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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatctcattttaaaccttttagatcagaggcattcacccggttttattaaggaatgctctccattttaacttgtcgcgcgcgtgtgtgtgcgtgtttgtttccagcatttcagttttcaaaacctcccaggccttcgcctgacagctgacattcccttttactttgccttcctttccagTTCTACCTCGATATGCAATTTGTGATCCTTTTCGGGCAAGGTCGTTTCTTATCTCGGCATGTGCATCAAGTCATATTGGACATCATTGATAGAGCGATGA

Basic information

species Zea mays
transcript GRMZM2G090573_T01
intron # 5
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|78118153|gb|DV536540.1|DV536540
EST:     AAGAGGTTGAAGAAGGACCAAGGGCTTTGGGTCCGGTTGGACTTCAGCAG                         TTTTACCTCGATATGCAATTTGTGATCCTTTTCGGGCAAGGTCGTTTTTTA
genomic: AAGAGGTTGAAGAAGGACCAAGGGCTCTGGGTCCGGTTGGACTTCAGCAGgtaatctcat ... tcctttccagTTCTACCTCGATATGCAATTTGTGATCCTTTTCGGGCAAGGTCGTTTCTTA
EST: gi|91054249|gb|EB164667.1|EB164667
EST:     AAGAGGTTGAAGAAGGACCAAGGGCTCTGGGTCCGGTTGGACTTCAGCAG                         TTCTACCTCGATATGCAATTTGTGATCCTTTTCGGGCAAGGTCGTTTCTTA
genomic: AAGAGGTTGAAGAAGGACCAAGGGCTCTGGGTCCGGTTGGACTTCAGCAGgtaatctcat ... tcctttccagTTCTACCTCGATATGCAATTTGTGATCCTTTTCGGGCAAGGTCGTTTCTTA
EST: gi|78023987|gb|DV492374.1|DV492374
EST:     GGACCAAGGGCTCTGGGTCCGG-TGGACTTCAGCAG                         TTCTACCTCGATATGCAATTTGTGATCCTTTTCGGGCAAGGTCGTTTCTTA
genomic: GGACCAAGGGCTCTGGGTCCGGTTGGACTTCAGCAGgtaatctcat ... tcctttccagTTCTACCTCGATATGCAATTTGTGATCCTTTTCGGGCAAGGTCGTTTCTTA
EST: gi|5455985|gb|AI833675.1|AI833675
EST:     AAGAGGTTGAAGAAGGACCAAGGGCTCTGGGTCCGGTTGGACTTCAGCAG                         TTCTACCTCGATATGCAATTTGTGATCCTTTTCGGGCAAGGTCGTTTCTTA
genomic: AAGAGGTTGAAGAAGGACCAAGGGCTCTGGGTCCGGTTGGACTTCAGCAGgtaatctcat ... tcctttccagTTCTACCTCGATATGCAATTTGTGATCCTTTTCGGGCAAGGTCGTTTCTTA
EST: gi|211223063|gb|FL465834.1|FL465834
EST:     TGGGTCCGGTTGGACTTCAGCAG                         TTYTACCTCGATATGCAATTTGTGATCCTTTTCGGGCAAGGTCGTTTYTTA
genomic: TGGGTCCGGTTGGACTTCAGCAGgtaatctcat ... tcctttccagTTCTACCTCGATATGCAATTTGTGATCCTTTTCGGGCAAGGTCGTTTCTTA
EST: gi|211223064|gb|FL465835.1|FL465835
EST:     AAGAGGTTGAAGAAGGACCAAGGGCTCTGGGTCCGGTTGGACTTCAGCAG                         TTCTACCTCGATATGCAATTTGTGATCCTTTTCGGGCAAGGTCGTTTCTTA
genomic: AAGAGGTTGAAGAAGGACCAAGGGCTCTGGGTCCGGTTGGACTTCAGCAGgtaatctcat ... tcctttccagTTCTACCTCGATATGCAATTTGTGATCCTTTTCGGGCAAGGTCGTTTCTTA
EST: gi|71758499|gb|DR956436.1|DR956436
EST:     AAGAGGTTGAAGAAGGACCAAGGGCTCTGGGTCCGGTTGGACTTCAGCAG                         TTCTACCTCGATATGCAATTTGTGATCCTTTTCGGGCAAGGTCGTTTCTTA
genomic: AAGAGGTTGAAGAAGGACCAAGGGCTCTGGGTCCGGTTGGACTTCAGCAGgtaatctcat ... tcctttccagTTCTACCTCGATATGCAATTTGTGATCCTTTTCGGGCAAGGTCGTTTCTTA
EST: gi|78023641|gb|DV492028.1|DV492028
EST:     TCCGGTTGGACTTCAGCAG                         TTCTACCTCGATATGCAATTTGTGATCCTTTTCGGGCAAGGTCGTTTCTTA
genomic: TCCGGTTGGACTTCAGCAGgtaatctcat ... tcctttccagTTCTACCTCGATATGCAATTTGTGATCCTTTTCGGGCAAGGTCGTTTCTTA
EST: gi|149094930|gb|EE180513.2|EE180513
EST:     AAGAGGTTGAAGAAGGACCAAGGGCTCTGGGTCCGGTTGGACTTCAGCAG                         TTCTACCTCGATATGCAATTTGTGATCCTTTTCGGGCAAGGTCGTTTCTTA
genomic: AAGAGGTTGAAGAAGGACCAAGGGCTCTGGGTCCGGTTGGACTTCAGCAGgtaatctcat ... tcctttccagTTCTACCTCGATATGCAATTTGTGATCCTTTTCGGGCAAGGTCGTTTCTTA
EST: gi|78111121|gb|DV529518.1|DV529518
EST:     GGGTCCGGTTGGACTTCAGCAG                         TTCTACCTCGATATGCAATTTGTGATCCTTTTCGGGCAAGGTCGTTTCTTA
genomic: GGGTCCGGTTGGACTTCAGCAGgtaatctcat ... tcctttccagTTCTACCTCGATATGCAATTTGTGATCCTTTTCGGGCAAGGTCGTTTCTTA
EST: gi|71307953|gb|DR790196.1|DR790196
EST:     AAGAGGTTGAAGAAGGACCAAGGGCTCTGGGTCCGGTTGGACTTCAGCAG                         TTCTACCTCGATATGCAATTTGTGATCCTTTTCGGGCAAGGTCGTTTCTTA
genomic: AAGAGGTTGAAGAAGGACCAAGGGCTCTGGGTCCGGTTGGACTTCAGCAGgtaatctcat ... tcctttccagTTCTACCTCGATATGCAATTTGTGATCCTTTTCGGGCAAGGTCGTTTCTTA

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: 44 (upstream exon), 47 (downstream exon)
Score: 45

ACTTACGGAGGCAGTCATGCTTTGGCTCTCAGACGACCAGAGCTTTTGGGAAGAGGTTGAAGAAGGACCAAGGGCTCTGGGTCCGGTTGGACTTCAGCAGgtaatctcat ... tcctttccagTTCTACCTCGATATGCAATTTGTGATCCTTTTCGGGCAAGGTCGTTTCTTATCTCGGCATGTGCATCAAGTCATATTGGACATCATTGATAGAGCGATGA


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 52

ACTTACGGAGGCAGTCATGCTTTGGCTCTCAGACGACCAGAGCTTTTGGGAAGAGGTTGAAGAAGGACCAAGGGCTCTGGGTCCGGTTGGACTTCAGCAGgtaatctcat ... tcctttccagTTCTACCTCGATATGCAATTTGTGATCCTTTTCGGGCAAGGTCGTTTCTTATCTCGGCATGTGCATCAAGTCATATTGGACATCATTGATAGAGCGATGA


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 45

ACTTACGGAGGCAGTCATGCTTTGGCTCTCAGACGACCAGAGCTTTTGGGAAGAGGTTGAAGAAGGACCAAGGGCTCTGGGTCCGGTTGGACTTCAGCAGgtaatctcat ... tcctttccagTTCTACCTCGATATGCAATTTGTGATCCTTTTCGGGCAAGGTCGTTTCTTATCTCGGCATGTGCATCAAGTCATATTGGACATCATTGATAGAGCGATGA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 56

ACTTACGGAGGCAGTCATGCTTTGGCTCTCAGACGACCAGAGCTTTTGGGAAGAGGTTGAAGAAGGACCAAGGGCTCTGGGTCCGGTTGGACTTCAGCAGgtaatctcat ... tcctttccagTTCTACCTCGATATGCAATTTGTGATCCTTTTCGGGCAAGGTCGTTTCTTATCTCGGCATGTGCATCAAGTCATATTGGACATCATTGATAGAGCGATGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcccaggccttcgcctgacagctgacattcccttttactttgccttcctttccagTTCTACCTCGATATGCAATTTGTGATCCTTTTCGGGCAAGGTCGTTTCTTATCTCGGCATGTGCATCAAGTCATATTGGACATCATTGATAGAGCGATGA
                   agctgac  putative branch site (score: 56)
                         cattcccttttacttt  CT-rich tract
                                ttttacttt  TA-rich tract