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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgcagtcttttgtgattgctttataagttattagtacaatactactggcgttaagacactatgacaatccacacaattttgcagGCTGTTAATTCATTTGGAGCTCTCACCGGTGGACAACTTCCAGTACGGAGTACAAACCTGGCCTGTTTCCTAGAAGCCATTGAAGCTGGCTGTACGAACA

Basic information

species Zea mays
transcript GRMZM2G051288_T01
intron # 5
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|50332926|gb|CO528052.1|CO528052
EST:     ATGTACGATCCATTAGGCCTCGAGTGCTTTTGGCACCCTCGCAGTGGCAT                         GCTGTTAATTCATTTGGAGCTCTCACCGGTGGACAACTTCCAGTACGGAGT
genomic: ATGTACGATCCATTAGGCCTCGAGTGCTTTTGGCACCCTCGCAGTGGCATgtatgcagtc ... aattttgcagGCTGTTAATTCATTTGGAGCTCTCACCGGTGGACAACTTCCAGTACGGAGT
EST: gi|71766289|gb|DR964226.1|DR964226
EST:     ATGTACGATCCATTAGGCCTCGAGTGCTTTTGGCACCCTCGCAGTGGCAT                         GCTGTTAATTCATTTGGAGCTCTCACCGGTGGACAACTTCCAGTACGGAGT
genomic: ATGTACGATCCATTAGGCCTCGAGTGCTTTTGGCACCCTCGCAGTGGCATgtatgcagtc ... aattttgcagGCTGTTAATTCATTTGGAGCTCTCACCGGTGGACAACTTCCAGTACGGAGT
EST: gi|211298369|gb|FL254613.1|FL254613
EST:     AGGCCTCGAGTGCTTTTGGCACCCTCGCATTGGCAT                         GCTGTTAGTTCATTTGGAGCTCTCACCGGTGGACAACTTCCAGTACGGAGT
genomic: AGGCCTCGAGTGCTTTTGGCACCCTCGCAGTGGCATgtatgcagtc ... aattttgcagGCTGTTAATTCATTTGGAGCTCTCACCGGTGGACAACTTCCAGTACGGAGT
EST: gi|71444036|gb|DR825086.1|DR825086
EST:     ATGTACGATCCATTAGGCCTCGAGTGCTTTTGGCACCCTCGCAGTGGCAT                         GCTGTTAATTCATTGGGAGCTCTCACCGGTGGACAACTTCCAGTACGGAGT
genomic: ATGTACGATCCATTAGGCCTCGAGTGCTTTTGGCACCCTCGCAGTGGCATgtatgcagtc ... aattttgcagGCTGTTAATTCATTTGGAGCTCTCACCGGTGGACAACTTCCAGTACGGAGT
EST: gi|67018199|gb|CO446948.1|CO446948
EST:     ATGTACGATCCATTAGGCCTCGAGTGCTTTTGGCACCCTCGCAGTGGCAT                         GCTGTTAATTCTTTTGGAGCTCTCACCGGTGGACAACTTCCATTACGGAGT
genomic: ATGTACGATCCATTAGGCCTCGAGTGCTTTTGGCACCCTCGCAGTGGCATgtatgcagtc ... aattttgcagGCTGTTAATTCATTTGGAGCTCTCACCGGTGGACAACTTCCAGTACGGAGT
EST: gi|71444037|gb|DR825087.1|DR825087
EST:     ATGTACGATCCATTAGGCCTCGAGTGCTTTTGGCACCCTCGCAGTGGCAT                         GCTGTTAATTCATTTGGAGCTCTCACGGGTGGACAACTTCCAGTACGGAGT
genomic: ATGTACGATCCATTAGGCCTCGAGTGCTTTTGGCACCCTCGCAGTGGCATgtatgcagtc ... aattttgcagGCTGTTAATTCATTTGGAGCTCTCACCGGTGGACAACTTCCAGTACGGAGT
EST: gi|71331074|gb|DR802367.1|DR802367
EST:     ATGTACGATCCATTAGGCCTCGAGTGCTTTTGGCACCCTCGCAGTGGCAT                         GCTGTTAATTCATTTGGAGCTCTCACCGGTGGACAACTTCCAGTACGGAGT
genomic: ATGTACGATCCATTAGGCCTCGAGTGCTTTTGGCACCCTCGCAGTGGCATgtatgcagtc ... aattttgcagGCTGTTAATTCATTTGGAGCTCTCACCGGTGGACAACTTCCAGTACGGAGT
EST: gi|149009260|gb|EE153872.2|EE153872
EST:     ATGTACGATCCATTAGGCCTCGAGTGCTTTTGGCACCCTCGCAGTGGCAT                         GCTGTTAATTCATTTGGAGCTCTCACCGGTGGACAACTTCCAGTACGGAGT
genomic: ATGTACGATCCATTAGGCCTCGAGTGCTTTTGGCACCCTCGCAGTGGCATgtatgcagtc ... aattttgcagGCTGTTAATTCATTTGGAGCTCTCACCGGTGGACAACTTCCAGTACGGAGT
EST: gi|71766290|gb|DR964227.1|DR964227
EST:     ATGTACGATCCATTAGGCCTCGAGTGCTTTTGGCACCCTCGCAGTGGCAT                         GCTGTTAATTCATTTGGAGCTCTCACCGGTGGACAACTTCCAGTACGGAGT
genomic: ATGTACGATCCATTAGGCCTCGAGTGCTTTTGGCACCCTCGCAGTGGCATgtatgcagtc ... aattttgcagGCTGTTAATTCATTTGGAGCTCTCACCGGTGGACAACTTCCAGTACGGAGT
EST: gi|211298370|gb|FL254614.1|FL254614
EST:     ATGTACGATCCATTAGGCCTCGAGTGCTTTTGGCACCCTCGCAGTGGCAT                         GCTGTTAATTCATTTGGAGCTCTCACCGGTGGACAACTTCCAGTACGGAGT
genomic: ATGTACGATCCATTAGGCCTCGAGTGCTTTTGGCACCCTCGCAGTGGCATgtatgcagtc ... aattttgcagGCTGTTAATTCATTTGGAGCTCTCACCGGTGGACAACTTCCAGTACGGAGT
EST: gi|91055876|gb|EB166294.1|EB166294
EST:     ATGTACGATCCATTAGGCCTCGAGTGCTTTTGGCACCCTCGCAGTGGCAT                         GCTGTTAATTCATTTGGAGCTCTCACCGGTGGACAACTTCCAGTACGGAGT
genomic: ATGTACGATCCATTAGGCCTCGAGTGCTTTTGGCACCCTCGCAGTGGCATgtatgcagtc ... aattttgcagGCTGTTAATTCATTTGGAGCTCTCACCGGTGGACAACTTCCAGTACGGAGT
EST: gi|78119952|gb|DV538336.1|DV538336
EST:     ATGTACGATCCATTAGGCCTCGAGTGCTTTTGGCACCCTCGCAGTGGCAT                         GCTGTTAATTCATTTGGAGCTCTCACCGGTGGACAACTTCCAGTACGGAGT
genomic: ATGTACGATCCATTAGGCCTCGAGTGCTTTTGGCACCCTCGCAGTGGCATgtatgcagtc ... aattttgcagGCTGTTAATTCATTTGGAGCTCTCACCGGTGGACAACTTCCAGTACGGAGT
EST: gi|148985352|gb|EE029662.2|EE029662
EST:     TTTGGCACCCTCGCAGTGGCAT                         GCTGTTAATTCATTTGGAGCTCTCACCGGTGGACAACTTCCAGTACGGAGT
genomic: TTTGGCACCCTCGCAGTGGCATgtatgcagtc ... aattttgcagGCTGTTAATTCATTTGGAGCTCTCACCGGTGGACAACTTCCAGTACGGAGT
EST: gi|67020173|gb|CO448922.1|CO448922
EST:     ATGTACGATCCATTACGCCTCGAGTGCTTTTGGCACCCTCGCAGTGGCAT                         GCTGTTAATTCATTTGGAGCTCTCACCGGTGGACAACTTCCAGTACGGAGT
genomic: ATGTACGATCCATTAGGCCTCGAGTGCTTTTGGCACCCTCGCAGTGGCATgtatgcagtc ... aattttgcagGCTGTTAATTCATTTGGAGCTCTCACCGGTGGACAACTTCCAGTACGGAGT
EST: gi|71331076|gb|DR802368.1|DR802368
EST:     ATGTACGATCCATTAGGCCTCGAGTGCTTTTGGCACCCTCGCAGTGGCAT                         GCNTGT-AATTCATTTGGAGCTCTCACCGGTGGACAACTTCCAGTACGGAG
genomic: ATGTACGATCCATTAGGCCTCGAGTGCTTTTGGCACCCTCGCAGTGGCATgtatgcagtc ... aattttgcagGC-TGTTAATTCATTTGGAGCTCTCACCGGTGGACAACTTCCAGTACGGAG

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: 46 (upstream exon), 49 (downstream exon)
Score: 61

ATTAAATACAGGAACATGACCCCTGAAGCAGCTTTGGATCATGTACGATCCATTAGGCCTCGAGTGCTTTTGGCACCCTCGCAGTGGCATgtatgcagtc ... aattttgcagGCTGTTAATTCATTTGGAGCTCTCACCGGTGGACAACTTCCAGTACGGAGTACAAACCTGGCCTGTTTCCTAGAAGCCATTGAAGCTGGCTGTACGAACA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 84

ATTAAATACAGGAACATGACCCCTGAAGCAGCTTTGGATCATGTACGATCCATTAGGCCTCGAGTGCTTTTGGCACCCTCGCAGTGGCATgtatgcagtc ... aattttgcagGCTGTTAATTCATTTGGAGCTCTCACCGGTGGACAACTTCCAGTACGGAGTACAAACCTGGCCTGTTTCCTAGAAGCCATTGAAGCTGGCTGTACGAACA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 104

ATTAAATACAGGAACATGACCCCTGAAGCAGCTTTGGATCATGTACGATCCATTAGGCCTCGAGTGCTTTTGGCACCCTCGCAGTGGCATgtatgcagtc ... aattttgcagGCTGTTAATTCATTTGGAGCTCTCACCGGTGGACAACTTCCAGTACGGAGTACAAACCTGGCCTGTTTCCTAGAAGCCATTGAAGCTGGCTGTACGAACA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 76

ATTAAATACAGGAACATGACCCCTGAAGCAGCTTTGGATCATGTACGATCCATTAGGCCTCGAGTGCTTTTGGCACCCTCGCAGTGGCATgtatgcagtc ... aattttgcagGCTGTTAATTCATTTGGAGCTCTCACCGGTGGACAACTTCCAGTACGGAGTACAAACCTGGCCTGTTTCCTAGAAGCCATTGAAGCTGGCTGTACGAACA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attagtacaatactactggcgttaagacactatgacaatccacacaattttgcagGCTGTTAATTCATTTGGAGCTCTCACCGGTGGACAACTTCCAGTACGGAGTACAAACCTGGCCTGTTTCCTAGAAGCCATTGAAGCTGGCTGTACGAACA
                                           acaatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgcagtcttttgtgattgctttataagttattagtacaatactactggcgttaagacactatgacaatccacacaattttgcagGCTGTTAATTCATTTGGAGCTCTCACCGGTGGACAACTTCCAGTACGGAGTACAAACCTGGCCTGTTTCCTAGAAGCCATTGAAGCTGGCTGTACGAACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG