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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AATGCAGTTGTATGCTGAACAAGTTTCTCAGCTTATGACTACTGAGAAGAACCTGCGGTTGCAACTAGCTTCTGACGGGGAAAGATTTCAGCACTTTCAGgtactttcacttctaagaccatttctaggttccaaatggttgccctgtagatgacgacaataacgacaacatttggctttggtccaaatcaagttgatgt...

Basic information

species Zea mays
transcript GRMZM2G107731_T01
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G107731_T01 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os03g17930.1 (Oryza sativa), 5'ss of exon 8
AATGCAGTTGTATGCTGAACAAGTTTCTCAGCTTATGACTACTGAGAAGAACCTGCGGTTGCAACTAGCTTCTGACGGGGAAAGATTTCAGCACTTTCAGgtactttcacttctaagaccatttc------------taggttccaaatggttgccctgtagatgacgacaataacgacaacatttggct--ttggtccaaatcaa--gttgatgt-----------------------------------------------
 |||||| | |||||||| ||||||||||| |||||| |||| ||||||||  |  ||||||| |||||| |||| || |||||||||||||| |||||||||| ||  ||  | || || |||             ||  | ||  ||||| |   |     ||  ||     | |  || |||       ||  |||   | ||  || |||                                                 
GATGCAGCTATATGCTGATCAAGTTTCTCAACTTATGTCTACCGAGAAGAATTTAAGGTTGCAGCTAGCTGCTGATGGAGAAAGATTTCAGCAGTTTCAGgtacctttgctgattaggcccttttcgtaatgacgagtatatgcctcatggtggttttccctttgcagatggctatgcaaatattcaagcagtttctccgttttaattgtggatagctctgccttgtactaaaattttaaaattgtctactttaccttatcag
















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|148994669|gb|EE034190.2|EE034190
EST:     ACCTGCGGTTGCAACTAGCTTCTGACGGGGAAAGATTTCAGCACTTTCAG                         GATGCCTTGTCAAAAAGCAATGAAGTCTTTGAAACTTACAAGCAGGAGATG
genomic: ACCTGCGGTTGCAACTAGCTTCTGACGGGGAAAGATTTCAGCACTTTCAGgtactttcac ... cctttatcagGATGCCTTGTCAAAAAGCAATGAAGTCTTTGAAACTTACAAGCAGGAGATG
EST: gi|149071350|gb|EE159745.2|EE159745
EST:     CAACTAGCTTCTGACGGGGAAAGATTTCAGCACTTTCAG                         GATGCCTTGTCAAAAAGCAATGAAGTCTTTGAAACTTACAAGCAGGAGATG
genomic: CAACTAGCTTCTGACGGGGAAAGATTTCAGCACTTTCAGgtactttcac ... cctttatcagGATGCCTTGTCAAAAAGCAATGAAGTCTTTGAAACTTACAAGCAGGAGATG
EST: gi|71758247|gb|DR956184.1|DR956184
EST:     ACCTGCGGTTGCAACTAGCTTCTGACGGGGAAAGATTTCAGCACTTTCAG                         GATGCCTTGTCAAAAAGCAATGAAGTCTTTGAAACTTACAAGCAGGAGATG
genomic: ACCTGCGGTTGCAACTAGCTTCTGACGGGGAAAGATTTCAGCACTTTCAGgtactttcac ... cctttatcagGATGCCTTGTCAAAAAGCAATGAAGTCTTTGAAACTTACAAGCAGGAGATG
EST: gi|60358220|gb|DN225193.1|DN225193
EST:     ACCTGCGGTTGCAACTAGCTTCTGACGGGGAAAGATTTCAGCACTTTCAG                         GATGCCTTGTCAAAAAGCAATGAAGTCTTTGAAACTTACA
genomic: ACCTGCGGTTGCAACTAGCTTCTGACGGGGAAAGATTTCAGCACTTTCAGgtactttcac ... cctttatcagGATGCCTTGTCAAAAAGCAATGAAGTCTTTGAAACTTACA
EST: gi|78022706|gb|DV491093.1|DV491093
EST:     CGGTTGCAACTAGCTTCTGACGGGGAAAGATTTCAGCACTTTCAG                         GATGCCTTGTCAAAAAGCAATGAAGTCTTTGAAACTTACAAGCAGGAGATG
genomic: CGGTTGCAACTAGCTTCTGACGGGGAAAGATTTCAGCACTTTCAGgtactttcac ... cctttatcagGATGCCTTGTCAAAAAGCAATGAAGTCTTTGAAACTTACAAGCAGGAGATG
EST: gi|37394977|gb|CF634768.1|CF634768
EST:     ACCTGCGGTTGCAACTAGCTTCTGACGGGGAAAGATTTCAGCACTTTCAG                         GATGCCTTGTCAAAAAGCAATGAAGTCTTTGAAACTTACAAGCAGGAGATG
genomic: ACCTGCGGTTGCAACTAGCTTCTGACGGGGAAAGATTTCAGCACTTTCAGgtactttcac ... cctttatcagGATGCCTTGTCAAAAAGCAATGAAGTCTTTGAAACTTACAAGCAGGAGATG
EST: gi|213169996|gb|FM189145.1|FM189145
EST:     ACCTGCGGTTGCAACTAGCTTCTGACGGGGAAAGATTTCAGCACTTTCAG                         GATGCCTTGTCAAAAAGCAATGAAGTCTTTGAAACTTACAAGCAGGAGATG
genomic: ACCTGCGGTTGCAACTAGCTTCTGACGGGGAAAGATTTCAGCACTTTCAGgtactttcac ... cctttatcagGATGCCTTGTCAAAAAGCAATGAAGTCTTTGAAACTTACAAGCAGGAGATG
EST: gi|71774541|gb|DR972419.1|DR972419
EST:     ACCTGCGGTTGCAACTAGCTTCTGACGGGGAAAGATTTCAGCACTTTCAG                         GATGCCTTGTCAAAAAGCAATGAAGTCTTTGAAACTTACAAGCAGGAGATG
genomic: ACCTGCGGTTGCAACTAGCTTCTGACGGGGAAAGATTTCAGCACTTTCAGgtactttcac ... cctttatcagGATGCCTTGTCAAAAAGCAATGAAGTCTTTGAAACTTACAAGCAGGAGATG
EST: gi|32931571|gb|CF036383.1|CF036383
EST:     ACCTGCGGTTGCAACTAGCTTCTGACGGGGAAAGATTTCAGCACTTTCAG                         GATGCCTTGTCAAAAAGCAATGAAGTCCTTGAAACCTACAAGCAGGAGATG
genomic: ACCTGCGGTTGCAACTAGCTTCTGACGGGGAAAGATTTCAGCACTTTCAGgtactttcac ... cctttatcagGATGCCTTGTCAAAAAGCAATGAAGTCTTTGAAACTTACAAGCAGGAGATG
EST: gi|78114092|gb|DV532481.1|DV532481
EST:     GGTTGCAACTAGCTTCTGACGGGGAAAGATTTCAGCACTTTCAG                         GATGCCTTGTCAAAAAGCAATGAAGTCTTTGAAACTTACAAGCAGGAGATG
genomic: GGTTGCAACTAGCTTCTGACGGGGAAAGATTTCAGCACTTTCAGgtactttcac ... cctttatcagGATGCCTTGTCAAAAAGCAATGAAGTCTTTGAAACTTACAAGCAGGAGATG
EST: gi|60337106|gb|DN204079.1|DN204079
EST:     GACGGTGAAAGATTTCAGCACTTTCAG                         GATGCCTTGTCAAAAAGCAATGAAGTCTTTGAAACTTACAAGCAGGAGATG
genomic: GACGGGGAAAGATTTCAGCACTTTCAGgtactttcac ... cctttatcagGATGCCTTGTCAAAAAGCAATGAAGTCTTTGAAACTTACAAGCAGGAGATG

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: 105

AATGCAGTTGTATGCTGAACAAGTTTCTCAGCTTATGACTACTGAGAAGAACCTGCGGTTGCAACTAGCTTCTGACGGGGAAAGATTTCAGCACTTTCAGgtactttcac ... cctttatcagGATGCCTTGTCAAAAAGCAATGAAGTCTTTGAAACTTACAAGCAGGAGATGGAAAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 125

AATGCAGTTGTATGCTGAACAAGTTTCTCAGCTTATGACTACTGAGAAGAACCTGCGGTTGCAACTAGCTTCTGACGGGGAAAGATTTCAGCACTTTCAGgtactttcac ... cctttatcagGATGCCTTGTCAAAAAGCAATGAAGTCTTTGAAACTTACAAGCAGGAGATGGAAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 119

AATGCAGTTGTATGCTGAACAAGTTTCTCAGCTTATGACTACTGAGAAGAACCTGCGGTTGCAACTAGCTTCTGACGGGGAAAGATTTCAGCACTTTCAGgtactttcac ... cctttatcagGATGCCTTGTCAAAAAGCAATGAAGTCTTTGAAACTTACAAGCAGGAGATGGAAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 74

AATGCAGTTGTATGCTGAACAAGTTTCTCAGCTTATGACTACTGAGAAGAACCTGCGGTTGCAACTAGCTTCTGACGGGGAAAGATTTCAGCACTTTCAGgtactttcac ... cctttatcagGATGCCTTGTCAAAAAGCAATGAAGTCTTTGAAACTTACAAGCAGGAGATGGAAAAG