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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttacgattttgaattcttgctgcagatgcctgaattgttgaagtattctgttccctattattttgattgtagaataaaaaatgaccgtatcagtatatgatatgttcgtatcttgatttgcaatctgcagATACAAGGGAGTTTATGAATACTGTAGATCAAAAGGGATAGATCTGGGCAAACCTGTTGCGCTTGACGTCGTTGTTGATGGCACAGTTCCTCAAG

Basic information

species Zea mays
transcript GRMZM2G458549_T01
intron # 3
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 3
lower sequence: LOC_Os03g61710.1 (Oryza sativa), 3'ss of exon 3
gtaagttacgattttgaattcttgctgcagatgcctgaattgttgaagt-attctgttccctattattttgattgtagaataaaaaatgaccgtatcagtatatgatatgttcgtatcttgatttgcaatctgcagATACAAGGGAGTTTATGAATACTGTAGATCAAAAGGGATAGATCTGGGCAAACCTGTTGCGCTTGACGTCGTTGTTGATGGCACAGTTCCTCAAG
||||||||    ||  |||  |   |   | ||| | ||| |   || |  |||  ||    ||    || ||||   |  | |||| ||    |  |  ||||    |||  ||   |  |||  | |||||||||||||||||||||||||| || ||||| ||||||||||||||| ||||   ||||||||  ||||| || |||||||||||||||||||||  ||
gtaagttaattcttataatattgtataatgttgcataaatagcgaaatttgttcactttttcatacacttcattggccacaagaaaaaga--aaacgaacatat--cctgtctgt---tcaattctctatctgcagATACAAGGGAGTTTATGAGTATTGTAGGTCAAAAGGGATAGATATGGGTGGACCTGTTGGCCTTGATGTAGTTGTTGATGGCACAGTTCCTACAG
















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:     GAAATTGACGTAAAAAATCACAAATGGGGGCACTATTTCCTGTGTGG                         ATACAAGGGAGTTTATGAATACTGTAGATCAAAAGGGATAGATCTGGGCAA
genomic: GAAATTGACGTAAAAAATCACAAATGGGGGCACTATTTCATGTGTGGgtaagttacg ... caatctgcagATACAAGGGAGTTTATGAATACTGTAGATCAAAAGGGATAGATCTGGGCAA
EST: gi|76290432|gb|DV030000.1|DV030000
EST:     GAAATTGACGTAAAAAATCACAAATGGGGGCACTATTTCATGTGTGG                         ATACAAGGGAGTTTATGAATACTGTAGATCAAAAGGGATAGATCTGGGCAA
genomic: GAAATTGACGTAAAAAATCACAAATGGGGGCACTATTTCATGTGTGGgtaagttacg ... caatctgcagATACAAGGGAGTTTATGAATACTGTAGATCAAAAGGGATAGATCTGGGCAA
EST: gi|50330093|gb|CO525219.1|CO525219
EST:     GAAATTGACGTAAAAAATCACAAATGGGGGCACTATTTCATGTGTGG                         ATACAAGGGAGTTTATGAATACTGTAGATCAAAAGGGATAGATCTGGGCAA
genomic: GAAATTGACGTAAAAAATCACAAATGGGGGCACTATTTCATGTGTGGgtaagttacg ... caatctgcagATACAAGGGAGTTTATGAATACTGTAGATCAAAAGGGATAGATCTGGGCAA
EST: gi|148960156|gb|EE153406.2|EE153406
EST:     GAAATTGACGTAAAAAATCACAAATGGGGGCACTATTTCATGTGTGG                         ATACAAGGGAGTTTATGAATACTGTAGATCAAAAGGGATAGATCTGGGCAA
genomic: GAAATTGACGTAAAAAATCACAAATGGGGGCACTATTTCATGTGTGGgtaagttacg ... caatctgcagATACAAGGGAGTTTATGAATACTGTAGATCAAAAGGGATAGATCTGGGCAA
EST: gi|76283981|gb|DV023549.1|DV023549
EST:     GAAATTGACGTAAAAAATCACAAATGGGGGCACTATTTCATGTGTGG                         ATACAAGGGAGTTTATGAATACTGTAGATCAAAAGGGATAGATCTGGGCAA
genomic: GAAATTGACGTAAAAAATCACAAATGGGGGCACTATTTCATGTGTGGgtaagttacg ... caatctgcagATACAAGGGAGTTTATGAATACTGTAGATCAAAAGGGATAGATCTGGGCAA
EST: gi|89764289|gb|DY691150.1|DY691150
EST:     GAAATTGACGTAAAAAATCACAAATGGGGGCACTATTTCATGTGTGG                         ATACAAGGGAGTTTATGAATACTGTAGATCAAAAGGGATAGATCTGGGCAA
genomic: GAAATTGACGTAAAAAATCACAAATGGGGGCACTATTTCATGTGTGGgtaagttacg ... caatctgcagATACAAGGGAGTTTATGAATACTGTAGATCAAAAGGGATAGATCTGGGCAA
EST: gi|93014044|gb|EB639564.1|EB639564
EST:     GAAATTGACGTAAAAAATCACAAATGGGGGCACTATTTCATGTGTGG                         ATACAAGGGAGTTTATGAATACTGTAGATCAAAAGGGATAGATCTGGGCAA
genomic: GAAATTGACGTAAAAAATCACAAATGGGGGCACTATTTCATGTGTGGgtaagttacg ... caatctgcagATACAAGGGAGTTTATGAATACTGTAGATCAAAAGGGATAGATCTGGGCAA
EST: gi|148955644|gb|EC901316.2|EC901316
EST:     GAAATTGACGTAAAAAATCACAAATGGGGGCACTATTTCATGTGTGG                         ATACAAGGGAGTTTATGAATACTGTAGATCAAAAGGGATAGATCTGGGCAA
genomic: GAAATTGACGTAAAAAATCACAAATGGGGGCACTATTTCATGTGTGGgtaagttacg ... caatctgcagATACAAGGGAGTTTATGAATACTGTAGATCAAAAGGGATAGATCTGGGCAA
EST: gi|149070820|gb|EE159229.2|EE159229
EST:     GAAATTGACGTAAAAAATCACAAATGGGGGCACTATTTCATGTGTGG                         ATACAAGGGAGTTTATGAATACTGTAGATCAAAAGGGATAGATCTGGGCAA
genomic: GAAATTGACGTAAAAAATCACAAATGGGGGCACTATTTCATGTGTGGgtaagttacg ... caatctgcagATACAAGGGAGTTTATGAATACTGTAGATCAAAAGGGATAGATCTGGGCAA
EST: gi|74231838|gb|DT639752.1|DT639752
EST:     GAAATTGACGTAAAAAATCACAAATGGGGGCACTATTTCATGTGTGG                         ATACAAGGGAGTTTATGAATACTGTAGATCAAAAGGGATAGATCTGGGCAA
genomic: GAAATTGACGTAAAAAATCACAAATGGGGGCACTATTTCATGTGTGGgtaagttacg ... caatctgcagATACAAGGGAGTTTATGAATACTGTAGATCAAAAGGGATAGATCTGGGCAA
EST: gi|148972046|gb|EE022887.2|EE022887
EST:     GAAATTGACGTAAAAAATCACAAATGGGGGCACTATTTCATGTGTGG                         ATACAAGGGAGTTTATGAATACTGTAGATCAAAAGGGATAGATCTGGGCAA
genomic: GAAATTGACGTAAAAAATCACAAATGGGGGCACTATTTCATGTGTGGgtaagttacg ... caatctgcagATACAAGGGAGTTTATGAATACTGTAGATCAAAAGGGATAGATCTGGGCAA
EST: gi|148982924|gb|EE028793.2|EE028793
EST:     GAAATTGACGTAAAAAATCACAAATGGGGGCACTATTTCATGTGTGG                         ATACA-GTGGAGTTTATGAATACTGTAAATCAA
genomic: GAAATTGACGTAAAAAATCACAAATGGGGGCACTATTTCATGTGTGGgtaagttacg ... caatctgcagATACAAG-GGAGTTTATGAATACTGTAGATCAA
EST: gi|149071533|gb|EE159924.2|EE159924
EST:     GAAATTGACGTAAAAAATCACAAATGGGGGCACTATTTCATGTGTGG                         ATACAAGGGAGTTTATGAATACTGTAGATCAAAAGGGATAGATCTGGGCAA
genomic: GAAATTGACGTAAAAAATCACAAATGGGGGCACTATTTCATGTGTGGgtaagttacg ... caatctgcagATACAAGGGAGTTTATGAATACTGTAGATCAAAAGGGATAGATCTGGGCAA
EST: gi|76912626|gb|DV164825.1|DV164825
EST:     GAAATTGACGTAAAAAATCACAAATGGGGGCACTATTTCATGTGTGG                         ATACAAGGGAGTTTATGAATACTGTAGATCAAAAGGGATAGATCTGGGCAA
genomic: GAAATTGACGTAAAAAATCACAAATGGGGGCACTATTTCATGTGTGGgtaagttacg ... caatctgcagATACAAGGGAGTTTATGAATACTGTAGATCAAAAGGGATAGATCTGGGCAA
EST: gi|148965140|gb|EE015956.2|EE015956
EST:     GAAATTGACGTAAAAAATCACAAATGGGGGCACTATTTCATGTGTGG                         ATACAAGGGAGTTTATGAATACTGTAGATCAAAAGGGATAGATCTGGGCAA
genomic: GAAATTGACGTAAAAAATCACAAATGGGGGCACTATTTCATGTGTGGgtaagttacg ... caatctgcagATACAAGGGAGTTTATGAATACTGTAGATCAAAAGGGATAGATCTGGGCAA
EST: gi|78085244|gb|DV513637.1|DV513637
EST:     GAAATTGACGTAAAAAATCACAAATGGGGGCACTATTTCATGTGTGG                         ATACAAGGGAGTTTATGAATACTGTAGATCAAAAGGGATAGATCTGGGCAA
genomic: GAAATTGACGTAAAAAATCACAAATGGGGGCACTATTTCATGTGTGGgtaagttacg ... caatctgcagATACAAGGGAGTTTATGAATACTGTAGATCAAAAGGGATAGATCTGGGCAA
EST: gi|93282954|gb|EB675218.1|EB675218
EST:     GAAATTGACGTAAAAAATCACAAATGGGGGCACTATTTCATGTGTGG                         ATACAAGGGAGTTTATGAATACTGTAGATCAAAAGGGATAGATCTGGGCAA
genomic: GAAATTGACGTAAAAAATCACAAATGGGGGCACTATTTCATGTGTGGgtaagttacg ... caatctgcagATACAAGGGAGTTTATGAATACTGTAGATCAAAAGGGATAGATCTGGGCAA
EST: gi|148991238|gb|EE032704.2|EE032704
EST:     GAAATTGACGTAAAAAATCACAAATGGGGGCACTATTTCATGTGTGG                         ATACAAGGGAGTTTATGAATACTGTAGATCAAAAGGGATAGATCTGGGCAA
genomic: GAAATTGACGTAAAAAATCACAAATGGGGGCACTATTTCATGTGTGGgtaagttacg ... caatctgcagATACAAGGGAGTTTATGAATACTGTAGATCAAAAGGGATAGATCTGGGCAA
EST: gi|148951727|gb|EC897480.2|EC897480
EST:     GAAATTGACGTAAAAAATCACAAATGGGGGCACTATTTCATGTGTGG                         ATACAAGGGAGTTTATGAATACTGTAGATCAAAAGGGATAGATCTGGGCAA
genomic: GAAATTGACGTAAAAAATCACAAATGGGGGCACTATTTCATGTGTGGgtaagttacg ... caatctgcagATACAAGGGAGTTTATGAATACTGTAGATCAAAAGGGATAGATCTGGGCAA
EST: gi|71318360|gb|DR795942.1|DR795942
EST:     GAAATTGACGTAAAAAATCACAAATGGGGGCACTATTTCATGTGTGG                         ATACAAGGGAGTTTATGAATACTGTAGATCAAAAGGGATAGATCTGGGCAA
genomic: GAAATTGACGTAAAAAATCACAAATGGGGGCACTATTTCATGTGTGGgtaagttacg ... caatctgcagATACAAGGGAGTTTATGAATACTGTAGATCAAAAGGGATAGATCTGGGCAA
EST: gi|148973013|gb|EE024065.2|EE024065
EST:     GAAATTGACGTAAAAAATCACAAATGGGGGCACTATTTCATGTGTGG                         ATACAAGGGAGTTTATGAATACTGTAGATCAAAAGGGATAGATCTGGGCAA
genomic: GAAATTGACGTAAAAAATCACAAATGGGGGCACTATTTCATGTGTGGgtaagttacg ... caatctgcagATACAAGGGAGTTTATGAATACTGTAGATCAAAAGGGATAGATCTGGGCAA
EST: gi|148942675|gb|EC887696.2|EC887696
EST:     GAAATTGACGTAAAAAATCACAAATGGGGGCACTATTTCATGTGTGG                         ATACAAGGGAGTTTATGAATACTGTAGATCAAAAGGGATAGATCTGGGCAA
genomic: GAAATTGACGTAAAAAATCACAAATGGGGGCACTATTTCATGTGTGGgtaagttacg ... caatctgcagATACAAGGGAGTTTATGAATACTGTAGATCAAAAGGGATAGATCTGGGCAA
EST: gi|148967123|gb|EE018297.2|EE018297
EST:     GAAATTGACGTAAAAAATCACAAATGGGGGCACTATTTCATGTGTGG                         ATACAAGGGAGTTTATGAATACTGTAGATCAAAAGGGATAGATCTGGGCAA
genomic: GAAATTGACGTAAAAAATCACAAATGGGGGCACTATTTCATGTGTGGgtaagttacg ... caatctgcagATACAAGGGAGTTTATGAATACTGTAGATCAAAAGGGATAGATCTGGGCAA
EST: gi|108824283|gb|EC278291.1|EC278291
EST:     TGGGGGCACTATTTCATGTGTGG                         ATACAAGGGAGTTTATGAATACTGTAGATCAAAAGGGATAGATCTGGGCAA
genomic: TGGGGGCACTATTTCATGTGTGGgtaagttacg ... caatctgcagATACAAGGGAGTTTATGAATACTGTAGATCAAAAGGGATAGATCTGGGCAA

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: 83

GAAATTGACGTAAAAAATCACAAATGGGGGCACTATTTCATGTGTGGgtaagttacg ... caatctgcagATACAAGGGAGTTTATGAATACTGTAGATCAAAAGGGATAGATCTGGGCAAACCTGTTGCGCTTGACGTCGTTGTTGATGGCACAGTTCCTCAAG


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 227

GAAATTGACGTAAAAAATCACAAATGGGGGCACTATTTCATGTGTGGgtaagttacg ... caatctgcagATACAAGGGAGTTTATGAATACTGTAGATCAAAAGGGATAGATCTGGGCAAACCTGTTGCGCTTGACGTCGTTGTTGATGGCACAGTTCCTCAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 222

GAAATTGACGTAAAAAATCACAAATGGGGGCACTATTTCATGTGTGGgtaagttacg ... caatctgcagATACAAGGGAGTTTATGAATACTGTAGATCAAAAGGGATAGATCTGGGCAAACCTGTTGCGCTTGACGTCGTTGTTGATGGCACAGTTCCTCAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 254

GAAATTGACGTAAAAAATCACAAATGGGGGCACTATTTCATGTGTGGgtaagttacg ... caatctgcagATACAAGGGAGTTTATGAATACTGTAGATCAAAAGGGATAGATCTGGGCAAACCTGTTGCGCTTGACGTCGTTGTTGATGGCACAGTTCCTCAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaaaatgaccgtatcagtatatgatatgttcgtatcttgatttgcaatctgcagATACAAGGGAGTTTATGAATACTGTAGATCAAAAGGGATAGATCTGGGCAAACCTGTTGCGCTTGACGTCGTTGTTGATGGCACAGTTCCTCAAG
                                   tcttgat  putative branch site (score: 254)
                  tatatgatat  TA-rich tract