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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattaagttttatccgctgctctgttctcaatttgtccaaaccacagtttttagcatctcgtcgtcggtcgtcatgctcaaatagtataatttcattcagGGCCAAGTCTCAGCGAAGCGTGTTACCGAGCTGAACCTGGACGAGTTCCTGTCCTACGGGCCGCAAAGAGACCAGGGGAAG

Basic information

species Zea mays
transcript GRMZM5G829946_T02
intron # 2
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|211430751|gb|FL131180.1|FL131180
EST:     ACGGCTGCCCTGTCATCTTCCATGACAACTTCATCTACACGCAACAAGAC                         GGCCAAGTCTCAGCGAAGCGTGTTACCGAGCTGAACCTGGACGAGTTCCTG
genomic: ACGGCTGCCCTGTCATCTTCCATGACAACTTCATCTACACGCAACAAGACgtaattaagt ... tttcattcagGGCCAAGTCTCAGCGAAGCGTGTTACCGAGCTGAACCTGGACGAGTTCCTG
EST: gi|148967494|gb|EE018731.2|EE018731
EST:     ACGGCTGCCCTGTCATCTTCCATGACAACTTCATCTACACGCAACAAGAC                         GGCCAAGTCTCAGCGAAGCGTGTTACCGAGCTGAACCTGGACGAGTTCCTG
genomic: ACGGCTGCCCTGTCATCTTCCATGACAACTTCATCTACACGCAACAAGACgtaattaagt ... tttcattcagGGCCAAGTCTCAGCGAAGCGTGTTACCGAGCTGAACCTGGACGAGTTCCTG
EST: gi|211430752|gb|FL131181.1|FL131181
EST:     ACGGCTGCCCTGTCATCTTCCATGACAACTTCATCTACACGCAACAAGAC                         GGCCAAGTCTCAGCGAAGCGTGTTACCGAGCTGAACCTGGACGAGTTCCTG
genomic: ACGGCTGCCCTGTCATCTTCCATGACAACTTCATCTACACGCAACAAGACgtaattaagt ... tttcattcagGGCCAAGTCTCAGCGAAGCGTGTTACCGAGCTGAACCTGGACGAGTTCCTG

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), 32 (downstream exon)
Score: 5

GTGACCAGGGACGGCTGCCCTGTCATCTTCCATGACAACTTCATCTACACGCAACAAGACgtaattaagt ... tttcattcagGGCCAAGTCTCAGCGAAGCGTGTTACCGAGCTGAACCTGGACGAGTTCCTGTCCTACGGGCCGCAAAGAGACCAGGGGAAG


Block sizes: 49 (upstream exon), 40 (downstream exon)
Score: 28

GTGACCAGGGACGGCTGCCCTGTCATCTTCCATGACAACTTCATCTACACGCAACAAGACgtaattaagt ... tttcattcagGGCCAAGTCTCAGCGAAGCGTGTTACCGAGCTGAACCTGGACGAGTTCCTGTCCTACGGGCCGCAAAGAGACCAGGGGAAG


Block sizes: 49 (upstream exon), 38 (downstream exon)
Score: 18

GTGACCAGGGACGGCTGCCCTGTCATCTTCCATGACAACTTCATCTACACGCAACAAGACgtaattaagt ... tttcattcagGGCCAAGTCTCAGCGAAGCGTGTTACCGAGCTGAACCTGGACGAGTTCCTGTCCTACGGGCCGCAAAGAGACCAGGGGAAG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 66

GTGACCAGGGACGGCTGCCCTGTCATCTTCCATGACAACTTCATCTACACGCAACAAGACgtaattaagt ... tttcattcagGGCCAAGTCTCAGCGAAGCGTGTTACCGAGCTGAACCTGGACGAGTTCCTGTCCTACGGGCCGCAAAGAGACCAGGGGAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtttttagcatctcgtcgtcggtcgtcatgctcaaatagtataatttcattcagGGCCAAGTCTCAGCGAAGCGTGTTACCGAGCTGAACCTGGACGAGTTCCTGTCCTACGGGCCGCAAAGAGACCAGGGGAAG
                                             tttcattc  CT-rich tract
                                  aaatagtataatttca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaattaagttttatccgctgctctgttctcaatttgtccaaaccacagtttttagcatctcgtcgtcggtcgtcatgctcaaatagtataatttcattcagGGCCAAGTCTCAGCGAAGCGTGTTACCGAGCTGAACCTGGACGAGTTCCTGTCCTACGGGCCGCAAAGAGACCAGGGGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA