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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtatatgttagcatccaatatttactgtccgttctttctgtttttattgctttttattatttggttctaatttgtgaactgctatccttatggatagGTATACTTACAAGGTCTGTGCATATAAGAAAGCATCACAGGCTGAAGGGCACAGTTCTACCAACCTGGG

Basic information

species Zea mays
transcript AC213600.3_FGT002
intron # 11
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|67012552|gb|CO441301.1|CO441301
EST:     AAGGAGTTCTATTCCTTTTATGATCAGTGTTTTGAGACCAAGGAAGGGAA                         GTATACTTACAAGGTCTGTGCATATAAGAAAGCATCACAGGCTGAAGGGCA
genomic: AAGGAGTTCTATTCCTTTTATGATCAGTGTTTTGAGACCAAGGAAGGGAAgtatgtatat ... ttatggatagGTATACTTACAAGGTCTGTGCATATAAGAAAGCATCACAGGCTGAAGGGCA
EST: gi|32834869|gb|CD974547.1|CD974547
EST:     AAGGAGTTCTATTCCTTTTATGATCAGTGTTTTGAGACCAAGGAAGGGAA                         GTATACTTACAAGGTCTGTGCATATAAGAAAGCATCACAGGCTGAAGGGCA
genomic: AAGGAGTTCTATTCCTTTTATGATCAGTGTTTTGAGACCAAGGAAGGGAAgtatgtatat ... ttatggatagGTATACTTACAAGGTCTGTGCATATAAGAAAGCATCACAGGCTGAAGGGCA
EST: gi|211410948|gb|FL407147.1|FL407147
EST:     AAGGAGTTCTATTCCTTTTATGATCAGTGTTTTGAGACCAAGGAAGGGAA                         GTATACTTACAAGGTCTGTGCATATAAGAAAGCATCACAGGCTGAAGGGCA
genomic: AAGGAGTTCTATTCCTTTTATGATCAGTGTTTTGAGACCAAGGAAGGGAAgtatgtatat ... ttatggatagGTATACTTACAAGGTCTGTGCATATAAGAAAGCATCACAGGCTGAAGGGCA
EST: gi|67033121|gb|CO461870.1|CO461870
EST:     A-GGAGT-CTATTCCTTT-ATGATCAGTGTTTTGAGAC-AAGGAAGGNAA                         GTATACTTACA-GGTCTGTGCATATAAGAAA-CATCACAG-CTGAAGGGC-
genomic: AAGGAGTTCTATTCCTTTTATGATCAGTGTTTTGAGACCAAGGAAGGGAAgtatgtatat ... ttatggatagGTATACTTACAAGGTCTGTGCATATAAGAAAGCATCACAGGCTGAAGGGCA
EST: gi|60340979|gb|DN207952.1|DN207952
EST:     AAGGAGTTCTATTCCTTTTATGATCAGTGTTTTGAGACCAAGGAAGGGAA                         GTATACTTACAAGGTCTGTGCATATAAGAAAGCATCACAGGCTGAAGGGCA
genomic: AAGGAGTTCTATTCCTTTTATGATCAGTGTTTTGAGACCAAGGAAGGGAAgtatgtatat ... ttatggatagGTATACTTACAAGGTCTGTGCATATAAGAAAGCATCACAGGCTGAAGGGCA

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), 48 (downstream exon)
Score: 107

GTAATGACAAGGAGTTCTATTCCTTTTATGATCAGTGTTTTGAGACCAAGGAAGGGAAgtatgtatat ... ttatggatagGTATACTTACAAGGTCTGTGCATATAAGAAAGCATCACAGGCTGAAGGGCACAGTTCTACCAACCTGGG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 90

GTAATGACAAGGAGTTCTATTCCTTTTATGATCAGTGTTTTGAGACCAAGGAAGGGAAgtatgtatat ... ttatggatagGTATACTTACAAGGTCTGTGCATATAAGAAAGCATCACAGGCTGAAGGGCACAGTTCTACCAACCTGGG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 119

GTAATGACAAGGAGTTCTATTCCTTTTATGATCAGTGTTTTGAGACCAAGGAAGGGAAgtatgtatat ... ttatggatagGTATACTTACAAGGTCTGTGCATATAAGAAAGCATCACAGGCTGAAGGGCACAGTTCTACCAACCTGGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 180

GTAATGACAAGGAGTTCTATTCCTTTTATGATCAGTGTTTTGAGACCAAGGAAGGGAAgtatgtatat ... ttatggatagGTATACTTACAAGGTCTGTGCATATAAGAAAGCATCACAGGCTGAAGGGCACAGTTCTACCAACCTGGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttattgctttttattatttggttctaatttgtgaactgctatccttatggatagGTATACTTACAAGGTCTGTGCATATAAGAAAGCATCACAGGCTGAAGGGCACAGTTCTACCAACCTGGG
                      ttctaat  putative branch site (score: 180)
                                       ctatcctt  putative PPT
        tttttattatttggtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtatatgttagcatccaatatttactgtccgttctttctgtttttattgctttttattatttggttctaatttgtgaactgctatccttatggatagGTATACTTACAAGGTCTGTGCATATAAGAAAGCATCACAGGCTGAAGGGCACAGTTCTACCAACCTGGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG