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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AATTCTTAGTGTAATACTAGCCAAGGAAGATTTGGCAGACGACGTTGATCTAGAAACTATAGCTAACCTGACAGAAGGGTACTCAGGCAGTGATCTCAAGgtatgatactaccgatgctagaattttttatggtacttgtttttacaatcaaataatgattgttgttaacctcttggctgtgattattttcag

Basic information

species Zea mays
transcript GRMZM2G168228_T01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G168228_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os03g22420.1 (Oryza sativa), 5'ss of exon 25
AATTCTTAGTGTAATACTAGCCAAGGAAGATTTGGCAGACGACGTTGATCTAGAAACTATAGCTAACCTGACAGAAGGGTACTCAGGCAGTGATCTCAAGgtatgatactaccgatgctagaatt--------ttttatggtacttgtttttacaatcaaataatgattgttgt-taacctcttggctgtgattatttt-cag
||||||||| || |||||||| || |||||||||||||| || || ||||| ||| || |||||| | |||| |||||||| || ||||||||||||||||||  |   |  |  |  ||||| |        |  | || || |  ||  |  |||  |||  || ||||||  |   ||| |||| || || ||||| |||
AATTCTTAGCGTGATACTAGCTAAAGAAGATTTGGCAGATGATGTCGATCTTGAAGCTGTAGCTAGCTTGACTGAAGGGTATTCTGGCAGTGATCTCAAGgtactactgttgcattcatagaagtagttccactgctgtgatattgattcctcaaattgaatgttgcttgttgagttgactcctggccgtaatcatttttcag
















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|211424428|gb|FK972465.1|FK972465
EST:     TAGAAACTATAGCTAACCTGACAGAAGGGTACTCAGGCAGTGATCTCAAG                         AATCTGTGTGTTACTGCTGCACACCGTCCTATTAGGGAGATTCTTGAAAAG
genomic: TAGAAACTATAGCTAACCTGACAGAAGGGTACTCAGGCAGTGATCTCAAGgtatgatact ... ttattttcagAATCTGTGTGTTACTGCTGCACACCGTCCTATTAGGGAGATTCTTGAAAAG
EST: gi|211424427|gb|FK972464.1|FK972464
EST:     TAGAAACTATAGCTAACCTGACAGAAGGGTACTCAGGCAGTGATCTCAAG                         AATCTGTGTGTTACTGCTGCACACCGTCCTATTAGGGAGATTCTTGAAAAG
genomic: TAGAAACTATAGCTAACCTGACAGAAGGGTACTCAGGCAGTGATCTCAAGgtatgatact ... ttattttcagAATCTGTGTGTTACTGCTGCACACCGTCCTATTAGGGAGATTCTTGAAAAG

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), 48 (downstream exon)
Score: 239

AATTCTTAGTGTAATACTAGCCAAGGAAGATTTGGCAGACGACGTTGATCTAGAAACTATAGCTAACCTGACAGAAGGGTACTCAGGCAGTGATCTCAAGgtatgatact ... ttattttcagAATCTGTGTGTTACTGCTGCACACCGTCCTATTAGGGAGATTCTTGAAAAGGAAAAGAAG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 283

AATTCTTAGTGTAATACTAGCCAAGGAAGATTTGGCAGACGACGTTGATCTAGAAACTATAGCTAACCTGACAGAAGGGTACTCAGGCAGTGATCTCAAGgtatgatact ... ttattttcagAATCTGTGTGTTACTGCTGCACACCGTCCTATTAGGGAGATTCTTGAAAAGGAAAAGAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 227

AATTCTTAGTGTAATACTAGCCAAGGAAGATTTGGCAGACGACGTTGATCTAGAAACTATAGCTAACCTGACAGAAGGGTACTCAGGCAGTGATCTCAAGgtatgatact ... ttattttcagAATCTGTGTGTTACTGCTGCACACCGTCCTATTAGGGAGATTCTTGAAAAGGAAAAGAAG


Block sizes: 46 (upstream exon), 48 (downstream exon)
Score: 192

AATTCTTAGTGTAATACTAGCCAAGGAAGATTTGGCAGACGACGTTGATCTAGAAACTATAGCTAACCTGACAGAAGGGTACTCAGGCAGTGATCTCAAGgtatgatact ... ttattttcagAATCTGTGTGTTACTGCTGCACACCGTCCTATTAGGGAGATTCTTGAAAAGGAAAAGAAG