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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcaactatatggtatatgctgatgggtcagagtggcttgtgtaatagtttttttgataaaaaaatgtaatagttttttttgtctatccatggtattgcagGATGGGTCAGAGTGGATATTTACAAACAAAAAAGCTGATGAAGCCCATCAGTTCACAATGCATGTGAATTTTGATAAGTTTTCTGAAG

Basic information

species Zea mays
transcript GRMZM2G177947_T02
intron # 1
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|149106831|gb|EE188728.2|EE188728
EST:     CCCAGCTCCTCGTCGCGGACCACGGAGGCGCCACCTCAGTCAAGGCCGAG                         GATGGGTCAGAGTGGATATTTACAAACAAAAAAGCTGATGAAGCCCATCAG
genomic: CCCAGCTCCTCGTCGCGGACCACGGAGGCGCCACCTCAGTCAAGGCCGAGgtaggttggt ... ggtattgcagGATGGGTCAGAGTGGATATTTACAAACAAAAAAGCTGATGAAGCCCATCAG
EST: gi|74236453|gb|DT644367.1|DT644367
EST:     CCCAGCTCCTCGTCGCGGACCACGGAGGCGCCACCTCAGTCAAGGCCGAG                         GATGGGTCAGAGTGGATATTTACAAACAAAAAAGCTGATGAAGCCCATCAG
genomic: CCCAGCTCCTCGTCGCGGACCACGGAGGCGCCACCTCAGTCAAGGCCGAGgtaggttggt ... ggtattgcagGATGGGTCAGAGTGGATATTTACAAACAAAAAAGCTGATGAAGCCCATCAG
EST: gi|148976014|gb|EE025872.2|EE025872
EST:     CCCAGCTCCTCGTCGCGGACCACGGAGGCGCCACCTCAGTCAAGGCCGAG                         GATGGGTCAGAGTGGATATTTACAAACAAAAAAGCTGATGAAGCCCATCAG
genomic: CCCAGCTCCTCGTCGCGGACCACGGAGGCGCCACCTCAGTCAAGGCCGAGgtaggttggt ... ggtattgcagGATGGGTCAGAGTGGATATTTACAAACAAAAAAGCTGATGAAGCCCATCAG
EST: gi|91052862|gb|EB163280.1|EB163280
EST:     CCCAGCTCCTCGTCGCGGACCACGGAGGCGCCACCTCAGTCAAGGCCGAG                         GATGGGTCAGAGTGGATATTTACAAACAAAAAAGCTGATGAAGCCCATCAG
genomic: CCCAGCTCCTCGTCGCGGACCACGGAGGCGCCACCTCAGTCAAGGCCGAGgtaggttggt ... ggtattgcagGATGGGTCAGAGTGGATATTTACAAACAAAAAAGCTGATGAAGCCCATCAG
EST: gi|101390104|gb|EB816984.1|EB816984
EST:     CCCAGCTCCTCGTCGCGGACCACGGAGGCGCCACCTCAGTCAAGGCCGAG                         GATGGGTCAGAGTGGATATTTACAAACAAAAAAGCTGATGAAGCCCATCAG
genomic: CCCAGCTCCTCGTCGCGGACCACGGAGGCGCCACCTCAGTCAAGGCCGAGgtaggttggt ... ggtattgcagGATGGGTCAGAGTGGATATTTACAAACAAAAAAGCTGATGAAGCCCATCAG
EST: gi|149008823|gb|EE041027.2|EE041027
EST:     CCCAGCTCCTCGTCGCGGACCACGGAGGCGCCACCTCAGTCAAGGCCGAG                         GATGGGTCAGAGTGGATATTTACAAACAAAAAAGCTGATGAAGCCCATCAG
genomic: CCCAGCTCCTCGTCGCGGACCACGGAGGCGCCACCTCAGTCAAGGCCGAGgtaggttggt ... ggtattgcagGATGGGTCAGAGTGGATATTTACAAACAAAAAAGCTGATGAAGCCCATCAG
EST: gi|76286649|gb|DV026217.1|DV026217
EST:     CCCAGCTCCTCGTCGCGGACCACGGAGGCGCCACCTCAGTCAAGGCCGAG                         GATGGGTCAGAGTGGATATTTACAAACAAAAAAGCTGATGAAGCCCATC
genomic: CCCAGCTCCTCGTCGCGGACCACGGAGGCGCCACCTCAGTCAAGGCCGAGgtaggttggt ... ggtattgcagGATGGGTCAGAGTGGATATTTACAAACAAAAAAGCTGATGAAGCCCATC
EST: gi|149076451|gb|EE165074.2|EE165074
EST:     CCCAGCTCCTCGTCGCGGACCACGGAGGCGCCACCTCAGTCAAGGCCGAG                         GATGGGTCAGAGTGGATATTTACAAACAAAAAAGCTGATGAAGCCCATCAG
genomic: CCCAGCTCCTCGTCGCGGACCACGGAGGCGCCACCTCAGTCAAGGCCGAGgtaggttggt ... ggtattgcagGATGGGTCAGAGTGGATATTTACAAACAAAAAAGCTGATGAAGCCCATCAG
EST: gi|148938916|gb|EC883275.2|EC883275
EST:     CCCAGCTCCTCGTCGCGGACCACGGAGGCGCCACCTCAGTCAAGGCCGAG                         GATGGGTCAGAGTGGATATTTACAAACAAAAAAGCTGATGAAGCCCATCAG
genomic: CCCAGCTCCTCGTCGCGGACCACGGAGGCGCCACCTCAGTCAAGGCCGAGgtaggttggt ... ggtattgcagGATGGGTCAGAGTGGATATTTACAAACAAAAAAGCTGATGAAGCCCATCAG
EST: gi|76012665|gb|DT939835.1|DT939835
EST:     CCCAGCTCCTCGTCGCGGACCACGGAGGCGCCACCTCAGTCAAGGCCGAG                         GATGGGTCAGAGTGGATATTTACAAACAAAAAAGCTGATGAAGCCCATCAG
genomic: CCCAGCTCCTCGTCGCGGACCACGGAGGCGCCACCTCAGTCAAGGCCGAGgtaggttggt ... ggtattgcagGATGGGTCAGAGTGGATATTTACAAACAAAAAAGCTGATGAAGCCCATCAG
EST: gi|148934162|gb|EC878181.2|EC878181
EST:     CCCAGCTCCTCGTCGCGGACCACGGAGGCGCCACCTCAGTCAAGGCCGAG                         GATGGGTCAGAGTGGATATTTACAA
genomic: CCCAGCTCCTCGTCGCGGACCACGGAGGCGCCACCTCAGTCAAGGCCGAGgtaggttggt ... ggtattgcagGATGGGTCAGAGTGGATATTTACAA
EST: gi|71764392|gb|DR962329.1|DR962329
EST:     CCCAGCTCCTCGTCGCGGACCACGGAGGCGCCACCTCAGTCAAGGCCGAA                         GATGGGTCAGAGTGGATATTTACAAACAAAAAAGCTGATGAAACCCATCAA
genomic: CCCAGCTCCTCGTCGCGGACCACGGAGGCGCCACCTCAGTCAAGGCCGAGgtaggttggt ... ggtattgcagGATGGGTCAGAGTGGATATTTACAAACAAAAAAGCTGATGAAGCCCATCAG

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), 47 (downstream exon)
Score: 85

CAACGAGGAGGGAGGATTCTGCGTGACGCTTATGGTCGACACCGAGGGTTCCCAGCTCCTCGTCGCGGACCACGGAGGCGCCACCTCAGTCAAGGCCGAGgtaggttggt ... ggtattgcagGATGGGTCAGAGTGGATATTTACAAACAAAAAAGCTGATGAAGCCCATCAGTTCACAATGCATGTGAATTTTGATAAGTTTTCTGAAG


Block sizes: 46 (upstream exon), 48 (downstream exon)
Score: 24

CAACGAGGAGGGAGGATTCTGCGTGACGCTTATGGTCGACACCGAGGGTTCCCAGCTCCTCGTCGCGGACCACGGAGGCGCCACCTCAGTCAAGGCCGAGgtaggttggt ... ggtattgcagGATGGGTCAGAGTGGATATTTACAAACAAAAAAGCTGATGAAGCCCATCAGTTCACAATGCATGTGAATTTTGATAAGTTTTCTGAAG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 34

CAACGAGGAGGGAGGATTCTGCGTGACGCTTATGGTCGACACCGAGGGTTCCCAGCTCCTCGTCGCGGACCACGGAGGCGCCACCTCAGTCAAGGCCGAGgtaggttggt ... ggtattgcagGATGGGTCAGAGTGGATATTTACAAACAAAAAAGCTGATGAAGCCCATCAGTTCACAATGCATGTGAATTTTGATAAGTTTTCTGAAG


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

CAACGAGGAGGGAGGATTCTGCGTGACGCTTATGGTCGACACCGAGGGTTCCCAGCTCCTCGTCGCGGACCACGGAGGCGCCACCTCAGTCAAGGCCGAGgtaggttggt ... ggtattgcagGATGGGTCAGAGTGGATATTTACAAACAAAAAAGCTGATGAAGCCCATCAGTTCACAATGCATGTGAATTTTGATAAGTTTTCTGAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtttttttgataaaaaaatgtaatagttttttttgtctatccatggtattgcagGATGGGTCAGAGTGGATATTTACAAACAAAAAAGCTGATGAAGCCCATCAGTTCACAATGCATGTGAATTTTGATAAGTTTTCTGAAG
     ttttgat  putative branch site (score: 87)
     ttttgataaaaaaatg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcaactatatggtatatgctgatgggtcagagtggcttgtgtaatagtttttttgataaaaaaatgtaatagttttttttgtctatccatggtattgcagGATGGGTCAGAGTGGATATTTACAAACAAAAAAGCTGATGAAGCCCATCAGTTCACAATGCATGTGAATTTTGATAAGTTTTCTGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG