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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGCTTCGGCGCCACCAAGTGGTACCACGTCTCCTGCTTACCCTCCTCGTCGTACCCGCTCGGCCCCATCGGGAGTATCAAGGGGTTCGACTCCATTAAGgttctctcattgggtggttagtttggtgccgttcgctatctcattctgtgttgttttggggattaatacgtggggctttgggatttgcag

Basic information

species Zea mays
transcript GRMZM2G111510_T01
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G111510_T01 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os01g53560.1 (Oryza sativa), 5'ss of exon 1
TGGCTTCGGCGCCACCAAGTGGTACCACGTCTCCTGCTTACCCTCCTCGTCGTACCCGCTCGGCCCCATCGGGAGTATCAAGGGGTTCGACTCCATTAAGgttctctcattgggtgg--ttagtttggtgccgttcgctatctcattctgtgttgttttggggattaatacgtggggctttgggatttgcag
 ||||||| |  ||||||||||||||||||| | ||||| |||||||||||| ||||| | | |||| ||| ||   ||||||||||||||||||| ||||||    |  || || |  |||  || |   | | ||    || ||    ||||| ||| |||   | | |                     
CGGCTTCGACAGCACCAAGTGGTACCACGTCGCTTGCTTCCCCTCCTCGTCGCACCCGATTGACCCCGTCGAGAAGGTCAAGGGGTTCGACTCCATCAAGgtttgggctctgagtcggtttacatttgcttcctacgggtgctaat---atgttgattttggggggagtgcag-------------------
















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|211319410|gb|FL056112.1|FL056112
EST:     CGTACCCGCTCGGCCCCATCGGGAGTATCAAGGGGTTCGACTCCATTAAG                         GACCATGATCGTGCGGAATTGCGAGAACTAGAGAAG
genomic: CGTACCCGCTCGGCCCCATCGGGAGTATCAAGGGGTTCGACTCCATTAAGgttctctcat ... ggatttgcagGACCATGATCGTGCGGAATTGCGAGAACTAGAGAAG
EST: gi|211319408|gb|FL056110.1|FL056110
EST:     CGTACCCGCTCGGCCCCATCGGGAGTATCAAGGGGTTCGACTCCATTAAG                         GACCATGATCGTGCGGAATTGCGAGAACTAGAGAAG
genomic: CGTACCCGCTCGGCCCCATCGGGAGTATCAAGGGGTTCGACTCCATTAAGgttctctcat ... ggatttgcagGACCATGATCGTGCGGAATTGCGAGAACTAGAGAAG
EST: gi|74242081|gb|DT649995.1|DT649995
EST:     CGTACCCGCTCGGCCCCATCGGGAGTATCAAGGGGTTCGACTCCATTAAG                         GACCATGATCGTGCGGAATTGCGAGAACTAGAGAAG
genomic: CGTACCCGCTCGGCCCCATCGGGAGTATCAAGGGGTTCGACTCCATTAAGgttctctcat ... ggatttgcagGACCATGATCGTGCGGAATTGCGAGAACTAGAGAAG
EST: gi|33095039|gb|CF055033.1|CF055033
EST:     GTACCCGCTCGGCCCCATCGGGAGTATCAAGGGGTTCGACTCCATTAAG                         GACCATGATCGTGCGGAATTGCGGGAACTAGAGAAG
genomic: GTACCCGCTCGGCCCCATCGGGAGTATCAAGGGGTTCGACTCCATTAAGgttctctcat ... ggatttgcagGACCATGATCGTGCGGAATTGCGAGAACTAGAGAAG
EST: gi|91053261|gb|EB163679.1|EB163679
EST:     CGTACCCGCTCGGCCCCATCGGGAGTATCAAGGGGTTCGACTCCATTAAG                         GACCATGATCGTGCGGAATTGCGAGAACTAGAGAAG
genomic: CGTACCCGCTCGGCCCCATCGGGAGTATCAAGGGGTTCGACTCCATTAAGgttctctcat ... ggatttgcagGACCATGATCGTGCGGAATTGCGAGAACTAGAGAAG
EST: gi|71432126|gb|DR813176.1|DR813176
EST:     CGTACCCGCTCGGCCCCATCGGGAGTATCAAGGGGTTCGACTCCATTAAG                         GACCATGATCGTGCGGAATTGCGAGAACTAGAGAAG
genomic: CGTACCCGCTCGGCCCCATCGGGAGTATCAAGGGGTTCGACTCCATTAAGgttctctcat ... ggatttgcagGACCATGATCGTGCGGAATTGCGAGAACTAGAGAAG
EST: gi|71316665|gb|DR795007.1|DR795007
EST:     CGTACCCGCTCGGCCCCATCGGGAGTATCAAGGGGTTCGACTCCATTAAG                         GACCATGATCGTGCGGAATTGCGAGAACTAGAGAAG
genomic: CGTACCCGCTCGGCCCCATCGGGAGTATCAAGGGGTTCGACTCCATTAAGgttctctcat ... ggatttgcagGACCATGATCGTGCGGAATTGCGAGAACTAGAGAAG
EST: gi|28984330|gb|BQ538995.2|BQ538995
EST:     CGACTCCATTAAG                         GACCCATGATCGTGCGGAATTGCGAGAACTAGAGAAG
genomic: CGACTCCATTAAGgttctctcat ... ggatttgcagGA-CCATGATCGTGCGGAATTGCGAGAACTAGAGAAG
EST: gi|211319405|gb|FL056107.1|FL056107
EST:     CGTACCCGCTCGGCCCCATCGGGAGTATCAAGGGGTTCGACTCCATTAAG                         GACCATGATCGTGCGGAATTGCGAGAACTAGAGAAG
genomic: CGTACCCGCTCGGCCCCATCGGGAGTATCAAGGGGTTCGACTCCATTAAGgttctctcat ... ggatttgcagGACCATGATCGTGCGGAATTGCGAGAACTAGAGAAG

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), 36 (downstream exon)
Score: 127

TGGCTTCGGCGCCACCAAGTGGTACCACGTCTCCTGCTTACCCTCCTCGTCGTACCCGCTCGGCCCCATCGGGAGTATCAAGGGGTTCGACTCCATTAAGgttctctcat ... ggatttgcagGACCATGATCGTGCGGAATTGCGAGAACTAGAGAAG


Block sizes: 44 (upstream exon), 34 (downstream exon)
Score: 16

TGGCTTCGGCGCCACCAAGTGGTACCACGTCTCCTGCTTACCCTCCTCGTCGTACCCGCTCGGCCCCATCGGGAGTATCAAGGGGTTCGACTCCATTAAGgttctctcat ... ggatttgcagGACCATGATCGTGCGGAATTGCGAGAACTAGAGAAG


Block sizes: 49 (upstream exon), 36 (downstream exon)
Score: 27

TGGCTTCGGCGCCACCAAGTGGTACCACGTCTCCTGCTTACCCTCCTCGTCGTACCCGCTCGGCCCCATCGGGAGTATCAAGGGGTTCGACTCCATTAAGgttctctcat ... ggatttgcagGACCATGATCGTGCGGAATTGCGAGAACTAGAGAAG


Block sizes: 49 (upstream exon), 36 (downstream exon)
Score: 23

TGGCTTCGGCGCCACCAAGTGGTACCACGTCTCCTGCTTACCCTCCTCGTCGTACCCGCTCGGCCCCATCGGGAGTATCAAGGGGTTCGACTCCATTAAGgttctctcat ... ggatttgcagGACCATGATCGTGCGGAATTGCGAGAACTAGAGAAG