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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcgctaaaatatgacattcttgtggtgtctagtttctgcagtattgttagtttgttggccctgaccttatcaacattgagtgttttgtttctggtgatagGAAATTGACGTAAAAAATCACAAATGGGGGCACTATTTCATGTGTGG

Basic information

species Zea mays
transcript GRMZM2G458549_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G458549_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os03g61710.1 (Oryza sativa), 3'ss of exon 2
tcgctaaaat----atgacattcttgtggtgtct-agtttctgcagtattgttagtttgttggccc--tgaccttatcaacattgagtgttttgtttctggtgatagGAAATTGACGTAAAAAATCACAAATGGGGGCACTATTTCATGTGTGG
  || |  ||     |||  ||  |||  | ||| || ||| |   | |  ||| ||  |||      |||  |  |      | | | ||||   |        ||||||||||| ||||||| ||||||||||| |||||||||||||||||
-tgccatgatccgtctgaagttgctgttttttcttagcttcagttatttgattatttctttgatatattgatttggttgttgataaatatttttcat------gcagGAAATTGACATAAAAAACCACAAATGGGGCCACTATTTCATGTGTGG
















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|148997911|gb|EE035899.2|EE035899
EST:     ACGTCGACGACAAGTACCCCCTCTGCGTTTACCCCGCCGACCCAGACAAG                         GAAATTGACGTAAAAAATCACAAATGGGGGCACTATTTCCTGTGTGG
genomic: ACGTCGACGACAAGTACCCCCTCTGCGTTTACCCCGCCGACCCAGACAAGgtgctccctg ... ctggtgatagGAAATTGACGTAAAAAATCACAAATGGGGGCACTATTTCATGTGTGG
EST: gi|76290432|gb|DV030000.1|DV030000
EST:     ACGTCGACGACAAGTACCCCCTCTGCGTTTACCCCGCCGACCCAGACAAG                         GAAATTGACGTAAAAAATCACAAATGGGGGCACTATTTCATGTGTGG
genomic: ACGTCGACGACAAGTACCCCCTCTGCGTTTACCCCGCCGACCCAGACAAGgtgctccctg ... ctggtgatagGAAATTGACGTAAAAAATCACAAATGGGGGCACTATTTCATGTGTGG
EST: gi|50330093|gb|CO525219.1|CO525219
EST:     ACGTCGACGACAAGTACCCCCTCTGCGTTTACCCCGCCGACCCAGACAAG                         GAAATTGACGTAAAAAATCACAAATGGGGGCACTATTTCATGTGTGG
genomic: ACGTCGACGACAAGTACCCCCTCTGCGTTTACCCCGCCGACCCAGACAAGgtgctccctg ... ctggtgatagGAAATTGACGTAAAAAATCACAAATGGGGGCACTATTTCATGTGTGG
EST: gi|148960156|gb|EE153406.2|EE153406
EST:     ACGTCGACGACAAGTACCCCCTCTGCGTTTACCCCGCCGACCCAGACAAG                         GAAATTGACGTAAAAAATCACAAATGGGGGCACTATTTCATGTGTGG
genomic: ACGTCGACGACAAGTACCCCCTCTGCGTTTACCCCGCCGACCCAGACAAGgtgctccctg ... ctggtgatagGAAATTGACGTAAAAAATCACAAATGGGGGCACTATTTCATGTGTGG
EST: gi|76283981|gb|DV023549.1|DV023549
EST:     ACGTCGACGACAAGTACCCCCTCTGCGTTTACCCCGCCGACCCAGACAAG                         GAAATTGACGTAAAAAATCACAAATGGGGGCACTATTTCATGTGTGG
genomic: ACGTCGACGACAAGTACCCCCTCTGCGTTTACCCCGCCGACCCAGACAAGgtgctccctg ... ctggtgatagGAAATTGACGTAAAAAATCACAAATGGGGGCACTATTTCATGTGTGG
EST: gi|89764289|gb|DY691150.1|DY691150
EST:     ACGTCGACGACAAGTACCCCCTCTGCGTTTACCCCGCCGACCCAGACAAG                         GAAATTGACGTAAAAAATCACAAATGGGGGCACTATTTCATGTGTGG
genomic: ACGTCGACGACAAGTACCCCCTCTGCGTTTACCCCGCCGACCCAGACAAGgtgctccctg ... ctggtgatagGAAATTGACGTAAAAAATCACAAATGGGGGCACTATTTCATGTGTGG
EST: gi|93014044|gb|EB639564.1|EB639564
EST:     CGTCGACGACAAGTACCCCCCTCTGCGTTTACCCCGCCGACCCAGACAAG                         GAAATTGACGTAAAAAATCACAAATGGGGGCACTATTTCATGTGTGG
genomic: CGTCGACGACAAGTACCCCC-TCTGCGTTTACCCCGCCGACCCAGACAAGgtgctccctg ... ctggtgatagGAAATTGACGTAAAAAATCACAAATGGGGGCACTATTTCATGTGTGG
EST: gi|148955644|gb|EC901316.2|EC901316
EST:     ACGTCGACGACAAGTACCCCCTCTGCGTTTACCCCGCCGACCCAGACAAG                         GAAATTGACGTAAAAAATCACAAATGGGGGCACTATTTCATGTGTGG
genomic: ACGTCGACGACAAGTACCCCCTCTGCGTTTACCCCGCCGACCCAGACAAGgtgctccctg ... ctggtgatagGAAATTGACGTAAAAAATCACAAATGGGGGCACTATTTCATGTGTGG
EST: gi|149070820|gb|EE159229.2|EE159229
EST:     ACGTCGACGACAAGTACCCCCTCTGCGTTTACCCCGCCGACCCAGACAAG                         GAAATTGACGTAAAAAATCACAAATGGGGGCACTATTTCATGTGTGG
genomic: ACGTCGACGACAAGTACCCCCTCTGCGTTTACCCCGCCGACCCAGACAAGgtgctccctg ... ctggtgatagGAAATTGACGTAAAAAATCACAAATGGGGGCACTATTTCATGTGTGG
EST: gi|74231838|gb|DT639752.1|DT639752
EST:     ACGTCGACGACAAGTACCCCCTCTGCGTTTACCCCGCCGACCCAGACAAG                         GAAATTGACGTAAAAAATCACAAATGGGGGCACTATTTCATGTGTGG
genomic: ACGTCGACGACAAGTACCCCCTCTGCGTTTACCCCGCCGACCCAGACAAGgtgctccctg ... ctggtgatagGAAATTGACGTAAAAAATCACAAATGGGGGCACTATTTCATGTGTGG
EST: gi|148972046|gb|EE022887.2|EE022887
EST:     ACGTCGACGACAAGTACCCCCTCTGCGTTTACCCCGCCGACCCAGACAAG                         GAAATTGACGTAAAAAATCACAAATGGGGGCACTATTTCATGTGTGG
genomic: ACGTCGACGACAAGTACCCCCTCTGCGTTTACCCCGCCGACCCAGACAAGgtgctccctg ... ctggtgatagGAAATTGACGTAAAAAATCACAAATGGGGGCACTATTTCATGTGTGG
EST: gi|148982924|gb|EE028793.2|EE028793
EST:     ACGTCGACGACAAGTACCCCCTCTGCGTTTACCCCGCCGACCCAGACAAG                         GAAATTGACGTAAAAAATCACAAATGGGGGCACTATTTCATGTGTGG
genomic: ACGTCGACGACAAGTACCCCCTCTGCGTTTACCCCGCCGACCCAGACAAGgtgctccctg ... ctggtgatagGAAATTGACGTAAAAAATCACAAATGGGGGCACTATTTCATGTGTGG
EST: gi|149071533|gb|EE159924.2|EE159924
EST:     ACGTCGACGACAAGTACCCCCTCTGCGTTTACCCCGCCGACCCAGACAAG                         GAAATTGACGTAAAAAATCACAAATGGGGGCACTATTTCATGTGTGG
genomic: ACGTCGACGACAAGTACCCCCTCTGCGTTTACCCCGCCGACCCAGACAAGgtgctccctg ... ctggtgatagGAAATTGACGTAAAAAATCACAAATGGGGGCACTATTTCATGTGTGG
EST: gi|76912626|gb|DV164825.1|DV164825
EST:     ACGTCGACGACAAGTACCCCCTCTGCGTTTACCCCGCCGACCCAGACAAG                         GAAATTGACGTAAAAAATCACAAATGGGGGCACTATTTCATGTGTGG
genomic: ACGTCGACGACAAGTACCCCCTCTGCGTTTACCCCGCCGACCCAGACAAGgtgctccctg ... ctggtgatagGAAATTGACGTAAAAAATCACAAATGGGGGCACTATTTCATGTGTGG
EST: gi|148965140|gb|EE015956.2|EE015956
EST:     ACGTCGACGACAAGTACCCCCTCTGCGTTTACCCCGCCGACCCAGACAAG                         GAAATTGACGTAAAAAATCACAAATGGGGGCACTATTTCATGTGTGG
genomic: ACGTCGACGACAAGTACCCCCTCTGCGTTTACCCCGCCGACCCAGACAAGgtgctccctg ... ctggtgatagGAAATTGACGTAAAAAATCACAAATGGGGGCACTATTTCATGTGTGG
EST: gi|78085244|gb|DV513637.1|DV513637
EST:     ACGTCGACGACAAGTACCCCCTCTGCGTTTACCCCGCCGACCCAGACAAG                         GAAATTGACGTAAAAAATCACAAATGGGGGCACTATTTCATGTGTGG
genomic: ACGTCGACGACAAGTACCCCCTCTGCGTTTACCCCGCCGACCCAGACAAGgtgctccctg ... ctggtgatagGAAATTGACGTAAAAAATCACAAATGGGGGCACTATTTCATGTGTGG
EST: gi|93282954|gb|EB675218.1|EB675218
EST:     ACGTCGACGACAAGTACCCCCTCTGCGTTTACCCCGCCGACCCAGACAAG                         GAAATTGACGTAAAAAATCACAAATGGGGGCACTATTTCATGTGTGG
genomic: ACGTCGACGACAAGTACCCCCTCTGCGTTTACCCCGCCGACCCAGACAAGgtgctccctg ... ctggtgatagGAAATTGACGTAAAAAATCACAAATGGGGGCACTATTTCATGTGTGG
EST: gi|148991238|gb|EE032704.2|EE032704
EST:     ACGTCGACGACAAGTACCCCCTCTGCGTTTACCCCGCCGACCCAGACAAG                         GAAATTGACGTAAAAAATCACAAATGGGGGCACTATTTCATGTGTGG
genomic: ACGTCGACGACAAGTACCCCCTCTGCGTTTACCCCGCCGACCCAGACAAGgtgctccctg ... ctggtgatagGAAATTGACGTAAAAAATCACAAATGGGGGCACTATTTCATGTGTGG
EST: gi|148951727|gb|EC897480.2|EC897480
EST:     ACGTCGACGACAAGTACCCCCTCTGCGTTTACCCCGCCGACCCAGACAAG                         GAAATTGACGTAAAAAATCACAAATGGGGGCACTATTTCATGTGTGG
genomic: ACGTCGACGACAAGTACCCCCTCTGCGTTTACCCCGCCGACCCAGACAAGgtgctccctg ... ctggtgatagGAAATTGACGTAAAAAATCACAAATGGGGGCACTATTTCATGTGTGG
EST: gi|71318360|gb|DR795942.1|DR795942
EST:     ACGTCGACGACAAGTACCCCCTCTGCGTTTACCCCGCCGACCCAGACAAG                         GAAATTGACGTAAAAAATCACAAATGGGGGCACTATTTCATGTGTGG
genomic: ACGTCGACGACAAGTACCCCCTCTGCGTTTACCCCGCCGACCCAGACAAGgtgctccctg ... ctggtgatagGAAATTGACGTAAAAAATCACAAATGGGGGCACTATTTCATGTGTGG
EST: gi|148973013|gb|EE024065.2|EE024065
EST:     ACGTCGACGACAAGTACCCCCTCTGCGTTTACCCCGCCGACCCAGACAAG                         GAAATTGACGTAAAAAATCACAAATGGGGGCACTATTTCATGTGTGG
genomic: ACGTCGACGACAAGTACCCCCTCTGCGTTTACCCCGCCGACCCAGACAAGgtgctccctg ... ctggtgatagGAAATTGACGTAAAAAATCACAAATGGGGGCACTATTTCATGTGTGG
EST: gi|148942675|gb|EC887696.2|EC887696
EST:     ACGTCGACGACAAGTACCCCCTCTGCGTTTACCCCGCCGACCCAGACAAG                         GAAATTGACGTAAAAAATCACAAATGGGGGCACTATTTCATGTGTGG
genomic: ACGTCGACGACAAGTACCCCCTCTGCGTTTACCCCGCCGACCCAGACAAGgtgctccctg ... ctggtgatagGAAATTGACGTAAAAAATCACAAATGGGGGCACTATTTCATGTGTGG
EST: gi|148967123|gb|EE018297.2|EE018297
EST:     ACGTCGACGACAAGTACCCCCTCTGCGTTTACCCCGCCGACCCAGACAAG                         GAAATTGACGTAAAAAATCACAAATGGGGGCACTATTTCATGTGTGG
genomic: ACGTCGACGACAAGTACCCCCTCTGCGTTTACCCCGCCGACCCAGACAAGgtgctccctg ... ctggtgatagGAAATTGACGTAAAAAATCACAAATGGGGGCACTATTTCATGTGTGG

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), 47 (downstream exon)
Score: 100

CATGATCGTCGCCATCCGAAGGGCCAACGGCGCCCAGGTGAGGGTCGCCAACGTCGACGACAAGTACCCCCTCTGCGTTTACCCCGCCGACCCAGACAAGgtgctccctg ... ctggtgatagGAAATTGACGTAAAAAATCACAAATGGGGGCACTATTTCATGTGTGG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 209

CATGATCGTCGCCATCCGAAGGGCCAACGGCGCCCAGGTGAGGGTCGCCAACGTCGACGACAAGTACCCCCTCTGCGTTTACCCCGCCGACCCAGACAAGgtgctccctg ... ctggtgatagGAAATTGACGTAAAAAATCACAAATGGGGGCACTATTTCATGTGTGG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 200

CATGATCGTCGCCATCCGAAGGGCCAACGGCGCCCAGGTGAGGGTCGCCAACGTCGACGACAAGTACCCCCTCTGCGTTTACCCCGCCGACCCAGACAAGgtgctccctg ... ctggtgatagGAAATTGACGTAAAAAATCACAAATGGGGGCACTATTTCATGTGTGG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 192

CATGATCGTCGCCATCCGAAGGGCCAACGGCGCCCAGGTGAGGGTCGCCAACGTCGACGACAAGTACCCCCTCTGCGTTTACCCCGCCGACCCAGACAAGgtgctccctg ... ctggtgatagGAAATTGACGTAAAAAATCACAAATGGGGGCACTATTTCATGTGTGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttagtttgttggccctgaccttatcaacattgagtgttttgtttctggtgatagGAAATTGACGTAAAAAATCACAAATGGGGGCACTATTTCATGTGTGG
             ccctgac  putative branch site (score: 192)
                                     ttttgtttct  putative PPT
                                     ttttgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcgctaaaatatgacattcttgtggtgtctagtttctgcagtattgttagtttgttggccctgaccttatcaacattgagtgttttgtttctggtgatagGAAATTGACGTAAAAAATCACAAATGGGGGCACTATTTCATGTGTGG

- - - - - -tgacatt
- - - - - - - - - - tgtggtg
- - - - - - - - - - - - - - - - - tctgcag
- - - - - - - - - - - - - - - - - - - - - - - - - tttgttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - atcaaca