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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCACTACCCTTGAGGAGGTGAAGTACGAGGACATCGACCGTCTGTTCCAGCCGTTCAGTCCGGAGCTGGAACTTCAGGTCCCATCTGATGATTCCAACAGgtgggctgtgactccccttgaatctcacacatcactcatggatcctgcatacatataaccaacgcatttgacatcatcaaaaccaacaaaatgcag

Basic information

species Zea mays
transcript GRMZM2G042818_T01
intron # 14
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G042818_T01 (Zea mays), 5'ss of exon 14
lower sequence: LOC_Os01g54860.1 (Oryza sativa), 5'ss of exon 14
CCACTACCCTTGAGGAGGTGAAGTACGAGGACATCGACCGTCTGTTCCAGCCGTTCAGTCCGGAGCTGGAACTTCAGGTCCCATCTGATGATTCCAACAGgtgggctgtgactcc--------ccttgaatctc-acacatcactcatggatcc-tgcatacatataaccaacgcatttgacatcatcaaaaccaacaaaatgcag
|  |||||||||||||||| ||| ||||||||||||||||||| ||| | || |||||| | ||   ||| || || ||||||||||| ||||||||||||||  |  |  ||||          |    ||||  | | |||| ||   | |  || || |  || | |  | |  ||  ||   |  | |   ||||    |||
CTGCTACCCTTGAGGAGGTCAAGAACGAGGACATCGACCGTCTTTTCGAACCATTCAGTTCAGAAAAGGAGCTCCAAGTCCCATCTGACGATTCCAACAGgtgaacaattgctccaaaatccatttcttttctctgcccttcacacaaacaacagtgtatcctaatcatctgcactatttccaattttgacatggacaatgcacag
















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|74240479|gb|DT648393.1|DT648393
EST:     CCGTTCAGTCCGGAGCTGGAACTTCAGGTCCCATCTGATGATTCCAACAG                         GTGGAGCGGCAAATACGAGAACACGGTCTATGGCAGAGCTTCCCAGTGACT
genomic: CCGTTCAGTCCGGAGCTGGAACTTCAGGTCCCATCTGATGATTCCAACAGgtgggctgtg ... caaaatgcagGTGGAGCGGCAAATACGAGAACACGGTCTATGGCAGAGCTTCCCAGTGACT
EST: gi|15053507|gb|BI359052.1|BI359052
EST:     CCGTTCAGTCCGGAGCTGGAACTTCAGGTCCCATCTGATGATTCCAACAG                         GTGGAGCGGCAAATACGAGAACACGGTCTATGGCAGAGCTTCCCCAGTGCC
genomic: CCGTTCAGTCCGGAGCTGGAACTTCAGGTCCCATCTGATGATTCCAACAGgtgggctgtg ... caaaatgcagGTGGAGCGGCAAATACGAGAACACGGTCTATGGCAGAGCTTCCC-AGTGAC
EST: gi|32938089|gb|CF042908.1|CF042908
EST:     CCGTTCAGTCCAGAGCTGGAACTTCAGGTCCCATCTGATGATTCCAACAG                         GTGGAGCGGCAAATACGAGAACCCGGTCTATGGCAGAGCTTCCCAGTGACT
genomic: CCGTTCAGTCCGGAGCTGGAACTTCAGGTCCCATCTGATGATTCCAACAGgtgggctgtg ... caaaatgcagGTGGAGCGGCAAATACGAGAACACGGTCTATGGCAGAGCTTCCCAGTGACT
EST: gi|29544823|gb|CB605431.1|CB605431
EST:     CCGTTCAGTCCGGAGCTGGAACTTCAGGTCCCATCTGATGATTCCAACAG                         GTGGAGCGGCAAATACGAGAACACGGTCTATGGCAGAGCTTCCCAGTGACT
genomic: CCGTTCAGTCCGGAGCTGGAACTTCAGGTCCCATCTGATGATTCCAACAGgtgggctgtg ... caaaatgcagGTGGAGCGGCAAATACGAGAACACGGTCTATGGCAGAGCTTCCCAGTGACT
EST: gi|37400624|gb|CF637668.1|CF637668
EST:     CCGTTCAGTCCGGAGCTGGAACTTCAGGTCCCATCTGATGATTCCAACAG                         GTGGAGCGGCAAATACGAGAACACGGTCTATGGCAGAGCTTCCCAGTGACT
genomic: CCGTTCAGTCCGGAGCTGGAACTTCAGGTCCCATCTGATGATTCCAACAGgtgggctgtg ... caaaatgcagGTGGAGCGGCAAATACGAGAACACGGTCTATGGCAGAGCTTCCCAGTGACT
EST: gi|161591487|gb|EY962862.1|EY962862
EST:     CGGAGCTGGAACTTCAGGTCCCATCTGATGATTCCAACAG                         GTGGAGCGGCAAATACGAGAACACGGTCTATGGCAGAGCTTCCCAGTGACT
genomic: CGGAGCTGGAACTTCAGGTCCCATCTGATGATTCCAACAGgtgggctgtg ... caaaatgcagGTGGAGCGGCAAATACGAGAACACGGTCTATGGCAGAGCTTCCCAGTGACT
EST: gi|15057208|gb|BI361180.1|BI361180
EST:     CCGTTCAGTCCGGAGCTGGAACTTCAGGTCCCATCTGATGATTCCAACAG                         GTGGAGCGGCAAATACGAGAACACGGTCTATGGCAGAGCTTCCCAGTGACT
genomic: CCGTTCAGTCCGGAGCTGGAACTTCAGGTCCCATCTGATGATTCCAACAGgtgggctgtg ... caaaatgcagGTGGAGCGGCAAATACGAGAACACGGTCTATGGCAGAGCTTCCCAGTGACT
EST: gi|148959114|gb|EC905254.2|EC905254
EST:     CCGTTCAGTCCGGAGCTGGAACTTCAGGTCCCATCTGATGATTCCAACAG                         GTGGAGCGGCAAATACGAGAACACGGTCTATGGCAGAGCTTCCCAGTGACT
genomic: CCGTTCAGTCCGGAGCTGGAACTTCAGGTCCCATCTGATGATTCCAACAGgtgggctgtg ... caaaatgcagGTGGAGCGGCAAATACGAGAACACGGTCTATGGCAGAGCTTCCCAGTGACT
EST: gi|45568357|gb|CK986026.1|CK986026
EST:     CCGTTCAGTCCGGAGCTGGAACTTCAGGTCCCATCTGATGATTCCAACAG                         GTGGAGCGGCAAATACGAGAACACGGTCTATGGCAGAGCTTCCCAGTGACT
genomic: CCGTTCAGTCCGGAGCTGGAACTTCAGGTCCCATCTGATGATTCCAACAGgtgggctgtg ... caaaatgcagGTGGAGCGGCAAATACGAGAACACGGTCTATGGCAGAGCTTCCCAGTGACT
EST: gi|45847153|gb|CN071096.1|CN071096
EST:     CCGTTCAGTCCGGAGCTGGAACTTCAGGTCCCATCTGATGATTCCAACAG                         GTGGAGCGGCAAATAACGAGAACACGGTCTATGGCAGAGCTTCCCA
genomic: CCGTTCAGTCCGGAGCTGGAACTTCAGGTCCCATCTGATGATTCCAACAGgtgggctgtg ... caaaatgcagGTGGAGCGGCAAATA-CGAGAACACGGTCTATGGCAGAGCTTCCCA
EST: gi|37392700|gb|CF633603.1|CF633603
EST:     CCGTTCAGTCCGGAGCTGGAACTTCAGGTCCCATCTGATGATTCCAACAG                         GTGGAGCGGCAAATACGAGAACACGGTCTATGGCAGAGCTTCCCAGTGACT
genomic: CCGTTCAGTCCGGAGCTGGAACTTCAGGTCCCATCTGATGATTCCAACAGgtgggctgtg ... caaaatgcagGTGGAGCGGCAAATACGAGAACACGGTCTATGGCAGAGCTTCCCAGTGACT
EST: gi|32849451|gb|CD989132.1|CD989132
EST:     CCGTTCAGTCCGGAGCTGGAACTTCAGGTCCCATCTGATGATTCCAACAG                         GTGGAGCGGCAAATACGAGAACACGGTCTATGGCAGAGCTTCCCAGTGACT
genomic: CCGTTCAGTCCGGAGCTGGAACTTCAGGTCCCATCTGATGATTCCAACAGgtgggctgtg ... caaaatgcagGTGGAGCGGCAAATACGAGAACACGGTCTATGGCAGAGCTTCCCAGTGACT
EST: gi|45847757|gb|CN071700.1|CN071700
EST:     CCGTTCAGTCCGGAGCTGGAACTTCAGGTCCCATCTGATGATTCCAACAG                         GTGGAGCGGCAAATACGAGAACACGGTCTA
genomic: CCGTTCAGTCCGGAGCTGGAACTTCAGGTCCCATCTGATGATTCCAACAGgtgggctgtg ... caaaatgcagGTGGAGCGGCAAATACGAGAACACGGTCTA
EST: gi|33092056|gb|CF052050.1|CF052050
EST:     CCGTTCAGTCCGGAGCTGGAACTTCAGGTCCCATCTGATGATTCCAACAG                         GTGGAGCGGCAAATACGAGAACACGGTCTATGGCAGAGCTTCCCAGTGACT
genomic: CCGTTCAGTCCGGAGCTGGAACTTCAGGTCCCATCTGATGATTCCAACAGgtgggctgtg ... caaaatgcagGTGGAGCGGCAAATACGAGAACACGGTCTATGGCAGAGCTTCCCAGTGACT
EST: gi|71304194|gb|DR788217.1|DR788217
EST:     CCGTTCAGTCCGGAGCTGGAACTTCAGGTCCCATCTGATGATTCCAACAG                         GTGGAGCGGCAAATACGAGAACACGGTCTATGGCAGAGCTTCCCAGTGACT
genomic: CCGTTCAGTCCGGAGCTGGAACTTCAGGTCCCATCTGATGATTCCAACAGgtgggctgtg ... caaaatgcagGTGGAGCGGCAAATACGAGAACACGGTCTATGGCAGAGCTTCCCAGTGACT
EST: gi|29544214|gb|CB604594.1|CB604594
EST:     CCGTTCAGTCCGGAGCTGGAACTTCAGGTCCCATCTGATGATTCCAACAG                         GTGGAGCGGCAAATACGAGAACNCGGTCTATGGCAGAGCTTCCCAGTGACT
genomic: CCGTTCAGTCCGGAGCTGGAACTTCAGGTCCCATCTGATGATTCCAACAGgtgggctgtg ... caaaatgcagGTGGAGCGGCAAATACGAGAACACGGTCTATGGCAGAGCTTCCCAGTGACT
EST: gi|37383733|gb|CF628896.1|CF628896
EST:     CCGTTCAGTCCGGAGCTGGAACTTCAGGTCCCATCTGATGATTCCAACAG                         GTGGAGCGGCAAATACGAGAACACGGTCTATGGCAGAGCTTCCCAGTGACT
genomic: CCGTTCAGTCCGGAGCTGGAACTTCAGGTCCCATCTGATGATTCCAACAGgtgggctgtg ... caaaatgcagGTGGAGCGGCAAATACGAGAACACGGTCTATGGCAGAGCTTCCCAGTGACT
EST: gi|40303747|gb|CK348134.1|CK348134
EST:     CCGTTCAGTCCGGAGCTGGAACTTCAGGTCCCATCTGATGATTCCAACAG                         GTGGAGCGGCAAATACGAGAACACGGTCTATGGCAGAGCTTCCCAGTGACT
genomic: CCGTTCAGTCCGGAGCTGGAACTTCAGGTCCCATCTGATGATTCCAACAGgtgggctgtg ... caaaatgcagGTGGAGCGGCAAATACGAGAACACGGTCTATGGCAGAGCTTCCCAGTGACT
EST: gi|84970253|gb|DW468603.1|DW468603
EST:     CCGTTCAGTCCGGAGCGGGAACTTCAGGTCCCATCTGATGATTCCAACAG                         GTGGAGCGGCAAATACGAGAACACGGTCTATGGCAGAGCTTCCCAGTGACT
genomic: CCGTTCAGTCCGGAGCTGGAACTTCAGGTCCCATCTGATGATTCCAACAGgtgggctgtg ... caaaatgcagGTGGAGCGGCAAATACGAGAACACGGTCTATGGCAGAGCTTCCCAGTGACT
EST: gi|91053743|gb|EB164161.1|EB164161
EST:     CCGTTCAGTCCGGAGCTGGAACTTCAGGTCCCATCTGATGATTCCAACAG                         GTGGAGCGGCAAATACGAGAACACGGTCTATGGCAGAGCTTCCCAGTGACT
genomic: CCGTTCAGTCCGGAGCTGGAACTTCAGGTCCCATCTGATGATTCCAACAGgtgggctgtg ... caaaatgcagGTGGAGCGGCAAATACGAGAACACGGTCTATGGCAGAGCTTCCCAGTGACT
EST: gi|74239819|gb|DT647733.1|DT647733
EST:     CCGTTCAGTCCGGAGCTGGAACTTCAGGTCCCATCTGATGATTCCAACAG                         GTGGAGCGGCAAATACGAGAACACGGTCTATGGCAGAGCTTCCCAGTGACT
genomic: CCGTTCAGTCCGGAGCTGGAACTTCAGGTCCCATCTGATGATTCCAACAGgtgggctgtg ... caaaatgcagGTGGAGCGGCAAATACGAGAACACGGTCTATGGCAGAGCTTCCCAGTGACT
EST: gi|211149870|gb|FL475634.1|FL475634
EST:     CCGTTCAGTCCGGAGCTGGAACTTCAGGTCCCATCTGATGATTCCAACAG                         GTGGAGCGGCAAATACGAGAACACGGTCTATGGCAGAGCTTCCCAGTGACT
genomic: CCGTTCAGTCCGGAGCTGGAACTTCAGGTCCCATCTGATGATTCCAACAGgtgggctgtg ... caaaatgcagGTGGAGCGGCAAATACGAGAACACGGTCTATGGCAGAGCTTCCCAGTGACT
EST: gi|37379687|gb|CF626591.1|CF626591
EST:     CCGTTCAGTCCGGAGCTGGAACTTCAGGTCCCATCTGATGATTCCAACAG                         GTGGAGCGGCAAATACGAGAACACGGTCTATGGCAGAGCTTCCCAGTGACT
genomic: CCGTTCAGTCCGGAGCTGGAACTTCAGGTCCCATCTGATGATTCCAACAGgtgggctgtg ... caaaatgcagGTGGAGCGGCAAATACGAGAACACGGTCTATGGCAGAGCTTCCCAGTGACT
EST: gi|71762792|gb|DR960729.1|DR960729
EST:     CCGTTCAGTCCGGAGCTGGAACTTCAGGTCCCATCTGATGATTCCAACAG                         GTGGAGCGGCAAATACGAGAACACGGTCTATGGCAGAGCTTCCCAGTGACT
genomic: CCGTTCAGTCCGGAGCTGGAACTTCAGGTCCCATCTGATGATTCCAACAGgtgggctgtg ... caaaatgcagGTGGAGCGGCAAATACGAGAACACGGTCTATGGCAGAGCTTCCCAGTGACT

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: 49 (upstream exon), 49 (downstream exon)
Score: 64

CCACTACCCTTGAGGAGGTGAAGTACGAGGACATCGACCGTCTGTTCCAGCCGTTCAGTCCGGAGCTGGAACTTCAGGTCCCATCTGATGATTCCAACAGgtgggctgtg ... caaaatgcagGTGGAGCGGCAAATACGAGAACACGGTCTATGGCAGAGCTTCCCAGTGACTGTATACAAGATCCCCCAGCCTTTTGTTATTTTCATCCGAACCACTGCAT


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 209

CCACTACCCTTGAGGAGGTGAAGTACGAGGACATCGACCGTCTGTTCCAGCCGTTCAGTCCGGAGCTGGAACTTCAGGTCCCATCTGATGATTCCAACAGgtgggctgtg ... caaaatgcagGTGGAGCGGCAAATACGAGAACACGGTCTATGGCAGAGCTTCCCAGTGACTGTATACAAGATCCCCCAGCCTTTTGTTATTTTCATCCGAACCACTGCAT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 130

CCACTACCCTTGAGGAGGTGAAGTACGAGGACATCGACCGTCTGTTCCAGCCGTTCAGTCCGGAGCTGGAACTTCAGGTCCCATCTGATGATTCCAACAGgtgggctgtg ... caaaatgcagGTGGAGCGGCAAATACGAGAACACGGTCTATGGCAGAGCTTCCCAGTGACTGTATACAAGATCCCCCAGCCTTTTGTTATTTTCATCCGAACCACTGCAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 298

CCACTACCCTTGAGGAGGTGAAGTACGAGGACATCGACCGTCTGTTCCAGCCGTTCAGTCCGGAGCTGGAACTTCAGGTCCCATCTGATGATTCCAACAGgtgggctgtg ... caaaatgcagGTGGAGCGGCAAATACGAGAACACGGTCTATGGCAGAGCTTCCCAGTGACTGTATACAAGATCCCCCAGCCTTTTGTTATTTTCATCCGAACCACTGCAT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCACTACCCTTGAGGAGGTGAAGTACGAGGACATCGACCGTCTGTTCCAGCCGTTCAGTCCGGAGCTGGAACTTCAGGTCCCATCTGATGATTCCAACAGgtgggctgtgactccccttgaatctcacacatcactcatggatcctgcatacatataaccaacgcatttgacatcatcaaaaccaacaaaatgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA