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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTGCAATTATGAGAAGTTTGCGACATCCGAACATTGTTCTTCTTATGGGTGCTGTCACTCAGCCACCTAACCTTTCAATTGTGACTGAATACCTATCAAGgtgtgtccttactttctgaatgccttttgaaatatactatctgtgcacctctagagttagtccaaggttccagaacttaacctttttgttttctatgtgcag

Basic information

species Zea mays
transcript GRMZM2G059671_T04
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G059671_T01 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os02g32610.2 (Oryza sativa), 5'ss of exon 10
TTGCAATTATGAGAAGTTTGCGACATCCGAACATTGTTCTTCTTATGGGTGCTGTCACTCAGCCACCTAACCTTTCAATTGTGACTGAATACCTATCAAGgtgtgtccttactttctgaatgccttttgaaa-------tatactatctgtgcacctctagagttagtccaaggttccagaacttaacctttttgttttctatgtgcag
|||||||||||| |||| |||| ||||| |||||||| ||| ||||||||||||| ||||||||||| || ||||| |||||||| ||||| ||||||||||||||    ||||||||| | |  ||| |||       || ||||| ||   ||||||||   |||      |||||   || |||  |||||  ||  |   |||||
TTGCAATTATGAAAAGTCTGCGCCATCCAAACATTGTCCTTTTTATGGGTGCTGTTACTCAGCCACCAAAACTTTCGATTGTGACAGAATATCTATCAAGgtgtgttga-actttctgattactatttcaaaattgatgtaaactatgtgcttacctctagt-ctagcttgtagttccc--acataagtttttt--ttcttgaatgcag

upper sequence: GRMZM2G059671_T01 (Zea mays), 5'ss of exon 8
lower sequence: GLYMA13G21480.1 (Glycine max), 5'ss of exon 9
TTGCAATTATGAGAAGTTTGCGACATCCGAACATTGTTCTTCTTATGGGTGCTGTCACTCAGCCACCTAACCTTTCAATTGTGACTGAATACCTATCAAGgt---gtgtccttactt--tctgaatgccttt---tgaaatatactatctgtgcacctctagagttagtccaaggt-tccagaacttaaccttttt---gtttt----ctatgtgcag
||||||| |||| | |||| || ||||| ||||||||| |  ||||||| || ||||||||||| |||||| | |||||||| || |||||  |||| ||||       |  ||| |  ||   || |||||   | ||| |    |  | | ||   ||| ||  | |  | | | |   || ||| || || |    ||| |    ||| ||||||
TTGCAATAATGAAACGTTTACGGCATCCAAACATTGTTTTGTTTATGGGGGCAGTCACTCAGCCTCCTAACTTATCAATTGTCACGGAATATTTATCTAGgttgtactcctctacctgttcctcatccctttccctaaaagagggaagtttttcaaggctatagg-attataggatattttgaccttgacattctaagagttcttgacctaagtgcag

upper sequence: GRMZM2G059671_T01 (Zea mays), 5'ss of exon 8
lower sequence: GLYMA10G07610.1 (Glycine max), 5'ss of exon 11
TTGCAATTATGAGAAGTTTGCGACATCCGAACATTGTTCTTCTTATGGGTGCTGTCACTCAGCCACCTAACCTTTCAATTGTGACTGAATACCTATCAAGgt-gtgtcctt----actttctgaatgccttt---tgaaatatactatctgtgcacctctagagttagtccaaggttccagaacttaaccttttt---gtttt----ctatgtgcag
   |||| |||| | |||| || ||||| ||||||||| |  ||||||| || ||||||||||| |||||| | |||||||| || |||||  ||||||||| ||   | |    |  |||   ||   |||   | ||| |    |  | | ||   |||  | || |   |  ||   || ||| |  || |    ||| |    ||| ||||||
---CAATAATGAAACGTTTACGGCATCCAAACATTGTTTTGTTTATGGGGGCAGTCACTCAGCCTCCTAACTTATCAATTGTCACAGAATATTTATCAAGGTTgtactcctctacatgttcctcatctttttccctcaaagagggaagtttttcaaggctatggataataggatatttt-gaccttgagattctaagagttcttgacctaagtgcag

upper sequence: GRMZM2G059671_T01 (Zea mays), 5'ss of exon 8
lower sequence: GLYMA03G34890.1 (Glycine max), 5'ss of exon 10
TTGCAATTATGAGAAGTTTGCGACATCCGAACATTGTTCTTCTTATGGGTGCTGTCACTCAGCCACCTAACCTTTCAATTGTGACTGAATACCTATCAAGgtgtgtc-----cttactttctgaat-----gccttttgaaatatacta------tctgtgcacctctagagttagtccaaggttccagaacttaacctttttgttttctatgtgcag
||||||| |||| | | || || ||||| ||||||||| | ||||||||||| |||||| |||| ||||| || |||||||| || |||||  | ||||||| |  |     || |  | | |  |      |||||     ||||  |      ||| | ||   ||| |     ||  |   |  ||| | |||    |||| ||    |||||||
TTGCAATAATGAAAGGCTTACGGCATCCAAACATTGTTTTACTTATGGGTGCAGTCACTAAGCCTCCTAATCTATCAATTGTCACAGAATATTTGTCAAGgttttacaatatctcatctaccggttcctttacctttcctcctataagagggatctcttttcatggctataaaatatcttacacttgaga-cctaaaggatttgattgaactgtgcag

upper sequence: GRMZM2G059671_T01 (Zea mays), 5'ss of exon 8
lower sequence: Vv13s0074g00430.t01 (Vitis vinifera), 5'ss of exon 9
TTGCAATTATGAGAAGTTTGCGACATCCGAACATTGTTCTTCTTATGGGTGCTGTCACTCAGCCACCTAACCTTTCAATTGTGACTGAATACCTATCAAGgtgtgtccttactttctgaat---gccttttgaaatatactatctgtgca------cctctagagttagtccaaggttccag-aacttaacctttttgttttctatgtgcag
||||||| |||| | | ||| | ||||| |||||||||||  ||||||||||||| |||||||| ||  | || || || || || |||||| |||||||||   |  | | ||| |  ||   || | ||    |||||  | | | ||      | |  | | | | || ||  |  ||   | |||   | || |||||  || |||||
TTGCAATCATGAAACGCTTGAGGCATCCAAACATTGTTCTCTTTATGGGTGCTGTTACTCAGCCTCCACATCTGTCCATAGTTACAGAATACTTATCAAGgttctttatgattttttagatattgcttattttcttataccctgtttacaagaagtcgtgcaaaatgaatctaatatatcactgaattagaatattggttttgcat-tgcag

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|20802940|gb|BQ293990.1|BQ293990
EST:     GCTGTCACTCAGCCACCTAACCTTTCAATTGTGACTGAATACCTATCAAG                         AGGTAGCTTATACAGACTTTTACACAGGCATGCTGCAAGGGAAAATCTGGA
genomic: GCTGTCACTCAGCCACCTAACCTTTCAATTGTGACTGAATACCTATCAAGgtgtgtcctt ... ctatgtgcagAGGTAGCTTATACAGACTTTTACACAGGCATGCTGCAAGGGAAAATCTGGA
EST: gi|76284240|gb|DV023808.1|DV023808
EST:     CAATTGTGACTGAAT-CCTTATCAAG                         AGGTAGCTTATACAGACTTTTACACAGGCATGCTGCAAGGGAAAATCTGG
genomic: CAATTGTGACTGAATACC-TATCAAGgtgtgtcctt ... ctatgtgcagAGGTAGCTTATACAGACTTTTACACAGGCATGCTGCAAGGGAAAATCTGG
EST: gi|32836824|gb|CD976502.1|CD976502
EST:     GCTGTCACTCAGCCACCTAACCTTTCAATTGTGACTGAATACCTATCAAG                         AGGTAGCTTATACAGACTTTTACACAGGCATGCTGCAAGGGAAAATCTGGA
genomic: GCTGTCACTCAGCCACCTAACCTTTCAATTGTGACTGAATACCTATCAAGgtgtgtcctt ... ctatgtgcagAGGTAGCTTATACAGACTTTTACACAGGCATGCTGCAAGGGAAAATCTGGA
EST: gi|26456437|gb|CA828020.1|CA828020
EST:     GCTGTCACTCAGCCACCTAACCTTTCAATTGTGACTGAATACCTATCAAG                         AGGTAGCTTATACAGACTTTTACACAGGCATGCTGCAAGGGAAAATCTGGA
genomic: GCTGTCACTCAGCCACCTAACCTTTCAATTGTGACTGAATACCTATCAAGgtgtgtcctt ... ctatgtgcagAGGTAGCTTATACAGACTTTTACACAGGCATGCTGCAAGGGAAAATCTGGA
EST: gi|32839244|gb|CD978925.1|CD978925
EST:     GCTGTCACTCAGCCACCTAACCTTTCAATTGTGACTGAATACCTATCAAG                         AGGTAGCTTATACAGACTTTTACACAGGCATGCTGCAAGGGAAAATCTGGA
genomic: GCTGTCACTCAGCCACCTAACCTTTCAATTGTGACTGAATACCTATCAAGgtgtgtcctt ... ctatgtgcagAGGTAGCTTATACAGACTTTTACACAGGCATGCTGCAAGGGAAAATCTGGA
EST: gi|32837172|gb|CD976850.1|CD976850
EST:     GCTGTCACTCAGCCACCTAACCTTTCAATTGTGACTGAATACCTATCAAG                         AGGTAGCTTATACAGACTTTTACACAGGCATGCTGCAAGGGAAAATCTGGA
genomic: GCTGTCACTCAGCCACCTAACCTTTCAATTGTGACTGAATACCTATCAAGgtgtgtcctt ... ctatgtgcagAGGTAGCTTATACAGACTTTTACACAGGCATGCTGCAAGGGAAAATCTGGA
EST: gi|60358265|gb|DN225238.1|DN225238
EST:     CTAACCTTTCAATTGTGACTGAATACCTATCAAG                         AGGTAGCTTATACAGACTTTTACACAGGCATGCTGCAAGGGAAAATCTGGA
genomic: CTAACCTTTCAATTGTGACTGAATACCTATCAAGgtgtgtcctt ... ctatgtgcagAGGTAGCTTATACAGACTTTTACACAGGCATGCTGCAAGGGAAAATCTGGA
EST: gi|60337361|gb|DN204334.1|DN204334
EST:     GCTGTCACTCAGCCACCTAACCTTTCAATTGTGACTGAATACCTATCAAG                         AGGTAGCTTATACAGACTTTTACACAGGCATGCTGCAAGGGAAAATCTGGA
genomic: GCTGTCACTCAGCCACCTAACCTTTCAATTGTGACTGAATACCTATCAAGgtgtgtcctt ... ctatgtgcagAGGTAGCTTATACAGACTTTTACACAGGCATGCTGCAAGGGAAAATCTGGA
EST: gi|32838830|gb|CD978511.1|CD978511
EST:     GCTGTCACTCAGCCACCTAACCTTTCAATTGTGACTGAATACCTATCAAG                         AGGTAGCTTATACAGACTTTTACACAGGCATGCTGCAAGGGAAAATCTGGA
genomic: GCTGTCACTCAGCCACCTAACCTTTCAATTGTGACTGAATACCTATCAAGgtgtgtcctt ... ctatgtgcagAGGTAGCTTATACAGACTTTTACACAGGCATGCTGCAAGGGAAAATCTGGA
EST: gi|32836743|gb|CD976421.1|CD976421
EST:     GCTGTCACTCAGCCACCTAACCTTTCAATTGTGACTGAATACCTATCAAG                         AGGTAGCTTATACAGACTTTTACACAGGCATGCTGCAAGGGAAAATCTGGA
genomic: GCTGTCACTCAGCCACCTAACCTTTCAATTGTGACTGAATACCTATCAAGgtgtgtcctt ... ctatgtgcagAGGTAGCTTATACAGACTTTTACACAGGCATGCTGCAAGGGAAAATCTGGA

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: 41 (upstream exon), 49 (downstream exon)
Score: 66

TTGCAATTATGAGAAGTTTGCGACATCCGAACATTGTTCTTCTTATGGGTGCTGTCACTCAGCCACCTAACCTTTCAATTGTGACTGAATACCTATCAAGgtgtgtcctt ... ctatgtgcagAGGTAGCTTATACAGACTTTTACACAGGCATGCTGCAAGGGAAAATCTGGAGGAGCGCCGCCGCTTGAGTATGGCTTTCGACGTG


Block sizes: 41 (upstream exon), 49 (downstream exon)
Score: 73

TTGCAATTATGAGAAGTTTGCGACATCCGAACATTGTTCTTCTTATGGGTGCTGTCACTCAGCCACCTAACCTTTCAATTGTGACTGAATACCTATCAAGgtgtgtcctt ... ctatgtgcagAGGTAGCTTATACAGACTTTTACACAGGCATGCTGCAAGGGAAAATCTGGAGGAGCGCCGCCGCTTGAGTATGGCTTTCGACGTG


Block sizes: 41 (upstream exon), 49 (downstream exon)
Score: 99

TTGCAATTATGAGAAGTTTGCGACATCCGAACATTGTTCTTCTTATGGGTGCTGTCACTCAGCCACCTAACCTTTCAATTGTGACTGAATACCTATCAAGgtgtgtcctt ... ctatgtgcagAGGTAGCTTATACAGACTTTTACACAGGCATGCTGCAAGGGAAAATCTGGAGGAGCGCCGCCGCTTGAGTATGGCTTTCGACGTG


Block sizes: 41 (upstream exon), 48 (downstream exon)
Score: 38

TTGCAATTATGAGAAGTTTGCGACATCCGAACATTGTTCTTCTTATGGGTGCTGTCACTCAGCCACCTAACCTTTCAATTGTGACTGAATACCTATCAAGgtgtgtcctt ... ctatgtgcagAGGTAGCTTATACAGACTTTTACACAGGCATGCTGCAAGGGAAAATCTGGAGGAGCGCCGCCGCTTGAGTATGGCTTTCGACGTG