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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttacattatgttccttctccagcatttctgttaggtttcaactctagcttacccaaacttgcttgggactaaaaggctttattgttgttttcttctccagCTGCTAGTAGCACTAAAAGTGAGGTACCCACATCGAATTACAATCCTTCGTGGAAACCATGAGAGTCGGCAG

Basic information

species Zea mays
transcript GRMZM2G112793_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G112793_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os03g07150.1 (Oryza sativa), 3'ss of exon 4
ttacattatgttccttctccagcatttctgttag-gtttcaactctagcttacccaaacttgc-ttgggactaaaaggctttattg--ttgt-tttcttctccagCTGCTAGTAGCACTAAAAGTGAGGTACCCACATCGAATTACAATCCTTCGTGGAAACCATGAGAGTCGGCAG
       |  |||  |  |  | |||  |   |   |||||| | |    |     |  |    |    |     | ||  || ||  | || || ||| |||||||  | ||||| || || ||| |  |||||||||| |||||||||||||| ||||| || ||||| ||||||
-----caaaattcgattactggaattctttcaaatatttcaattgttttatgtttgagatcatgtcattatgtgtaagcactactgagtggtattccttatccagCTTTTGGTAGCGCTGAAGGTGCGTCACCCACATCGGATTACAATCCTTCGCGGAAATCACGAGAGCCGGCAG
















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|22818811|gb|BU498901.1|BU498901
EST:     TTATGGGGGATTATGTAGATCGTGGCTACTATTCTGTTGAGACTGTCACT                         CTGCTAGTAGCACTAAAAGTGAGGTACCCACATCGAATTACAATCCTTCGT
genomic: TTATGGGGGATTATGTAGATCGTGGCTACTATTCTGTTGAGACTGTCACTgtaagaaatt ... tcttctccagCTGCTAGTAGCACTAAAAGTGAGGTACCCACATCGAATTACAATCCTTCGT
EST: gi|22490124|gb|BU050047.1|BU050047
EST:     TTATGGGGGATTATGTAGATCGTGGCTACTATTCTGTTGAGACTGTCACT                         CTGCTAGTAGCACTAAAAGTGAGGTACCCACATCGAATTACAATCCTTCGT
genomic: TTATGGGGGATTATGTAGATCGTGGCTACTATTCTGTTGAGACTGTCACTgtaagaaatt ... tcttctccagCTGCTAGTAGCACTAAAAGTGAGGTACCCACATCGAATTACAATCCTTCGT
EST: gi|211046221|gb|FL204514.1|FL204514
EST:     TTATGGGGGATTATGTAGATCGTGGCTACTATTCTGTTGAGACTGTCACT                         CTGCTAGTAGCACTAAAAGTGAGGT
genomic: TTATGGGGGATTATGTAGATCGTGGCTACTATTCTGTTGAGACTGTCACTgtaagaaatt ... tcttctccagCTGCTAGTAGCACTAAAAGTGAGGT
EST: gi|211043271|gb|FL204511.1|FL204511
EST:     TTATGGGGGATTATGTAGATCGTGGCTACTATTCTGTTGAGACTGTCACT                         CTGCTAGTAGCACTAAAAGTGAGGTACCCACATCGAATTACAATCCTTCGT
genomic: TTATGGGGGATTATGTAGATCGTGGCTACTATTCTGTTGAGACTGTCACTgtaagaaatt ... tcttctccagCTGCTAGTAGCACTAAAAGTGAGGTACCCACATCGAATTACAATCCTTCGT
EST: gi|211046223|gb|FL204516.1|FL204516
EST:     TTATGGGGGATTATGTAGATCGTGGCTACTATTCTGTTGAGACTGTCACT                         CTGCTAGTAGCACTAAAAGTGAGGTACCCACATCGAATTACGATCCTTCGT
genomic: TTATGGGGGATTATGTAGATCGTGGCTACTATTCTGTTGAGACTGTCACTgtaagaaatt ... tcttctccagCTGCTAGTAGCACTAAAAGTGAGGTACCCACATCGAATTACAATCCTTCGT
EST: gi|211046224|gb|FL204517.1|FL204517
EST:     TTATGGNGGATTATGTAGATCGTGGCTACTATTCTGTTGAGACTGTCACT                         CTGCTAGTAGCACTAAAAGTGAGGTACCCACATCGAATTACAATCCTTCGT
genomic: TTATGGGGGATTATGTAGATCGTGGCTACTATTCTGTTGAGACTGTCACTgtaagaaatt ... tcttctccagCTGCTAGTAGCACTAAAAGTGAGGTACCCACATCGAATTACAATCCTTCGT
EST: gi|211043272|gb|FL204512.1|FL204512
EST:     TTATGGGGGATTATGTAGATCGTGGCTACTATTCTGTTGAGACTGTCACT                         CTGCTAGTAGCACTAAAAGTGAG
genomic: TTATGGGGGATTATGTAGATCGTGGCTACTATTCTGTTGAGACTGTCACTgtaagaaatt ... tcttctccagCTGCTAGTAGCACTAAAAGTGAG
EST: gi|78118757|gb|DV537141.1|DV537141
EST:     TTATGGGGGATTATGTAGATCGTGGCTACTATTCTGTTGAGACTGTCACT                         CTGCTAGTAGCACTAAAAGTGAGGTACCCACATCGAATTACAATCCTTCGT
genomic: TTATGGGGGATTATGTAGATCGTGGCTACTATTCTGTTGAGACTGTCACTgtaagaaatt ... tcttctccagCTGCTAGTAGCACTAAAAGTGAGGTACCCACATCGAATTACAATCCTTCGT
EST: gi|26559743|gb|CA831978.1|CA831978
EST:     TTATGGGGGATTATGTAGATCGTGGCTACTATTCTGTTGAGACTGTCACT                         CTGCTAGTAGCACTAAAAGTGAGGTACCCACATCGAATTACAATCCTTCGT
genomic: TTATGGGGGATTATGTAGATCGTGGCTACTATTCTGTTGAGACTGTCACTgtaagaaatt ... tcttctccagCTGCTAGTAGCACTAAAAGTGAGGTACCCACATCGAATTACAATCCTTCGT
EST: gi|211043270|gb|FL204510.1|FL204510
EST:     TTATGGGGGATTATGTAGATCGTGGCTACTATTCTGTTGAGACTGTCACT                         CTGCTAGTAGCACTAAAAGTGAGGTACCCACATCGAATTACAATCCTTCGT
genomic: TTATGGGGGATTATGTAGATCGTGGCTACTATTCTGTTGAGACTGTCACTgtaagaaatt ... tcttctccagCTGCTAGTAGCACTAAAAGTGAGGTACCCACATCGAATTACAATCCTTCGT
EST: gi|211046225|gb|FL204518.1|FL204518
EST:     TTATGGGGGATTATGTAGATCGTGGCTACTATTCTGTTGAGACTGTCACT                         CTGCTAGTAGCACTAAAAGTGAGGTACCCACATCGAATTACAATCCTTCGT
genomic: TTATGGGGGATTATGTAGATCGTGGCTACTATTCTGTTGAGACTGTCACTgtaagaaatt ... tcttctccagCTGCTAGTAGCACTAAAAGTGAGGTACCCACATCGAATTACAATCCTTCGT
EST: gi|6021718|gb|AW066646.1|AW066646
EST:     TTATGGGGGATTATGTAGATCGTGGCTACTATTCTGTTGAGACTGTCACT                         CTGCTAGTAGCACTAAAAGTGAGGTACCCACATCGAATTACAATCCTTCGT
genomic: TTATGGGGGATTATGTAGATCGTGGCTACTATTCTGTTGAGACTGTCACTgtaagaaatt ... tcttctccagCTGCTAGTAGCACTAAAAGTGAGGTACCCACATCGAATTACAATCCTTCGT
EST: gi|31360213|gb|CD444570.1|CD444570
EST:     TTATGGGGGATTATGTAGATCGTGGCTACTATTCTGTTGAGACTGTCACT                         CTGCTAGTAGCACTAAAAGTGAGGTACCCACATCGAATTACAATCCTTCGT
genomic: TTATGGGGGATTATGTAGATCGTGGCTACTATTCTGTTGAGACTGTCACTgtaagaaatt ... tcttctccagCTGCTAGTAGCACTAAAAGTGAGGTACCCACATCGAATTACAATCCTTCGT
EST: gi|87153205|gb|DY397994.1|DY397994
EST:     TTATGGGGGATTATGTAGATCGTGGCTACTATTCTGTTGAGACTGTCACT                         CTGCTAGTAGCACTAAAAGTGAGGTACCCACATCGAATTACAATCCTTCGT
genomic: TTATGGGGGATTATGTAGATCGTGGCTACTATTCTGTTGAGACTGTCACTgtaagaaatt ... tcttctccagCTGCTAGTAGCACTAAAAGTGAGGTACCCACATCGAATTACAATCCTTCGT
EST: gi|22541924|gb|BU092362.1|BU092362
EST:     TTATGGGGGATTATGTAGATCGTGGCTACTATTCTGTTGAGACTGTCACT                         CTGCTAGTAGCACTAAAAGTGAGGTACCCACATCGAATTACAATCCTTCGT
genomic: TTATGGGGGATTATGTAGATCGTGGCTACTATTCTGTTGAGACTGTCACTgtaagaaatt ... tcttctccagCTGCTAGTAGCACTAAAAGTGAGGTACCCACATCGAATTACAATCCTTCGT
EST: gi|211046226|gb|FL204519.1|FL204519
EST:     TTATGGGGGATTATGTAGATCGTGGCTACTATTCTGTTGAGACTGTCACT                         CTGCTAGTAGCACTAAAAGTGAGGTACCCACATCGAATTACAATCCTTCGT
genomic: TTATGGGGGATTATGTAGATCGTGGCTACTATTCTGTTGAGACTGTCACTgtaagaaatt ... tcttctccagCTGCTAGTAGCACTAAAAGTGAGGTACCCACATCGAATTACAATCCTTCGT

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: 269

TGTCCAGACACCAATTACTTATTTATGGGGGATTATGTAGATCGTGGCTACTATTCTGTTGAGACTGTCACTgtaagaaatt ... tcttctccagCTGCTAGTAGCACTAAAAGTGAGGTACCCACATCGAATTACAATCCTTCGTGGAAACCATGAGAGTCGGCAG


Block sizes: 48 (upstream exon), 45 (downstream exon)
Score: 158

TGTCCAGACACCAATTACTTATTTATGGGGGATTATGTAGATCGTGGCTACTATTCTGTTGAGACTGTCACTgtaagaaatt ... tcttctccagCTGCTAGTAGCACTAAAAGTGAGGTACCCACATCGAATTACAATCCTTCGTGGAAACCATGAGAGTCGGCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 169

TGTCCAGACACCAATTACTTATTTATGGGGGATTATGTAGATCGTGGCTACTATTCTGTTGAGACTGTCACTgtaagaaatt ... tcttctccagCTGCTAGTAGCACTAAAAGTGAGGTACCCACATCGAATTACAATCCTTCGTGGAAACCATGAGAGTCGGCAG


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 148

TGTCCAGACACCAATTACTTATTTATGGGGGATTATGTAGATCGTGGCTACTATTCTGTTGAGACTGTCACTgtaagaaatt ... tcttctccagCTGCTAGTAGCACTAAAAGTGAGGTACCCACATCGAATTACAATCCTTCGTGGAAACCATGAGAGTCGGCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agcttacccaaacttgcttgggactaaaaggctttattgttgttttcttctccagCTGCTAGTAGCACTAAAAGTGAGGTACCCACATCGAATTACAATCCTTCGTGGAAACCATGAGAGTCGGCAG
                     gactaaa  putative branch site (score: 148)
                               ctttattgttgttttc  putative PPT
                                tttattgttgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttacattatgttccttctccagcatttctgttaggtttcaactctagcttacccaaacttgcttgggactaaaaggctttattgttgttttcttctccagCTGCTAGTAGCACTAAAAGTGAGGTACCCACATCGAATTACAATCCTTCGTGGAAACCATGAGAGTCGGCAG

- - - - tgttcct
- - - - - - - - ctccagc
- - - - - - - - - - - - -ttctgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcttgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgttgtt