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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTACCACCATATCACCATGGATTGTTACTCTTGATGCTTTGAAGCCTTTCATGTGTGAGGCTCCTAAGCAGgtgaggaaatagtgtctttaagatttattattgaaataatcaatagttttaagctaacattgactgattctgttagtttttctaatcagcattttatgtaacttcagcccatgggcacctaattctctttgcattacag

Basic information

species Zea mays
transcript GRMZM2G093359_T01
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G093359_T02 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os02g10310.1 (Oryza sativa), 5'ss of exon 9
GTACCACCATATCACCATGGATTGTTACTCTTGATGCTTTGAAGCCTTTCATGTGTGAGGCTCCTAAGCAGgtgaggaaatagtgtctttaagatttattattgaaataatcaatagttttaagctaacattgactgattctgttagtttttctaatcagcattttatgtaacttcagcccatgggcacctaattctctttgcattacag
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GTACCACAGTATCACCCTGGATCGTTACTATGGATGCCCTAAAGCCTTTCACCTGTGAAGCTCCTAAGCAGgtgagcatgtcttagtattatagtatatagttaaccatattt-tccttgagaatcatcattttattgttctatggataaattaaattg---ctttgcgtggcag-----------------------------------
















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|60358486|gb|DN225459.1|DN225459
EST:     TTGTTACTCTTGATGCTTTGAAGCCTTTCATGTGTGAGGCTCCTAAGCAG                         GAACCCGAACCTTTACCATACCTAGCTGAAAAGAATCACATAAACTATGAC
genomic: TTGTTACTCTTGATGCTTTGAAGCCTTTCATGTGTGAGGCTCCTAAGCAGgtgaggaaat ... tgcattacagGAACCCGAACCTTTACCATACCTAGCTGAAAAGAATCACATAAACTATGAC
EST: gi|32937713|gb|CF042532.1|CF042532
EST:     TTGTTACTCTTGATGCTTTGAAGCCTTTCATGTGTGAGGCTCCTAAGCAG                         GAACCCGAACCTTTACCATACCTAGCTGAAAAGAATCACATAAACTATGAC
genomic: TTGTTACTCTTGATGCTTTGAAGCCTTTCATGTGTGAGGCTCCTAAGCAGgtgaggaaat ... tgcattacagGAACCCGAACCTTTACCATACCTAGCTGAAAAGAATCACATAAACTATGAC
EST: gi|60351022|gb|DN217995.1|DN217995
EST:     GAGGCTCCTAAGCAG                         GAACCCGAACCTTTACCATACCTAGCTGAAAAGAATCACATAAACTATGAC
genomic: GAGGCTCCTAAGCAGgtgaggaaat ... tgcattacagGAACCCGAACCTTTACCATACCTAGCTGAAAAGAATCACATAAACTATGAC
EST: gi|60401451|gb|DN234258.1|DN234258
EST:     TTGTTACTCTTGATGCTTTGAAGCCTTTCATGTGTGAGGCTCCTAAGCAG                         GAACCCGAACCTTTACCATACCTAGCTGAAAAGAATCACATAAACTATGAC
genomic: TTGTTACTCTTGATGCTTTGAAGCCTTTCATGTGTGAGGCTCCTAAGCAGgtgaggaaat ... tgcattacagGAACCCGAACCTTTACCATACCTAGCTGAAAAGAATCACATAAACTATGAC
EST: gi|16918483|gb|BM073768.1|BM073768
EST:     TTTGAAGCCTTTCATGTGTGAGGCTCCTAAGCAG                         GAACCCGAACCTTTACCATACCTAGCTGAAAAGAATCACATAAACTATGAC
genomic: TTTGAAGCCTTTCATGTGTGAGGCTCCTAAGCAGgtgaggaaat ... tgcattacagGAACCCGAACCTTTACCATACCTAGCTGAAAAGAATCACATAAACTATGAC
EST: gi|60338752|gb|DN205725.1|DN205725
EST:     TTGTTACTCTTGATGCTTTGAAGCCTTTCATGTGTGAGGCTCCTAAGCAG                         GAACCCGAACCTTTACCATACCTAGCTGAAAAGAATCACATAAACTATGAC
genomic: TTGTTACTCTTGATGCTTTGAAGCCTTTCATGTGTGAGGCTCCTAAGCAGgtgaggaaat ... tgcattacagGAACCCGAACCTTTACCATACCTAGCTGAAAAGAATCACATAAACTATGAC
EST: gi|60358733|gb|DN225706.1|DN225706
EST:     TTGTTACTCTTGATGCTTTGAAGCCTTTCATGTGTGAGGCTCCTAAGCAG                         GAACCCGAACCTTTACCATACCTAGCTGAAAAGAATCACATAAACTATGAC
genomic: TTGTTACTCTTGATGCTTTGAAGCCTTTCATGTGTGAGGCTCCTAAGCAGgtgaggaaat ... tgcattacagGAACCCGAACCTTTACCATACCTAGCTGAAAAGAATCACATAAACTATGAC
EST: gi|12046552|gb|BF728691.1|BF728691
EST:     TTGGTACTCTTGATGCTTTGAAGCCTTTCATGTGTGAGGCTCCTAAGCAG                         GAACCCGAACCTTTACCATACCTAGCTGAAAAGAATCACATAAACTATG
genomic: TTGTTACTCTTGATGCTTTGAAGCCTTTCATGTGTGAGGCTCCTAAGCAGgtgaggaaat ... tgcattacagGAACCCGAACCTTTACCATACCTAGCTGAAAAGAATCACATAAACTATG
EST: gi|19058676|gb|BM737343.1|BM737343
EST:     TTGTTACTCTTGATGCTTTGAAGCCTTTCATGTGTGAGGCTCCTAAGCAG                         GAACCCGAACCTTTACCATACCTAGCTGAAAAGAATCACATAAACTATGAC
genomic: TTGTTACTCTTGATGCTTTGAAGCCTTTCATGTGTGAGGCTCCTAAGCAGgtgaggaaat ... tgcattacagGAACCCGAACCTTTACCATACCTAGCTGAAAAGAATCACATAAACTATGAC
EST: gi|24769868|gb|CA404997.1|CA404997
EST:     TTGTTACTCTTGATGCTTTGAACCCTTTCATGTGTGAGGCTCCTAAGCAG                         GAACCCGAACCTTTACCATACCTAGCTGAAAAGAATCACATAAACTATGAC
genomic: TTGTTACTCTTGATGCTTTGAAGCCTTTCATGTGTGAGGCTCCTAAGCAGgtgaggaaat ... tgcattacagGAACCCGAACCTTTACCATACCTAGCTGAAAAGAATCACATAAACTATGAC
EST: gi|211126137|gb|FL125779.1|FL125779
EST:     TTGTTACTCTTGATGCTTTGAAGCCTTTCATGTGTGAGGCTCCTAAGCAG                         GAACCCGAACCTTTACCATACCTAGCTGAAAAGAATCACATAAACTATGAC
genomic: TTGTTACTCTTGATGCTTTGAAGCCTTTCATGTGTGAGGCTCCTAAGCAGgtgaggaaat ... tgcattacagGAACCCGAACCTTTACCATACCTAGCTGAAAAGAATCACATAAACTATGAC
EST: gi|94474487|gb|EB703445.1|EB703445
EST:     TTGTTACTCTTGATGCTTTGAAGCCTTTCATGTGTGAGGCTCCTAAGCAG                         GAACCCGAACCTTTACCATACCTAGCTGAAAAGAATCACATAAACTATGAC
genomic: TTGTTACTCTTGATGCTTTGAAGCCTTTCATGTGTGAGGCTCCTAAGCAGgtgaggaaat ... tgcattacagGAACCCGAACCTTTACCATACCTAGCTGAAAAGAATCACATAAACTATGAC
EST: gi|87154062|gb|DY398851.1|DY398851
EST:     TTGTTACTCTTGATGCTTTGAAGCCTTTCATGTGTGAGGCTCCTAAGCAG                         GAACCCGAACCTTTACCATACCTAGCTGAAAAGAATCACATAAACTATGAC
genomic: TTGTTACTCTTGATGCTTTGAAGCCTTTCATGTGTGAGGCTCCTAAGCAGgtgaggaaat ... tgcattacagGAACCCGAACCTTTACCATACCTAGCTGAAAAGAATCACATAAACTATGAC
EST: gi|71424524|gb|DR806343.1|DR806343
EST:     TTGTTACTCTTGATGCTTTGAAGCCTTTCATGTGTGAGGCTCCTAAGCAG                         GAACCCGAACCTTTACCATACCTAGCTGAAAAGAATCACATAAACTATGAC
genomic: TTGTTACTCTTGATGCTTTGAAGCCTTTCATGTGTGAGGCTCCTAAGCAGgtgaggaaat ... tgcattacagGAACCCGAACCTTTACCATACCTAGCTGAAAAGAATCACATAAACTATGAC
EST: gi|60397238|gb|DN230054.1|DN230054
EST:     TTGTTACTCTTGATGCTTTGAAGCCTTTCATGTGTGAGGCTCCTAAGCAG                         GAACCCGAACCTTTACCATACCTAGCTGAAAAGAATCACATAAACTATGAC
genomic: TTGTTACTCTTGATGCTTTGAAGCCTTTCATGTGTGAGGCTCCTAAGCAGgtgaggaaat ... tgcattacagGAACCCGAACCTTTACCATACCTAGCTGAAAAGAATCACATAAACTATGAC
EST: gi|149106512|gb|EE188404.2|EE188404
EST:     TTGTTACTCTTGATGCTTTGAAGCCTTTCATGTGTGAGGCTCCTAAGCAG                         GAACCCGAACCTTTACCATACCTAGCTGAAAAGAATCACATAAACTATGAC
genomic: TTGTTACTCTTGATGCTTTGAAGCCTTTCATGTGTGAGGCTCCTAAGCAGgtgaggaaat ... tgcattacagGAACCCGAACCTTTACCATACCTAGCTGAAAAGAATCACATAAACTATGAC
EST: gi|86466217|gb|DY232590.1|DY232590
EST:     TTGTTACTCTTGATGCTTTGAAGCCTTTCATGTGTGAGGCTCCTAAGCAG                         GAACCCGAACCTTTACCATACCTAGCTGAAAAGAATCACATAAACTATGAC
genomic: TTGTTACTCTTGATGCTTTGAAGCCTTTCATGTGTGAGGCTCCTAAGCAGgtgaggaaat ... tgcattacagGAACCCGAACCTTTACCATACCTAGCTGAAAAGAATCACATAAACTATGAC

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: 48 (upstream exon), 49 (downstream exon)
Score: 196

GTACCACCATATCACCATGGATTGTTACTCTTGATGCTTTGAAGCCTTTCATGTGTGAGGCTCCTAAGCAGgtgaggaaat ... tgcattacagGAACCCGAACCTTTACCATACCTAGCTGAAAAGAATCACATAAACTATGACATTCCTCTTGAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 159

GTACCACCATATCACCATGGATTGTTACTCTTGATGCTTTGAAGCCTTTCATGTGTGAGGCTCCTAAGCAGgtgaggaaat ... tgcattacagGAACCCGAACCTTTACCATACCTAGCTGAAAAGAATCACATAAACTATGACATTCCTCTTGAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 159

GTACCACCATATCACCATGGATTGTTACTCTTGATGCTTTGAAGCCTTTCATGTGTGAGGCTCCTAAGCAGgtgaggaaat ... tgcattacagGAACCCGAACCTTTACCATACCTAGCTGAAAAGAATCACATAAACTATGACATTCCTCTTGAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 188

GTACCACCATATCACCATGGATTGTTACTCTTGATGCTTTGAAGCCTTTCATGTGTGAGGCTCCTAAGCAGgtgaggaaat ... tgcattacagGAACCCGAACCTTTACCATACCTAGCTGAAAAGAATCACATAAACTATGACATTCCTCTTGAA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTACCACCATATCACCATGGATTGTTACTCTTGATGCTTTGAAGCCTTTCATGTGTGAGGCTCCTAAGCAGgtgaggaaatagtgtctttaagatttattattgaaataatcaatagttttaagctaacattgactgattctgttagtttttctaatcagcattttatgtaacttcagcccatgggcacctaattctctttgcattacag

- - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - -  TGAAGC