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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TAGATTTGGGACCATGGCGTCAATCTGGCTGTTTGGCAATTTCGCCCATTCATTTCTACAGAGTTCTGGTGCCTTTGAAGTTTATTGCAACGGGCAACTGgtaggttcctgtgaacacctagttttgctgcaatgttgttctcaagtacttttacttttgtttgcaacattatatttttttcgaaatcatttcatttctt...

Basic information

species Zea mays
transcript GRMZM5G897342_T02
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G897342_T02 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os01g61580.2 (Oryza sativa), 5'ss of exon 4
TAGATTTGGGACCATGGCGTCAATCTGGCTGTTTGGCAATTTCGCCCATTCATTTCTACAGAGTTCTGGTGCCTTTGAAGTTTATTGCAACGGGCAACTGgtaggttc-ctgtgaacac----ctagttttgctgcaatgttgttctcaagtacttttacttttgtt-tgcaacattatatttttttcgaaatcatttcatttctt
||||||||| || |||||  |||||||||||||||||||||||||||| ||||||||||| ||||||||||||||||||||||| ||||| || ||| ||||| |||   | || | ||     |  |||||||||| ||  ||||   ||||||||| ||| |||| || ||  ||| | |     |     |     |      
TAGATTTGGAACAATGGCAACAATCTGGCTGTTTGGCAATTTCGCCCAGTCATTTCTACAAAGTTCTGGTGCCTTTGAAGTTTACTGCAATGGACAATTGgtatgtttgttatgcatacatccttttttttgctgcagtg--gttcagtagtacttttgcttgtgttatgtaatgttagaatcccccccccccccaaaaaaa----
















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|211241957|gb|FL454430.1|FL454430
EST:     CATTTCTACAGAGTTCTGGTGCCTTTGAAGTTTATTGCAACGGGCAACTG                         GTTTTCTCCAAACTGTCTGAGCAGAGGTTTCCTAGTGAACTTGAGCTACAG
genomic: CATTTCTACAGAGTTCTGGTGCCTTTGAAGTTTATTGCAACGGGCAACTGgtaggttcct ... cacttttcagGTTTTCTCCAAACTGTCTGAGCAGAGGTTTCCTAGTGAACTTGAGCTACAG
EST: gi|31349680|gb|CD434037.1|CD434037
EST:     CATTTCTACAGAGTTCTGGTGCCTTTGAAGTTTATTGCAACGGGCAACTG                         GTTTTCTCCAAACTGTCTGAGCAGAGGTTTCCTAGTGAACTTGAGCTACAG
genomic: CATTTCTACAGAGTTCTGGTGCCTTTGAAGTTTATTGCAACGGGCAACTGgtaggttcct ... cacttttcagGTTTTCTCCAAACTGTCTGAGCAGAGGTTTCCTAGTGAACTTGAGCTACAG
EST: gi|32942636|gb|CF047455.1|CF047455
EST:     CATTTCTACAGAGTTCTGGTGCCTTTGAAGTTTATTGCAACGGGCAACTG                         GTTTTCTCCAAACTGTCTGAGCAGAGGTTTCCTAGTGAACTTGAGCTACAG
genomic: CATTTCTACAGAGTTCTGGTGCCTTTGAAGTTTATTGCAACGGGCAACTGgtaggttcct ... cacttttcagGTTTTCTCCAAACTGTCTGAGCAGAGGTTTCCTAGTGAACTTGAGCTACAG
EST: gi|101398258|gb|EB821002.1|EB821002
EST:     CATTTCTACAGAGTTCTGGTGCCTTTGAAGTTTATTGCAACGGGCAACTG                         GTTTTCTCCAAACTGTCTGAGCAGAGGTTTCCTAGTGAACTTGAGCTAC
genomic: CATTTCTACAGAGTTCTGGTGCCTTTGAAGTTTATTGCAACGGGCAACTGgtaggttcct ... cacttttcagGTTTTCTCCAAACTGTCTGAGCAGAGGTTTCCTAGTGAACTTGAGCTAC
EST: gi|56382517|gb|CV985186.1|CV985186
EST:     CATTTCTACAGAGTTCTGGTGCCTTTGAAGTTTATTGCAACGGGCAACTG                         GTGTTCTCCAAACTGTCTGAGCAGAGGTTTCCTAGTGAACTTGAGCTACAG
genomic: CATTTCTACAGAGTTCTGGTGCCTTTGAAGTTTATTGCAACGGGCAACTGgtaggttcct ... cacttttcagGTTTTCTCCAAACTGTCTGAGCAGAGGTTTCCTAGTGAACTTGAGCTACAG
EST: gi|29946845|gb|CB816354.1|CB816354
EST:     CATTTCTACAGAGTTCTGGTGCCTTTGAAGTTTATTGCAACGGGCAACTG                         GTTTTCTCCAAACTGTCTGAGCAGAGGTTTCCTAGTGAACTTGAGCTACAG
genomic: CATTTCTACAGAGTTCTGGTGCCTTTGAAGTTTATTGCAACGGGCAACTGgtaggttcct ... cacttttcagGTTTTCTCCAAACTGTCTGAGCAGAGGTTTCCTAGTGAACTTGAGCTACAG
EST: gi|37383739|gb|CF628900.1|CF628900
EST:     CATTTCTACAGAGTTCTGGTGCCTTTGAAGTTTATTGCAACGGGCAACTG                         GTTTTCTCCAAACTGTCTGAGCAGAGGTTTCCTAGTGAACTTGAGCTACAG
genomic: CATTTCTACAGAGTTCTGGTGCCTTTGAAGTTTATTGCAACGGGCAACTGgtaggttcct ... cacttttcagGTTTTCTCCAAACTGTCTGAGCAGAGGTTTCCTAGTGAACTTGAGCTACAG
EST: gi|32834618|gb|CD974296.1|CD974296
EST:     CATTTCTACAGAGTTCTGGTGCCTTTGAAGTTTATTGCAACGGGCAACTG                         GTTTTCTCCAAACTGTCTGAGCAGAGGTTTCCTAGTGAACTTGAGCTACAG
genomic: CATTTCTACAGAGTTCTGGTGCCTTTGAAGTTTATTGCAACGGGCAACTGgtaggttcct ... cacttttcagGTTTTCTCCAAACTGTCTGAGCAGAGGTTTCCTAGTGAACTTGAGCTACAG
EST: gi|24763701|gb|CA398872.1|CA398872
EST:     CATTTCTACAGAGTTCTGGTGCCTTTGAAGTTTATTGCAACGGGCAACTG                         GTTTTCTCCAAACTGTCTGAGCAGAGGTTTCCTAGTGAACTTGAGCTACAG
genomic: CATTTCTACAGAGTTCTGGTGCCTTTGAAGTTTATTGCAACGGGCAACTGgtaggttcct ... cacttttcagGTTTTCTCCAAACTGTCTGAGCAGAGGTTTCCTAGTGAACTTGAGCTACAG
EST: gi|213171748|gb|FM196206.1|FM196206
EST:     CATTTCTACAGAGTTCTGGTGCCTTTGAAGTTTATTGCAACGGGCAACTG                         GTTTTCTCCAAACTGTCTGAGCAGAGGTTTCCTAGTGAACTTGAGCTACAG
genomic: CATTTCTACAGAGTTCTGGTGCCTTTGAAGTTTATTGCAACGGGCAACTGgtaggttcct ... cacttttcagGTTTTCTCCAAACTGTCTGAGCAGAGGTTTCCTAGTGAACTTGAGCTACAG
EST: gi|14203675|gb|BG837352.1|BG837352
EST:     CATTTCTACAGAGTTCTGGTGCCTTTGAAGTTTATTGCAACGGGCAACTG                         GTTTTCTCCAAACTGTCTGAGCAGAGGTTTCCTAGTGAACTTGAGCTACAG
genomic: CATTTCTACAGAGTTCTGGTGCCTTTGAAGTTTATTGCAACGGGCAACTGgtaggttcct ... cacttttcagGTTTTCTCCAAACTGTCTGAGCAGAGGTTTCCTAGTGAACTTGAGCTACAG
EST: gi|213192800|gb|FM186079.1|FM186079
EST:     CATTTCTACAGAGTTCTGGTGCCTTTGGAGTTTATTGCAACGGGCAACTG                         GTTTTCTCCAAACTGTCTGAGCAGAGGTTTCCTAGTGAACTTGAGCTACAG
genomic: CATTTCTACAGAGTTCTGGTGCCTTTGAAGTTTATTGCAACGGGCAACTGgtaggttcct ... cacttttcagGTTTTCTCCAAACTGTCTGAGCAGAGGTTTCCTAGTGAACTTGAGCTACAG
EST: gi|78122045|gb|DV540429.1|DV540429
EST:     CATTTCTACAGAGTTCTGGTGCCTTTGAAGTTTATTGCAACGGGCAACTG                         GTTTTCTCCAAACTGTCTGAGCAGAGGTTTCCTAGTGAACTTGAGCTACAG
genomic: CATTTCTACAGAGTTCTGGTGCCTTTGAAGTTTATTGCAACGGGCAACTGgtaggttcct ... cacttttcagGTTTTCTCCAAACTGTCTGAGCAGAGGTTTCCTAGTGAACTTGAGCTACAG
EST: gi|76923684|gb|DV169607.1|DV169607
EST:     CATTTCTACAGAGTTCTGGTGCCTTTGAAGTTTATTGCAACGGGCAACTG                         GTTTTCTCCAAACTGTCTGAGCAGAGGTTTCCTAGTGAACTTGAGCTACAG
genomic: CATTTCTACAGAGTTCTGGTGCCTTTGAAGTTTATTGCAACGGGCAACTGgtaggttcct ... cacttttcagGTTTTCTCCAAACTGTCTGAGCAGAGGTTTCCTAGTGAACTTGAGCTACAG
EST: gi|24764209|gb|CA399375.1|CA399375
EST:     CATTTCTACAGAGTTCTGGTGCCTTTGAAGTTTATTGCAACGGGCAACTG                         GTTTTCTCCAAACTGTCTGAGCAGAGGTTTCCTAGTGAACTTGAGCTACAG
genomic: CATTTCTACAGAGTTCTGGTGCCTTTGAAGTTTATTGCAACGGGCAACTGgtaggttcct ... cacttttcagGTTTTCTCCAAACTGTCTGAGCAGAGGTTTCCTAGTGAACTTGAGCTACAG
EST: gi|37376649|gb|CF624876.1|CF624876
EST:     CATTTCTACAGAGTTCTGGTGCCTTTGAAGTTTATTGCAACGGGCAACTG                         GTTTTCTCCAAACTGTCTGAGCAGAGGTTTCCTAGTGAACTTGAGCTACAG
genomic: CATTTCTACAGAGTTCTGGTGCCTTTGAAGTTTATTGCAACGGGCAACTGgtaggttcct ... cacttttcagGTTTTCTCCAAACTGTCTGAGCAGAGGTTTCCTAGTGAACTTGAGCTACAG
EST: gi|166528496|gb|EG045154.1|EG045154
EST:     CATTTCTACAGAGTTCTGGTGCCTTTGAAGTTTATTGCAACGGGCAACTG                         GTTTTCTCCAAACTGTCTGAGCAGAGGTTTCCTAGTG
genomic: CATTTCTACAGAGTTCTGGTGCCTTTGAAGTTTATTGCAACGGGCAACTGgtaggttcct ... cacttttcagGTTTTCTCCAAACTGTCTGAGCAGAGGTTTCCTAGTG
EST: gi|29945799|gb|CB815825.1|CB815825
EST:     CATTTCTACAGAGTTCTGGTGCCTTTGAAGTTTATTGCAACGGGCAACTG                         GTTTTCTCCAAACTGTCTGAGCAGAGGTTTCCTAGTGAACTTGAGCTACAG
genomic: CATTTCTACAGAGTTCTGGTGCCTTTGAAGTTTATTGCAACGGGCAACTGgtaggttcct ... cacttttcagGTTTTCTCCAAACTGTCTGAGCAGAGGTTTCCTAGTGAACTTGAGCTACAG
EST: gi|24763702|gb|CA398873.1|CA398873
EST:     CATTTCTACAGAGTTCTGGTGCCTTTGAAGTTTATTGCAACGGGCAACTG                         GTTTTCTCCAAACTGTCTGAGCAGAGGTTTCCTAGTGAACTTGAGCTACAG
genomic: CATTTCTACAGAGTTCTGGTGCCTTTGAAGTTTATTGCAACGGGCAACTGgtaggttcct ... cacttttcagGTTTTCTCCAAACTGTCTGAGCAGAGGTTTCCTAGTGAACTTGAGCTACAG
EST: gi|37400793|gb|CF637756.1|CF637756
EST:     CATTTCTACAGAGTTCTGGTGCCTTTGAAGTTTATTGCAACGGGCAACTG                         GTTTTCTCCAAACTGTCTGAGCAGAGGTTTCCTAGTGAACTTGAGCTACAG
genomic: CATTTCTACAGAGTTCTGGTGCCTTTGAAGTTTATTGCAACGGGCAACTGgtaggttcct ... cacttttcagGTTTTCTCCAAACTGTCTGAGCAGAGGTTTCCTAGTGAACTTGAGCTACAG

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: 47 (upstream exon), 47 (downstream exon)
Score: 74

TAGATTTGGGACCATGGCGTCAATCTGGCTGTTTGGCAATTTCGCCCATTCATTTCTACAGAGTTCTGGTGCCTTTGAAGTTTATTGCAACGGGCAACTGgtaggttcct ... cacttttcagGTTTTCTCCAAACTGTCTGAGCAGAGGTTTCCTAGTGAACTTGAGCTACAGGAGCTCATTGGCAGTAGGATACCGGATTCTCAGATTGTAGAAAATCTGG


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 214

TAGATTTGGGACCATGGCGTCAATCTGGCTGTTTGGCAATTTCGCCCATTCATTTCTACAGAGTTCTGGTGCCTTTGAAGTTTATTGCAACGGGCAACTGgtaggttcct ... cacttttcagGTTTTCTCCAAACTGTCTGAGCAGAGGTTTCCTAGTGAACTTGAGCTACAGGAGCTCATTGGCAGTAGGATACCGGATTCTCAGATTGTAGAAAATCTGG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 250

TAGATTTGGGACCATGGCGTCAATCTGGCTGTTTGGCAATTTCGCCCATTCATTTCTACAGAGTTCTGGTGCCTTTGAAGTTTATTGCAACGGGCAACTGgtaggttcct ... cacttttcagGTTTTCTCCAAACTGTCTGAGCAGAGGTTTCCTAGTGAACTTGAGCTACAGGAGCTCATTGGCAGTAGGATACCGGATTCTCAGATTGTAGAAAATCTGG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 179

TAGATTTGGGACCATGGCGTCAATCTGGCTGTTTGGCAATTTCGCCCATTCATTTCTACAGAGTTCTGGTGCCTTTGAAGTTTATTGCAACGGGCAACTGgtaggttcct ... cacttttcagGTTTTCTCCAAACTGTCTGAGCAGAGGTTTCCTAGTGAACTTGAGCTACAGGAGCTCATTGGCAGTAGGATACCGGATTCTCAGATTGTAGAAAATCTGG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TAGATTTGGGACCATGGCGTCAATCTGGCTGTTTGGCAATTTCGCCCATTCATTTCTACAGAGTTCTGGTGCCTTTGAAGTTTATTGCAACGGGCAACTGgtaggttcctgtgaacacctagttttgctgcaatgttgttctcaagtacttttacttttgtttgcaacattatatttttttcgaaatcatttcatttctt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG