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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tacaaaattaaaacgagccgagtcgagccgagtcgagcgagttatcgagccacgagtattttgtccagctctacctgcaacatcgtcccacttgttccagGTGAAACAGAACACCGTGTCAAGGGAGCGTCAGAACGTTGAGCTTCTAGCAAGAGGGCGCCATGACCCATGCGTCGCCCCTCGAG

Basic information

species Zea mays
transcript GRMZM2G036861_T01
intron # 11
splice site 3'
intron type U2

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|211012763|gb|FL448392.1|FL448392
EST:     GTGAGATTGTGCACTTCAAAGTTGCTTTTAAGCCGACACCATCTATCGGG                         GTGAAACAGAACACCGTGTCAAGGGAGCGTCAGAACGTTGAGCTTCTAGCA
genomic: GTGAGATTGTGCACTTCAAAGTTGCTTTTAAGCCGACACCATCTATCGGGgtaaggcatt ... cttgttccagGTGAAACAGAACACCGTGTCAAGGGAGCGTCAGAACGTTGAGCTTCTAGCA
EST: gi|16925294|gb|BM078362.1|BM078362
EST:     GTGAGATTGTGCACTTCAAAGTTGCTTTTAAGCCGACACCATCTATCGGG                         GTGAAACAGAACACCGTGTCAAGGGAGCGTCAGAACGTTGAGCTTCTAGCA
genomic: GTGAGATTGTGCACTTCAAAGTTGCTTTTAAGCCGACACCATCTATCGGGgtaaggcatt ... cttgttccagGTGAAACAGAACACCGTGTCAAGGGAGCGTCAGAACGTTGAGCTTCTAGCA
EST: gi|148951093|gb|EC896758.2|EC896758
EST:     GTGAGATTGTGCACTTCAAAGTTGCTTTTAAGCCGACACCATCTATCGGG                         GTGAAACAGAACACCGTGTCAAGGGAGCGTCAGAACGTTGAGCTTCTAGCA
genomic: GTGAGATTGTGCACTTCAAAGTTGCTTTTAAGCCGACACCATCTATCGGGgtaaggcatt ... cttgttccagGTGAAACAGAACACCGTGTCAAGGGAGCGTCAGAACGTTGAGCTTCTAGCA
EST: gi|78109643|gb|DV528059.1|DV528059
EST:     GTGAGATTGTGCACTTCAAAGTTGCTTTTAAGCCGACACCATCTATCGGG                         GTGAAACAGAACACCGTGTCAAGGGAGCGTCAGAACGTTGAGCTTCTAGCA
genomic: GTGAGATTGTGCACTTCAAAGTTGCTTTTAAGCCGACACCATCTATCGGGgtaaggcatt ... cttgttccagGTGAAACAGAACACCGTGTCAAGGGAGCGTCAGAACGTTGAGCTTCTAGCA
EST: gi|76281789|gb|DV021357.1|DV021357
EST:     GTGAGATTGTGCACTTCAAAGTTGCTTTTAAGCCGACACCATCTATCGGG                         GTGAAACAGAACACCGTGTCAAGGGAGCGTCAGAACGTTGAGCTTCTAGCA
genomic: GTGAGATTGTGCACTTCAAAGTTGCTTTTAAGCCGACACCATCTATCGGGgtaaggcatt ... cttgttccagGTGAAACAGAACACCGTGTCAAGGGAGCGTCAGAACGTTGAGCTTCTAGCA
EST: gi|148940355|gb|EC885142.2|EC885142
EST:     GTGAGATTGTGCACTTCAAAGTTGCTTTTAAGCCGACACCATCTATCGGG                         GTGAAACAGAACACCGTGTCAAGGGAGCGTCAGAACGTTGAGCTTCTAGCA
genomic: GTGAGATTGTGCACTTCAAAGTTGCTTTTAAGCCGACACCATCTATCGGGgtaaggcatt ... cttgttccagGTGAAACAGAACACCGTGTCAAGGGAGCGTCAGAACGTTGAGCTTCTAGCA
EST: gi|76934910|gb|DV174082.1|DV174082
EST:     GTGAGATTGTGCACTTCAAAGTTGCTTTTAAGCCGACACCATCTATCGGG                         GTGAAACAGAACACCGTGTCAAGGGAGCGTCAGAACGTTGAGCTTCTAGCA
genomic: GTGAGATTGTGCACTTCAAAGTTGCTTTTAAGCCGACACCATCTATCGGGgtaaggcatt ... cttgttccagGTGAAACAGAACACCGTGTCAAGGGAGCGTCAGAACGTTGAGCTTCTAGCA
EST: gi|149098824|gb|EE184837.2|EE184837
EST:     GTGAGATTGTGCACTTCAAAGTTGCTTTTAAGCCGACACCATCTATCGGG                         GTGAAACAGAACACCGTGTCAAGGGAGCGTCAGAACGTTGAGCTTTTAGCA
genomic: GTGAGATTGTGCACTTCAAAGTTGCTTTTAAGCCGACACCATCTATCGGGgtaaggcatt ... cttgttccagGTGAAACAGAACACCGTGTCAAGGGAGCGTCAGAACGTTGAGCTTCTAGCA

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), 46 (downstream exon)
Score: 33

GGAGGGATATCGAATGGTGAGATTGTGCACTTCAAAGTTGCTTTTAAGCCGACACCATCTATCGGGgtaaggcatt ... cttgttccagGTGAAACAGAACACCGTGTCAAGGGAGCGTCAGAACGTTGAGCTTCTAGCAAGAGGGCGCCATGACCCATGCGTCGCCCCTCGAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 633

GGAGGGATATCGAATGGTGAGATTGTGCACTTCAAAGTTGCTTTTAAGCCGACACCATCTATCGGGgtaaggcatt ... cttgttccagGTGAAACAGAACACCGTGTCAAGGGAGCGTCAGAACGTTGAGCTTCTAGCAAGAGGGCGCCATGACCCATGCGTCGCCCCTCGAG


Block sizes: 46 (upstream exon), 21 (downstream exon)
Score: 4

GGAGGGATATCGAATGGTGAGATTGTGCACTTCAAAGTTGCTTTTAAGCCGACACCATCTATCGGGgtaaggcatt ... cttgttccagGTGAAACAGAACACCGTGTCAAGGGAGCGTCAGAACGTTGAGCTTCTAGCAAGAGGGCGCCATGACCCATGCGTCGCCCCTCGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 288

GGAGGGATATCGAATGGTGAGATTGTGCACTTCAAAGTTGCTTTTAAGCCGACACCATCTATCGGGgtaaggcatt ... cttgttccagGTGAAACAGAACACCGTGTCAAGGGAGCGTCAGAACGTTGAGCTTCTAGCAAGAGGGCGCCATGACCCATGCGTCGCCCCTCGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgagccacgagtattttgtccagctctacctgcaacatcgtcccacttgttccagGTGAAACAGAACACCGTGTCAAGGGAGCGTCAGAACGTTGAGCTTCTAGCAAGAGGGCGCCATGACCCATGCGTCGCCCCTCGAG
                                        tcccactt  CT-rich tract
         agtatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tacaaaattaaaacgagccgagtcgagccgagtcgagcgagttatcgagccacgagtattttgtccagctctacctgcaacatcgtcccacttgttccagGTGAAACAGAACACCGTGTCAAGGGAGCGTCAGAACGTTGAGCTTCTAGCAAGAGGGCGCCATGACCCATGCGTCGCCCCTCGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG