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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttttaaacagaaggatacataatagatctgtgtagtactggaaactatctgctgtctgaaatcaatttgattgtgcttccttttctgttatgcaatgcagGTAGTGGAGTTGGATTTTCTTTATCCTAGTGAAGGTATTCACCGACGATGGGAGAACGGATATAGAATAACTTCTACAGCAGCTACTGGCGATCAAGCTG

Basic information

species Zea mays
transcript GRMZM2G116086_T01
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G116086_T01 (Zea mays), 3'ss of exon 15
lower sequence: LOC_Os01g56580.1 (Oryza sativa), 3'ss of exon 15
ttttaaacagaaggatacat---aatagatctgtgtagtactggaaactat-ctgctgtctgaaatcaatttgattgtgcttccttttctgttatgcaatgcagGTAGTGGAGTTGGATTTTCTTTATCCTAGTGAAGGTATTCACCGACGATGGGAGAACGGATATAGAATAACTTCTACAGCAGCTACTGGCGATCAAGCTG
   | |   |  | ||  ||   ||    ||| | |    |||  |   || ||    ||  | ||||| |||||| | |||| | | || | ||| | |||||||||| || ||||||||| | ||||||||||||||||| ||||| || |||||||| || ||||||||||||||||||||||| ||||| || |||||||
---tgagttgtcgtattgatggaaaccagtctttttgaacctgacagggattcttacatcatatatcaagttgattatacttcatct-ctctcatgtactgcagGTAGTAGAATTGGATTTTTTATATCCTAGTGAAGGTATCCACCGGCGTTGGGAGAATGGCTATAGAATAACTTCTACAGCAGCCACTGGTGACCAAGCTG
















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|67026637|gb|CO455386.1|CO455386
EST:     GAAGCCGCTGGGGTGTAGTTATGTCAAGGAACTCTGGATACTCTGAACAG                         GTAGTGGAGTTGGATTTTCTTTATCCTAGTGAAGGTATTCACCGACGATGG
genomic: GAAGCCGCTGGGGTGTAGTTATGTCAAGGAACTCTGGATACTCTGAACAGgtattgggga ... tgcaatgcagGTAGTGGAGTTGGATTTTCTTTATCCTAGTGAAGGTATTCACCGACGATGG
EST: gi|113702279|gb|EE679783.1|EE679783
EST:     GAAGCCGCTGGGGTGTAGTTATGTCAAGGAACTCTGGATACTCTGAACAG                         GTAGTGGAGTTGGATTTTCTTTATCCTAGTGAAGGTATTCACCGACGATGG
genomic: GAAGCCGCTGGGGTGTAGTTATGTCAAGGAACTCTGGATACTCTGAACAGgtattgggga ... tgcaatgcagGTAGTGGAGTTGGATTTTCTTTATCCTAGTGAAGGTATTCACCGACGATGG
EST: gi|211469458|gb|FK962973.1|FK962973
EST:     GAAGCCGCTGGGGTGTAGTTATGTCAAGGAACTCTGGATACTCTGAACAG                         GTAGTGGAGTTGGATTTTCTTTATCCTAGTGAAGGTATTCACCGACGATGG
genomic: GAAGCCGCTGGGGTGTAGTTATGTCAAGGAACTCTGGATACTCTGAACAGgtattgggga ... tgcaatgcagGTAGTGGAGTTGGATTTTCTTTATCCTAGTGAAGGTATTCACCGACGATGG
EST: gi|211466933|gb|FK962961.1|FK962961
EST:     GAAGCCGCTGGGGTGTAGTTATGTCAAGGAACTCTGGATACTCTGAACAG                         GTAGTGGAGTTGGATTTTCTTTATCCTAGTGAAGGTATTCACCGACGATGG
genomic: GAAGCCGCTGGGGTGTAGTTATGTCAAGGAACTCTGGATACTCTGAACAGgtattgggga ... tgcaatgcagGTAGTGGAGTTGGATTTTCTTTATCCTAGTGAAGGTATTCACCGACGATGG
EST: gi|211469456|gb|FK962971.1|FK962971
EST:     GAAGCCGCTGGGGTGTAGTTATGTCAAGGAACTCTGGATACTCTGAACAG                         GTAGTGGAGTTGGATTTTCTTTATCCTAGTGAAGGTATTCACCGACGATGG
genomic: GAAGCCGCTGGGGTGTAGTTATGTCAAGGAACTCTGGATACTCTGAACAGgtattgggga ... tgcaatgcagGTAGTGGAGTTGGATTTTCTTTATCCTAGTGAAGGTATTCACCGACGATGG
EST: gi|211469453|gb|FK962968.1|FK962968
EST:     GAAGCCGCTGGGGTGTAGTTATGTCAAGGAACTCTGGATACTCTGAACAG                         GTAGTGGAGTTGGATTTTCTTTATCCTAGTGAAGGTATTCACCGACGATGG
genomic: GAAGCCGCTGGGGTGTAGTTATGTCAAGGAACTCTGGATACTCTGAACAGgtattgggga ... tgcaatgcagGTAGTGGAGTTGGATTTTCTTTATCCTAGTGAAGGTATTCACCGACGATGG
EST: gi|13249885|gb|BG360790.1|BG360790
EST:     GAAGCCGCTGGGGTGTAGTTATGTCAAGGAACTCTGGATACTCTGAACAG                         GTAGTGGAGTTGGATTTTCTTTATCCTAGTGAAGGTATTCACCGACGATGG
genomic: GAAGCCGCTGGGGTGTAGTTATGTCAAGGAACTCTGGATACTCTGAACAGgtattgggga ... tgcaatgcagGTAGTGGAGTTGGATTTTCTTTATCCTAGTGAAGGTATTCACCGACGATGG
EST: gi|211469457|gb|FK962972.1|FK962972
EST:     GAAGCCGCTGGGGTGTAGTTATGTCAAGGAACTCTGGATACTCTGAACAG                         GTAGTGGAGTTGGATTTTCTTTATCCTAGTGAAGGTATTCACCGACGATGG
genomic: GAAGCCGCTGGGGTGTAGTTATGTCAAGGAACTCTGGATACTCTGAACAGgtattgggga ... tgcaatgcagGTAGTGGAGTTGGATTTTCTTTATCCTAGTGAAGGTATTCACCGACGATGG
EST: gi|211466936|gb|FK962964.1|FK962964
EST:     GAAGCCGCTGGGGTGTAGTTATGTCAAGGAACTCTGGATACTCTGAACAG                         GTAGTGGAGTTGGATTTTCTTTATCCTAGTGAAGGTATTCACCGACGATGG
genomic: GAAGCCGCTGGGGTGTAGTTATGTCAAGGAACTCTGGATACTCTGAACAGgtattgggga ... tgcaatgcagGTAGTGGAGTTGGATTTTCTTTATCCTAGTGAAGGTATTCACCGACGATGG
EST: gi|211469452|gb|FK962967.1|FK962967
EST:     GAAGCCGCTGGGGTGTAGTTATGTCAAGGAACTCTGGATACTCTGAACAG                         GTAGTGGAGTTGGATTTTCTTTATCCTAGTGAAGGTATTCACCGACGATGG
genomic: GAAGCCGCTGGGGTGTAGTTATGTCAAGGAACTCTGGATACTCTGAACAGgtattgggga ... tgcaatgcagGTAGTGGAGTTGGATTTTCTTTATCCTAGTGAAGGTATTCACCGACGATGG
EST: gi|67014743|gb|CO443492.1|CO443492
EST:     GAAGCCGCTGGGGTGTAGTTATGTCAAGGAACTCTGGATACTCTGAACAG                         GTAGTGGAGTTGGATTTTCTTTATCCTAGTGAAGGTATTCACCGACGATGG
genomic: GAAGCCGCTGGGGTGTAGTTATGTCAAGGAACTCTGGATACTCTGAACAGgtattgggga ... tgcaatgcagGTAGTGGAGTTGGATTTTCTTTATCCTAGTGAAGGTATTCACCGACGATGG
EST: gi|211466937|gb|FK962965.1|FK962965
EST:     GAAGCCGCTGGGGTGTAGTTATGTCAAGGAACTCTGGATACTCTGAACAG                         GTAGTGGAGTTGGATTTTCTTTATCCTAGTGAAGGTATTCACCGACGATGG
genomic: GAAGCCGCTGGGGTGTAGTTATGTCAAGGAACTCTGGATACTCTGAACAGgtattgggga ... tgcaatgcagGTAGTGGAGTTGGATTTTCTTTATCCTAGTGAAGGTATTCACCGACGATGG
EST: gi|18650292|gb|BM499111.1|BM499111
EST:     GAAGCCGCTGGGGTGTAGTTATGTCAAGGAACTCTGGATACTCTGAACAG                         GTAGTGGAGTTGGATTTTCTTTATCCTAGTGAAGGTATTCACCGACGATGG
genomic: GAAGCCGCTGGGGTGTAGTTATGTCAAGGAACTCTGGATACTCTGAACAGgtattgggga ... tgcaatgcagGTAGTGGAGTTGGATTTTCTTTATCCTAGTGAAGGTATTCACCGACGATGG
EST: gi|71318166|gb|DR795847.1|DR795847
EST:     CTCTGGATACTCTGAACAG                         GTAGTGGAGTTGGATTTTCTTTATCCTAGTGAAGGTATTCACCGACGATGG
genomic: CTCTGGATACTCTGAACAGgtattgggga ... tgcaatgcagGTAGTGGAGTTGGATTTTCTTTATCCTAGTGAAGGTATTCACCGACGATGG
EST: gi|211469455|gb|FK962970.1|FK962970
EST:     GAAGCCGCTGGGGTGTAGTTATGTCAAGGAACTCTGGATACTCTGAACAG                         GTAGTGGAGTTGGATTTTCTTTATCCTAGTGAAGGTATTCACCGACGATGG
genomic: GAAGCCGCTGGGGTGTAGTTATGTCAAGGAACTCTGGATACTCTGAACAGgtattgggga ... tgcaatgcagGTAGTGGAGTTGGATTTTCTTTATCCTAGTGAAGGTATTCACCGACGATGG
EST: gi|60349444|gb|DN216417.1|DN216417
EST:     GAAGCCGCTGGGGTGTAGTTATGTCAAGGAACTCTGGATACTCTGAACAG                         GTAGTGGAGTTGGATTTTCTTTATCCTAGTGAAGGTATTCACCGACGATGG
genomic: GAAGCCGCTGGGGTGTAGTTATGTCAAGGAACTCTGGATACTCTGAACAGgtattgggga ... tgcaatgcagGTAGTGGAGTTGGATTTTCTTTATCCTAGTGAAGGTATTCACCGACGATGG
EST: gi|211466934|gb|FK962962.1|FK962962
EST:     GAAGCCGCTGGGGTGTAGTTATGTCAAGGAACTCTGGATACTCTGAACAG                         GTAGTGGAGTTGGATTTTCTTTATCCTAGTGAAGGTATTCACCGACGATGG
genomic: GAAGCCGCTGGGGTGTAGTTATGTCAAGGAACTCTGGATACTCTGAACAGgtattgggga ... tgcaatgcagGTAGTGGAGTTGGATTTTCTTTATCCTAGTGAAGGTATTCACCGACGATGG
EST: gi|71439628|gb|DR820678.1|DR820678
EST:     GAAGCCGCTGGGGTGTAGTTATGTCAAGGAACTCTGGATACTCTGAACAG                         GTAGTGGAGTTGGATTTTCTTTATCCTAGTGAAGGTATTCACCGACGATGG
genomic: GAAGCCGCTGGGGTGTAGTTATGTCAAGGAACTCTGGATACTCTGAACAGgtattgggga ... tgcaatgcagGTAGTGGAGTTGGATTTTCTTTATCCTAGTGAAGGTATTCACCGACGATGG

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: 428

CAACAAGAAATGGAAAGAAGGTTTTCATGTTACATCAATGACAACTGCAGGAAGCCGCTGGGGTGTAGTTATGTCAAGGAACTCTGGATACTCTGAACAGgtattgggga ... tgcaatgcagGTAGTGGAGTTGGATTTTCTTTATCCTAGTGAAGGTATTCACCGACGATGGGAGAACGGATATAGAATAACTTCTACAGCAGCTACTGGCGATCAAGCTG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 334

CAACAAGAAATGGAAAGAAGGTTTTCATGTTACATCAATGACAACTGCAGGAAGCCGCTGGGGTGTAGTTATGTCAAGGAACTCTGGATACTCTGAACAGgtattgggga ... tgcaatgcagGTAGTGGAGTTGGATTTTCTTTATCCTAGTGAAGGTATTCACCGACGATGGGAGAACGGATATAGAATAACTTCTACAGCAGCTACTGGCGATCAAGCTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 383

CAACAAGAAATGGAAAGAAGGTTTTCATGTTACATCAATGACAACTGCAGGAAGCCGCTGGGGTGTAGTTATGTCAAGGAACTCTGGATACTCTGAACAGgtattgggga ... tgcaatgcagGTAGTGGAGTTGGATTTTCTTTATCCTAGTGAAGGTATTCACCGACGATGGGAGAACGGATATAGAATAACTTCTACAGCAGCTACTGGCGATCAAGCTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 548

CAACAAGAAATGGAAAGAAGGTTTTCATGTTACATCAATGACAACTGCAGGAAGCCGCTGGGGTGTAGTTATGTCAAGGAACTCTGGATACTCTGAACAGgtattgggga ... tgcaatgcagGTAGTGGAGTTGGATTTTCTTTATCCTAGTGAAGGTATTCACCGACGATGGGAGAACGGATATAGAATAACTTCTACAGCAGCTACTGGCGATCAAGCTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatctgctgtctgaaatcaatttgattgtgcttccttttctgttatgcaatgcagGTAGTGGAGTTGGATTTTCTTTATCCTAGTGAAGGTATTCACCGACGATGGGAGAACGGATATAGAATAACTTCTACAGCAGCTACTGGCGATCAAGCTG
                   atttgat  putative branch site (score: 548)
                              cttccttttctgttat  putative PPT
             aaatcaatttgatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttttaaacagaaggatacataatagatctgtgtagtactggaaactatctgctgtctgaaatcaatttgattgtgcttccttttctgttatgcaatgcagGTAGTGGAGTTGGATTTTCTTTATCCTAGTGAAGGTATTCACCGACGATGGGAGAACGGATATAGAATAACTTCTACAGCAGCTACTGGCGATCAAGCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - aaacaga
- - - - - - - - - - - - - - - - - - - - - - - -tctgctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaaatcaa