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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaccagcggccaagcgctgccttcgctcaaaaaactaattccaaaagattcctcgatcgatctcggccggcggcggcggcggcggcgctgattctgtttttctttggtttctctgctctgcagTTTGCTCAAGATTTGGAACCTGAACAAGTGCGGTGGCGTGGTGGGTGTGTTCAACTGCCAGGGAGCCGGGTGGTGCCGCGTGACCAAGCGGACGCGCGTG

Basic information

species Zea mays
transcript GRMZM2G340656_T03
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G340656_T05 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os07g10840.1 (Oryza sativa), 3'ss of exon 7
gtgaccagcggccaagcgctgccttcgctcaaaaaactaattccaaaagattcctcgatcgatctcggccggcggcggcggcggcggcgctgattctgtttttctttggtttctctgctctgcagTTTGCTCAAGATTTGGAACCTGAACAAGTGCGGTGGCGTGGTGGGTGTGTTCAACTGCCAGGGAGCCGGGTGGTGCCGCGTGACCAAGCGGACGCGCGTG
                                     |||     ||||||| |   ||   | |         |    ||   ||    ||  |     |||  | |  || | ||      |||||||||||||| |||||||||||||| ||||| |||||||| || ||||||||||||||||| |||||||||||| | ||| |||||  ||||||||||
------------------------------------gtaacaaacaaagatttcgaaatttgtgt---------gaaatggtttcgaatttgggttaaaatttgatggaattttttgt-----agTTTGCTCAAGATATGGAACCTGAACAATTGCGGCGGCGTGGTCGGGGTGTTCAACTGCCAGGGCGCCGGGTGGTGCAGGGTGGCCAAGAAGACGCGCGTG
















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|154130378|gb|EC872174.2|EC872174
EST:     CGGCCCACACGGGACTGCCTCTTCTCCGACCCGGCGCGCGACGGCGCGAG                         TTTGCTCAAGATTTGGAACCTGAACAAGTGCGGTGGCGTGGTGGGTGTGTT
genomic: CGGCCCACACGGGACTGCCTCTTCTCCGACCCGGCGCGCGACGGCGCGAGgtgaccagcg ... tgctctgcagTTTGCTCAAGATTTGGAACCTGAACAAGTGCGGTGGCGTGGTGGGTGTGTT
EST: gi|76012353|gb|DT939523.1|DT939523
EST:     CGGCCCACACGGGACTGCCTCTTCTCCGACCCGGCGCGCGACGGCGCGAG                         TTTGCTCAAGATTTGGAACCTGAACAAGTGCGGTGGCGTGGTGGGTGTGTT
genomic: CGGCCCACACGGGACTGCCTCTTCTCCGACCCGGCGCGCGACGGCGCGAGgtgaccagcg ... tgctctgcagTTTGCTCAAGATTTGGAACCTGAACAAGTGCGGTGGCGTGGTGGGTGTGTT
EST: gi|148996151|gb|EE035420.2|EE035420
EST:     CGGCCCACACGGGATTGCCTCTTCTCCGACCCGGCGCGCGACGGCGCGAG                         TTTGCTCAAGATTTGGAACCTGAACAAGTGCGGTGGGGTGGTGGGTGTGTT
genomic: CGGCCCACACGGGACTGCCTCTTCTCCGACCCGGCGCGCGACGGCGCGAGgtgaccagcg ... tgctctgcagTTTGCTCAAGATTTGGAACCTGAACAAGTGCGGTGGCGTGGTGGGTGTGTT
EST: gi|149086838|gb|EE176387.2|EE176387
EST:     CGGCCCACACGGGACTGCCTCTTCTCCGACCCGGCGCGCGACGGCGCGAG                         TTTGCTCAAGATTTGGAACCTGAACAAGTGCGGTGGCGTGGTGGGTGTGTT
genomic: CGGCCCACACGGGACTGCCTCTTCTCCGACCCGGCGCGCGACGGCGCGAGgtgaccagcg ... tgctctgcagTTTGCTCAAGATTTGGAACCTGAACAAGTGCGGTGGCGTGGTGGGTGTGTT
EST: gi|149084331|gb|EE173770.2|EE173770
EST:     CGGCCCACACGGGACTGCCTCTTCTCCGACCCGGCGCGCGACGGCGCGAG                         TTTGCTCAAGATTTGGAACCTGAACAAGTGCGGTGGCGTGGTGGGTGTGTT
genomic: CGGCCCACACGGGACTGCCTCTTCTCCGACCCGGCGCGCGACGGCGCGAGgtgaccagcg ... tgctctgcagTTTGCTCAAGATTTGGAACCTGAACAAGTGCGGTGGCGTGGTGGGTGTGTT
EST: gi|211172040|gb|FL103285.1|FL103285
EST:     CGGCCCACACGGGACTGCCTCTTCTCCGACCCGGCGCGCGACGGCGCGAG                         TTTGCTCAAGATTTGGAACCTGAANCA-GTGCGGTGGCGTGGTGGGTGTGT
genomic: CGGCCCACACGGGACTGCCTCTTCTCCGACCCGGCGCGCGACGGCGCGAGgtgaccagcg ... tgctctgcagTTTGCTCAAGATTTGGAACCTGAA-CAAGTGCGGTGGCGTGGTGGGTGTGT
EST: gi|12047418|gb|BF729557.1|BF729557
EST:     CGGCCCACACGGGACTGCCTCTTCTCCGACCCGGCGCGCGACGGCGCGAG                         TTTGCTCAAGATTTGGAACCTGAACAAGTGCGGTGGCGTGGTGGGTGTGTT
genomic: CGGCCCACACGGGACTGCCTCTTCTCCGACCCGGCGCGCGACGGCGCGAGgtgaccagcg ... tgctctgcagTTTGCTCAAGATTTGGAACCTGAACAAGTGCGGTGGCGTGGTGGGTGTGTT
EST: gi|78180926|gb|DV551299.1|DV551299
EST:     CGGCCCACACGGGACTGCCTCTTCTCCGACCCGGCGCGCGACGGCGCGAG                         TTTGCTCAAGATTTGGAACCTGAACAAGTGCGGTGGCGTGGTGGGTGTGTT
genomic: CGGCCCACACGGGACTGCCTCTTCTCCGACCCGGCGCGCGACGGCGCGAGgtgaccagcg ... tgctctgcagTTTGCTCAAGATTTGGAACCTGAACAAGTGCGGTGGCGTGGTGGGTGTGTT
EST: gi|8930236|gb|BE225000.1|BE225000
EST:     CGGCCCACACGGGACTGCCTCTTCTCCGACCCGGCGCGCGACGGCGCGAG                         TTTGCTCAAGATTTGGAACCTGAACAAGTGCGGTGGCGTGGTGGGTGTGTT
genomic: CGGCCCACACGGGACTGCCTCTTCTCCGACCCGGCGCGCGACGGCGCGAGgtgaccagcg ... tgctctgcagTTTGCTCAAGATTTGGAACCTGAACAAGTGCGGTGGCGTGGTGGGTGTGTT
EST: gi|149070806|gb|EE159216.2|EE159216
EST:     CGGCCCACACGGGACTGCCTCTTCTCCGACCCGGCGCGCGACGGCGCGAG                         TTTGCTCAAGATTTGGAACCTGAACAAGTGCGGTGGCGTGGTGGGTGTGTT
genomic: CGGCCCACACGGGACTGCCTCTTCTCCGACCCGGCGCGCGACGGCGCGAGgtgaccagcg ... tgctctgcagTTTGCTCAAGATTTGGAACCTGAACAAGTGCGGTGGCGTGGTGGGTGTGTT
EST: gi|67015729|gb|CO444478.1|CO444478
EST:     CGGCCCACACGCGACTGCCTCTTCTCCGACCCGGCGCGCGACGGCGCGAG                         TTTGCTCAAGATCTGGAACCTGAACAAGTGCGGTGGCGTGGTGGGTGTGTT
genomic: CGGCCCACACGGGACTGCCTCTTCTCCGACCCGGCGCGCGACGGCGCGAGgtgaccagcg ... tgctctgcagTTTGCTCAAGATTTGGAACCTGAACAAGTGCGGTGGCGTGGTGGGTGTGTT
EST: gi|148941549|gb|EC886485.2|EC886485
EST:     CGGCCCACACGGGACTGCCTCTTCTCCGACCCGGCGCGCGACGGCGCGAG                         TTTGCTCAAGATTTGGAACCTGAACAAGTGCGGTGGCGTGGTGGGTGTGTT
genomic: CGGCCCACACGGGACTGCCTCTTCTCCGACCCGGCGCGCGACGGCGCGAGgtgaccagcg ... tgctctgcagTTTGCTCAAGATTTGGAACCTGAACAAGTGCGGTGGCGTGGTGGGTGTGTT
EST: gi|149010052|gb|EE041855.2|EE041855
EST:     CGGCCCACACGGGACTGCCTCTTCTCCGACCCGGCGCGCGACGGCGCGAG                         TTTGCTCAAGATTTGGAACCTGAACAAGTGCGGTGGCGTGGTGGGTGTGTT
genomic: CGGCCCACACGGGACTGCCTCTTCTCCGACCCGGCGCGCGACGGCGCGAGgtgaccagcg ... tgctctgcagTTTGCTCAAGATTTGGAACCTGAACAAGTGCGGTGGCGTGGTGGGTGTGTT
EST: gi|67020306|gb|CO449055.1|CO449055
EST:     CGGCCCACACGCGACTGCCTCTTCTCCGACCCGGCGCGCGACGGCGCGAG                         TTTGCTCAAGATCTGGAACCTGAACAAGTGCGGTGGCGTGGTGGGTGTGTT
genomic: CGGCCCACACGGGACTGCCTCTTCTCCGACCCGGCGCGCGACGGCGCGAGgtgaccagcg ... tgctctgcagTTTGCTCAAGATTTGGAACCTGAACAAGTGCGGTGGCGTGGTGGGTGTGTT
EST: gi|149087714|gb|EE177063.2|EE177063
EST:     CGGCCCACACGGGACTGCCTCTTCTCCGACCCGGCGCGCGACGGCGCGAG                         TTTGCTCAAGATTTGGAACCTGAACAAGTGCGGTGGCGTGGTGGGTGTGTT
genomic: CGGCCCACACGGGACTGCCTCTTCTCCGACCCGGCGCGCGACGGCGCGAGgtgaccagcg ... tgctctgcagTTTGCTCAAGATTTGGAACCTGAACAAGTGCGGTGGCGTGGTGGGTGTGTT
EST: gi|78090795|gb|DV519169.1|DV519169
EST:     CGGCCCACACGGGACTGCCTCTTCTCCGACCCGGCGCGCGACGGCGCGAG                         TTTGCTCAAGATTTGGAACCTGAACAAGTGCGGTGGCGTGGTGGGTGTGTT
genomic: CGGCCCACACGGGACTGCCTCTTCTCCGACCCGGCGCGCGACGGCGCGAGgtgaccagcg ... tgctctgcagTTTGCTCAAGATTTGGAACCTGAACAAGTGCGGTGGCGTGGTGGGTGTGTT
EST: gi|148932434|gb|EC876140.2|EC876140
EST:     CGGCCCACACGGGACTGCCTCTTCTCCGACCCGGCGCGCGACGGCGCGAG                         TTTGCTCAAGATTTGGAACCTGAACAAGTGCGGTGGCGTGGTGGGTGTGTT
genomic: CGGCCCACACGGGACTGCCTCTTCTCCGACCCGGCGCGCGACGGCGCGAGgtgaccagcg ... tgctctgcagTTTGCTCAAGATTTGGAACCTGAACAAGTGCGGTGGCGTGGTGGGTGTGTT
EST: gi|148983163|gb|EE029102.2|EE029102
EST:     CGGCCCACACGGGACTGCCTCTTCTCCGACCCGGCGCGCGACGGCGCGAG                         TTTGCTCAAGATTTGGAAC
genomic: CGGCCCACACGGGACTGCCTCTTCTCCGACCCGGCGCGCGACGGCGCGAGgtgaccagcg ... tgctctgcagTTTGCTCAAGATTTGGAAC
EST: gi|148939693|gb|EC884359.2|EC884359
EST:     CGGCCCACACGGGACTGCCTCTTCTCCGACCCGGCGCGCGACGGCGCGAG                         TTTGCTCAAGATTTGGAACCTGAACAAGTGCGGTGGCGTGGTGGGTGTGTT
genomic: CGGCCCACACGGGACTGCCTCTTCTCCGACCCGGCGCGCGACGGCGCGAGgtgaccagcg ... tgctctgcagTTTGCTCAAGATTTGGAACCTGAACAAGTGCGGTGGCGTGGTGGGTGTGTT
EST: gi|149024936|gb|EE045966.2|EE045966
EST:     CGGCCCACACGGGACTGCCTCTTCTCCGACCCGGCGCGCGACGGCGCGAG                         TTTGCTCAAGATTTGGAACCTGAACAAGTGCGGTGGCGTGGTGGGTGTGTT
genomic: CGGCCCACACGGGACTGCCTCTTCTCCGACCCGGCGCGCGACGGCGCGAGgtgaccagcg ... tgctctgcagTTTGCTCAAGATTTGGAACCTGAACAAGTGCGGTGGCGTGGTGGGTGTGTT
EST: gi|149111646|gb|EE190788.2|EE190788
EST:     CGGCCCACACGGGACTGCCTCTTCTCCGACCCGGCGCGCGACGGCGCGAG                         TTTGCTCAAGATTTGGAACCTGAACAAGTGCGGTGGCGTGGTGGGTGTGTT
genomic: CGGCCCACACGGGACTGCCTCTTCTCCGACCCGGCGCGCGACGGCGCGAGgtgaccagcg ... tgctctgcagTTTGCTCAAGATTTGGAACCTGAACAAGTGCGGTGGCGTGGTGGGTGTGTT
EST: gi|148997335|gb|EE035830.2|EE035830
EST:     CGGCCCACACGGGACTGCCTCTTCTCCGACCCGGCGCGCGACGGCGCGAG                         TTTGCTCAAGATTTGGAACCTGAACAAGTGCGGTGGCGTGGTGGGTGTGTT
genomic: CGGCCCACACGGGACTGCCTCTTCTCCGACCCGGCGCGCGACGGCGCGAGgtgaccagcg ... tgctctgcagTTTGCTCAAGATTTGGAACCTGAACAAGTGCGGTGGCGTGGTGGGTGTGTT

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: 47 (upstream exon), 49 (downstream exon)
Score: 270

GGAAGCTCGTGCTCCCCGACGGCACCGTGCTACGCGCGCAGCTTCCCGGCCGGCCCACACGGGACTGCCTCTTCTCCGACCCGGCGCGCGACGGCGCGAGgtgaccagcg ... tgctctgcagTTTGCTCAAGATTTGGAACCTGAACAAGTGCGGTGGCGTGGTGGGTGTGTTCAACTGCCAGGGAGCCGGGTGGTGCCGCGTGACCAAGCGGACGCGCGTG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 371

GGAAGCTCGTGCTCCCCGACGGCACCGTGCTACGCGCGCAGCTTCCCGGCCGGCCCACACGGGACTGCCTCTTCTCCGACCCGGCGCGCGACGGCGCGAGgtgaccagcg ... tgctctgcagTTTGCTCAAGATTTGGAACCTGAACAAGTGCGGTGGCGTGGTGGGTGTGTTCAACTGCCAGGGAGCCGGGTGGTGCCGCGTGACCAAGCGGACGCGCGTG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 145

GGAAGCTCGTGCTCCCCGACGGCACCGTGCTACGCGCGCAGCTTCCCGGCCGGCCCACACGGGACTGCCTCTTCTCCGACCCGGCGCGCGACGGCGCGAGgtgaccagcg ... tgctctgcagTTTGCTCAAGATTTGGAACCTGAACAAGTGCGGTGGCGTGGTGGGTGTGTTCAACTGCCAGGGAGCCGGGTGGTGCCGCGTGACCAAGCGGACGCGCGTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 434

GGAAGCTCGTGCTCCCCGACGGCACCGTGCTACGCGCGCAGCTTCCCGGCCGGCCCACACGGGACTGCCTCTTCTCCGACCCGGCGCGCGACGGCGCGAGgtgaccagcg ... tgctctgcagTTTGCTCAAGATTTGGAACCTGAACAAGTGCGGTGGCGTGGTGGGTGTGTTCAACTGCCAGGGAGCCGGGTGGTGCCGCGTGACCAAGCGGACGCGCGTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggcggcggcggcggcggcgctgattctgtttttctttggtttctctgctctgcagTTTGCTCAAGATTTGGAACCTGAACAAGTGCGGTGGCGTGGTGGGTGTGTTCAACTGCCAGGGAGCCGGGTGGTGCCGCGTGACCAAGCGGACGCGCGTG
                 cgctgat  putative branch site (score: 434)
                       ttctgtttttctttgg  CT-rich tract
                            tttttcttt  TA-rich tract