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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgcccaggggccgcgattcttttttttttccgtattccgaattccagtcccaatcccaatccagtgtgtgtgtgtgtgtgtcagtcagtgtgtgcctccttaaacctcactgacgattcttcgttcatgtctccctcgcccagGGGCCGCAAGAGGGCCTGCGTCACCTATTGCATCAGCTACATCCTCAGCTGCATCACCAAGCACTCCCCCGAGTACAGGGTCCTCATGATCGGCCGCATC

Basic information

species Zea mays
transcript GRMZM2G064563_T03
intron # 2
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|149105632|gb|EE291180.2|EE291180
EST:     GGATCCTCCATGCTCTTCGGCACCATCGTCGGCTCCCTCGCCGACAAACA                         GGGCCGCAAGAGGGCCTGCGTCACCTATTGCATCAGCTACATCCTCAGCTG
genomic: GGATCCTCCATGCTCTTCGGCACCATCGTCGGCTCCCTCGCCGACAAACAgtacgcccag ... cctcgcccagGGGCCGCAAGAGGGCCTGCGTCACCTATTGCATCAGCTACATCCTCAGCTG
EST: gi|211429139|gb|FL408429.1|FL408429
EST:     GGATCCTCCATGCTCTTCGGCACCATCGTCGGCTCCCTCGCCGACAAACA                         GGGCCGCAAGAGGGCCTGCGTCACCTATTGCATCAGCTACATCCTCAGCTG
genomic: GGATCCTCCATGCTCTTCGGCACCATCGTCGGCTCCCTCGCCGACAAACAgtacgcccag ... cctcgcccagGGGCCGCAAGAGGGCCTGCGTCACCTATTGCATCAGCTACATCCTCAGCTG
EST: gi|211385926|gb|FL097275.1|FL097275
EST:     GGATCCTCCATGCTCTTCGGCACCATCGTCGGCTCCCTCGCCGACAAACA                         GGGCCGCAAGAGGGCCTGCGTCACCTATTGCATCAGCTACATCCTCAGCTG
genomic: GGATCCTCCATGCTCTTCGGCACCATCGTCGGCTCCCTCGCCGACAAACAgtacgcccag ... cctcgcccagGGGCCGCAAGAGGGCCTGCGTCACCTATTGCATCAGCTACATCCTCAGCTG
EST: gi|32802659|gb|CD954895.1|CD954895
EST:     GATCCTCCATGCTCTTCGGCACCATCGTCGGCTCCCTCGCCGACAAACA                         GGGCCGCAAGAGGGCCTGCGTTACCTACTGCATCAGCTACATCCTCAGCTG
genomic: GATCCTCCATGCTCTTCGGCACCATCGTCGGCTCCCTCGCCGACAAACAgtacgcccag ... cctcgcccagGGGCCGCAAGAGGGCCTGCGTCACCTATTGCATCAGCTACATCCTCAGCTG
EST: gi|211344703|gb|FL214763.1|FL214763
EST:     GGATCCTCCATGCTCTTCGGCACCATCGTCGGCTCCCTCGCCGACAAACA                         GGGCCGCAAGAGGGCCTGCGTCACCTATTGCATCAGCTACATCCTCAGCTG
genomic: GGATCCTCCATGCTCTTCGGCACCATCGTCGGCTCCCTCGCCGACAAACAgtacgcccag ... cctcgcccagGGGCCGCAAGAGGGCCTGCGTCACCTATTGCATCAGCTACATCCTCAGCTG
EST: gi|211383298|gb|FL097268.1|FL097268
EST:     GGATCCTCCATGCTCTTCGGCACCATCGTCGGCTCCCTCGCCGACAAACA                         GGGCCGCAAGAGGGCCTGCGTCACCTATTGCATCAGCTACATCCTCAGCTG
genomic: GGATCCTCCATGCTCTTCGGCACCATCGTCGGCTCCCTCGCCGACAAACAgtacgcccag ... cctcgcccagGGGCCGCAAGAGGGCCTGCGTCACCTATTGCATCAGCTACATCCTCAGCTG
EST: gi|149086869|gb|EE176413.2|EE176413
EST:     GGATCCTCCATGCTCTTCGGCACCATCGTCGGCTCCCTCGCCGACAAACA                         GGGCCGCAAGAGGGCCTGCGTCACCTATTGCATCAGCTACATCCTCAGCTG
genomic: GGATCCTCCATGCTCTTCGGCACCATCGTCGGCTCCCTCGCCGACAAACAgtacgcccag ... cctcgcccagGGGCCGCAAGAGGGCCTGCGTCACCTATTGCATCAGCTACATCCTCAGCTG
EST: gi|211385929|gb|FL097278.1|FL097278
EST:     GGATCCTCCATGCTCTTCGGCACCATCGTCGGCTCCCTCGCCGACAAACA                         GGGCCGCAAGAGGGCCTGCGTCACCTATTGCATCAGCTACATCCTCAGCTG
genomic: GGATCCTCCATGCTCTTCGGCACCATCGTCGGCTCCCTCGCCGACAAACAgtacgcccag ... cctcgcccagGGGCCGCAAGAGGGCCTGCGTCACCTATTGCATCAGCTACATCCTCAGCTG
EST: gi|93012444|gb|EB637964.1|EB637964
EST:     GGATCCTCCATGCTCTTCGGCACCATCGTCGGCTCCCTCGCCGACAAACA                         GGGCCGCAAGAGGGCCTGCGTCACCTATTGCATCAGCTACATCCTCAGCTG
genomic: GGATCCTCCATGCTCTTCGGCACCATCGTCGGCTCCCTCGCCGACAAACAgtacgcccag ... cctcgcccagGGGCCGCAAGAGGGCCTGCGTCACCTATTGCATCAGCTACATCCTCAGCTG
EST: gi|211344698|gb|FL214758.1|FL214758
EST:     GGATCCTCCATGCTCTTCGGCACCATCGTCGGCTCCCTCGCCGACAAACA                         GGGCCGCAAGAGGGCCTGCGTCACCTATTGCATCAGCTACATCCTCAGCTG
genomic: GGATCCTCCATGCTCTTCGGCACCATCGTCGGCTCCCTCGCCGACAAACAgtacgcccag ... cctcgcccagGGGCCGCAAGAGGGCCTGCGTCACCTATTGCATCAGCTACATCCTCAGCTG
EST: gi|87156350|gb|DY401139.1|DY401139
EST:     GGATCCTCCATGCTCTTCGGCACCATCGTCGGCTCCCTCGCCGACAAACA                         GGGCCGCAAGAGGGCCTGCGTCACCTATTGCATCAGCTACATCCTCAGCTG
genomic: GGATCCTCCATGCTCTTCGGCACCATCGTCGGCTCCCTCGCCGACAAACAgtacgcccag ... cctcgcccagGGGCCGCAAGAGGGCCTGCGTCACCTATTGCATCAGCTACATCCTCAGCTG
EST: gi|101390561|gb|EB817215.1|EB817215
EST:     GGATCCTCCATGCTCTTCGGCACCATCGTCGGCTCCCTCGCCGACAAACA                         GGGCCGCAAGAGGGCCTGCGTCACCTATTGCATCAGCTACATCCTCAGCTG
genomic: GGATCCTCCATGCTCTTCGGCACCATCGTCGGCTCCCTCGCCGACAAACAgtacgcccag ... cctcgcccagGGGCCGCAAGAGGGCCTGCGTCACCTATTGCATCAGCTACATCCTCAGCTG
EST: gi|211383301|gb|FL097271.1|FL097271
EST:     GGATCCTCCATGCTCTTCGGCACCATCGTCGGCTCCCTCGCCGACAAACA                         GGGCCGCAAGAGGGCCTGCGTCACCTATTGCATCAGCTACATCCTCAGCTG
genomic: GGATCCTCCATGCTCTTCGGCACCATCGTCGGCTCCCTCGCCGACAAACAgtacgcccag ... cctcgcccagGGGCCGCAAGAGGGCCTGCGTCACCTATTGCATCAGCTACATCCTCAGCTG
EST: gi|32804659|gb|CD956895.1|CD956895
EST:     GATCCCCCATGCTCTTCGGCACCATCGTCGGCTCCCTCGCCGACAAACA                         GGGCCGCAAGAGGGCCTGCGTTACCTACTGCATCAGCTACATCCTCAGCTG
genomic: GATCCTCCATGCTCTTCGGCACCATCGTCGGCTCCCTCGCCGACAAACAgtacgcccag ... cctcgcccagGGGCCGCAAGAGGGCCTGCGTCACCTATTGCATCAGCTACATCCTCAGCTG
EST: gi|211383297|gb|FL097267.1|FL097267
EST:     GGATCCTCCATGCTCTTCGGCACCATCGTCGGCTCCCTCGCCGACAAACA                         GGGCCGCAAGAGGGCCTGCGTCACCTATT
genomic: GGATCCTCCATGCTCTTCGGCACCATCGTCGGCTCCCTCGCCGACAAACAgtacgcccag ... cctcgcccagGGGCCGCAAGAGGGCCTGCGTCACCTATT
EST: gi|211383300|gb|FL097270.1|FL097270
EST:     GGATCCTCCATGCTCTTCGGCACCATCGTCGGCTCCCTCGCCGACAAACA                         GGGCCGCAAGAGGGCCTGCGTCACCTATTGCATCAGCTACATCCTCAGCTG
genomic: GGATCCTCCATGCTCTTCGGCACCATCGTCGGCTCCCTCGCCGACAAACAgtacgcccag ... cctcgcccagGGGCCGCAAGAGGGCCTGCGTCACCTATTGCATCAGCTACATCCTCAGCTG
EST: gi|148971109|gb|EE021954.2|EE021954
EST:     GGATCCTCCATGCTCTTCGGCACCATCGTCGGCTCCCTCGCCGACAAACA                         GGGCCGCAAGAGGGCCTGCGTCACCTATTGCATCAGCTACATCCTCAGCTG
genomic: GGATCCTCCATGCTCTTCGGCACCATCGTCGGCTCCCTCGCCGACAAACAgtacgcccag ... cctcgcccagGGGCCGCAAGAGGGCCTGCGTCACCTATTGCATCAGCTACATCCTCAGCTG
EST: gi|149071690|gb|EE160082.2|EE160082
EST:     GGATCCTCCATGCTCTTCGGCACCATCGTCGGCTCCCTCGCCGACAAACA                         GGGCCGCAAGAGGGCCTGCGTCACCTATTGCATCAGCTACATCCTCAGCTG
genomic: GGATCCTCCATGCTCTTCGGCACCATCGTCGGCTCCCTCGCCGACAAACAgtacgcccag ... cctcgcccagGGGCCGCAAGAGGGCCTGCGTCACCTATTGCATCAGCTACATCCTCAGCTG
EST: gi|211344704|gb|FL214764.1|FL214764
EST:     GGATCCTCCATGCTCTTCGGCACCATCGTCGGCTCCCTCGCCGACAAACA                         GGGCCGCAAGAGGGCCTGCGTCACCTATTGCATCAGCTACATCCTCAGCTG
genomic: GGATCCTCCATGCTCTTCGGCACCATCGTCGGCTCCCTCGCCGACAAACAgtacgcccag ... cctcgcccagGGGCCGCAAGAGGGCCTGCGTCACCTATTGCATCAGCTACATCCTCAGCTG

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), 48 (downstream exon)
Score: 81

AGTATGGCTTCGACAAGGGCGACATCGGCCGCCTCTTCATCGCCGGCTTCGGATCCTCCATGCTCTTCGGCACCATCGTCGGCTCCCTCGCCGACAAACAgtacgcccag ... cctcgcccagGGGCCGCAAGAGGGCCTGCGTCACCTATTGCATCAGCTACATCCTCAGCTGCATCACCAAGCACTCCCCCGAGTACAGGGTCCTCATGATCGGCCGCATC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 36

AGTATGGCTTCGACAAGGGCGACATCGGCCGCCTCTTCATCGCCGGCTTCGGATCCTCCATGCTCTTCGGCACCATCGTCGGCTCCCTCGCCGACAAACAgtacgcccag ... cctcgcccagGGGCCGCAAGAGGGCCTGCGTCACCTATTGCATCAGCTACATCCTCAGCTGCATCACCAAGCACTCCCCCGAGTACAGGGTCCTCATGATCGGCCGCATC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 154

AGTATGGCTTCGACAAGGGCGACATCGGCCGCCTCTTCATCGCCGGCTTCGGATCCTCCATGCTCTTCGGCACCATCGTCGGCTCCCTCGCCGACAAACAgtacgcccag ... cctcgcccagGGGCCGCAAGAGGGCCTGCGTCACCTATTGCATCAGCTACATCCTCAGCTGCATCACCAAGCACTCCCCCGAGTACAGGGTCCTCATGATCGGCCGCATC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 116

AGTATGGCTTCGACAAGGGCGACATCGGCCGCCTCTTCATCGCCGGCTTCGGATCCTCCATGCTCTTCGGCACCATCGTCGGCTCCCTCGCCGACAAACAgtacgcccag ... cctcgcccagGGGCCGCAAGAGGGCCTGCGTCACCTATTGCATCAGCTACATCCTCAGCTGCATCACCAAGCACTCCCCCGAGTACAGGGTCCTCATGATCGGCCGCATC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtgtgcctccttaaacctcactgacgattcttcgttcatgtctccctcgcccagGGGCCGCAAGAGGGCCTGCGTCACCTATTGCATCAGCTACATCCTCAGCTGCATCACCAAGCACTCCCCCGAGTACAGGGTCCTCATGATCGGCCGCATC
                   cactgac  putative branch site (score: 116)
                            ttcttcgttcatgtct  putative PPT
           ttaaa  TA-rich tract