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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatatatttttctgtctttcatatacatttagaattacaaagaaaagagattctgacataatgatgatatttattcatctagAGGATGGTGAGAGTGCTAATGAGAAAGAAAAATCATATGGTTCCATTATGATGGAAAGGTTGACCAGTTCACCGAATGGTCGAATTGATCATGTGCTTCA

Basic information

species Zea mays
transcript GRMZM2G318860_T02
intron # 18
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G318860_T02 (Zea mays), 3'ss of exon 18
lower sequence: LOC_Os08g01920.1 (Oryza sativa), 3'ss of exon 18
----gtatatatt---tttctgtctttcatatacatttagaattacaaagaaaagagattctgacataatgatgatatttattcatctagAGGATGGTGAGAGTGCTAATGAGAAAGAAAAATCATATGGTTCCATTATGATGGAAAGGTTGACCAGTTCACCGAATGGTCGAATTGATCATGTGCTTCA
    | ||||| |   ||| | | | |  || |||||   | | ||||| || |  | |      ||  |       |||  |  |  |||||| | ||| ||   |||||||||||| || |||||||||| ||| |||||||||||| ||||  |||||||  ||||||| ||||| ||||| |||||
gtatgcatatagtagatttttttgtcttctacacattgcaagtcacaaaaaacaatgctctgagtatgtt-------tttggttgttcagAGGACGTTGACAGCAATAATGAGAAAGAGAAGTCATATGGTTACATGATGATGGAAAGGCTGACAGGTTCACCAGATGGTCGGATTGACCATGTACTTCA
















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|67015052|gb|CO443801.1|CO443801
EST:     GTCAAAGCAGTAGCTGCTATACTAGCATTGAGCAGAAATGACACAGAAG                         AGGATGGTGAGAGTGCTAATGAGAAAGAAAAATCATATGGTTCCATTATGA
genomic: GTCAAAGCAGTAGCTGCTATACTAGCATTGAGCAGAAATGACACAGAAGgtatatattt ... attcatctagAGGATGGTGAGAGTGCTAATGAGAAAGAAAAATCATATGGTTCCATTATGA
EST: gi|78075263|gb|DV503697.1|DV503697
EST:     GTCAAAGCAGTAGCTGCTATACTAGCATTGAGCAGAAATGACACAGAAG                         AGGATGGTGAGAGTGCTAATGAGAAAGAAAAATCATATGGTTCCATTATGA
genomic: GTCAAAGCAGTAGCTGCTATACTAGCATTGAGCAGAAATGACACAGAAGgtatatattt ... attcatctagAGGATGGTGAGAGTGCTAATGAGAAAGAAAAATCATATGGTTCCATTATGA
EST: gi|71767650|gb|DR965587.1|DR965587
EST:     GTCAAAGCAGTAGCTGCTATACTAGCATTGAGCAGAAATGACACAGAAG                         AGGATGGTGAGAGTGCTAATGAG
genomic: GTCAAAGCAGTAGCTGCTATACTAGCATTGAGCAGAAATGACACAGAAGgtatatattt ... attcatctagAGGATGGTGAGAGTGCTAATGAG
EST: gi|28873574|gb|CB329545.1|CB329545
EST:     GTCAAAGCAGTAGCTGCTATACTAGCATTGAGCAGAAATGACACAGAAG                         AGGATGGTGAGAGTGCTAATGAGAAAGAAAAATCATATGGTTCCATTATGA
genomic: GTCAAAGCAGTAGCTGCTATACTAGCATTGAGCAGAAATGACACAGAAGgtatatattt ... attcatctagAGGATGGTGAGAGTGCTAATGAGAAAGAAAAATCATATGGTTCCATTATGA
EST: gi|211270821|gb|FL023496.1|FL023496
EST:     GTCAAAGCAGTAGCTGCTATACTAGCATTGAGCAGAAATGACACAGAAG                         AGGATGGTGAGAGTGCTAATGAGAAAGAAAAATCATATGGTTCCATTATGA
genomic: GTCAAAGCAGTAGCTGCTATACTAGCATTGAGCAGAAATGACACAGAAGgtatatattt ... attcatctagAGGATGGTGAGAGTGCTAATGAGAAAGAAAAATCATATGGTTCCATTATGA

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: 104

GTCAAAGCAGTAGCTGCTATACTAGCATTGAGCAGAAATGACACAGAAGgtatatattt ... attcatctagAGGATGGTGAGAGTGCTAATGAGAAAGAAAAATCATATGGTTCCATTATGATGGAAAGGTTGACCAGTTCACCGAATGGTCGAATTGATCATGTGCTTCA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 187

GTCAAAGCAGTAGCTGCTATACTAGCATTGAGCAGAAATGACACAGAAGgtatatattt ... attcatctagAGGATGGTGAGAGTGCTAATGAGAAAGAAAAATCATATGGTTCCATTATGATGGAAAGGTTGACCAGTTCACCGAATGGTCGAATTGATCATGTGCTTCA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 240

GTCAAAGCAGTAGCTGCTATACTAGCATTGAGCAGAAATGACACAGAAGgtatatattt ... attcatctagAGGATGGTGAGAGTGCTAATGAGAAAGAAAAATCATATGGTTCCATTATGATGGAAAGGTTGACCAGTTCACCGAATGGTCGAATTGATCATGTGCTTCA


Block sizes: 48 (upstream exon), 42 (downstream exon)
Score: 102

GTCAAAGCAGTAGCTGCTATACTAGCATTGAGCAGAAATGACACAGAAGgtatatattt ... attcatctagAGGATGGTGAGAGTGCTAATGAGAAAGAAAAATCATATGGTTCCATTATGATGGAAAGGTTGACCAGTTCACCGAATGGTCGAATTGATCATGTGCTTCA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttagaattacaaagaaaagagattctgacataatgatgatatttattcatctagAGGATGGTGAGAGTGCTAATGAGAAAGAAAAATCATATGGTTCCATTATGATGGAAAGGTTGACCAGTTCACCGAATGGTCGAATTGATCATGTGCTTCA
                       ttctgac  putative branch site (score: 102)
                                          tttattc  putative PPT
                              ataatgatgatattta  TA-rich tract