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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGCTACGTGTCTCAGGAAGATGTTGACATGGCCATCCGTGTCTTGCTTGACTCTTTTATTTCGACTCAGAAGTTCGGTGTGCAGAAAGCACTTCAAAAGgtaagttttgttggtgttgagctgttattacatcatccagtgctacacaagtacatgcacttgataaacaatttaatgtaaaagtgctcatccatttaac...

Basic information

species Zea mays
transcript GRMZM2G139894_T01
intron # 16
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G139894_T02 (Zea mays), 5'ss of exon 16
lower sequence: LOC_Os11g29380.1 (Oryza sativa), 5'ss of exon 16
GAGCTACGTGTCTCAGGAAGATGTTGACATGGCCATCCGTGTCTTGCTTGACTCTTTTATTTCGACTCAGAAGTTCGGTGTGCAGAAAGCACTTCAAAAGgtaagttttg---ttggtgttgagctgttattacatcatccagtgctacacaagtacatgcacttgataaacaatttaatgtaaaagtgctcatccatttaac
|||||||||||||||||||||||| |||||||| ||||| ||| |||||||||| |||||||| ||||||||||| ||||| |||||||||||||||||||||| |||||   ||| |||||   || ||||  ||||||   | | ||  | | | |   |           |  |  |||||     || |    ||||  
GAGCTACGTGTCTCAGGAAGATGTCGACATGGCTATCCGCGTCCTGCTTGACTCATTTATTTCAACTCAGAAGTTTGGTGTACAGAAAGCACTTCAAAAGgtaaattttgattttgctgttgtattgctattctatcatct--tccaactgatgcatacctagcatgagtttgaactgttgtaagctgccttagttttttag-

upper sequence: GRMZM2G139894_T02 (Zea mays), 5'ss of exon 16
lower sequence: Vv01s0150g00390.t01 (Vitis vinifera), 5'ss of exon 15
GAGCTACGTGTCTCAGGAAGATGTTGACATGGCCATCCGTGTCTTGCTTGACTCTTTTATTTCGACTCAGAAGTTCGGTGTGCAGAAAGCACTTCAAAAGgtaagttttgttggtgttgagctgttattacatcatccagtgctacacaagtaca-tgcacttgataaacaatttaatgtaaaagtgctcatccatttaac
     | ||  | |||||||||||||||||||| || |||||| ||||||| ||||| ||||| || || || ||||| ||||||||||| || |||||||||           | ||   || |   | | | | ||| |  |   |   || | |  | |  |||      |  |  | |   |     |  | | || 
ACAGCATGTTACCCAGGAAGATGTTGACATGGCTATTCGTGTCCTGCTTGATTCTTTCATTTCAACACAAAAATTCGGGGTGCAGAAAGCCCTACAAAAGgtactgaaaagatatatttgcctttgcattccttaaccattctttttctcttagaatatattctatatgtttgtcca-atgatcctatcattggaatcaat
















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|29544223|gb|CB604603.1|CB604603
EST:     ACTCTTTTATTTCGACTCAGAAGTTCGGTGTGCAGAAAGCACTTCAAAAG                         AATTTCCGGAAGTACATGACATTCAAGAAGGACTACAACGAGCTGCTCCTG
genomic: ACTCTTTTATTTCGACTCAGAAGTTCGGTGTGCAGAAAGCACTTCAAAAGgtaagttttg ... gtgtccacagAATTTCCGGAAGTACATGACATTCAAGAAGGACTACAACGAGCTGCTCCTG
EST: gi|87153156|gb|DY397945.1|DY397945
EST:     ACTCTTTTATTTCGACTCAGAAATTCGGTGTGCAGAAAGCACTCCAAAAG                         AATTTCCGGAAGTACATGACATTCAAGAAGGACTACAACGAGCTGCTCCTG
genomic: ACTCTTTTATTTCGACTCAGAAGTTCGGTGTGCAGAAAGCACTTCAAAAGgtaagttttg ... gtgtccacagAATTTCCGGAAGTACATGACATTCAAGAAGGACTACAACGAGCTGCTCCTG
EST: gi|60340933|gb|DN207906.1|DN207906
EST:     ACTCTTTTATTTCGACTCAGAAGTTCGGTGTGCAGAAAGCACTTCAAAAG                         AATTTCCGGAAGTACATGACATTCAAGAAGGACTACAACGAGCTGCTCCTG
genomic: ACTCTTTTATTTCGACTCAGAAGTTCGGTGTGCAGAAAGCACTTCAAAAGgtaagttttg ... gtgtccacagAATTTCCGGAAGTACATGACATTCAAGAAGGACTACAACGAGCTGCTCCTG
EST: gi|78125563|gb|DV543947.1|DV543947
EST:     ACTCTTTTATTTCGACTCAGAAGTTCGGTGTGCAGAAAGCACTTCAAAAG                         AATTTCCGGAAGTACATGACATTCAAGAAGGACTACAACGAGCTGCTCCTG
genomic: ACTCTTTTATTTCGACTCAGAAGTTCGGTGTGCAGAAAGCACTTCAAAAGgtaagttttg ... gtgtccacagAATTTCCGGAAGTACATGACATTCAAGAAGGACTACAACGAGCTGCTCCTG
EST: gi|33093214|gb|CF053208.1|CF053208
EST:     ACTCTTTTATTTCGACTCAGAAATTCGGTGTGCAGAAAGCACTCCAAAAG                         AATTTCCGGAAGT
genomic: ACTCTTTTATTTCGACTCAGAAGTTCGGTGTGCAGAAAGCACTTCAAAAGgtaagttttg ... gtgtccacagAATTTCCGGAAGT
EST: gi|78109714|gb|DV528130.1|DV528130
EST:     ACTCTTTTATTTCGACTCAGAAGTTCGGTGTGCAGAAAGCACTTCAAAAG                         AATTTCCGGAAGTACATGACATTCAAGAAGGATTACAACGAGCTGCTCCTG
genomic: ACTCTTTTATTTCGACTCAGAAGTTCGGTGTGCAGAAAGCACTTCAAAAGgtaagttttg ... gtgtccacagAATTTCCGGAAGTACATGACATTCAAGAAGGACTACAACGAGCTGCTCCTG
EST: gi|76286756|gb|DV026324.1|DV026324
EST:     GCACTTCAAAAG                         AATTTCCGGAAGTACATGACATTCAAGAAGGACTACAACGAGCTGCTCCTG
genomic: GCACTTCAAAAGgtaagttttg ... gtgtccacagAATTTCCGGAAGTACATGACATTCAAGAAGGACTACAACGAGCTGCTCCTG
EST: gi|5055638|gb|AI734525.1|AI734525
EST:     ACTCTTTTATTTCGACTCAGAAATTCGGTGTGCAGAAAGCACTTCAAAAG                         AATTTCCGAAAGTACATGACATTCAAGAAGGACTCCAACGAGCTGCTCCTG
genomic: ACTCTTTTATTTCGACTCAGAAGTTCGGTGTGCAGAAAGCACTTCAAAAGgtaagttttg ... gtgtccacagAATTTCCGGAAGTACATGACATTCAAGAAGGACTACAACGAGCTGCTCCTG
EST: gi|19822702|gb|BQ048726.1|BQ048726
EST:     ACTCTTTTATTTCGACTCAGAAATTCGGTGTGCAGAAAGCACTCCAAAAG                         AATTTCCGGAAGTACATGACATTCAAGAAGGACTACAACGAGCTGCTCCTG
genomic: ACTCTTTTATTTCGACTCAGAAGTTCGGTGTGCAGAAAGCACTTCAAAAGgtaagttttg ... gtgtccacagAATTTCCGGAAGTACATGACATTCAAGAAGGACTACAACGAGCTGCTCCTG
EST: gi|32931979|gb|CF036791.1|CF036791
EST:     ACTCTTTTATTTCGACTCAGAAATTCGGTGTGCAGAAAGCACTCCAAAAG                         AATTTCCGGAAGT
genomic: ACTCTTTTATTTCGACTCAGAAGTTCGGTGTGCAGAAAGCACTTCAAAAGgtaagttttg ... gtgtccacagAATTTCCGGAAGT
EST: gi|78023863|gb|DV492250.1|DV492250
EST:     ACTCTTTTATTTCGACTCAGAAATTCGGTGTGCAGAAAGCACTTCAAAAG                         AATTTCCGGAAGTACATGACATTCAAGAAGGACTACAACGAGCTGCTCCTG
genomic: ACTCTTTTATTTCGACTCAGAAGTTCGGTGTGCAGAAAGCACTTCAAAAGgtaagttttg ... gtgtccacagAATTTCCGGAAGTACATGACATTCAAGAAGGACTACAACGAGCTGCTCCTG
EST: gi|32934497|gb|CF039309.1|CF039309
EST:     ACTCTTTTATTTCGACTCAGAAATTCGGTGTGCAGAAAGCACTCCAAAAG                         AATTTCCGGAAGT
genomic: ACTCTTTTATTTCGACTCAGAAGTTCGGTGTGCAGAAAGCACTTCAAAAGgtaagttttg ... gtgtccacagAATTTCCGGAAGT
EST: gi|76280576|gb|DV020144.1|DV020144
EST:     GCACTTCAAAAG                         AATTTCCGGAAGTACATGACATTCAAGAAGGACTACAACGAGCTGCTCCTG
genomic: GCACTTCAAAAGgtaagttttg ... gtgtccacagAATTTCCGGAAGTACATGACATTCAAGAAGGACTACAACGAGCTGCTCCTG
EST: gi|60351822|gb|DN218795.1|DN218795
EST:     ACTCTTTTATTTCGACTCAGAAGTTCGGTGTGCAGAAAGCACTTCAAAAG                         AATTTCCGGAAGTACATGACATTCAAGAAGGACTACAACGAGCTGCTCCTG
genomic: ACTCTTTTATTTCGACTCAGAAGTTCGGTGTGCAGAAAGCACTTCAAAAGgtaagttttg ... gtgtccacagAATTTCCGGAAGTACATGACATTCAAGAAGGACTACAACGAGCTGCTCCTG
EST: gi|18450515|gb|BM428793.1|BM428793
EST:     ACTCTTTTATTTCGACTCAGAAATTCGGTGTGCAGAAAGCACTCCAAAAG                         AATTTCCGGAAGTACATGACATTCAAGAAGGACTACAACGAGCTGCTCCTG
genomic: ACTCTTTTATTTCGACTCAGAAGTTCGGTGTGCAGAAAGCACTTCAAAAGgtaagttttg ... gtgtccacagAATTTCCGGAAGTACATGACATTCAAGAAGGACTACAACGAGCTGCTCCTG
EST: gi|22521025|gb|BU079836.1|BU079836
EST:     AGAAATTCGGTGTGCAGAAAGCCCTTCAAAAG                         AATTTCCGGAAGTACATGACATTCAAGAAGGGCTACAACGAGCTGCTCCTG
genomic: AGAAGTTCGGTGTGCAGAAAGCACTTCAAAAGgtaagttttg ... gtgtccacagAATTTCCGGAAGTACATGACATTCAAGAAGGACTACAACGAGCTGCTCCTG
EST: gi|32932452|gb|CF037264.1|CF037264
EST:     ACTCTTTTATTTCGACTCAGAAATTCGGTGTGCAGAAAGCACTCCAAAAG                         AATTTCCGGAAGT
genomic: ACTCTTTTATTTCGACTCAGAAGTTCGGTGTGCAGAAAGCACTTCAAAAGgtaagttttg ... gtgtccacagAATTTCCGGAAGT
EST: gi|22521026|gb|BU079837.1|BU079837
EST:     ACTCTTTTATTTCGACTCAGAAATTCGGTGTGCAGAAAGCACTTCAAAAG                         AATTTCCGGAAGTACATGACATTCAAGAAGGACTACAACGAGCTGCTCCTG
genomic: ACTCTTTTATTTCGACTCAGAAGTTCGGTGTGCAGAAAGCACTTCAAAAGgtaagttttg ... gtgtccacagAATTTCCGGAAGTACATGACATTCAAGAAGGACTACAACGAGCTGCTCCTG
EST: gi|22715477|gb|BU197786.1|BU197786
EST:     ACTCTTTTATTTCGACTCAGAAATTCGG-GTGCAGAAAGCACTTCAAAAG                         AATTTCCGGAAGTACATGACATTCAAGAAGGACTACAACGAGCTGCTCCTG
genomic: ACTCTTTTATTTCGACTCAGAAGTTCGGTGTGCAGAAAGCACTTCAAAAGgtaagttttg ... gtgtccacagAATTTCCGGAAGTACATGACATTCAAGAAGGACTACAACGAGCTGCTCCTG
EST: gi|32932490|gb|CF037302.1|CF037302
EST:     ACTCTTTTATTTCGACTCAGAAATTCGGTGTGCAGAAAGCACTCCAAAAG                         AATTTCCGGAAGT
genomic: ACTCTTTTATTTCGACTCAGAAGTTCGGTGTGCAGAAAGCACTTCAAAAGgtaagttttg ... gtgtccacagAATTTCCGGAAGT
EST: gi|4646684|gb|AI491541.2|AI491541
EST:     ACTCTTTTATTTCGACTCAGAAGTTCGGTGTGCAGAAAGCACTTCAAAAG                         AATTTCCGGAAGTACATGACATTCAAGAAGGACTACAACGAGCTGCTCCTG
genomic: ACTCTTTTATTTCGACTCAGAAGTTCGGTGTGCAGAAAGCACTTCAAAAGgtaagttttg ... gtgtccacagAATTTCCGGAAGTACATGACATTCAAGAAGGACTACAACGAGCTGCTCCTG
EST: gi|60352083|gb|DN219056.1|DN219056
EST:     ACTCTTTTATTTCGACTCAGAAATTCGGTGTGCAGAAAGCACTTCAAAAG                         AATTTCCGGAAGTACATGACATTCAAGAAGGACTACAACGAGCTGCTCCTG
genomic: ACTCTTTTATTTCGACTCAGAAGTTCGGTGTGCAGAAAGCACTTCAAAAGgtaagttttg ... gtgtccacagAATTTCCGGAAGTACATGACATTCAAGAAGGACTACAACGAGCTGCTCCTG
EST: gi|32911609|gb|CF016421.1|CF016421
EST:     ACTCTTTTATTTCGACTCAGAAATTCGGTGTGCAGAAAGCACTCCAAAAG                         AATTTCCGGAAGTACATGACATTCAAGAAGGACTACAACGAGCTGCTCCTG
genomic: ACTCTTTTATTTCGACTCAGAAGTTCGGTGTGCAGAAAGCACTTCAAAAGgtaagttttg ... gtgtccacagAATTTCCGGAAGTACATGACATTCAAGAAGGACTACAACGAGCTGCTCCTG

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: 47 (upstream exon), 49 (downstream exon)
Score: 824

GAGCTACGTGTCTCAGGAAGATGTTGACATGGCCATCCGTGTCTTGCTTGACTCTTTTATTTCGACTCAGAAGTTCGGTGTGCAGAAAGCACTTCAAAAGgtaagttttg ... gtgtccacagAATTTCCGGAAGTACATGACATTCAAGAAGGACTACAACGAGCTGCTCCTGCTGCTCCTGCGCACACTGGTCAAGGACGCCGTGCACTTCGAAGAAATCA


Block sizes: 42 (upstream exon), 48 (downstream exon)
Score: 152

GAGCTACGTGTCTCAGGAAGATGTTGACATGGCCATCCGTGTCTTGCTTGACTCTTTTATTTCGACTCAGAAGTTCGGTGTGCAGAAAGCACTTCAAAAGgtaagttttg ... gtgtccacagAATTTCCGGAAGTACATGACATTCAAGAAGGACTACAACGAGCTGCTCCTGCTGCTCCTGCGCACACTGGTCAAGGACGCCGTGCACTTCGAAGAAATCA


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 87

GAGCTACGTGTCTCAGGAAGATGTTGACATGGCCATCCGTGTCTTGCTTGACTCTTTTATTTCGACTCAGAAGTTCGGTGTGCAGAAAGCACTTCAAAAGgtaagttttg ... gtgtccacagAATTTCCGGAAGTACATGACATTCAAGAAGGACTACAACGAGCTGCTCCTGCTGCTCCTGCGCACACTGGTCAAGGACGCCGTGCACTTCGAAGAAATCA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 78

GAGCTACGTGTCTCAGGAAGATGTTGACATGGCCATCCGTGTCTTGCTTGACTCTTTTATTTCGACTCAGAAGTTCGGTGTGCAGAAAGCACTTCAAAAGgtaagttttg ... gtgtccacagAATTTCCGGAAGTACATGACATTCAAGAAGGACTACAACGAGCTGCTCCTGCTGCTCCTGCGCACACTGGTCAAGGACGCCGTGCACTTCGAAGAAATCA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAGCTACGTGTCTCAGGAAGATGTTGACATGGCCATCCGTGTCTTGCTTGACTCTTTTATTTCGACTCAGAAGTTCGGTGTGCAGAAAGCACTTCAAAAGgtaagttttgttggtgttgagctgttattacatcatccagtgctacacaagtacatgcacttgataaacaatttaatgtaaaagtgctcatccatttaac

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ataaacaa