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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaatgcaaaattatttgatcttgctttttaaaaacataaacttcttttcaggaaataaagtgatgtatttgtgcaccacttctagagcagttatatgcgtcaagcataagacctacatgcatatgttgtgactgacatgatatgatgtattctgttttgcagCCTGATTTACCTCATGCATATGTTTGCGCAGAAAGCTACATATTTGATGTCACTGAGTGGTTCAACTGTCAG

Basic information

species Zea mays
transcript GRMZM2G138511_T01
intron # 8
splice site 3'
intron type U2

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|15312804|gb|BI478394.1|BI478394
EST:     GATGGGTTGAACAGTCCTTTCAACCTGTTCTATTTGGCATGCTGCAGAAG                         CCTGATTTACCTCATGCATATGTTTGCGCAGAAAGCTACATATTTGATGTC
genomic: GATGGGTTGAACAGTCCTTTCAACCTGTTCTATTTGGCATGCTGCAGAAGgtaaatgcaa ... tgttttgcagCCTGATTTACCTCATGCATATGTTTGCGCAGAAAGCTACATATTTGATGTC
EST: gi|32836644|gb|CD976322.1|CD976322
EST:     GATGGGTCGAACAGTCCTTTCAACCTGTTCTATTTGGCATGCTGCAGAAG                         CCTGATTTACCTCATGCATATGTTTGCGCAGAAAGCTACATATTTGATGTC
genomic: GATGGGTTGAACAGTCCTTTCAACCTGTTCTATTTGGCATGCTGCAGAAGgtaaatgcaa ... tgttttgcagCCTGATTTACCTCATGCATATGTTTGCGCAGAAAGCTACATATTTGATGTC
EST: gi|33102124|gb|CF062084.1|CF062084
EST:     GATGGGTTGAACAGTCCTTTCAACCTGTTCTATTTGGCATGCTGCAGAAG                         CCTGATTTACCTCATGCATATGTTTGCGCAGAAAGCTACATATTTGATGTC
genomic: GATGGGTTGAACAGTCCTTTCAACCTGTTCTATTTGGCATGCTGCAGAAGgtaaatgcaa ... tgttttgcagCCTGATTTACCTCATGCATATGTTTGCGCAGAAAGCTACATATTTGATGTC
EST: gi|60345046|gb|DN212019.1|DN212019
EST:     GATGGGTTGAACAGTCCTTTCAACCTGTTCTATTTGGCATGCTGCAGAAG                         CCTGATTTACCTCATGCATATGTTTGCGCAGAAAGCTACATATTTGATGTC
genomic: GATGGGTTGAACAGTCCTTTCAACCTGTTCTATTTGGCATGCTGCAGAAGgtaaatgcaa ... tgttttgcagCCTGATTTACCTCATGCATATGTTTGCGCAGAAAGCTACATATTTGATGTC
EST: gi|101385815|gb|EB814956.1|EB814956
EST:     GATGGGTTGAACAGTCCTTTCAACCTGTTCTATTTGGCATGCTGCAGAAG                         CCTGATTTACCTCATGCATATGTTTGCGCAGAAAGCTACATATTTGATGTC
genomic: GATGGGTTGAACAGTCCTTTCAACCTGTTCTATTTGGCATGCTGCAGAAGgtaaatgcaa ... tgttttgcagCCTGATTTACCTCATGCATATGTTTGCGCAGAAAGCTACATATTTGATGTC
EST: gi|32837356|gb|CD977034.1|CD977034
EST:     GATGGGTCGAACAGTCCTTTCAACCTGTTCTATTTGGCATGCTGCAGAAG                         CCTGATTTACCTCATGCATATGTTTGCGCAGAAAGCTACATATTTGATGTC
genomic: GATGGGTTGAACAGTCCTTTCAACCTGTTCTATTTGGCATGCTGCAGAAGgtaaatgcaa ... tgttttgcagCCTGATTTACCTCATGCATATGTTTGCGCAGAAAGCTACATATTTGATGTC
EST: gi|67020498|gb|CO449247.1|CO449247
EST:     GATGGGTTGAACAGTCCTTTCAACCTGTTCTATTTGGCATGCTGCAGAAG                         CCTGATTTACCTCATGCATATGTTTGCGCAGAAAGCTACATATTTGATGTC
genomic: GATGGGTTGAACAGTCCTTTCAACCTGTTCTATTTGGCATGCTGCAGAAGgtaaatgcaa ... tgttttgcagCCTGATTTACCTCATGCATATGTTTGCGCAGAAAGCTACATATTTGATGTC
EST: gi|211314726|gb|FL246031.1|FL246031
EST:     GATGGGTTGAACAGTCCTTTCAACCTGTTCTATTTGGCATGCTGCAGAAG                         CCTGATTTACCTCATGCATATGTTTGCGCAGAAAGCTACATATTTGATGTC
genomic: GATGGGTTGAACAGTCCTTTCAACCTGTTCTATTTGGCATGCTGCAGAAGgtaaatgcaa ... tgttttgcagCCTGATTTACCTCATGCATATGTTTGCGCAGAAAGCTACATATTTGATGTC
EST: gi|120481228|gb|EH211231.1|EH211231
EST:     CCTGTTCTATTTGGCATGCTGCAGAAG                         CCTGATTTACCTCATGCATATGTTTGCGCAGAAAGCTACATATTTGATGTC
genomic: CCTGTTCTATTTGGCATGCTGCAGAAGgtaaatgcaa ... tgttttgcagCCTGATTTACCTCATGCATATGTTTGCGCAGAAAGCTACATATTTGATGTC

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), 47 (downstream exon)
Score: 99

GACTGCAAGGAGTTCCATCAAGCTAAAGATGGCGATGGATGGGTTGAACAGTCCTTTCAACCTGTTCTATTTGGCATGCTGCAGAAGgtaaatgcaa ... tgttttgcagCCTGATTTACCTCATGCATATGTTTGCGCAGAAAGCTACATATTTGATGTCACTGAGTGGTTCAACTGTCAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 77

GACTGCAAGGAGTTCCATCAAGCTAAAGATGGCGATGGATGGGTTGAACAGTCCTTTCAACCTGTTCTATTTGGCATGCTGCAGAAGgtaaatgcaa ... tgttttgcagCCTGATTTACCTCATGCATATGTTTGCGCAGAAAGCTACATATTTGATGTCACTGAGTGGTTCAACTGTCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 85

GACTGCAAGGAGTTCCATCAAGCTAAAGATGGCGATGGATGGGTTGAACAGTCCTTTCAACCTGTTCTATTTGGCATGCTGCAGAAGgtaaatgcaa ... tgttttgcagCCTGATTTACCTCATGCATATGTTTGCGCAGAAAGCTACATATTTGATGTCACTGAGTGGTTCAACTGTCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 81

GACTGCAAGGAGTTCCATCAAGCTAAAGATGGCGATGGATGGGTTGAACAGTCCTTTCAACCTGTTCTATTTGGCATGCTGCAGAAGgtaaatgcaa ... tgttttgcagCCTGATTTACCTCATGCATATGTTTGCGCAGAAAGCTACATATTTGATGTCACTGAGTGGTTCAACTGTCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagacctacatgcatatgttgtgactgacatgatatgatgtattctgttttgcagCCTGATTTACCTCATGCATATGTTTGCGCAGAAAGCTACATATTTGATGTCACTGAGTGGTTCAACTGTCAG
                      gactgac  putative branch site (score: 81)
                                          ttctgtttt  putative PPT
             atatgtt  TA-rich tract