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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTATATAGGCTCAGTTTCCTTTTTAGATACTGTGCTACAAGTTGTTGAGAAATTGCGATCAGTTAATCCTGATCTTGTATATGgtaatcttttctcatcttttgttatttgtatgcttgcttcttctttaataaatttaatttaacagggacaatttaggtcatagctagagactgactagacatggttaattcttctgtttgctaattgcaaacatgctgcag

Basic information

species Zea mays
transcript GRMZM2G069758_T01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G069758_T02 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os12g40830.3 (Oryza sativa), 5'ss of exon 5
GTTATATAGGCTCAGTTTCCTTTTTAGATACTGTGCTACAAGTTGTTGAGAAATTGCGATCAGTTAATCCTGATCTTGTATATGgtaatcttttctcatcttttgttatttgtatgcttgcttcttctttaataa--atttaatttaacagggacaatttaggtcatagctagagactgactagacatggttaattcttctgtttgctaattgcaaacatgctgcag
||||||| || || ||||||||||||  |||||| |||||||||||||| ||||| |||||||| ||||||||||||||||||||||||||||||||||||||  |||| | |     |   |  | |||  |    |   ||||| | |||| |||||   |||||||||  ||||||| ||   |||  | ||   |||||||||||||        | ||||||
GTTATATTGGATCTGTTTCCTTTTTAACTACTGTACTACAAGTTGTTGACAAATTACGATCAGTCAATCCTGATCTTGTATATGgtaatcttttctcatctttcattatctattcttctctatggtgttttgtctctaccaaattttataggg-caatt-gtgtcatagctcaagactgattacgaatgactgata--tctgtttgctaat-------gttctgcag
















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|211278750|gb|FL388232.1|FL388232
EST:     GCTACAAGTTGTTGAGAAATTGCGATCAGTTAATCCTGATCTTGTATATG                         TTTGTGACCCAGTTCTAGGTGATGAAGGAAAACTATATGTTCCTCAGGAGC
genomic: GCTACAAGTTGTTGAGAAATTGCGATCAGTTAATCCTGATCTTGTATATGgtaatctttt ... catgctgcagTTTGTGACCCAGTTCTAGGTGATGAAGGAAAACTATATGTTCCTCAGGAGC
EST: gi|86471052|gb|DY237422.1|DY237422
EST:     GCTACAAGTTGTTGAGAAATTGCGATCAGTTAATCCTGATCTTGTATATG                         TTTGTGACCCAGTTCTAGGTGATGAAGGAAAACTATATGTTCCTCAGGAGC
genomic: GCTACAAGTTGTTGAGAAATTGCGATCAGTTAATCCTGATCTTGTATATGgtaatctttt ... catgctgcagTTTGTGACCCAGTTCTAGGTGATGAAGGAAAACTATATGTTCCTCAGGAGC
EST: gi|33096068|gb|CF056062.1|CF056062
EST:     GCGATCAGTTAATCCTGATCTTGTATATG                         TTTGTGACCCAGTTCTAGGTGATGAAGGAAAACTATATGTTCCTCAGGGGC
genomic: GCGATCAGTTAATCCTGATCTTGTATATGgtaatctttt ... catgctgcagTTTGTGACCCAGTTCTAGGTGATGAAGGAAAACTATATGTTCCTCAGGAGC
EST: gi|17931888|gb|BM268848.1|BM268848
EST:     GCT-CAAGTTGTTGAGAAATTGCGATCAGTTAATCCTGATCTTGTATATG                         TTTGTGACCCAGTTCTAGGTGATGAAGGAAAACTATATGTTCCTCAGGAGC
genomic: GCTACAAGTTGTTGAGAAATTGCGATCAGTTAATCCTGATCTTGTATATGgtaatctttt ... catgctgcagTTTGTGACCCAGTTCTAGGTGATGAAGGAAAACTATATGTTCCTCAGGAGC
EST: gi|67022839|gb|CO451588.1|CO451588
EST:     GCTACAAGTTGTTGAGAAATTGCGATCAGTTAATCCTGATCTTGTATATG                         TTTGTGACCCAGTTCTAGGTGATGAAGGAAAACTATATGTTCCTCAGGAGC
genomic: GCTACAAGTTGTTGAGAAATTGCGATCAGTTAATCCTGATCTTGTATATGgtaatctttt ... catgctgcagTTTGTGACCCAGTTCTAGGTGATGAAGGAAAACTATATGTTCCTCAGGAGC
EST: gi|40303606|gb|CK347993.1|CK347993
EST:     GCTACAAGTTGTTGAGAAATTGCGATCAGTTAATCCTGATCTTGTATATG                         TTTGTGACCCAGTTCTAGGTGATGAAGGAAAACTATATGTTCCTCAGGAGC
genomic: GCTACAAGTTGTTGAGAAATTGCGATCAGTTAATCCTGATCTTGTATATGgtaatctttt ... catgctgcagTTTGTGACCCAGTTCTAGGTGATGAAGGAAAACTATATGTTCCTCAGGAGC
EST: gi|16922789|gb|BM075781.1|BM075781
EST:     AAGTTGTTGAGAAATTGCGATCAGTTAATCCTGATCTTGTATATG                         TTTGTGACCCAGTTCTAGGTGATGAAGGAAAACTATATGTTCCTCAGGAGC
genomic: AAGTTGTTGAGAAATTGCGATCAGTTAATCCTGATCTTGTATATGgtaatctttt ... catgctgcagTTTGTGACCCAGTTCTAGGTGATGAAGGAAAACTATATGTTCCTCAGGAGC

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), 49 (downstream exon)
Score: 46

GTTATATAGGCTCAGTTTCCTTTTTAGATACTGTGCTACAAGTTGTTGAGAAATTGCGATCAGTTAATCCTGATCTTGTATATGgtaatctttt ... catgctgcagTTTGTGACCCAGTTCTAGGTGATGAAGGAAAACTATATGTTCCTCAGGAGCTAATATCTGTTTATCAACAGAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 162

GTTATATAGGCTCAGTTTCCTTTTTAGATACTGTGCTACAAGTTGTTGAGAAATTGCGATCAGTTAATCCTGATCTTGTATATGgtaatctttt ... catgctgcagTTTGTGACCCAGTTCTAGGTGATGAAGGAAAACTATATGTTCCTCAGGAGCTAATATCTGTTTATCAACAGAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 228

GTTATATAGGCTCAGTTTCCTTTTTAGATACTGTGCTACAAGTTGTTGAGAAATTGCGATCAGTTAATCCTGATCTTGTATATGgtaatctttt ... catgctgcagTTTGTGACCCAGTTCTAGGTGATGAAGGAAAACTATATGTTCCTCAGGAGCTAATATCTGTTTATCAACAGAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 135

GTTATATAGGCTCAGTTTCCTTTTTAGATACTGTGCTACAAGTTGTTGAGAAATTGCGATCAGTTAATCCTGATCTTGTATATGgtaatctttt ... catgctgcagTTTGTGACCCAGTTCTAGGTGATGAAGGAAAACTATATGTTCCTCAGGAGCTAATATCTGTTTATCAACAGAAG