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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggttgtaggcaattgactccatggtccatgctaagtcagcaaagtcactgagtcgtaacattatatgagatgttgctattctgataaattactgtaacagGCTCCTGCTAAAGAGGAGCAACCCGCAAAGAAGGACGACGAGCTGAGGTTCCAAGCGTTCAGCGGGAAGAGCTACTCATTGAAACGTTAGCTGCTTCAGT

Basic information

species Zea mays
transcript GRMZM2G114220_T01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G114220_T01 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os04g48770.2 (Oryza sativa), 3'ss of exon 5
-------ggttgtaggcaattgactccatg-gtccatgctaagtcagcaaagtcactgagtcgtaacattatatgagatgttgctattctgataaattactgt-aacagGCTCCTGCTAAAGAGGAGCAACCCGCAAAGAAGGACGACGAGCTGAGGTTCCAAGCGTTCAGCGGGAAGAGCTACTCATTGAAACGTTAGCTGC-TTCAGT--
        ||| |     | ||     |   ||  |||||  | | |||   |   |  | ||     |||| |||    ||  | || |      ||  ||| |||||||| | | ||| || ||  |  |  |||||||||||||   ||  | ||||||||| || || |||||||||||||| |||||||||||||||  ||  ||  
tgagcagagttttgattgagtggaatgacatgtttatgct--gcctgcattatggatatgccgactagttat-tgattcttttttttttt------tttttgtgaacagGCTTCCGTTAAGGATGATGAGTCTCCAAAGAAGGACGA---GCCCAAGTTCCAAGCATTTAGTGGGAAGAGCTACTCCTTGAAACGTTAGCTGGATTTTGTAG
















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|211226982|gb|FL456596.1|FL456596
EST:     GGAAACTTGTTTTTGGTTCAAGTGCAAGCAACAATAAGGAACCACAAAAG                         GCTCCTGCTAAAGAGGAGCAACCCGCAAAGAAGGACGACGAGCTGAGGTTC
genomic: GGAAACTTGTTTTTGGTTCAAGTGCAAGCAACAATAAGGAACCACAAAAGgtatatccta ... actgtaacagGCTCCTGCTAAAGAGGAGCAACCCGCAAAGAAGGACGACGAGCTGAGGTTC
EST: gi|5080966|gb|AI738228.1|AI738228
EST:     GAAAACTTGTTTTTGGTTCAAGCGCAAGCAATAATAAGGAACCACAAAAG                         GCTCCTGCTAAAGAGGAGCAACCCGCAAAGAAGGACGACGAGCTGAGGTTC
genomic: GGAAACTTGTTTTTGGTTCAAGTGCAAGCAACAATAAGGAACCACAAAAGgtatatccta ... actgtaacagGCTCCTGCTAAAGAGGAGCAACCCGCAAAGAAGGACGACGAGCTGAGGTTC
EST: gi|89251784|gb|DY623570.1|DY623570
EST:     GGAAACTTGTTTTTGGTTCAAGTGCAAGCAACAATAAGGAACCACAAAAG                         GCTCCTGCTAAAGAGGAGCAACCCGCAAAGAAGGACGACGAGCTGAGGTTC
genomic: GGAAACTTGTTTTTGGTTCAAGTGCAAGCAACAATAAGGAACCACAAAAGgtatatccta ... actgtaacagGCTCCTGCTAAAGAGGAGCAACCCGCAAAGAAGGACGACGAGCTGAGGTTC
EST: gi|37384441|gb|CF629292.1|CF629292
EST:     GGAAACTTGTTTTTGGTTCAAGTGCAAGCAACAATAAGGAACCACAAAAG                         GCTCCTGCTAAAGAGGAGCAACCCGCAAAG--G-ACGACGAGCTGAGGTTC
genomic: GGAAACTTGTTTTTGGTTCAAGTGCAAGCAACAATAAGGAACCACAAAAGgtatatccta ... actgtaacagGCTCCTGCTAAAGAGGAGCAACCCGCAAAGAAGGACGACGAGCTGAGGTTC
EST: gi|93282993|gb|EB675257.1|EB675257
EST:     GGAAACTTGTTTTTGGTTCAAGTGCAAGCAACAATAAGGAACCACAAAAG                         GCTCCTGCTAAAGAGGAGCAACCCGCAAAGAAGGACGACGAGCTGAGGTTC
genomic: GGAAACTTGTTTTTGGTTCAAGTGCAAGCAACAATAAGGAACCACAAAAGgtatatccta ... actgtaacagGCTCCTGCTAAAGAGGAGCAACCCGCAAAGAAGGACGACGAGCTGAGGTTC
EST: gi|60355921|gb|DN222894.1|DN222894
EST:     GGAAACTTGTTTTTGGTTCAAGTGCAAGCAACAATAAGGAACCACAAAAG                         GCTCCTGCTAAAGAGGAGCAACCCGCAAAGAAGGACGACGAGCTGAGGTTC
genomic: GGAAACTTGTTTTTGGTTCAAGTGCAAGCAACAATAAGGAACCACAAAAGgtatatccta ... actgtaacagGCTCCTGCTAAAGAGGAGCAACCCGCAAAGAAGGACGACGAGCTGAGGTTC
EST: gi|37389693|gb|CF632067.1|CF632067
EST:     GGAAACTTGTTTTTGGTTCAAGTGCAAGCAACAATAAGGAACCACAAAAG                         GCTCCTGCTAAAGAGGAGCAACCCGC--A-AAGGACGACGAGCTGAGGTTC
genomic: GGAAACTTGTTTTTGGTTCAAGTGCAAGCAACAATAAGGAACCACAAAAGgtatatccta ... actgtaacagGCTCCTGCTAAAGAGGAGCAACCCGCAAAGAAGGACGACGAGCTGAGGTTC
EST: gi|211469293|gb|FL298426.1|FL298426
EST:     GGAAACTTGTTTTTGGTTCAAGTGCAAGCAACAATAAGGAACCACAAAAG                         GCTCCTGCTAAAGAGGAGCAACCCGCAAAGAAGGACGACGAGCTGAGGTTC
genomic: GGAAACTTGTTTTTGGTTCAAGTGCAAGCAACAATAAGGAACCACAAAAGgtatatccta ... actgtaacagGCTCCTGCTAAAGAGGAGCAACCCGCAAAGAAGGACGACGAGCTGAGGTTC
EST: gi|60342371|gb|DN209344.1|DN209344
EST:     GGAAACTTGTTTTTGGTTCAAGTGCAAGCAACAATAAGGAACCACAAAAG                         GCTCCTGCTAAAGAGGAGCAACCCGCAAAGAAGGACGACGAGCTGAGGTTC
genomic: GGAAACTTGTTTTTGGTTCAAGTGCAAGCAACAATAAGGAACCACAAAAGgtatatccta ... actgtaacagGCTCCTGCTAAAGAGGAGCAACCCGCAAAGAAGGACGACGAGCTGAGGTTC
EST: gi|18174639|gb|BM350027.1|BM350027
EST:     GGAAACTTGTTTTTGGTTCAAGTGCAAGCAACAATAAGGAACCACAAAAG                         GCTCCTGCTAAAGAGGAGCAACCCGCAAAGAAGGACGACGAGCTGAGGTTC
genomic: GGAAACTTGTTTTTGGTTCAAGTGCAAGCAACAATAAGGAACCACAAAAGgtatatccta ... actgtaacagGCTCCTGCTAAAGAGGAGCAACCCGCAAAGAAGGACGACGAGCTGAGGTTC
EST: gi|76909134|gb|DV163239.1|DV163239
EST:     GGAAACTTGTTTTTGGTTCAAGTGCAAGCAACAATAAGGAACCACAAAAG                         GCTCCTGCTAAAGAGGAGCAACCCGCAAAGAAGGACGACGAGCTGAGGTTC
genomic: GGAAACTTGTTTTTGGTTCAAGTGCAAGCAACAATAAGGAACCACAAAAGgtatatccta ... actgtaacagGCTCCTGCTAAAGAGGAGCAACCCGCAAAGAAGGACGACGAGCTGAGGTTC
EST: gi|60352454|gb|DN219427.1|DN219427
EST:     GGAAACTTGTTTTTGGTTCAAGTGCAAGCAACAATAAGGAACCACAAAAG                         GCTCCTGCTAAAGAGGAGCAACCCGCAAAGAAGGACGACGAGCTGAGGTTC
genomic: GGAAACTTGTTTTTGGTTCAAGTGCAAGCAACAATAAGGAACCACAAAAGgtatatccta ... actgtaacagGCTCCTGCTAAAGAGGAGCAACCCGCAAAGAAGGACGACGAGCTGAGGTTC
EST: gi|88746722|gb|DY530863.1|DY530863
EST:     GGAAACTTGTTTTTGGTTCAAGTGCAAGCAACAATAAGGAACCACAAAAG                         GCTCCTGCTAAAGAGGAGCAACCCGCAAAGAAGGACGACGAGCTGAGGTTC
genomic: GGAAACTTGTTTTTGGTTCAAGTGCAAGCAACAATAAGGAACCACAAAAGgtatatccta ... actgtaacagGCTCCTGCTAAAGAGGAGCAACCCGCAAAGAAGGACGACGAGCTGAGGTTC
EST: gi|211469294|gb|FL298427.1|FL298427
EST:     GGAAACTTGTTTTTGGTTCAAGTGCAAGCAACAATAAGGAACCACAAAAG                         GCTCCTGCTAAAGAGGAGCAACCCGCAAAGAAGGACGACGAGCTGAGGTTC
genomic: GGAAACTTGTTTTTGGTTCAAGTGCAAGCAACAATAAGGAACCACAAAAGgtatatccta ... actgtaacagGCTCCTGCTAAAGAGGAGCAACCCGCAAAGAAGGACGACGAGCTGAGGTTC
EST: gi|60399898|gb|DN232708.1|DN232708
EST:     GGAAACTTGTTTTTGGTTCAAGTGCAAGCAACAATAAGGAACCACAAAAG                         GCTCCTGCTAAAGAGGAGCAACCCGCAAAGAAGGACGACGAGCTGAGGTTC
genomic: GGAAACTTGTTTTTGGTTCAAGTGCAAGCAACAATAAGGAACCACAAAAGgtatatccta ... actgtaacagGCTCCTGCTAAAGAGGAGCAACCCGCAAAGAAGGACGACGAGCTGAGGTTC
EST: gi|28986284|gb|CB351059.1|CB351059
EST:     GGAAACTTGTTTTTGGTTCAAGTGCAAGCAACAATAAGGAACCACAAAAG                         GCTCCTGCTAAAGAGGAGCAACCCGCAAAGAAGGACGACGAGCTGAGGTTC
genomic: GGAAACTTGTTTTTGGTTCAAGTGCAAGCAACAATAAGGAACCACAAAAGgtatatccta ... actgtaacagGCTCCTGCTAAAGAGGAGCAACCCGCAAAGAAGGACGACGAGCTGAGGTTC
EST: gi|60354663|gb|DN221636.1|DN221636
EST:     GGAAACTTGTTTTTGGTTCAAGTGCAAGCAACAATAAGGAACCACAAAAG                         GCTCCTGCTAAAGAGGAGCAACCCGCAAAGAAGGACGACGAGCTGAGGTTC
genomic: GGAAACTTGTTTTTGGTTCAAGTGCAAGCAACAATAAGGAACCACAAAAGgtatatccta ... actgtaacagGCTCCTGCTAAAGAGGAGCAACCCGCAAAGAAGGACGACGAGCTGAGGTTC
EST: gi|60350571|gb|DN217544.1|DN217544
EST:     GGAAACTTGTTTTTGGTTCAAGTGCAAGCAACAATAAGGAACCACAAAAG                         GCTCCTGCTAAAGAGGAGCAACCCGCAAAGAAGGACGACGAGCTGAGGTTC
genomic: GGAAACTTGTTTTTGGTTCAAGTGCAAGCAACAATAAGGAACCACAAAAGgtatatccta ... actgtaacagGCTCCTGCTAAAGAGGAGCAACCCGCAAAGAAGGACGACGAGCTGAGGTTC
EST: gi|4628232|gb|AI619106.1|AI619106
EST:     GGAAACTTGTTTTTGGTTCAAGTGCAAGCAACAATAAGGAACCACAAAAG                         GCTCCTGCTAAAGAGGAGCAACCCGCAAAGAAGGACGACGAGCTGAGGTTC
genomic: GGAAACTTGTTTTTGGTTCAAGTGCAAGCAACAATAAGGAACCACAAAAGgtatatccta ... actgtaacagGCTCCTGCTAAAGAGGAGCAACCCGCAAAGAAGGACGACGAGCTGAGGTTC
EST: gi|60349374|gb|DN216347.1|DN216347
EST:     GGAAACTTGTTTTTGGTTCAAGTGCAAGCAACAATAAGGAACCACAAAAG                         GCTCCTGCTAAAGAGGAGCAACCCGCAAAGAAGGACGACGAGCTGAGGTTC
genomic: GGAAACTTGTTTTTGGTTCAAGTGCAAGCAACAATAAGGAACCACAAAAGgtatatccta ... actgtaacagGCTCCTGCTAAAGAGGAGCAACCCGCAAAGAAGGACGACGAGCTGAGGTTC
EST: gi|32859778|gb|CD999459.1|CD999459
EST:     GGAAACTTGTTTTTGGTTCAAGTGCAAGCAACAATAAGGAACCACAAAAG                         GCTCCTGCTAAAGAGGAGCAACCCGCAAAGAAGGACGACGAGCTGAGGTTC
genomic: GGAAACTTGTTTTTGGTTCAAGTGCAAGCAACAATAAGGAACCACAAAAGgtatatccta ... actgtaacagGCTCCTGCTAAAGAGGAGCAACCCGCAAAGAAGGACGACGAGCTGAGGTTC
EST: gi|14243258|gb|BG840910.2|BG840910
EST:     GGAAACTTGTTTTTGGTTCAAGTGCAAGCAACAATAAGGAACCCCAAAAG                         GCTCCTGCTAAAGAGGAGCAACCCGCAAAGAAGGACGACGAGCTGAGGTTC
genomic: GGAAACTTGTTTTTGGTTCAAGTGCAAGCAACAATAAGGAACCACAAAAGgtatatccta ... actgtaacagGCTCCTGCTAAAGAGGAGCAACCCGCAAAGAAGGACGACGAGCTGAGGTTC
EST: gi|60396597|gb|DN229466.1|DN229466
EST:     GGAAACTTGTTTTTGGTTCAAGTGCAAGCAACAATAAGGAACCACAAAAG                         GCTCCTGCTAAAGAGGAGCAACCCGCAAAGAAGGACGACGAGCTGAGGTTC
genomic: GGAAACTTGTTTTTGGTTCAAGTGCAAGCAACAATAAGGAACCACAAAAGgtatatccta ... actgtaacagGCTCCTGCTAAAGAGGAGCAACCCGCAAAGAAGGACGACGAGCTGAGGTTC
EST: gi|50338445|gb|CO533571.1|CO533571
EST:     GGAAACTTGTTTTTGGTTCAAGTGCAAGCAACAATAAGGAACCACAAAAG                         GCTCCTGCTAAAGAGGAGCAACCCGCAAAGAAGGACGACGAGCTGAGGTTC
genomic: GGAAACTTGTTTTTGGTTCAAGTGCAAGCAACAATAAGGAACCACAAAAGgtatatccta ... actgtaacagGCTCCTGCTAAAGAGGAGCAACCCGCAAAGAAGGACGACGAGCTGAGGTTC
EST: gi|84970179|gb|DW468529.1|DW468529
EST:     GGAAACTTGTTTTTGGTTCAAGTGCAAGCAACAATAAGGAACCACAAAAG                         GCTCCTGCTAAAGAGGAGCAACCCGCAAAGAAGGAGGACGAGCTGAGGTTC
genomic: GGAAACTTGTTTTTGGTTCAAGTGCAAGCAACAATAAGGAACCACAAAAGgtatatccta ... actgtaacagGCTCCTGCTAAAGAGGAGCAACCCGCAAAGAAGGACGACGAGCTGAGGTTC
EST: gi|60353567|gb|DN220540.1|DN220540
EST:     GGAAACTTGTTTTTGGTTCAAGTGCAAGCAACAATAAGGAACCACAAAAG                         GCTCCTGCTAAAGAGGAGCAACCCGCAAAGAAGGACGACGAGCTGAGGTTC
genomic: GGAAACTTGTTTTTGGTTCAAGTGCAAGCAACAATAAGGAACCACAAAAGgtatatccta ... actgtaacagGCTCCTGCTAAAGAGGAGCAACCCGCAAAGAAGGACGACGAGCTGAGGTTC

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: 40 (upstream exon), 49 (downstream exon)
Score: 37

CTCAGCACCCGCAGCTTCAGGAGCTAGCAATTACAGTCGACAGAAAACTGGGAAACTTGTTTTTGGTTCAAGTGCAAGCAACAATAAGGAACCACAAAAGgtatatccta ... actgtaacagGCTCCTGCTAAAGAGGAGCAACCCGCAAAGAAGGACGACGAGCTGAGGTTCCAAGCGTTCAGCGGGAAGAGCTACTCATTGAAACGTTAGCTGCTTCAGT


Block sizes: 40 (upstream exon), 49 (downstream exon)
Score: 66

CTCAGCACCCGCAGCTTCAGGAGCTAGCAATTACAGTCGACAGAAAACTGGGAAACTTGTTTTTGGTTCAAGTGCAAGCAACAATAAGGAACCACAAAAGgtatatccta ... actgtaacagGCTCCTGCTAAAGAGGAGCAACCCGCAAAGAAGGACGACGAGCTGAGGTTCCAAGCGTTCAGCGGGAAGAGCTACTCATTGAAACGTTAGCTGCTTCAGT


Block sizes: 40 (upstream exon), 49 (downstream exon)
Score: 67

CTCAGCACCCGCAGCTTCAGGAGCTAGCAATTACAGTCGACAGAAAACTGGGAAACTTGTTTTTGGTTCAAGTGCAAGCAACAATAAGGAACCACAAAAGgtatatccta ... actgtaacagGCTCCTGCTAAAGAGGAGCAACCCGCAAAGAAGGACGACGAGCTGAGGTTCCAAGCGTTCAGCGGGAAGAGCTACTCATTGAAACGTTAGCTGCTTCAGT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 93

CTCAGCACCCGCAGCTTCAGGAGCTAGCAATTACAGTCGACAGAAAACTGGGAAACTTGTTTTTGGTTCAAGTGCAAGCAACAATAAGGAACCACAAAAGgtatatccta ... actgtaacagGCTCCTGCTAAAGAGGAGCAACCCGCAAAGAAGGACGACGAGCTGAGGTTCCAAGCGTTCAGCGGGAAGAGCTACTCATTGAAACGTTAGCTGCTTCAGT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cactgagtcgtaacattatatgagatgttgctattctgataaattactgtaacagGCTCCTGCTAAAGAGGAGCAACCCGCAAAGAAGGACGACGAGCTGAGGTTCCAAGCGTTCAGCGGGAAGAGCTACTCATTGAAACGTTAGCTGCTTCAGT
                               tattctgataaatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggttgtaggcaattgactccatggtccatgctaagtcagcaaagtcactgagtcgtaacattatatgagatgttgctattctgataaattactgtaacagGCTCCTGCTAAAGAGGAGCAACCCGCAAAGAAGGACGACGAGCTGAGGTTCCAAGCGTTCAGCGGGAAGAGCTACTCATTGAAACGTTAGCTGCTTCAGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT