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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCCTCCTGCCTCTCTCCCCCTGCGAGCGATCGTGAGGGGATCGGGATGGCCTCCCACCATTCCGAGCCCCTCGACCCCGCCGACGCTGACGACCCCTCAGgtgcggcacttacctatgcctctcccctctctcttcatcctcctggtggctcggctctcccagtgttgctctactcgcggtgtaaatcgtggcgcgttag...

Basic information

species Zea mays
transcript GRMZM2G142984_T02
intron # 1
splice site 5'
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|67014473|gb|CO443222.1|CO443222
EST:     CTCCCACCATTCCGAGCCCCTCGACCCCGCCGACGCTGACGATCCCTCAG                         ATAACAACCCAGAATTACCATGCCCCTCCTATCATATCGTTACCAAACCTG
genomic: CTCCCACCATTCCGAGCCCCTCGACCCCGCCGACGCTGACGACCCCTCAGgtgcggcact ... tctcttgcagATAACAACCCAGAATTACCATGCCCCTCCTATCATATCGTTACCAAACCTG
EST: gi|211299166|gb|FL411034.1|FL411034
EST:     CTCCCACCATTCCGAGCCCCTCGACCCCGCCGACGCTGACGACCCCTCAG                         ATAACAACCCAGAATTACCATGCCCCTCCTATCATATCGTTACCAAACCTG
genomic: CTCCCACCATTCCGAGCCCCTCGACCCCGCCGACGCTGACGACCCCTCAGgtgcggcact ... tctcttgcagATAACAACCCAGAATTACCATGCCCCTCCTATCATATCGTTACCAAACCTG
EST: gi|149070923|gb|EE159330.2|EE159330
EST:     CTCCCACCATTCCGAGCCCCTCGACCCCGCCGACGCTGACGACCCCTCAG                         ATAACAACCCAGAATTACCATGCCCCTCCTATCATATCGTTACCAAACCTG
genomic: CTCCCACCATTCCGAGCCCCTCGACCCCGCCGACGCTGACGACCCCTCAGgtgcggcact ... tctcttgcagATAACAACCCAGAATTACCATGCCCCTCCTATCATATCGTTACCAAACCTG
EST: gi|211426112|gb|FL387512.1|FL387512
EST:     CTCCCACCATTCCGAGCCCCTCGACCCCGCCGACGCTGACGACCCCTCAG                         ATAACAACCCAGAATTACCATGCCCCTCCTATCATATCGTTACCAAACCTG
genomic: CTCCCACCATTCCGAGCCCCTCGACCCCGCCGACGCTGACGACCCCTCAGgtgcggcact ... tctcttgcagATAACAACCCAGAATTACCATGCCCCTCCTATCATATCGTTACCAAACCTG
EST: gi|149000223|gb|EE037369.2|EE037369
EST:     CTCCCACCATTCCGAGCCCCTCGACCCCGCCGACGCTGACGACCCCTCAG                         ATAACAACCCAGAATTACCATGCCCCTCCTATCATATCGTTACCAAACCTG
genomic: CTCCCACCATTCCGAGCCCCTCGACCCCGCCGACGCTGACGACCCCTCAGgtgcggcact ... tctcttgcagATAACAACCCAGAATTACCATGCCCCTCCTATCATATCGTTACCAAACCTG
EST: gi|211288495|gb|FL414818.1|FL414818
EST:     CTCCCACCATTCCGAGCCCCTCGACCCCGCCGACGCTGACGACCCCTCAG                         ATAACAACCCAGAATTACCATGCCCCTCCTATCATATCGTTACCAAACCTG
genomic: CTCCCACCATTCCGAGCCCCTCGACCCCGCCGACGCTGACGACCCCTCAGgtgcggcact ... tctcttgcagATAACAACCCAGAATTACCATGCCCCTCCTATCATATCGTTACCAAACCTG
EST: gi|89758395|gb|DY687589.1|DY687589
EST:     CTCCCACCATTCCGAGCCCCTCGACCCCGCCGACGCTGACGACCCCTCAG                         ATAACAACCCAGAATTACCATGCCCCTCCTATCATATCGTTACCAAACCTG
genomic: CTCCCACCATTCCGAGCCCCTCGACCCCGCCGACGCTGACGACCCCTCAGgtgcggcact ... tctcttgcagATAACAACCCAGAATTACCATGCCCCTCCTATCATATCGTTACCAAACCTG
EST: gi|211321691|gb|FL409781.1|FL409781
EST:     CTCCCACCATTCCGAGCCCCTCGACCCCGCCGACGCTGACGACCCCTCAG                         ATAACAACCCAGAATTACCATGCCCCTCCTATCATATCGTTACCAAACCTG
genomic: CTCCCACCATTCCGAGCCCCTCGACCCCGCCGACGCTGACGACCCCTCAGgtgcggcact ... tctcttgcagATAACAACCCAGAATTACCATGCCCCTCCTATCATATCGTTACCAAACCTG
EST: gi|211062502|gb|FL371367.1|FL371367
EST:     CTCCCACCATTCCGAGCCCCTCGACCCCGCCGACGCTGACGACCCCTCAG                         ATAACAACCCAGAATTACCATGCCCCTCCTATCATATCGTTACCAAACCTG
genomic: CTCCCACCATTCCGAGCCCCTCGACCCCGCCGACGCTGACGACCCCTCAGgtgcggcact ... tctcttgcagATAACAACCCAGAATTACCATGCCCCTCCTATCATATCGTTACCAAACCTG
EST: gi|211515755|gb|FL378376.1|FL378376
EST:     CTCCCACCATTCCGAGCCCCTCGACCCCGCCGACGCTGACGACCCCTCAG                         ATAACAACCCAGAATTACCATGCCCCTCCTATCATATCGTTACCAAACCTG
genomic: CTCCCACCATTCCGAGCCCCTCGACCCCGCCGACGCTGACGACCCCTCAGgtgcggcact ... tctcttgcagATAACAACCCAGAATTACCATGCCCCTCCTATCATATCGTTACCAAACCTG
EST: gi|211338816|gb|FL389703.1|FL389703
EST:     CTCCCACCATTCCGAGCYCCTCGACCCCGCCGACGCTGACGACCCCTCAG                         ATAACAACCCAGAATTACCATGCYCCTCCTATCATATCGTTACCAAACCTG
genomic: CTCCCACCATTCCGAGCCCCTCGACCCCGCCGACGCTGACGACCCCTCAGgtgcggcact ... tctcttgcagATAACAACCCAGAATTACCATGCCCCTCCTATCATATCGTTACCAAACCTG
EST: gi|211298560|gb|FL375542.1|FL375542
EST:     CTCCCACCATTCCGAG-CCCTCGACCCCGCCGACGCTGACGACCCCTCAG                         ATAACAACCCAGAATTACCATGCMCCTCCTATCATATCGTTACCAAACCTG
genomic: CTCCCACCATTCCGAGCCCCTCGACCCCGCCGACGCTGACGACCCCTCAGgtgcggcact ... tctcttgcagATAACAACCCAGAATTACCATGCCCCTCCTATCATATCGTTACCAAACCTG
EST: gi|211256766|gb|FL400906.1|FL400906
EST:     CTCCCACCATTCCGAGCCCCTCGACCCCGCCGACGCTGACGACCCCTCAG                         ATAACAACCCAGAATTACCATGCCCCTCCTATCATATCGTTACCAAACCTG
genomic: CTCCCACCATTCCGAGCCCCTCGACCCCGCCGACGCTGACGACCCCTCAGgtgcggcact ... tctcttgcagATAACAACCCAGAATTACCATGCCCCTCCTATCATATCGTTACCAAACCTG
EST: gi|149102743|gb|EE188274.2|EE188274
EST:     CTCCCACCATTCCGAGCCCCTCGACCCCGCCGACGCTGACGACCCCTCAG                         ATAACAACCCAGAATTACCATGCCCCTCCTATCATATCGTTACCAAACCTG
genomic: CTCCCACCATTCCGAGCCCCTCGACCCCGCCGACGCTGACGACCCCTCAGgtgcggcact ... tctcttgcagATAACAACCCAGAATTACCATGCCCCTCCTATCATATCGTTACCAAACCTG
EST: gi|211301280|gb|FL410221.1|FL410221
EST:     CTCCCACCATTCCGAGCCCCTCGACCCCGCCGACGCTGACGACCCCTCAG                         ATAACAACCCAGAATTACCATGCACCTCCTATCATATCGTTACCAAACCTG
genomic: CTCCCACCATTCCGAGCCCCTCGACCCCGCCGACGCTGACGACCCCTCAGgtgcggcact ... tctcttgcagATAACAACCCAGAATTACCATGCCCCTCCTATCATATCGTTACCAAACCTG
EST: gi|67016231|gb|CO444980.1|CO444980
EST:     CTCCCACCATTCCGAGCCCCTCGACCCCGCCGACGCTGACGATCCCTCAG                         ATAACAACCCAGAATTACCATGCCCCTCCTATCATATCGTTACCAAACCTG
genomic: CTCCCACCATTCCGAGCCCCTCGACCCCGCCGACGCTGACGACCCCTCAGgtgcggcact ... tctcttgcagATAACAACCCAGAATTACCATGCCCCTCCTATCATATCGTTACCAAACCTG
EST: gi|148965239|gb|EC906094.2|EC906094
EST:     CTCCCACCATTCCGAGCCCCTCGACCCCGCCGACGCTGACGACCCCTCAG                         ATAACAACCCAGAATTACCATGCCCCTCCTATCATATCGTTACCAAACCTG
genomic: CTCCCACCATTCCGAGCCCCTCGACCCCGCCGACGCTGACGACCCCTCAGgtgcggcact ... tctcttgcagATAACAACCCAGAATTACCATGCCCCTCCTATCATATCGTTACCAAACCTG
EST: gi|211448014|gb|FL403750.1|FL403750
EST:     CTCCCACCATTCCGAGCCCCTCGACCCCGCCGACACTGACGACCCCTCAG                         ATAACAACCCAGAATTACCATGCCCCTCCTATCATATCGTTACCAAACCTG
genomic: CTCCCACCATTCCGAGCCCCTCGACCCCGCCGACGCTGACGACCCCTCAGgtgcggcact ... tctcttgcagATAACAACCCAGAATTACCATGCCCCTCCTATCATATCGTTACCAAACCTG
EST: gi|148995982|gb|EE035233.2|EE035233
EST:     CTCCCACCATTCCGAGCCCCTCGACCCCGCCGACGCTGACGACCCCTCAG                         ATAACAACCCAGAATTACCATGCCCCTCCTATCATATCGTTACCAAACCTG
genomic: CTCCCACCATTCCGAGCCCCTCGACCCCGCCGACGCTGACGACCCCTCAGgtgcggcact ... tctcttgcagATAACAACCCAGAATTACCATGCCCCTCCTATCATATCGTTACCAAACCTG
EST: gi|211487590|gb|FL383666.1|FL383666
EST:     CTCCCACCATTCCGAGCCCCTCGACCCCGCCGACGCTGACGACCCCTCAG                         ATAACAACCCAGAATTACCATGCCCCTCCTATCATATCGTTACCAAACCTG
genomic: CTCCCACCATTCCGAGCCCCTCGACCCCGCCGACGCTGACGACCCCTCAGgtgcggcact ... tctcttgcagATAACAACCCAGAATTACCATGCCCCTCCTATCATATCGTTACCAAACCTG

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), 43 (downstream exon)
Score: 164

GCCTCCTGCCTCTCTCCCCCTGCGAGCGATCGTGAGGGGATCGGGATGGCCTCCCACCATTCCGAGCCCCTCGACCCCGCCGACGCTGACGACCCCTCAGgtgcggcact ... tctcttgcagATAACAACCCAGAATTACCATGCCCCTCCTATCATATCGTTACCAAACCTGGTCAACTCCCAGTCGAGTTTCTTGAACCCTCAGCTGCCCAGAAGTTGGT


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 320

GCCTCCTGCCTCTCTCCCCCTGCGAGCGATCGTGAGGGGATCGGGATGGCCTCCCACCATTCCGAGCCCCTCGACCCCGCCGACGCTGACGACCCCTCAGgtgcggcact ... tctcttgcagATAACAACCCAGAATTACCATGCCCCTCCTATCATATCGTTACCAAACCTGGTCAACTCCCAGTCGAGTTTCTTGAACCCTCAGCTGCCCAGAAGTTGGT


Block sizes: 48 (upstream exon), 43 (downstream exon)
Score: 310

GCCTCCTGCCTCTCTCCCCCTGCGAGCGATCGTGAGGGGATCGGGATGGCCTCCCACCATTCCGAGCCCCTCGACCCCGCCGACGCTGACGACCCCTCAGgtgcggcact ... tctcttgcagATAACAACCCAGAATTACCATGCCCCTCCTATCATATCGTTACCAAACCTGGTCAACTCCCAGTCGAGTTTCTTGAACCCTCAGCTGCCCAGAAGTTGGT


Block sizes: 49 (upstream exon), 43 (downstream exon)
Score: 337

GCCTCCTGCCTCTCTCCCCCTGCGAGCGATCGTGAGGGGATCGGGATGGCCTCCCACCATTCCGAGCCCCTCGACCCCGCCGACGCTGACGACCCCTCAGgtgcggcact ... tctcttgcagATAACAACCCAGAATTACCATGCCCCTCCTATCATATCGTTACCAAACCTGGTCAACTCCCAGTCGAGTTTCTTGAACCCTCAGCTGCCCAGAAGTTGGT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCCTCCTGCCTCTCTCCCCCTGCGAGCGATCGTGAGGGGATCGGGATGGCCTCCCACCATTCCGAGCCCCTCGACCCCGCCGACGCTGACGACCCCTCAGgtgcggcacttacctatgcctctcccctctctcttcatcctcctggtggctcggctctcccagtgttgctctactcgcggtgtaaatcgtggcgcgttag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cctctccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctctctct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -catcctcc