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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttcccttttgtaatatattaaaatttctacaaaaaatgttgcatttttggactatctatcatatcattttgctgacgtttacaaatcctacattacccagGCACAGTTTTCTCAGATGCGCCCTGCTGTACCAATGACACCCACTCTAGCCCCGCGCCTTCCAATGTACCCTCCTATGGCTCCTCAGCAACTCTTCTATG

Basic information

species Zea mays
transcript GRMZM2G352129_T01
intron # 5
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|211179932|gb|FL049123.1|FL049123
EST:     TGTATGTTGCATTTGCGCAGCGCAAAGAAGATAGAAAAGCGATGTTGCAG                         GCACAGTTTTCTCAGATGCGCCCTGCTGTACCAATGACACCCACTCTAGCC
genomic: TGTATGTTGCATTTGCGCAGCGCAAAGAAGATAGAAAAGCGATGTTGCAGgcaagtgtcc ... cattacccagGCACAGTTTTCTCAGATGCGCCCTGCTGTACCAATGACACCCACTCTAGCC
EST: gi|32850911|gb|CD990592.1|CD990592
EST:     TGTATGTTGCATTTGCGCAGCGCAAAGAAGATAGAAAAGCGATGTTGCAG                         GCACAGTTTTCTCAGATGCGCCCTGCTGTACCAATGACACCCACTCTAGCC
genomic: TGTATGTTGCATTTGCGCAGCGCAAAGAAGATAGAAAAGCGATGTTGCAGgcaagtgtcc ... cattacccagGCACAGTTTTCTCAGATGCGCCCTGCTGTACCAATGACACCCACTCTAGCC
EST: gi|211205761|gb|FL339666.1|FL339666
EST:     TGTATGTTGCATTTGCGCAGCGCAAAGAAGATAGAAAAGCGATGTTGCAG                         GCACAGTTTTCTCAGATGCGCCCTGCTGTACCAATGACACCCACTCTAGCC
genomic: TGTATGTTGCATTTGCGCAGCGCAAAGAAGATAGAAAAGCGATGTTGCAGgcaagtgtcc ... cattacccagGCACAGTTTTCTCAGATGCGCCCTGCTGTACCAATGACACCCACTCTAGCC
EST: gi|32929766|gb|CF034578.1|CF034578
EST:     TGTATGTTGCATTTGCACAGCGCAAAGAAGATAGAAAAGCGATGTTGCAG                         GCACAGTTTTCTCAGATGCGCCCTGCTGTA
genomic: TGTATGTTGCATTTGCGCAGCGCAAAGAAGATAGAAAAGCGATGTTGCAGgcaagtgtcc ... cattacccagGCACAGTTTTCTCAGATGCGCCCTGCTGTA
EST: gi|211182327|gb|FL049124.1|FL049124
EST:     T-TATGTTGCATTTGCGCAGCGCAAAGAAGATAGAAAAGCGATGTTGCAG                         GCACAGTTTTCTCAGATGCGCCCTGCTGTACCAATGACACCCACTCTAGCC
genomic: TGTATGTTGCATTTGCGCAGCGCAAAGAAGATAGAAAAGCGATGTTGCAGgcaagtgtcc ... cattacccagGCACAGTTTTCTCAGATGCGCCCTGCTGTACCAATGACACCCACTCTAGCC
EST: gi|32928646|gb|CF033458.1|CF033458
EST:     TGTATGTTGCATTTGCACAGCGCAAAGAAGATAGAAAAGCGATGTTGCAG                         GCACAGTTTTCTCAGATGCGCCCTGCTGTA
genomic: TGTATGTTGCATTTGCGCAGCGCAAAGAAGATAGAAAAGCGATGTTGCAGgcaagtgtcc ... cattacccagGCACAGTTTTCTCAGATGCGCCCTGCTGTA
EST: gi|211193131|gb|FL329966.1|FL329966
EST:     TGTATGTTGCATTTGCGCAGCGCAAAGAAGATAGAAAAGCGATGTTGCAG                         GCACAGTTTTCTCAGATGCGCCCTGCTGTACCAATGACACCCACTCTAGCC
genomic: TGTATGTTGCATTTGCGCAGCGCAAAGAAGATAGAAAAGCGATGTTGCAGgcaagtgtcc ... cattacccagGCACAGTTTTCTCAGATGCGCCCTGCTGTACCAATGACACCCACTCTAGCC
EST: gi|101391361|gb|EB817615.1|EB817615
EST:     TGTATGTTGCATTTGCGCAGCGCAAAGAAGATAGAAAAGCGATGTTGCAG                         GCACAGTTTTCTCAGATGCGCCCTGGTGTACCAATGACACCCACTCTAGCC
genomic: TGTATGTTGCATTTGCGCAGCGCAAAGAAGATAGAAAAGCGATGTTGCAGgcaagtgtcc ... cattacccagGCACAGTTTTCTCAGATGCGCCCTGCTGTACCAATGACACCCACTCTAGCC
EST: gi|211157245|gb|FL334278.1|FL334278
EST:     TGTATGTTGCATTTGCGCAGCGCAAAGAAGATAGAAAAGCGATGTTGCAG                         GCACAGTTTTCTCAGATGCGCCCTGCTGTACCAATGACACCCACTCTARCC
genomic: TGTATGTTGCATTTGCGCAGCGCAAAGAAGATAGAAAAGCGATGTTGCAGgcaagtgtcc ... cattacccagGCACAGTTTTCTCAGATGCGCCCTGCTGTACCAATGACACCCACTCTAGCC
EST: gi|211461945|gb|FL313813.1|FL313813
EST:     TGTATGTTGCATTTGCGCAGCGCAAAGAAGATAGAAAAGCGATGTTGCAG                         GCACAGTTTTCTCAGATGCGCCCTGCTGTACCAATGACACCCACTCTAGCC
genomic: TGTATGTTGCATTTGCGCAGCGCAAAGAAGATAGAAAAGCGATGTTGCAGgcaagtgtcc ... cattacccagGCACAGTTTTCTCAGATGCGCCCTGCTGTACCAATGACACCCACTCTAGCC
EST: gi|33097147|gb|CF057107.1|CF057107
EST:     TGCGCAGTGCATAGAATATAGAAAAGCGATGTTGCAG                         GCACAGTTTTCTCAGATGCGCCCTGCTGTACCAATGACACCCACTCTAGCC
genomic: TGCGCAGCGCAAAGAAGATAGAAAAGCGATGTTGCAGgcaagtgtcc ... cattacccagGCACAGTTTTCTCAGATGCGCCCTGCTGTACCAATGACACCCACTCTAGCC
EST: gi|32848176|gb|CD987857.1|CD987857
EST:     TGTATGTTGCATTTGCACAGCGCAAAGAAGATAGAAAAGCGATGTTGCAG                         GCACAGTTTTCTCAGATGCGCCCTGCTGT
genomic: TGTATGTTGCATTTGCGCAGCGCAAAGAAGATAGAAAAGCGATGTTGCAGgcaagtgtcc ... cattacccagGCACAGTTTTCTCAGATGCGCCCTGCTGT
EST: gi|211437282|gb|FL309165.1|FL309165
EST:     TGTATGTTGCATTTGCGCAGCGCAAAGAAGATAGAAAAGCGATGTTGCAG                         GCACAGTTTTCTCAGATGCGCCCTGCTGTACCAATGACACCCACTCTAGCC
genomic: TGTATGTTGCATTTGCGCAGCGCAAAGAAGATAGAAAAGCGATGTTGCAGgcaagtgtcc ... cattacccagGCACAGTTTTCTCAGATGCGCCCTGCTGTACCAATGACACCCACTCTAGCC
EST: gi|13490826|gb|BG517590.1|BG517590
EST:     TGTATGTTGCATTTGCGCAGCGCAAAGAAGATAGAAAAGCGATGTTGCAG                         GCACAGTTTTCTCAGATGCGCCCTGCTGTACCAATGACACCCACT
genomic: TGTATGTTGCATTTGCGCAGCGCAAAGAAGATAGAAAAGCGATGTTGCAGgcaagtgtcc ... cattacccagGCACAGTTTTCTCAGATGCGCCCTGCTGTACCAATGACACCCACT
EST: gi|211179931|gb|FL049122.1|FL049122
EST:     TGTATGTTGCATTTGCGCAGCGCAAAGAAGATAGAAAAGCGATGTTGCAG                         GCACAGTTTTCTCAGATGCGCCCTGCTGTACCAATGACACCCACTCTAGCC
genomic: TGTATGTTGCATTTGCGCAGCGCAAAGAAGATAGAAAAGCGATGTTGCAGgcaagtgtcc ... cattacccagGCACAGTTTTCTCAGATGCGCCCTGCTGTACCAATGACACCCACTCTAGCC

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: 788

TTAACTGAAATGAATGGCAAAATGATATCTGGAAAACCATTGTATGTTGCATTTGCGCAGCGCAAAGAAGATAGAAAAGCGATGTTGCAGgcaagtgtcc ... cattacccagGCACAGTTTTCTCAGATGCGCCCTGCTGTACCAATGACACCCACTCTAGCCCCGCGCCTTCCAATGTACCCTCCTATGGCTCCTCAGCAACTCTTCTATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 651

TTAACTGAAATGAATGGCAAAATGATATCTGGAAAACCATTGTATGTTGCATTTGCGCAGCGCAAAGAAGATAGAAAAGCGATGTTGCAGgcaagtgtcc ... cattacccagGCACAGTTTTCTCAGATGCGCCCTGCTGTACCAATGACACCCACTCTAGCCCCGCGCCTTCCAATGTACCCTCCTATGGCTCCTCAGCAACTCTTCTATG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 755

TTAACTGAAATGAATGGCAAAATGATATCTGGAAAACCATTGTATGTTGCATTTGCGCAGCGCAAAGAAGATAGAAAAGCGATGTTGCAGgcaagtgtcc ... cattacccagGCACAGTTTTCTCAGATGCGCCCTGCTGTACCAATGACACCCACTCTAGCCCCGCGCCTTCCAATGTACCCTCCTATGGCTCCTCAGCAACTCTTCTATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 901

TTAACTGAAATGAATGGCAAAATGATATCTGGAAAACCATTGTATGTTGCATTTGCGCAGCGCAAAGAAGATAGAAAAGCGATGTTGCAGgcaagtgtcc ... cattacccagGCACAGTTTTCTCAGATGCGCCCTGCTGTACCAATGACACCCACTCTAGCCCCGCGCCTTCCAATGTACCCTCCTATGGCTCCTCAGCAACTCTTCTATG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttggactatctatcatatcattttgctgacgtttacaaatcctacattacccagGCACAGTTTTCTCAGATGCGCCCTGCTGTACCAATGACACCCACTCTAGCCCCGCGCCTTCCAATGTACCCTCCTATGGCTCCTCAGCAACTCTTCTATG
                        tgctgac  putative branch site (score: 901)
           tatcatatcatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttcccttttgtaatatattaaaatttctacaaaaaatgttgcatttttggactatctatcatatcattttgctgacgtttacaaatcctacattacccagGCACAGTTTTCTCAGATGCGCCCTGCTGTACCAATGACACCCACTCTAGCCCCGCGCCTTCCAATGTACCCTCCTATGGCTCCTCAGCAACTCTTCTATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC
- - - - - - - - - - - - - - - aaaaaat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgctgac