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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCAGGATTGGTTATATATGGACGGTGAAGATGCTCAAGCTAATGAATTCAAAGAGCGTCTTGACCAACTTAAAGCCATTGGTGACCCAATTCTTTTCAGgtaactaactgtttatattataccctttagttcatatgagtcaatgactgagattgtattgttttcctttacccag

Basic information

species Zea mays
transcript GRMZM2G020040_T02
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G020040_T01 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os02g48110.1 (Oryza sativa), 5'ss of exon 9
TGCAGGATTGGTTATATATGGACGGTGAAGATGCTCAAGCTAATGAATTCAAAGAGCGTCTTGACCAACTTAAAGCCATTGGTGACCCAATTCTTTTCAGgtaactaactgtttatattataccctttagttcatatgagtcaatgactgagattg-tattgttttccttta---cccag
| || |||||||| |||||||| ||||||||||||||||| ||||||||||| || || |||||||||||||| ||||| ||||||||||||||||||||||||||  || | |||      | |||  ||||||||  |||| ||||||| |||| | || |||| |||||   |||||
TACAAGATTGGTTGTATATGGATGGTGAAGATGCTCAAGCAAATGAATTCAAGGAACGCCTTGACCAACTTAAGGCCATCGGTGACCCAATTCTTTTCAGgtaacttgctctgtatc-----cacttaggttcatataggtcattgactgacattgattttttttttctttattgcccag
















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|5901244|gb|AW042344.1|AW042344
EST:     AAAGAGCGTCTTGACCAACTTAAAGTCATTGGTGACCCAATTCTTTTCAG                         ATTGAGTGAATTAAAAACCCGACCAACGGCCTGTGAAAATGCTCGATTGTA
genomic: AAAGAGCGTCTTGACCAACTTAAAGCCATTGGTGACCCAATTCTTTTCAGgtaactaact ... ctttacccagATTGAATGAATTAAAAACCCGACCAACGGCCTGTGAAAATGCTCGATTGTA
EST: gi|32932694|gb|CF037506.1|CF037506
EST:     ATTGGTGACCCAATTCTTTTCAG                         ATTGAGTGAATTAAAAACCCGACCAACGGCCTGTGAAAATGCTCGATTGTA
genomic: ATTGGTGACCCAATTCTTTTCAGgtaactaact ... ctttacccagATTGAATGAATTAAAAACCCGACCAACGGCCTGTGAAAATGCTCGATTGTA
EST: gi|32932673|gb|CF037485.1|CF037485
EST:     CCCAATTCTTTTCAG                         ATTGAGTGAATTAAAAACCCGACCAACGGCCTGTGAAAATGCTCGATTGTA
genomic: CCCAATTCTTTTCAGgtaactaact ... ctttacccagATTGAATGAATTAAAAACCCGACCAACGGCCTGTGAAAATGCTCGATTGTA
EST: gi|26557797|gb|CA830032.1|CA830032
EST:     AAAGAGCGTCTTGACCAACTTAAAGCCATTGGTGACCCAATTCTTTTCAG                         ATTGAATGAATTAAAAACCCGACCAACGGCCTGTGAAAATGCTCGATTGTA
genomic: AAAGAGCGTCTTGACCAACTTAAAGCCATTGGTGACCCAATTCTTTTCAGgtaactaact ... ctttacccagATTGAATGAATTAAAAACCCGACCAACGGCCTGTGAAAATGCTCGATTGTA
EST: gi|116828779|gb|EC861048.1|EC861048
EST:     AAAGAGCGTCTTGACCAACTTAAAGCCATTGGTGACCCAATTCTTTTCAG                         ATTGAGTGAATTAAAAACCCGACCAACGGCCTGTGAAAATGCTCGATTGTA
genomic: AAAGAGCGTCTTGACCAACTTAAAGCCATTGGTGACCCAATTCTTTTCAGgtaactaact ... ctttacccagATTGAATGAATTAAAAACCCGACCAACGGCCTGTGAAAATGCTCGATTGTA

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: 91

TGCAGGATTGGTTATATATGGACGGTGAAGATGCTCAAGCTAATGAATTCAAAGAGCGTCTTGACCAACTTAAAGCCATTGGTGACCCAATTCTTTTCAGgtaactaact ... ctttacccagATTGAATGAATTAAAAACCCGACCAACGGCCTGTGAAAATGCTCGATTGTATCTTGATGAGCTGCAAAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 163

TGCAGGATTGGTTATATATGGACGGTGAAGATGCTCAAGCTAATGAATTCAAAGAGCGTCTTGACCAACTTAAAGCCATTGGTGACCCAATTCTTTTCAGgtaactaact ... ctttacccagATTGAATGAATTAAAAACCCGACCAACGGCCTGTGAAAATGCTCGATTGTATCTTGATGAGCTGCAAAAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 156

TGCAGGATTGGTTATATATGGACGGTGAAGATGCTCAAGCTAATGAATTCAAAGAGCGTCTTGACCAACTTAAAGCCATTGGTGACCCAATTCTTTTCAGgtaactaact ... ctttacccagATTGAATGAATTAAAAACCCGACCAACGGCCTGTGAAAATGCTCGATTGTATCTTGATGAGCTGCAAAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 416

TGCAGGATTGGTTATATATGGACGGTGAAGATGCTCAAGCTAATGAATTCAAAGAGCGTCTTGACCAACTTAAAGCCATTGGTGACCCAATTCTTTTCAGgtaactaact ... ctttacccagATTGAATGAATTAAAAACCCGACCAACGGCCTGTGAAAATGCTCGATTGTATCTTGATGAGCTGCAAAAG