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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcgtgcagtctcatcatatgttgttctcagtttgtgtcagtattgaaacactgctcctaaacttcaaacagtcataaaccatgtaattttctggatgcagAACGTCTTGCTTTAATAAGACAGCAAAGGGCTGATGCTGCAAAGAAACGCGATGAGGAGAAAGCTG

Basic information

species Zea mays
transcript GRMZM2G093535_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G093535_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os01g54920.1 (Oryza sativa), 3'ss of exon 6
gcgtgcagtct-catcatatgttgttctcagtttgtgtcagtattgaaacactgctcctaaacttcaaacagtcataaaccat-gtaattttctggatgcagAACGTCTTGCTTTAATAAGACAGCAAAGGGCTGATGCTGCAAAGAAACGCGATGAGGAGAAAGCTG
  ||  | |   |||  ||| || || |  | |    ||| |||||||  | | |   | || | | ||||| ||| | || |  |||||||    |||||||||||||||||||||||||||| ||||| |||||||||||||||||||| || |||||||||||||
--gtagaattggcattgtatattttttttgggtgcgttcaatattgaagaattacctgtgaattgccaacagccatgaccctttataattttgcaaatgcagAACGTCTTGCTTTAATAAGACAACAAAGAGCTGATGCTGCAAAGAAACGTGAAGAGGAGAAAGCTG
















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|211192189|gb|FL404823.1|FL404823
EST:     TATGAAACTTCAGGAGCAAGGAAAAACAGAACAAGCACGGAAAGATTTGG                         AACGTCTTGCTTTAATAAGACAGCAAAGGGCTGATGCTGCAAAGAAACGCG
genomic: TATGAAACTTCAGGAGCAAGGAAAAACAGAACAAGCACGGAAAGATTTGGgtgagaactc ... ctggatgcagAACGTCTTGCTTTAATAAGACAGCAAAGGGCTGATGCTGCAAAGAAACGCG
EST: gi|211213892|gb|FL469120.1|FL469120
EST:     TATGAAACTTCAGGAGCAAGGAAAAACAGAACAAGCACGGAAAGATTTGG                         AACGTCTTGCTTTAATAAGRCAGCAAAGGGCTGATGCTGCAAAGAAACGCG
genomic: TATGAAACTTCAGGAGCAAGGAAAAACAGAACAAGCACGGAAAGATTTGGgtgagaactc ... ctggatgcagAACGTCTTGCTTTAATAAGACAGCAAAGGGCTGATGCTGCAAAGAAACGCG
EST: gi|32837519|gb|CD977197.1|CD977197
EST:     TATGGAACTTCAGGAGCAAGGAAAAACAGAACAAGCTCGGAAAGATTTGG                         AACGTCTTGCTTTAATAAGACAGCAAAGGGCTGATGCTGCAAAGAAACGCG
genomic: TATGAAACTTCAGGAGCAAGGAAAAACAGAACAAGCACGGAAAGATTTGGgtgagaactc ... ctggatgcagAACGTCTTGCTTTAATAAGACAGCAAAGGGCTGATGCTGCAAAGAAACGCG
EST: gi|213167496|gb|FM196281.1|FM196281
EST:     ATGAAACTTCANNNAGCAAGGAAAAACAGAACAAGCACGGAAAGATTTGG                         AACGTCTTGCTTTAATAAGACAGCAAAGGGCTGATGCTGCAAAGAAACGCG
genomic: ATGAAACTTCA-GGAGCAAGGAAAAACAGAACAAGCACGGAAAGATTTGGgtgagaactc ... ctggatgcagAACGTCTTGCTTTAATAAGACAGCAAAGGGCTGATGCTGCAAAGAAACGCG
EST: gi|211273115|gb|FL373254.1|FL373254
EST:     TATGAAACTTCAGGAGCAAGGAAAAACAGAACAAGCACGGAAAGATTTGG                         AACGTCTTGCTTTAATAAGACAGCAAAGGGCTGATGCTGCAAAGAAACGCG
genomic: TATGAAACTTCAGGAGCAAGGAAAAACAGAACAAGCACGGAAAGATTTGGgtgagaactc ... ctggatgcagAACGTCTTGCTTTAATAAGACAGCAAAGGGCTGATGCTGCAAAGAAACGCG
EST: gi|113847453|gb|DW961445.1|DW961445
EST:     TATGAAACTTCAGGAGCAAGGAAAAACAGAACAAGCACGGAAAGATTTGG                         AACGTCTTGCTTTAATAAGACAGCAAAGGGCTGATGCTGC
genomic: TATGAAACTTCAGGAGCAAGGAAAAACAGAACAAGCACGGAAAGATTTGGgtgagaactc ... ctggatgcagAACGTCTTGCTTTAATAAGACAGCAAAGGGCTGATGCTGC
EST: gi|12970294|gb|BG266911.1|BG266911
EST:     ACGGAAAGATTTGG                         AACGTCTTGCTTTAATAAGACAGCAAAGGGCTGATGCTGCAAAGAA-CGCG
genomic: ACGGAAAGATTTGGgtgagaactc ... ctggatgcagAACGTCTTGCTTTAATAAGACAGCAAAGGGCTGATGCTGCAAAGAAACGCG
EST: gi|32937462|gb|CF042281.1|CF042281
EST:     TATGAAACTTCAGGAGCAAGGAAAAACAGAACAAGCCCGGAAAGATTTGG                         AACGTCTTGCTTTAATAAGACAGCAAAGGGCTGATGCTGCAAAGAAACGCG
genomic: TATGAAACTTCAGGAGCAAGGAAAAACAGAACAAGCACGGAAAGATTTGGgtgagaactc ... ctggatgcagAACGTCTTGCTTTAATAAGACAGCAAAGGGCTGATGCTGCAAAGAAACGCG
EST: gi|32944737|gb|CF049556.1|CF049556
EST:     TATGAAACTTCAGGAGCAAGGAAAACCAGAACAAGCACGGAAAGATTTGG                         AACGTCTTGCTTTAATAAGGCAGCAAAGGGCTGATACTGCAAAGAAACGCG
genomic: TATGAAACTTCAGGAGCAAGGAAAAACAGAACAAGCACGGAAAGATTTGGgtgagaactc ... ctggatgcagAACGTCTTGCTTTAATAAGACAGCAAAGGGCTGATGCTGCAAAGAAACGCG
EST: gi|78026071|gb|DV494458.1|DV494458
EST:     ACGGAAAGATTTGG                         AACGTCTTGCTTTAATAAGACAGCAAAGGGCTGATGCTGCAAAGAAACGCG
genomic: ACGGAAAGATTTGGgtgagaactc ... ctggatgcagAACGTCTTGCTTTAATAAGACAGCAAAGGGCTGATGCTGCAAAGAAACGCG

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: 580

GGAGGAGCTTGAGAAACAAAAAGCTCATGAACGTTATATGAAACTTCAGGAGCAAGGAAAAACAGAACAAGCACGGAAAGATTTGGgtgagaactc ... ctggatgcagAACGTCTTGCTTTAATAAGACAGCAAAGGGCTGATGCTGCAAAGAAACGCGATGAGGAGAAAGCTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 323

GGAGGAGCTTGAGAAACAAAAAGCTCATGAACGTTATATGAAACTTCAGGAGCAAGGAAAAACAGAACAAGCACGGAAAGATTTGGgtgagaactc ... ctggatgcagAACGTCTTGCTTTAATAAGACAGCAAAGGGCTGATGCTGCAAAGAAACGCGATGAGGAGAAAGCTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 512

GGAGGAGCTTGAGAAACAAAAAGCTCATGAACGTTATATGAAACTTCAGGAGCAAGGAAAAACAGAACAAGCACGGAAAGATTTGGgtgagaactc ... ctggatgcagAACGTCTTGCTTTAATAAGACAGCAAAGGGCTGATGCTGCAAAGAAACGCGATGAGGAGAAAGCTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 266

GGAGGAGCTTGAGAAACAAAAAGCTCATGAACGTTATATGAAACTTCAGGAGCAAGGAAAAACAGAACAAGCACGGAAAGATTTGGgtgagaactc ... ctggatgcagAACGTCTTGCTTTAATAAGACAGCAAAGGGCTGATGCTGCAAAGAAACGCGATGAGGAGAAAGCTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaacactgctcctaaacttcaaacagtcataaaccatgtaattttctggatgcagAACGTCTTGCTTTAATAAGACAGCAAAGGGCTGATGCTGCAAAGAAACGCGATGAGGAGAAAGCTG
         tcctaaa  putative branch site (score: 266)
                                         ttttct  putative PPT
                                   atgtaatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcgtgcagtctcatcatatgttgttctcagtttgtgtcagtattgaaacactgctcctaaacttcaaacagtcataaaccatgtaattttctggatgcagAACGTCTTGCTTTAATAAGACAGCAAAGGGCTGATGCTGCAAAGAAACGCGATGAGGAGAAAGCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
gcgtgca
- - - - - - - - - tgttgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -catgtaa