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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGATGATGTTTTGGATGATCCCGTATCAAAGAAACCCAAGGGATCCTCTTCTTATTCGAAGCAAAATGTCGGGAAAAGGTCTAGGAAGGTTATGACTGAGgtaaatatagcaaagataccattttaatatcagtattttgtttttttaatctttgcctctgatacatgtagttgccccctctgaccaaatgtccatgagg...

Basic information

species Zea mays
transcript GRMZM2G461793_T01
intron # 8
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|71431372|gb|DR812422.1|DR812422
EST:     CTTATTCGAAGCAAAATGTCGGGAAAAGGTCTAGGAAGGTTATGACTGAG                         GTGGAAGAAGACGAGGAGATAAATACGAGGCAAAGGCAAAGGGCGTGAGTG
genomic: CTTATTCGAAGCAAAATGTCGGGAAAAGGTCTAGGAAGGTTATGACTGAGgtaaatatag ... cctgtggcagGTGGAAGAAGACGAGGAGATAAATACGAGGCAAAGGCAAAGGGCGTGAGTG
EST: gi|33468206|gb|CF245255.1|CF245255
EST:     CTTATTCGAAGCAAAATGTCGGGAAAAGGTCTAGGAAGGTTATGACTGAG                         GTGGAAGAAGACGAGGAGATAAATACGAGGCAAAGGCAAAGGGCGTGAGTG
genomic: CTTATTCGAAGCAAAATGTCGGGAAAAGGTCTAGGAAGGTTATGACTGAGgtaaatatag ... cctgtggcagGTGGAAGAAGACGAGGAGATAAATACGAGGCAAAGGCAAAGGGCGTGAGTG
EST: gi|211374387|gb|FK951695.1|FK951695
EST:     CTTATTCGAAGCAAAATGTCGGGAAAAGGTCTAGGAAGGTTATGACTGAG                         GTGGAAGAAGACGAGGAGA
genomic: CTTATTCGAAGCAAAATGTCGGGAAAAGGTCTAGGAAGGTTATGACTGAGgtaaatatag ... cctgtggcagGTGGAAGAAGACGAGGAGA
EST: gi|71322070|gb|DR797725.1|DR797725
EST:     TTTATTCGAAGCAAAATGTCGGGAAAAGGTCTAGGAAGGTTATGACTGAG                         GTGGAAGAAGACGAGGAGATAAATACGAGGCAAAGGCAAAGGGCGTGAGTG
genomic: CTTATTCGAAGCAAAATGTCGGGAAAAGGTCTAGGAAGGTTATGACTGAGgtaaatatag ... cctgtggcagGTGGAAGAAGACGAGGAGATAAATACGAGGCAAAGGCAAAGGGCGTGAGTG
EST: gi|211371734|gb|FK951691.1|FK951691
EST:     CTTATTCGAAGCAAAATGTCGGGAAAAGGTCTAGGAAGGTTATGACTGAG                         GTGGAAGAAGACGAGGAGATAAATACGAGGCAAAGGCAAAGGGCGTGAGTG
genomic: CTTATTCGAAGCAAAATGTCGGGAAAAGGTCTAGGAAGGTTATGACTGAGgtaaatatag ... cctgtggcagGTGGAAGAAGACGAGGAGATAAATACGAGGCAAAGGCAAAGGGCGTGAGTG
EST: gi|30087565|gb|CB885771.1|CB885771
EST:     CTTATTCGAAGCAAAATGTCGGGAAAAGGTCTAGGAAGGTTATGACTGAG                         GTGGAAGAAGACGAGGAGATAAATGCGAGGCAAAGGCAAAGGGCGAAAATA
genomic: CTTATTCGAAGCAAAATGTCGGGAAAAGGTCTAGGAAGGTTATGACTGAGgtaaatatag ... cctgtggcagGTGGAAGAAGACGAGGAGATAAATACGAGGCAAAGGCAAAGGGCGTGAGTG
EST: gi|148953457|gb|EE152960.2|EE152960
EST:     CTTATTCGAAGCAAAATGTCGGGAAAAGGTCTAGGAAGGTTATGACTGAG                         GTGGAAGAAGACGAGGAGATAAATACGAGGCAAAGGCAAAGGGCGTGAGTG
genomic: CTTATTCGAAGCAAAATGTCGGGAAAAGGTCTAGGAAGGTTATGACTGAGgtaaatatag ... cctgtggcagGTGGAAGAAGACGAGGAGATAAATACGAGGCAAAGGCAAAGGGCGTGAGTG
EST: gi|148987549|gb|EE031414.2|EE031414
EST:     CTTATTCGAAGCAAAATGTCGGGAAAAGGTCTAGGAAGGTTATGACTGAG                         GTGGAAGAAGACGAGGAGATAAATACGAGGCAAAGGCAAAGGGCGTGAGTG
genomic: CTTATTCGAAGCAAAATGTCGGGAAAAGGTCTAGGAAGGTTATGACTGAGgtaaatatag ... cctgtggcagGTGGAAGAAGACGAGGAGATAAATACGAGGCAAAGGCAAAGGGCGTGAGTG
EST: gi|88749612|gb|DY533753.1|DY533753
EST:     CTTATTCGAAGCAAAATGTCGGGAAAAGGTCTAGGAAGGTTATGACTGAG                         GTGGAAGAAGACGAGGAGATAAATACGAGGCAAAGGCAAAGGGCGTGAGTG
genomic: CTTATTCGAAGCAAAATGTCGGGAAAAGGTCTAGGAAGGTTATGACTGAGgtaaatatag ... cctgtggcagGTGGAAGAAGACGAGGAGATAAATACGAGGCAAAGGCAAAGGGCGTGAGTG
EST: gi|32805532|gb|CD957766.1|CD957766
EST:     CTTATTCGAAGCAAAATGTCGGGAAAAGGTCTAGGAAGGTTATGACTGAG                         GTGGAAGAAGACGAGGAGATAAATACGAGGCAAAGGCAAAGGGCGTGAGTG
genomic: CTTATTCGAAGCAAAATGTCGGGAAAAGGTCTAGGAAGGTTATGACTGAGgtaaatatag ... cctgtggcagGTGGAAGAAGACGAGGAGATAAATACGAGGCAAAGGCAAAGGGCGTGAGTG
EST: gi|60395012|gb|DN227881.1|DN227881
EST:     CTTATTCGAAGCAAAATGTCGGGAAAAGGTCTAGGAAGGTTATGACTGAG                         GTGGAAGAAGACGAGGAGATAAATACGAGGCAAAGGCAAAGGGCGTGAGTG
genomic: CTTATTCGAAGCAAAATGTCGGGAAAAGGTCTAGGAAGGTTATGACTGAGgtaaatatag ... cctgtggcagGTGGAAGAAGACGAGGAGATAAATACGAGGCAAAGGCAAAGGGCGTGAGTG
EST: gi|211374384|gb|FK951692.1|FK951692
EST:     CTTATTCGAAGCAAAATGTCGGGAAAAGGTCTAGGAAGGTTATGACTGAG                         GTGGAAGAAGACGAGGAGATAAATACGAGGCAAAGGCAAAGGGCGTGAGTG
genomic: CTTATTCGAAGCAAAATGTCGGGAAAAGGTCTAGGAAGGTTATGACTGAGgtaaatatag ... cctgtggcagGTGGAAGAAGACGAGGAGATAAATACGAGGCAAAGGCAAAGGGCGTGAGTG
EST: gi|91872817|gb|EB402774.1|EB402774
EST:     NNNATTTGAAGCAAAATGTCGGGAAAAGGTCTAGGAAGGTTATGACTGAG                         GTGGAAGAAGACGAGGAGATAAATACGAGGCAAAGGCAAAGGGCGTGAGTG
genomic: CTTATTCGAAGCAAAATGTCGGGAAAAGGTCTAGGAAGGTTATGACTGAGgtaaatatag ... cctgtggcagGTGGAAGAAGACGAGGAGATAAATACGAGGCAAAGGCAAAGGGCGTGAGTG

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), 49 (downstream exon)
Score: 90

AGATGATGTTTTGGATGATCCCGTATCAAAGAAACCCAAGGGATCCTCTTCTTATTCGAAGCAAAATGTCGGGAAAAGGTCTAGGAAGGTTATGACTGAGgtaaatatag ... cctgtggcagGTGGAAGAAGACGAGGAGATAAATACGAGGCAAAGGCAAAGGGCGTGAGTGCGAAATGTGCAACTGCAACGACGGTTATATGATGTTAGATGCCGGCAGG


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 84

AGATGATGTTTTGGATGATCCCGTATCAAAGAAACCCAAGGGATCCTCTTCTTATTCGAAGCAAAATGTCGGGAAAAGGTCTAGGAAGGTTATGACTGAGgtaaatatag ... cctgtggcagGTGGAAGAAGACGAGGAGATAAATACGAGGCAAAGGCAAAGGGCGTGAGTGCGAAATGTGCAACTGCAACGACGGTTATATGATGTTAGATGCCGGCAGG


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 56

AGATGATGTTTTGGATGATCCCGTATCAAAGAAACCCAAGGGATCCTCTTCTTATTCGAAGCAAAATGTCGGGAAAAGGTCTAGGAAGGTTATGACTGAGgtaaatatag ... cctgtggcagGTGGAAGAAGACGAGGAGATAAATACGAGGCAAAGGCAAAGGGCGTGAGTGCGAAATGTGCAACTGCAACGACGGTTATATGATGTTAGATGCCGGCAGG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 36

AGATGATGTTTTGGATGATCCCGTATCAAAGAAACCCAAGGGATCCTCTTCTTATTCGAAGCAAAATGTCGGGAAAAGGTCTAGGAAGGTTATGACTGAGgtaaatatag ... cctgtggcagGTGGAAGAAGACGAGGAGATAAATACGAGGCAAAGGCAAAGGGCGTGAGTGCGAAATGTGCAACTGCAACGACGGTTATATGATGTTAGATGCCGGCAGG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGATGATGTTTTGGATGATCCCGTATCAAAGAAACCCAAGGGATCCTCTTCTTATTCGAAGCAAAATGTCGGGAAAAGGTCTAGGAAGGTTATGACTGAGgtaaatatagcaaagataccattttaatatcagtattttgtttttttaatctttgcctctgatacatgtagttgccccctctgaccaaatgtccatgagg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccccctc