTCACCCAGTTCGACAGGACCCGAGAGgtgcttcctc ... atatgtacagGCAGAGCGTGAAATACAGAAGGGGCCGCATGAGAACCTTCAAGGTTTCCTAGATGCAGTTGATCGCTTGAGAAGTATTGAGCGTTTCTTTAGTTCAAATC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 79

GTGAGGACGCACGCCGTTCGGACCGCGCACGAGAACATCGACCGCACGCTGCGCTCCGCGGATGTGATCCTCACCCAGTTCGACAGGACCCGAGAGgtgcttcctc ... atatgtacagGCAGAGCGTGAAATACAGAAGGGGCCGCATGAGAACCTTCAAGGTTTCCTAGATGCAGTTGATCGCTTGAGAAGTATTGAGCGTTTCTTTAGTTCAAATC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGAGGACGCACGCCGTTCGGACCGCGCACGAGAACATCGACCGCACGCTGCGCTCCGCGGATGTGATCCTCACCCAGTTCGACAGGACCCGAGAGgtgcttcctcctaacttcactcctcccatgctcgtcgattgagtttcacgctatgtgcatccccgcgtacttgcaagtcggacctgcagtttaatctagc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctcctccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tccccgc