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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gacatcctcgtataaatacttaatgtttgacactgctccaatacgagataccaattaacctggcttgttttgttgtgaatatttgtggtggacttcacagGTTTACGACGAAGACAAACTTCAGCAAGACAAGAGACTAGGTGTGGCAAAACTAGCAGTAAACACTCTTGAATCTGAGATTACCCAAGACGCCACTCTGA

Basic information

species Zea mays
transcript GRMZM2G092129_T02
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G092129_T02 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os07g22640.3 (Oryza sativa), 3'ss of exon 3
gacatcctcgtataaat--acttaatgt-ttgacactgctccaatacgagataccaattaacctggcttgttttgttgtga-atatttgtggtggacttcacagGTTTACGACGAAGACAAACTTCAGCAAGACAAGAGACTAGGTGTGGCAAAACTAGCAGTAAACACTCTTGAATCTGAGATTACCCAAGACGCCACTCTGA
    |     | |  ||  | || |||| ||   | |  |    | | |  |  ||||  ||      |  |      | | ||  |||||      ||  ||||| || || ||||||| ||||||||||||||| |  || ||||| || ||||||||||| |||| |||| || |||||  ||||   ||   |||| |||
---gtttctatcttgattgattttatgtgttcttaatattatgcttctatgtgtcaatctactcaatgtagtaccagataacatgcttgtga-attttttgcagGTATATGATGAAGACAGACTTCAGCAAGACAAAAAGCTTGGTGTAGCTAAACTAGCAGTGAACAGTCTTCAACCTGAGGCTACCAGTGAAATCACTTTGA
















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|211220819|gb|FL457378.1|FL457378
EST:     CATTTGACTTGATTGTCGAAGACAAAGAAACCCAATCTGTTATTTTTGAG                         GTTTACGACGAAGACAAACTTCAGCAAGACAAGAGACTAGGTGTGGCAAAA
genomic: CATTTGACTTGATTGTCGAAGACAAAGAAACCCAATCTGTTATTTTTGAGgtaattctat ... gacttcacagGTTTACGACGAAGACAAACTTCAGCAAGACAAGAGACTAGGTGTGGCAAAA
EST: gi|211335355|gb|FL444766.1|FL444766
EST:     CATTTGACTTGATTGTCGAAGACAAAGAAACCCAATCTGTTATTTTTGAG                         GTTTACGACGAAGACAAACTTCAGCAAGACAAGAGACTAGGTGTGGCAAAA
genomic: CATTTGACTTGATTGTCGAAGACAAAGAAACCCAATCTGTTATTTTTGAGgtaattctat ... gacttcacagGTTTACGACGAAGACAAACTTCAGCAAGACAAGAGACTAGGTGTGGCAAAA
EST: gi|32803298|gb|CD955534.1|CD955534
EST:     CATTTGACTTGATTGTCGAAGACAAAGAAACCCAATCTGTTATTTTTGAG                         GTTTACGACGAAGACAAACTTCAGCAAGACAAGAGACTAGGTGTGGCAAAA
genomic: CATTTGACTTGATTGTCGAAGACAAAGAAACCCAATCTGTTATTTTTGAGgtaattctat ... gacttcacagGTTTACGACGAAGACAAACTTCAGCAAGACAAGAGACTAGGTGTGGCAAAA
EST: gi|67025946|gb|CO454695.1|CO454695
EST:     CATTTGACTTGATTGTCGAAGACAAAGAAACCCAATCTGTTATTTTTGAG                         GTTTACGACGAAGACAAACTTCAGCAAGACAAGAGACTAGGTGTGGCAAAA
genomic: CATTTGACTTGATTGTCGAAGACAAAGAAACCCAATCTGTTATTTTTGAGgtaattctat ... gacttcacagGTTTACGACGAAGACAAACTTCAGCAAGACAAGAGACTAGGTGTGGCAAAA
EST: gi|71331352|gb|DR802510.1|DR802510
EST:     CATTTGACTTGATTGTCGAAGACAAAGAAACCCAATCTGTTA-TTTTGAG                         GTTTACGACGAAGACAAACTTCAGCAAGACAAGAGACTAGGTGTGGCAAAA
genomic: CATTTGACTTGATTGTCGAAGACAAAGAAACCCAATCTGTTATTTTTGAGgtaattctat ... gacttcacagGTTTACGACGAAGACAAACTTCAGCAAGACAAGAGACTAGGTGTGGCAAAA
EST: gi|67011685|gb|CO440434.1|CO440434
EST:     CATTTGACTTGATTGTCGAAGACAAAGAAACCCAATCTGTTATTTTTGAG                         GTTTACGACGAAGACAAACTTCAGCAAGACAAGAGACTAGGTGTGGCAAAA
genomic: CATTTGACTTGATTGTCGAAGACAAAGAAACCCAATCTGTTATTTTTGAGgtaattctat ... gacttcacagGTTTACGACGAAGACAAACTTCAGCAAGACAAGAGACTAGGTGTGGCAAAA
EST: gi|211220820|gb|FL457379.1|FL457379
EST:     CATTTGACTTGATTGTCGAAGACAAAGAAACCCAATCTGTTATTTTTGAG                         GTTTACGACGAAGACAAACTTCAGCAAGACAAGAGACTAGGTGTGGCAAAA
genomic: CATTTGACTTGATTGTCGAAGACAAAGAAACCCAATCTGTTATTTTTGAGgtaattctat ... gacttcacagGTTTACGACGAAGACAAACTTCAGCAAGACAAGAGACTAGGTGTGGCAAAA
EST: gi|111145863|gb|EE258112.1|EE258112
EST:     ATTTGACTTGATTGTCGAAGACAAAGAAAACCCAATCTGTTATTTTTGAG                         GGTTTATGATGGAAGACAAACTTCAGCAAGACNAAGAAGACTAGG
genomic: ATTTGACTTGATTGTCGAAGACAAAGAAA-CCCAATCTGTTATTTTTGAGgtaattctat ... gacttcacagG-TTTACGACG-AAGACAAACTTCAGCAAGAC-AAGA-GACTAGG

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: 165

GGTCAAAACAAAAGTCATAGATGATGACCTGAATCCGGAATGGAATGAAACATTTGACTTGATTGTCGAAGACAAAGAAACCCAATCTGTTATTTTTGAGgtaattctat ... gacttcacagGTTTACGACGAAGACAAACTTCAGCAAGACAAGAGACTAGGTGTGGCAAAACTAGCAGTAAACACTCTTGAATCTGAGATTACCCAAGACGCCACTCTGA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 251

GGTCAAAACAAAAGTCATAGATGATGACCTGAATCCGGAATGGAATGAAACATTTGACTTGATTGTCGAAGACAAAGAAACCCAATCTGTTATTTTTGAGgtaattctat ... gacttcacagGTTTACGACGAAGACAAACTTCAGCAAGACAAGAGACTAGGTGTGGCAAAACTAGCAGTAAACACTCTTGAATCTGAGATTACCCAAGACGCCACTCTGA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 257

GGTCAAAACAAAAGTCATAGATGATGACCTGAATCCGGAATGGAATGAAACATTTGACTTGATTGTCGAAGACAAAGAAACCCAATCTGTTATTTTTGAGgtaattctat ... gacttcacagGTTTACGACGAAGACAAACTTCAGCAAGACAAGAGACTAGGTGTGGCAAAACTAGCAGTAAACACTCTTGAATCTGAGATTACCCAAGACGCCACTCTGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 191

GGTCAAAACAAAAGTCATAGATGATGACCTGAATCCGGAATGGAATGAAACATTTGACTTGATTGTCGAAGACAAAGAAACCCAATCTGTTATTTTTGAGgtaattctat ... gacttcacagGTTTACGACGAAGACAAACTTCAGCAAGACAAGAGACTAGGTGTGGCAAAACTAGCAGTAAACACTCTTGAATCTGAGATTACCCAAGACGCCACTCTGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agataccaattaacctggcttgttttgttgtgaatatttgtggtggacttcacagGTTTACGACGAAGACAAACTTCAGCAAGACAAGAGACTAGGTGTGGCAAAACTAGCAGTAAACACTCTTGAATCTGAGATTACCCAAGACGCCACTCTGA
       aattaac  putative branch site (score: 191)
                              tgaatattt  TA-rich tract