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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagtctttttgatactacgtgttgcctatcattttctaaatttctggatactgatctgattaatgtttttaaaatattaccagTATAGAGCAACCGGTAGAGGTTTTGTGGTACGACATATCAAGTTTGCTGAGAACTACCGTATTTATTCTCGAAGCCATTTTGTGAAAGG

Basic information

species Zea mays
transcript GRMZM2G453794_T01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G453794_T01 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os03g02756.2 (Oryza sativa), 3'ss of exon 10
gtagtctt-tttgatactacgtgttgcctatcattttctaaattt--ctggatactgatctgattaatgtttttaaaatattaccagTATAGAGCAACCGGTAGAGGTTTTGTGGTACGACATATCAAGTTTGCTGAGAACTACCGTATTTATTCTCGAAGCCATTTTGTGAAAGG
||||  |  |||| |  || ||| ||| ||||   |||| | |||  ||   || |||||||||   ||||| |     ||||||||||||||||||||||||| ||||||||||||||||||||||| |||||||| ||||||||| |||||||  | |||||||||||||||||
gtagggtcctttgtttttaagtgatgcttatctacttctgatttttactctgtattgatctgat--gtgtttcttctggattaccagTATAGAGCAACCGGTAGGGGTTTTGTGGTACGACATATCAAATTTGCTGAAAACTACCGTCTTTATTCCAGGAGCCATTTTGTGAAAGG
















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|32837827|gb|CD977505.1|CD977505
EST:     GAACAAGAACCCACTACTTTGGCCGTGCAATATTACATGGAGGTGCAAAG                         TATAGAGCAACCGGTAGAGGTTTTGTGGT
genomic: GAACAAGAACCCACTACTTTGGCCGTGCAATATTACATGGAGGTGCAAAGgtagtctttt ... atattaccagTATAGAGCAACCGGTAGAGGTTTTGTGGT
EST: gi|22543019|gb|BU093457.1|BU093457
EST:     GAACAAGAACCCACTACTTTGGNCGTGCAATATTACATGGAGGTGCAAAG                         TATAGAGCAACCGGTAGAGGTTTTGTGGTACGACATATCAAGTTTGCTGAG
genomic: GAACAAGAACCCACTACTTTGGCCGTGCAATATTACATGGAGGTGCAAAGgtagtctttt ... atattaccagTATAGAGCAACCGGTAGAGGTTTTGTGGTACGACATATCAAGTTTGCTGAG
EST: gi|22935757|gb|BU572032.1|BU572032
EST:     GAACAAGAACCCACTACTTTGGCCGTGCAATATTACATGGAGGTGCAAAG                         TATAGAGCAACCGGTAGAGGTTTTGTGGTACGACATATCAAGTTTGCTGAG
genomic: GAACAAGAACCCACTACTTTGGCCGTGCAATATTACATGGAGGTGCAAAGgtagtctttt ... atattaccagTATAGAGCAACCGGTAGAGGTTTTGTGGTACGACATATCAAGTTTGCTGAG
EST: gi|32838890|gb|CD978571.1|CD978571
EST:     GAACAAGAACCCACTACTTTGGCCGTGCAATATTACATGGAGGTGCAAAG                         TATAGAGCAACCGGTAGAGGTTTTGTGGT
genomic: GAACAAGAACCCACTACTTTGGCCGTGCAATATTACATGGAGGTGCAAAGgtagtctttt ... atattaccagTATAGAGCAACCGGTAGAGGTTTTGTGGT
EST: gi|78118622|gb|DV537006.1|DV537006
EST:     GAACAAGAACCCACTACTTTGGCCGTGCAATATTACATGGAGGTGCAAAG                         TATAGAGCAACCGGTAGAGGTTTTGTGGTACGACATATCAAGTTTGCTGAG
genomic: GAACAAGAACCCACTACTTTGGCCGTGCAATATTACATGGAGGTGCAAAGgtagtctttt ... atattaccagTATAGAGCAACCGGTAGAGGTTTTGTGGTACGACATATCAAGTTTGCTGAG
EST: gi|67031292|gb|CO460041.1|CO460041
EST:     GAACAAGAACCCACTACTTTGGCCGTGCAATATTACATGGAGGTGCAAAG                         TATAGAGCAACCGGTAGAGGTTTTGTGGTACGACATATCAAGTTTGCTGAG
genomic: GAACAAGAACCCACTACTTTGGCCGTGCAATATTACATGGAGGTGCAAAGgtagtctttt ... atattaccagTATAGAGCAACCGGTAGAGGTTTTGTGGTACGACATATCAAGTTTGCTGAG
EST: gi|32838192|gb|CD977870.1|CD977870
EST:     GAACAAGAACCCACTACTTTGGCCGTGCAATATTACATGGAGGTGCAAAG                         TATAGAGCAACCGGTAGAGGTTTTGTGGT
genomic: GAACAAGAACCCACTACTTTGGCCGTGCAATATTACATGGAGGTGCAAAGgtagtctttt ... atattaccagTATAGAGCAACCGGTAGAGGTTTTGTGGT
EST: gi|50322941|gb|CO518067.1|CO518067
EST:     GAACAAGAACCCACTACTTTGGCCGTGCAATATTACATGGAGGTGCAAAG                         TATAGAGCAACCGGTAGAGGTTTTGTGGTACGACATATCAAGTTTGCTGAG
genomic: GAACAAGAACCCACTACTTTGGCCGTGCAATATTACATGGAGGTGCAAAGgtagtctttt ... atattaccagTATAGAGCAACCGGTAGAGGTTTTGTGGTACGACATATCAAGTTTGCTGAG
EST: gi|22549115|gb|BU101316.1|BU101316
EST:     GAACAAGAACCCACTACTTTGGCCGTGCAATATTACATGGAGGTGCAAAG                         TATAGAGCAACCGGTAGAGGTTTTGTGGTACGACATATCAAGTTTGCTGAG
genomic: GAACAAGAACCCACTACTTTGGCCGTGCAATATTACATGGAGGTGCAAAGgtagtctttt ... atattaccagTATAGAGCAACCGGTAGAGGTTTTGTGGTACGACATATCAAGTTTGCTGAG
EST: gi|211408045|gb|FL038492.1|FL038492
EST:     GAACAAGAACCCACTACTTTGGCCGTGCAATATTACATGGAGGTGCAAAG                         TATAGAGCAACCGGTAGAGGTTTTGTGGTACGACATATCAAGTTTGCTGAG
genomic: GAACAAGAACCCACTACTTTGGCCGTGCAATATTACATGGAGGTGCAAAGgtagtctttt ... atattaccagTATAGAGCAACCGGTAGAGGTTTTGTGGTACGACATATCAAGTTTGCTGAG

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), 49 (downstream exon)
Score: 407

TATTACAATGCAGTTCCAAATGTGCTCTGTATTTTTTACTTTCTCACTTGGAACAAGAACCCACTACTTTGGCCGTGCAATATTACATGGAGGTGCAAAGgtagtctttt ... atattaccagTATAGAGCAACCGGTAGAGGTTTTGTGGTACGACATATCAAGTTTGCTGAGAACTACCGTATTTATTCTCGAAGCCATTTTGTGAAAGG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 174

TATTACAATGCAGTTCCAAATGTGCTCTGTATTTTTTACTTTCTCACTTGGAACAAGAACCCACTACTTTGGCCGTGCAATATTACATGGAGGTGCAAAGgtagtctttt ... atattaccagTATAGAGCAACCGGTAGAGGTTTTGTGGTACGACATATCAAGTTTGCTGAGAACTACCGTATTTATTCTCGAAGCCATTTTGTGAAAGG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 194

TATTACAATGCAGTTCCAAATGTGCTCTGTATTTTTTACTTTCTCACTTGGAACAAGAACCCACTACTTTGGCCGTGCAATATTACATGGAGGTGCAAAGgtagtctttt ... atattaccagTATAGAGCAACCGGTAGAGGTTTTGTGGTACGACATATCAAGTTTGCTGAGAACTACCGTATTTATTCTCGAAGCCATTTTGTGAAAGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 231

TATTACAATGCAGTTCCAAATGTGCTCTGTATTTTTTACTTTCTCACTTGGAACAAGAACCCACTACTTTGGCCGTGCAATATTACATGGAGGTGCAAAGgtagtctttt ... atattaccagTATAGAGCAACCGGTAGAGGTTTTGTGGTACGACATATCAAGTTTGCTGAGAACTACCGTATTTATTCTCGAAGCCATTTTGTGAAAGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcattttctaaatttctggatactgatctgattaatgtttttaaaatattaccagTATAGAGCAACCGGTAGAGGTTTTGTGGTACGACATATCAAGTTTGCTGAGAACTACCGTATTTATTCTCGAAGCCATTTTGTGAAAGG
                       tgatctgattaatgtt  TA-rich tract