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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACGAATGGTTCGGCCGTCAGGGATGACCTTTGGGGTTCAAAGCTTGCTAGCAAATTTTATGGGTGCAGCAACTCAAGCAGCAGGTTTCTTGgtaggcaaactttttaaaatccactgttggtagaaatttggtgaaactgcattggacaattttatttgttccacagttctacaaggctacaaatgctaggtgtttagttgtaattaatgcttttgagattcgggaaatagttttgactgcatcttttgttaaattttacctgaagcagtttttgtttcaaaattgtgtag

Basic information

species Zea mays
transcript GRMZM2G131699_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G131699_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os08g44015.1 (Oryza sativa), 5'ss of exon 3
ACGAATGGTTCGGCCGTCAGGGATGACCTTTGGGGTTCAAAGCTTGCTAGCAAATTTTATGGGTGCAGCAACTCAAGCAGCAGGTTTCTTGgtaggcaaactttttaaaatccactgttggtagaaatttggtgaaactgcattggacaattttatttgttccacagttctacaaggctacaaatgctaggtgtttagttgtaattaatgcttttgagattcgggaaatagttttgactgcatcttttgttaaattttacctgaagcagtttttgtttcaaaattgtgtag
               |     |||| |||||||||||| ||| |||| |||| ||| ||||||||||||||||||||||||||||| ||||||  |||   |||||     ||||||  |||  ||||||| |  |||||  | |            ||||  | | || ||            |||  | |  | ||  | | |  |    |  ||| ||   |    |||  | |||     || |  ||    |||||||||  |||   ||||| ||| ||||| ||
------------AAAGAGGCAGATGGCCTTTGGGGTTCTAAGTTTGCGAGCAGATTCTATGGGTGCAGCAACTCAAGCAGCAGGTTCCTTGgtgcgcattattttt-----ccactgacggttaaaatttgctcgaactgagtag------------tgttttagatttgta---------gtgtgcatgtttctgag--gcattctacatataggaggttttagtggcagtggt-actattctttgttgtatggattacctgaaatagtcaatgttttaaa-ttgtgcag
















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|76010763|gb|DT937933.1|DT937933
EST:     GCTTGCTAGCAAATTTTATGGGTGCAGCAACTCAAGCAGCAGGTTTCTTG                         ACTCAAATATTACTACCCAACCAGAGCGCTATTTGATGATTGTTACAAGTG
genomic: GCTTGCTAGCAAATTTTATGGGTGCAGCAACTCAAGCAGCAGGTTTCTTGgtaggcaaac ... aattgtgtagACTCAAATATTACTACCCAACCAGAGCGCTATTTGATGATTGTTACAAGTG
EST: gi|89249642|gb|DY621428.1|DY621428
EST:     GCTTGCTAGCAAATTTTATGGGTGCAGCAACTCAAGCAGCAGGTTTCTTG                         ACTCAAATATTACTACCCAACCAGAGCGCTATTTGATGATTGTTACAAGTG
genomic: GCTTGCTAGCAAATTTTATGGGTGCAGCAACTCAAGCAGCAGGTTTCTTGgtaggcaaac ... aattgtgtagACTCAAATATTACTACCCAACCAGAGCGCTATTTGATGATTGTTACAAGTG
EST: gi|149110252|gb|EE190310.2|EE190310
EST:     GCTTGCTAGCAAATTTTATGGGTGCAGCAACTCAAGCAGCAGGTTTCTTG                         ACTCAAATATTACTACCCAACCAGAGCGCTATTTGATGATTGTTACAAGTG
genomic: GCTTGCTAGCAAATTTTATGGGTGCAGCAACTCAAGCAGCAGGTTTCTTGgtaggcaaac ... aattgtgtagACTCAAATATTACTACCCAACCAGAGCGCTATTTGATGATTGTTACAAGTG
EST: gi|31909461|gb|CD650930.1|CD650930
EST:     GCTTGCTAGCAAATTTTATGGGTGCAGCAACTCAAGCAGCAGGTTTCTTG                         ACTCAAATATTACTACCCAACCAGAGCGCTATTTGATGATTGTTACAAGTG
genomic: GCTTGCTAGCAAATTTTATGGGTGCAGCAACTCAAGCAGCAGGTTTCTTGgtaggcaaac ... aattgtgtagACTCAAATATTACTACCCAACCAGAGCGCTATTTGATGATTGTTACAAGTG
EST: gi|78111344|gb|DV529741.1|DV529741
EST:     GCTTGCTAGCAAATTTTATGGGTGCAGCAACTCAAGCAGCAGGTTTCTTG                         ACTTCAA-TATTACTACCCAACCAGAGCGCTATTTGATGATTGTTACAAGT
genomic: GCTTGCTAGCAAATTTTATGGGTGCAGCAACTCAAGCAGCAGGTTTCTTGgtaggcaaac ... aattgtgtagACT-CAAATATTACTACCCAACCAGAGCGCTATTTGATGATTGTTACAAGT
EST: gi|71322750|gb|DR798057.1|DR798057
EST:     GCTTGCTAGCAAATTTTATGGGTGCAGCAACTCAAGCAGCAGGTTTCTTG                         ACTCAAATATTACTACCCAACCAGAGCGCTATTTGATGATTGTTACAAGTG
genomic: GCTTGCTAGCAAATTTTATGGGTGCAGCAACTCAAGCAGCAGGTTTCTTGgtaggcaaac ... aattgtgtagACTCAAATATTACTACCCAACCAGAGCGCTATTTGATGATTGTTACAAGTG
EST: gi|211056621|gb|FL260439.1|FL260439
EST:     GCTTGCTAGCAAATTTTATGGGTGCAGCAACTCAAGCAGCAGGTTTCTTG                         ACTCAAATATTACTACCCAACCAGAGCGCTATTTGATGATTGTTACAAGTG
genomic: GCTTGCTAGCAAATTTTATGGGTGCAGCAACTCAAGCAGCAGGTTTCTTGgtaggcaaac ... aattgtgtagACTCAAATATTACTACCCAACCAGAGCGCTATTTGATGATTGTTACAAGTG
EST: gi|71308473|gb|DR790475.1|DR790475
EST:     GCTTGCTAGCAAATTTTATGGGTGCAGCAACTCAAGCAGCAGGTTTCTTG                         ACTCAAATATTACTACCCAACCAGAGCGCTATTTGATGATTGTTACAAGTG
genomic: GCTTGCTAGCAAATTTTATGGGTGCAGCAACTCAAGCAGCAGGTTTCTTGgtaggcaaac ... aattgtgtagACTCAAATATTACTACCCAACCAGAGCGCTATTTGATGATTGTTACAAGTG

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: 48 (upstream exon), 45 (downstream exon)
Score: 58

ACGAATGGTTCGGCCGTCAGGGATGACCTTTGGGGTTCAAAGCTTGCTAGCAAATTTTATGGGTGCAGCAACTCAAGCAGCAGGTTTCTTGgtaggcaaac ... aattgtgtagACTCAAATATTACTACCCAACCAGAGCGCTATTTGATGATTGTTACAAGTGGAGGCCTGAATCAACAGAGAACAGGG


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

ACGAATGGTTCGGCCGTCAGGGATGACCTTTGGGGTTCAAAGCTTGCTAGCAAATTTTATGGGTGCAGCAACTCAAGCAGCAGGTTTCTTGgtaggcaaac ... aattgtgtagACTCAAATATTACTACCCAACCAGAGCGCTATTTGATGATTGTTACAAGTGGAGGCCTGAATCAACAGAGAACAGGG


Block sizes: 45 (upstream exon), 47 (downstream exon)
Score: 53

ACGAATGGTTCGGCCGTCAGGGATGACCTTTGGGGTTCAAAGCTTGCTAGCAAATTTTATGGGTGCAGCAACTCAAGCAGCAGGTTTCTTGgtaggcaaac ... aattgtgtagACTCAAATATTACTACCCAACCAGAGCGCTATTTGATGATTGTTACAAGTGGAGGCCTGAATCAACAGAGAACAGGG


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 69

ACGAATGGTTCGGCCGTCAGGGATGACCTTTGGGGTTCAAAGCTTGCTAGCAAATTTTATGGGTGCAGCAACTCAAGCAGCAGGTTTCTTGgtaggcaaac ... aattgtgtagACTCAAATATTACTACCCAACCAGAGCGCTATTTGATGATTGTTACAAGTGGAGGCCTGAATCAACAGAGAACAGGG