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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTTTGCATATGGACAGAAACGACTACTATGGAGGAGATTCCACCTCGCTCAACCTTAATCAGgtaagcaactcctataacttctgtttaagtacagagtgttttagatttgtgcatcgatttcttgtcataacaaagcttttgattgattttgctggaacttctaaactgacgtgctttccgctaccttttggaacag

Basic information

species Zea mays
transcript GRMZM2G435373_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G435373_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os05g34540.1 (Oryza sativa), 5'ss of exon 2
GTTTTGCATATGGACAGAAACGACTACTATGGAGGAGATTCCACCTCGCTCAACCTTAATCAGgtaagcaactcctataacttctgtttaagtacagagtgttttagatttgtgcatcgatttctt----------------gtcataacaaag----------cttttgattgattttgctggaacttctaaactgacgt--gctttccgctaccttttggaacag-
|| ||||| ||||| ||||| |||||||||||||| ||||||||||||||||||||||| ||||||||||||||| || |  |   ||| | ||      |||| | ||| | |     |||||||                || || ||  ||          | ||||||| ||| |        || |  |||||| |  | |||    |  ||||||||  |  
GTGTTGCACATGGATAGAAATGACTACTATGGAGGGGATTCCACCTCGCTCAACCTTAACCAGgtaagcaactccaatgaactaaatttgaatagtagaggtttcatattcgcgtgcttatttcttgcgaagggatgcttatgttattacggagtacattatatcctttgattaattctatctttgtttgtttactgacattggttttgaattcgcttttggattaag

upper sequence: GRMZM2G435373_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os05g23860.1 (Oryza sativa), 5'ss of exon 2
GTTTTGCATATGGACAGAAACGACTACTATGGAGGAGATTCCACCTCGCTCAACCTTAATCAGgtaagcaa-ctcctataacttctgtttaa---gtacagagt----gttttagatttgtg------catcgatttct--tgtcataacaaagcttttgattgattttg----ctggaacttctaaactgacgt-gctttccgct--accttttggaacag
|| ||||| ||||| || || |||||||||||||||||||||||||||||||||||||| ||||||||||| || | || |  |   ||| |   |||||| ||     | ||    |  |       ||  || | ||  ||| || ||| ||    | |||  ||||      | |  ||| |  |||||| | | ||||| ||   | |||||||| ||
GTCTTGCACATGGATAGGAATGACTACTATGGAGGAGATTCCACCTCGCTCAACCTTAACCAGgtaagcaaactgcaatgaacttaatttgaccagtacagggtctatatcttgtcgtcatatcatgtcaaggaatgcttatgttattacagagtacattatttcttttaattttttgtccttgttcactgacattgttttccacttcgctttttggaatag
















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|149050331|gb|EE048608.2|EE048608
EST:     ACAGAAACGACTACTATGGAGGAGATTCCACCTCGCTCAACCTTAATCAG                         CTCTGGAAGAGGTTTAGAGGGGAAGACAAGCCCCCAGCACATCTAGGTGCA
genomic: ACAGAAACGACTACTATGGAGGAGATTCCACCTCGCTCAACCTTAATCAGgtaagcaact ... tttggaacagCTCTGGAAGAGGTTTAGAGGGGAAGACAAGCCCCCAGCACATCTAGGTGCA
EST: gi|211064222|gb|FL094759.1|FL094759
EST:     ACAGAAACGACTACTATGGAGGAGATTCCACCTCGCTCAACCTTAATCAG                         CTCTGGAAGAGGTTTAGAGGGGAAGACAAGCCCCCAGCACATCTAGGTGCA
genomic: ACAGAAACGACTACTATGGAGGAGATTCCACCTCGCTCAACCTTAATCAGgtaagcaact ... tttggaacagCTCTGGAAGAGGTTTAGAGGGGAAGACAAGCCCCCAGCACATCTAGGTGCA
EST: gi|31612099|gb|CD568721.1|CD568721
EST:     ACAGAAACGACTACTATGGAGGAGATTCCACCTCGCTCAACCTTAATCAG                         CTCTGGAAGAGGTTTAGAGGGGAAGACAAGCCCCCAGCACATCTAGGTGCA
genomic: ACAGAAACGACTACTATGGAGGAGATTCCACCTCGCTCAACCTTAATCAGgtaagcaact ... tttggaacagCTCTGGAAGAGGTTTAGAGGGGAAGACAAGCCCCCAGCACATCTAGGTGCA
EST: gi|211064219|gb|FL094756.1|FL094756
EST:     ACAGAAACGACTACTATGGAGGAGATTCCACCTCGCTCAACCTTAATCAG                         CTCTGGAAGAGGTTTAGAGGGGAAGACAAGCCCCCAGCACATCTAGGTGCA
genomic: ACAGAAACGACTACTATGGAGGAGATTCCACCTCGCTCAACCTTAATCAGgtaagcaact ... tttggaacagCTCTGGAAGAGGTTTAGAGGGGAAGACAAGCCCCCAGCACATCTAGGTGCA
EST: gi|211066961|gb|FL094765.1|FL094765
EST:     ACAGAAACGACTACTATGGAGGAGATTCCACCTCGCTCAACCTTAATCAG                         CTCTGGAAGAGGTTTAGAGGGGAAGACAAGCCCCCAGCACATCTAGGTGCA
genomic: ACAGAAACGACTACTATGGAGGAGATTCCACCTCGCTCAACCTTAATCAGgtaagcaact ... tttggaacagCTCTGGAAGAGGTTTAGAGGGGAAGACAAGCCCCCAGCACATCTAGGTGCA
EST: gi|211064226|gb|FL094763.1|FL094763
EST:     ACAGAAACGACTACTATGGAGGAGATTCCACCTCGCTCAACCTTAATCAG                         CTCTGGAAGAGGTTTAGAGGGGAAGACAAGCCCCCAGCACATCTAGGTGCA
genomic: ACAGAAACGACTACTATGGAGGAGATTCCACCTCGCTCAACCTTAATCAGgtaagcaact ... tttggaacagCTCTGGAAGAGGTTTAGAGGGGAAGACAAGCCCCCAGCACATCTAGGTGCA
EST: gi|211455108|gb|FL094747.1|FL094747
EST:     ACAGAAACGACTACTATGGAGGAGATTCCACCTCGCTCAACCTTAATCAG                         CTCTGGAAGAGGTTTAGAGGGGAAGACAAGCCCCCAGCACATCTAGGTGCA
genomic: ACAGAAACGACTACTATGGAGGAGATTCCACCTCGCTCAACCTTAATCAGgtaagcaact ... tttggaacagCTCTGGAAGAGGTTTAGAGGGGAAGACAAGCCCCCAGCACATCTAGGTGCA
EST: gi|30087663|gb|CB885869.1|CB885869
EST:     ACAGAAACGACTACTATGGAGGAGATTCCACCTCGCTCAACCTTAATCAG                         CTCTGGAAGAGGTTTAGAGGGGAAGACAAGCCCCCAGCTCTTTTATTTGCA
genomic: ACAGAAACGACTACTATGGAGGAGATTCCACCTCGCTCAACCTTAATCAGgtaagcaact ... tttggaacagCTCTGGAAGAGGTTTAGAGGGGAAGACAAGCCCCCAGCACATCTAGGTGCA
EST: gi|211064223|gb|FL094760.1|FL094760
EST:     ACAGAAACGACTACTATGGAGGAGATTCCACCTCGCTCAACCTTAATCAG                         CTCTGGAAGAGGTTTAGAGGGGAAGACAAGCCCCCAGCACATCTAGGTGCA
genomic: ACAGAAACGACTACTATGGAGGAGATTCCACCTCGCTCAACCTTAATCAGgtaagcaact ... tttggaacagCTCTGGAAGAGGTTTAGAGGGGAAGACAAGCCCCCAGCACATCTAGGTGCA
EST: gi|211064213|gb|FL094750.1|FL094750
EST:     ACAGAAACGACTACTATGGAGGAGATTCCACCTCGCTCAACCTTAATCAG                         CTCTGGAAGAGGTTTAGAGGGGAAGACAAGCCCCCAGCACATCTAGGTGCA
genomic: ACAGAAACGACTACTATGGAGGAGATTCCACCTCGCTCAACCTTAATCAGgtaagcaact ... tttggaacagCTCTGGAAGAGGTTTAGAGGGGAAGACAAGCCCCCAGCACATCTAGGTGCA
EST: gi|149098467|gb|EE184446.2|EE184446
EST:     ACAGAAACGACTACTATGGAGGAGATTCCACCTCGCTCAACCTTAATCAG                         CTCTGGAAGAGGTTTAGAGGGGAAGACAAGCCCCCAGCACATCTAGGTGCA
genomic: ACAGAAACGACTACTATGGAGGAGATTCCACCTCGCTCAACCTTAATCAGgtaagcaact ... tttggaacagCTCTGGAAGAGGTTTAGAGGGGAAGACAAGCCCCCAGCACATCTAGGTGCA
EST: gi|211066964|gb|FL094768.1|FL094768
EST:     ACAGAAACGACTACTATGGAGGAGATTCCACCTCGCTCAACCTTAATCAG                         CTCTGGAAGAGGTTTAGAGGGGAAGACAAGCCCCCAGCACATCTAGGTGCA
genomic: ACAGAAACGACTACTATGGAGGAGATTCCACCTCGCTCAACCTTAATCAGgtaagcaact ... tttggaacagCTCTGGAAGAGGTTTAGAGGGGAAGACAAGCCCCCAGCACATCTAGGTGCA
EST: gi|211066963|gb|FL094767.1|FL094767
EST:     ACAGAAACGACTACTATGGAGGAGATTCCACCTCGCTCAACCTTAATCAG                         CTCTGGAAGAGGTTTAGAGGGGAAGACAAGCCCCCAGCACATCTAGGTGCA
genomic: ACAGAAACGACTACTATGGAGGAGATTCCACCTCGCTCAACCTTAATCAGgtaagcaact ... tttggaacagCTCTGGAAGAGGTTTAGAGGGGAAGACAAGCCCCCAGCACATCTAGGTGCA
EST: gi|149103159|gb|EE288530.2|EE288530
EST:     ACAGAAACGACTACTATGGAGGAGATTCCACCTCGCTCAACCTTAATCAG                         CTCTGGAAGAGGTTTAGAGGGGAAGACAAGCCCCCAGCACATCTAGGTGCA
genomic: ACAGAAACGACTACTATGGAGGAGATTCCACCTCGCTCAACCTTAATCAGgtaagcaact ... tttggaacagCTCTGGAAGAGGTTTAGAGGGGAAGACAAGCCCCCAGCACATCTAGGTGCA
EST: gi|211455107|gb|FL094746.1|FL094746
EST:     ACAGAAACGACTACTATGGAGGAGATTCCACCTCGCTCAACCTTAATCAG                         CTCTGGAAGARGTTTAGAGGGGAAGACAAGCCCCCAGCACATCTAGGTGCA
genomic: ACAGAAACGACTACTATGGAGGAGATTCCACCTCGCTCAACCTTAATCAGgtaagcaact ... tttggaacagCTCTGGAAGAGGTTTAGAGGGGAAGACAAGCCCCCAGCACATCTAGGTGCA
EST: gi|211064225|gb|FL094762.1|FL094762
EST:     ACAGAAACGACTACTATGGAGGAGATTCCACCTCGCTCAACCTTAATCAG                         CTCTGGAAGAGGTTTAGAGGGGAAGACAAGCCCCCAGCACATCTAGGTGCA
genomic: ACAGAAACGACTACTATGGAGGAGATTCCACCTCGCTCAACCTTAATCAGgtaagcaact ... tttggaacagCTCTGGAAGAGGTTTAGAGGGGAAGACAAGCCCCCAGCACATCTAGGTGCA
EST: gi|211064221|gb|FL094758.1|FL094758
EST:     ACAGAAACGACTACTATGGAGGAGATTCCACCTCGCTCAACCTTAATCAG                         CTCTGGAARAGGTTTAGAGGGGAAGACAAGCCCCCAGCACATCTAGGTGCA
genomic: ACAGAAACGACTACTATGGAGGAGATTCCACCTCGCTCAACCTTAATCAGgtaagcaact ... tttggaacagCTCTGGAAGAGGTTTAGAGGGGAAGACAAGCCCCCAGCACATCTAGGTGCA
EST: gi|211064220|gb|FL094757.1|FL094757
EST:     ACAGAAACGACTACTATGGAGGAGATTCCACCTCGCTCAACCTTAATCAG                         CTCTGGAAGAGGTTTAGAGGGGAAGACAAGCCCCCAGCACATCTAGGTGCA
genomic: ACAGAAACGACTACTATGGAGGAGATTCCACCTCGCTCAACCTTAATCAGgtaagcaact ... tttggaacagCTCTGGAAGAGGTTTAGAGGGGAAGACAAGCCCCCAGCACATCTAGGTGCA
EST: gi|211064224|gb|FL094761.1|FL094761
EST:     ACAGAAACGACTACTATGGAGGAGATTCCACCTCGCTCAACCTTAATCAG                         CTCTGGAAGAGGTTTAGAGGGGAAGACAAGCCCCCAGCACATCTAGGTGCA
genomic: ACAGAAACGACTACTATGGAGGAGATTCCACCTCGCTCAACCTTAATCAGgtaagcaact ... tttggaacagCTCTGGAAGAGGTTTAGAGGGGAAGACAAGCCCCCAGCACATCTAGGTGCA
EST: gi|211064214|gb|FL094751.1|FL094751
EST:     ACAGAAACGACTACTATGGAGGAGATTCCACCTCGCTCAACCTTAATCAG                         CTCTGGAAGAGGTTTAGAGGGGAAGACAAGCCCCCAGCACATCTAGGTGCA
genomic: ACAGAAACGACTACTATGGAGGAGATTCCACCTCGCTCAACCTTAATCAGgtaagcaact ... tttggaacagCTCTGGAAGAGGTTTAGAGGGGAAGACAAGCCCCCAGCACATCTAGGTGCA
EST: gi|211064212|gb|FL094749.1|FL094749
EST:     ACAGAAACGACTACTATGGAGGAGATTCCACCTCGCTCAACCTTAATCAG                         CTCTGGAAGAGGTTTAGAGGGGAAGACAAGCCCCCAGCACATCTAGGTGCA
genomic: ACAGAAACGACTACTATGGAGGAGATTCCACCTCGCTCAACCTTAATCAGgtaagcaact ... tttggaacagCTCTGGAAGAGGTTTAGAGGGGAAGACAAGCCCCCAGCACATCTAGGTGCA
EST: gi|211066962|gb|FL094766.1|FL094766
EST:     ACAGAAACGACTACTATGGAGGAGATTCCACCTCGCTCAACCTTAATCAG                         CTCTGGAAGAGGTTTAGAGGGGAAGACAAGCCCCCAGCACATCTAGGTGCA
genomic: ACAGAAACGACTACTATGGAGGAGATTCCACCTCGCTCAACCTTAATCAGgtaagcaact ... tttggaacagCTCTGGAAGAGGTTTAGAGGGGAAGACAAGCCCCCAGCACATCTAGGTGCA
EST: gi|211064215|gb|FL094752.1|FL094752
EST:     ACAGAAACGACTACTATGGAGGAGATTCCACCTCGCTCAACCTTAATCAG                         CTCTGGAAGAGGTTTAGAGGGGAAGACAAGCCCCCAGCACATCTAGGTGCA
genomic: ACAGAAACGACTACTATGGAGGAGATTCCACCTCGCTCAACCTTAATCAGgtaagcaact ... tttggaacagCTCTGGAAGAGGTTTAGAGGGGAAGACAAGCCCCCAGCACATCTAGGTGCA
EST: gi|211064216|gb|FL094753.1|FL094753
EST:     ACAGAAACGACTACTATGGAGGAGATTCCACCTCGCTCAACCTTAATCAG                         CTCTGGAAGARGTTTAGAGGGGAAGACAAGCCCCCAGCACATCTAGGTGCR
genomic: ACAGAAACGACTACTATGGAGGAGATTCCACCTCGCTCAACCTTAATCAGgtaagcaact ... tttggaacagCTCTGGAAGAGGTTTAGAGGGGAAGACAAGCCCCCAGCACATCTAGGTGCA
EST: gi|211455109|gb|FL094748.1|FL094748
EST:     ACAGAAACGACTACTATGGAGGAGATTCCACCTCGCTCAACCTTAATCAG                         CTCTGGAAGAGGTTTAGAGGGGAAGACAAGCCCCCAGCACATCTAGGTGCA
genomic: ACAGAAACGACTACTATGGAGGAGATTCCACCTCGCTCAACCTTAATCAGgtaagcaact ... tttggaacagCTCTGGAAGAGGTTTAGAGGGGAAGACAAGCCCCCAGCACATCTAGGTGCA
EST: gi|211064217|gb|FL094754.1|FL094754
EST:     ACAGAAACGACTACTATGGAGGAGATTCCACCTCGCTCAACCTTAATCAG                         CTCTGGAAGAGGTTTAGAGGGGAAGACAAGCCCCCAGCACATCTAGGTGCA
genomic: ACAGAAACGACTACTATGGAGGAGATTCCACCTCGCTCAACCTTAATCAGgtaagcaact ... tttggaacagCTCTGGAAGAGGTTTAGAGGGGAAGACAAGCCCCCAGCACATCTAGGTGCA

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: 796

GTTTTGCATATGGACAGAAACGACTACTATGGAGGAGATTCCACCTCGCTCAACCTTAATCAGgtaagcaact ... tttggaacagCTCTGGAAGAGGTTTAGAGGGGAAGACAAGCCCCCAGCACATCTAGGTGCAAGCAGAGACTACAATGTGGACATGGTGCCAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 871

GTTTTGCATATGGACAGAAACGACTACTATGGAGGAGATTCCACCTCGCTCAACCTTAATCAGgtaagcaact ... tttggaacagCTCTGGAAGAGGTTTAGAGGGGAAGACAAGCCCCCAGCACATCTAGGTGCAAGCAGAGACTACAATGTGGACATGGTGCCAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 927

GTTTTGCATATGGACAGAAACGACTACTATGGAGGAGATTCCACCTCGCTCAACCTTAATCAGgtaagcaact ... tttggaacagCTCTGGAAGAGGTTTAGAGGGGAAGACAAGCCCCCAGCACATCTAGGTGCAAGCAGAGACTACAATGTGGACATGGTGCCAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 418

GTTTTGCATATGGACAGAAACGACTACTATGGAGGAGATTCCACCTCGCTCAACCTTAATCAGgtaagcaact ... tttggaacagCTCTGGAAGAGGTTTAGAGGGGAAGACAAGCCCCCAGCACATCTAGGTGCAAGCAGAGACTACAATGTGGACATGGTGCCAAAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTTTGCATATGGACAGAAACGACTACTATGGAGGAGATTCCACCTCGCTCAACCTTAATCAGgtaagcaactcctataacttctgtttaagtacagagtgttttagatttgtgcatcgatttcttgtcataacaaagcttttgattgattttgctggaacttctaaactgacgtgctttccgctaccttttggaacag

- - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - -  GGAGAT