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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattctacattttatattccataaattgttatttcgtcgtagatttcagaggcgtgctttttatagccttccttaattgtttacagATTCAGTGGGACAATTATTGGTATGGGATGCATGCCAGCTAACTCAACATCTCCATGGGCTAACTCTGAATGGAGATCATTGAAG

Basic information

species Zea mays
transcript GRMZM2G702026_T01
intron # 9
splice site 3'
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|211284606|gb|FL307740.1|FL307740
EST:     GGTATGAGGTTTAAAATGAGATTTGAGGGTGATGAATCCCCTGAAAGAAG                         ATTCAGTGGGACAATTATTGGTATGGGATGCATGCCAGCTAACTCAACATC
genomic: GGTATGAGGTTTAAAATGAGATTTGAGGGTGATGAATCCCCTGAAAGAAGgtattctaca ... ttgtttacagATTCAGTGGGACAATTATTGGTATGGGATGCATGCCAGCTAACTCAACATC
EST: gi|31358117|gb|CD442474.1|CD442474
EST:     GGTATGAGGTTTAAAATGAGATTTGAGGGTGATGAATCCCCTGAAAGAAG                         ATTCAGTGGGACAATTATTGGTATGGGATGCATGCCAGCTAACTCAACATC
genomic: GGTATGAGGTTTAAAATGAGATTTGAGGGTGATGAATCCCCTGAAAGAAGgtattctaca ... ttgtttacagATTCAGTGGGACAATTATTGGTATGGGATGCATGCCAGCTAACTCAACATC
EST: gi|211531197|gb|FL317039.1|FL317039
EST:     GGTATGAGGTTTAAAATGAGATTTGAGGGTGATGAATCCCCTGAAAGAAG                         ATTCAGTGGGACAATTATTGGTATGGGATGCATGCCAGCTAACTCAACATC
genomic: GGTATGAGGTTTAAAATGAGATTTGAGGGTGATGAATCCCCTGAAAGAAGgtattctaca ... ttgtttacagATTCAGTGGGACAATTATTGGTATGGGATGCATGCCAGCTAACTCAACATC
EST: gi|211498503|gb|FL359837.1|FL359837
EST:     GGTATGAGGTTTAAAATGAGATTTGAGGGTGATGAATCCCCTGAAAGAAG                         ATTCAGTGGGACAATTATTGGTATGGGATGCATGCCAGCTAACTCAACATC
genomic: GGTATGAGGTTTAAAATGAGATTTGAGGGTGATGAATCCCCTGAAAGAAGgtattctaca ... ttgtttacagATTCAGTGGGACAATTATTGGTATGGGATGCATGCCAGCTAACTCAACATC

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), 48 (downstream exon)
Score: 190

TCGTTAGTGTAAACAAGTACCTCGAAGCTAAGAATCACAAGATGTCTGTTGGTATGAGGTTTAAAATGAGATTTGAGGGTGATGAATCCCCTGAAAGAAGgtattctaca ... ttgtttacagATTCAGTGGGACAATTATTGGTATGGGATGCATGCCAGCTAACTCAACATCTCCATGGGCTAACTCTGAATGGAGATCATTGAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 167

TCGTTAGTGTAAACAAGTACCTCGAAGCTAAGAATCACAAGATGTCTGTTGGTATGAGGTTTAAAATGAGATTTGAGGGTGATGAATCCCCTGAAAGAAGgtattctaca ... ttgtttacagATTCAGTGGGACAATTATTGGTATGGGATGCATGCCAGCTAACTCAACATCTCCATGGGCTAACTCTGAATGGAGATCATTGAAG


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

TCGTTAGTGTAAACAAGTACCTCGAAGCTAAGAATCACAAGATGTCTGTTGGTATGAGGTTTAAAATGAGATTTGAGGGTGATGAATCCCCTGAAAGAAGgtattctaca ... ttgtttacagATTCAGTGGGACAATTATTGGTATGGGATGCATGCCAGCTAACTCAACATCTCCATGGGCTAACTCTGAATGGAGATCATTGAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 92

TCGTTAGTGTAAACAAGTACCTCGAAGCTAAGAATCACAAGATGTCTGTTGGTATGAGGTTTAAAATGAGATTTGAGGGTGATGAATCCCCTGAAAGAAGgtattctaca ... ttgtttacagATTCAGTGGGACAATTATTGGTATGGGATGCATGCCAGCTAACTCAACATCTCCATGGGCTAACTCTGAATGGAGATCATTGAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttcgtcgtagatttcagaggcgtgctttttatagccttccttaattgtttacagATTCAGTGGGACAATTATTGGTATGGGATGCATGCCAGCTAACTCAACATCTCCATGGGCTAACTCTGAATGGAGATCATTGAAG
                                       ccttaat  putative branch site (score: 92)
                                         ttaattgttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattctacattttatattccataaattgttatttcgtcgtagatttcagaggcgtgctttttatagccttccttaattgtttacagATTCAGTGGGACAATTATTGGTATGGGATGCATGCCAGCTAACTCAACATCTCCATGGGCTAACTCTGAATGGAGATCATTGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG