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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taattaaaggtccatacacatgaatcaactagtgtttttttattttttgttttgagaaaagtgaaagtactaccgttttgctaatttacatgccattcagGTTTTCGGCCTGCTGACGAAGCCGCTTCTCAGTCTCCTCATCCCACCAAGGACTGGACTGAACACGTCGTCTCTGCTCTCAAGCCAGTCTATGCTGGACC

Basic information

species Zea mays
transcript GRMZM2G063492_T01
intron # 14
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|18964172|gb|BM660852.1|BM660852
EST:     ATGCTATCATGATCACCAGCACAGTTATTGTTGTTCTATTCAGCACA-TG                         GTTTTCGGCCTGCTGACGAAGCCGCTTCTCAGTCTCCTCATCC
genomic: ATGCTATCATGATCACCAGCACAGTTATTGTTGTTCTATTCAGCACAATGgtaagccgtc ... tgccattcagGTTTTCGGCCTGCTGACGAAGCCGCTTCTCAGTCTCCTCATCC
EST: gi|37397420|gb|CF636007.1|CF636007
EST:     ATGCTATCATGATCACCAGCACAGTTATTGTTGTTCTATTCAGCACAATG                         GTTTTCGGCCTGCTGACGAAGCCGCTGCTCAGTCTCCTCATCCCACCAAGG
genomic: ATGCTATCATGATCACCAGCACAGTTATTGTTGTTCTATTCAGCACAATGgtaagccgtc ... tgccattcagGTTTTCGGCCTGCTGACGAAGCCGCTTCTCAGTCTCCTCATCCCACCAAGG
EST: gi|211218430|gb|FL445376.1|FL445376
EST:     ATGCTATCATGATCACCAGCACAGTTATTGTTGTTCTATTCAGCACAATG                         GTTTTCGGCCTGCTGACGAAGCCGCTGCTCAGTCTCCTCATCCCACCAAGG
genomic: ATGCTATCATGATCACCAGCACAGTTATTGTTGTTCTATTCAGCACAATGgtaagccgtc ... tgccattcagGTTTTCGGCCTGCTGACGAAGCCGCTTCTCAGTCTCCTCATCCCACCAAGG
EST: gi|71311178|gb|DR791899.1|DR791899
EST:     ATGCTATCATGATCACCAGCACAGTTATTGTTGTTCTATTCAGCACAATG                         GTTTTCGGCCTGCTGACGAAGCCGCTGCTCAGTCTCCTCATCTCACAAAG-
genomic: ATGCTATCATGATCACCAGCACAGTTATTGTTGTTCTATTCAGCACAATGgtaagccgtc ... tgccattcagGTTTTCGGCCTGCTGACGAAGCCGCTTCTCAGTCTCCTCATCCCACCAAGG
EST: gi|89106454|gb|DY576671.1|DY576671
EST:     ATGCTATCATGATCACCAGCACAGTTATTGTTGTTCTATTCAGCACAATG                         GTTTTCGGCCTGCTGACGAAGCCGCTTCTCAGTCTCCTCATCCCACCAAGG
genomic: ATGCTATCATGATCACCAGCACAGTTATTGTTGTTCTATTCAGCACAATGgtaagccgtc ... tgccattcagGTTTTCGGCCTGCTGACGAAGCCGCTTCTCAGTCTCCTCATCCCACCAAGG
EST: gi|78078432|gb|DV506846.1|DV506846
EST:     ATGCTATCATGATCACCAGCACAGTTATTGTTGTTCTATTCAGCACAATG                         GTTTTCGGCCTGCTGACGAAGCCGCTGCTCAGTCTCCTCATCCCACCAAGG
genomic: ATGCTATCATGATCACCAGCACAGTTATTGTTGTTCTATTCAGCACAATGgtaagccgtc ... tgccattcagGTTTTCGGCCTGCTGACGAAGCCGCTTCTCAGTCTCCTCATCCCACCAAGG
EST: gi|18963602|gb|BM660527.1|BM660527
EST:     ATGCTATCATGATCACCAGCACAGTTATTGTTGTTCTATTCAGC-CAATG                         GTTTTCGGCCTGCTG-CGAAGCCGCTTCTCAGTCTCCTCATCCCACCAAGG
genomic: ATGCTATCATGATCACCAGCACAGTTATTGTTGTTCTATTCAGCACAATGgtaagccgtc ... tgccattcagGTTTTCGGCCTGCTGACGAAGCCGCTTCTCAGTCTCCTCATCCCACCAAGG
EST: gi|91872697|gb|EB402654.1|EB402654
EST:     ATGCTATCATGATCACCAGCACAGTTATTGTTGTTCTATTCAGCACAATG                         GTTTTCGGCCTGCTGACGAAGCCGCTTCTCAGTCTCCTCATCCCACCAAGG
genomic: ATGCTATCATGATCACCAGCACAGTTATTGTTGTTCTATTCAGCACAATGgtaagccgtc ... tgccattcagGTTTTCGGCCTGCTGACGAAGCCGCTTCTCAGTCTCCTCATCCCACCAAGG

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), 40 (downstream exon)
Score: 90

TTTACAGCATCTGGTCACACTGAAGTGCGAGTCAATGCTATCATGATCACCAGCACAGTTATTGTTGTTCTATTCAGCACAATGgtaagccgtc ... tgccattcagGTTTTCGGCCTGCTGACGAAGCCGCTTCTCAGTCTCCTCATCCCACCAAGGACTGGACTGAACACGTCGTCTCTGCTCTCAAGCCAGTCTATGCTGGACC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 110

TTTACAGCATCTGGTCACACTGAAGTGCGAGTCAATGCTATCATGATCACCAGCACAGTTATTGTTGTTCTATTCAGCACAATGgtaagccgtc ... tgccattcagGTTTTCGGCCTGCTGACGAAGCCGCTTCTCAGTCTCCTCATCCCACCAAGGACTGGACTGAACACGTCGTCTCTGCTCTCAAGCCAGTCTATGCTGGACC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 52

TTTACAGCATCTGGTCACACTGAAGTGCGAGTCAATGCTATCATGATCACCAGCACAGTTATTGTTGTTCTATTCAGCACAATGgtaagccgtc ... tgccattcagGTTTTCGGCCTGCTGACGAAGCCGCTTCTCAGTCTCCTCATCCCACCAAGGACTGGACTGAACACGTCGTCTCTGCTCTCAAGCCAGTCTATGCTGGACC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 103

TTTACAGCATCTGGTCACACTGAAGTGCGAGTCAATGCTATCATGATCACCAGCACAGTTATTGTTGTTCTATTCAGCACAATGgtaagccgtc ... tgccattcagGTTTTCGGCCTGCTGACGAAGCCGCTTCTCAGTCTCCTCATCCCACCAAGGACTGGACTGAACACGTCGTCTCTGCTCTCAAGCCAGTCTATGCTGGACC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgttttgagaaaagtgaaagtactaccgttttgctaatttacatgccattcagGTTTTCGGCCTGCTGACGAAGCCGCTTCTCAGTCTCCTCATCCCACCAAGGACTGGACTGAACACGTCGTCTCTGCTCTCAAGCCAGTCTATGCTGGACC
                                 tgctaat  putative branch site (score: 103)
                                    taatttacat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taattaaaggtccatacacatgaatcaactagtgtttttttattttttgttttgagaaaagtgaaagtactaccgttttgctaatttacatgccattcagGTTTTCGGCCTGCTGACGAAGCCGCTTCTCAGTCTCCTCATCCCACCAAGGACTGGACTGAACACGTCGTCTCTGCTCTCAAGCCAGTCTATGCTGGACC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - catacac
- - - - - - - - - - - aatcaac
- - - - - - - - - - - - - - - - tgttttt
- - - - - - - - - - - - - - - - - - - - - - - - - - -gagaaaag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttttgct