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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagaacacagcaagacttgcaatttcattattttggatttgcattcatgttgcatttacaatttgtagcaagttcatctagtctgattctttaacttgtgcaatgtgttaatctcctgctacctctaatccagCATATATTAGATAGCTTTGGTTTTCGGAAGCAGCATTTCCCCCTACATGCGACCCAATTAGATTGCTTATTGGTACTCGGGTTGGACAAGGATTAATAGG

Basic information

species Zea mays
transcript GRMZM2G097726_T01
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|18450467|gb|BM428745.1|BM428745
EST:     CCAGATCG-ATAGCAG-                         CATATATTAGATAGCTTTGGTTTTCGGAAGCAGCATTTCCCCCTACATGCG
genomic: CCAGATCGTATAGCAGTgtaagaacac ... tctaatccagCATATATTAGATAGCTTTGGTTTTCGGAAGCAGCATTTCCCCCTACATGCG
EST: gi|19822612|gb|BQ048636.1|BQ048636
EST:     TTCGAGTATAAATCAGCTACTGGCAGCTTTGTACCAGATCGTATAGCAGT                         CATATATTAGATAGCTTTGGTTTTCGGAAGCAGCATTTCCCCCTACATGCG
genomic: TTCGAGTATAAATCAGCTACTGGCAGCTTTGTACCAGATCGTATAGCAGTgtaagaacac ... tctaatccagCATATATTAGATAGCTTTGGTTTTCGGAAGCAGCATTTCCCCCTACATGCG
EST: gi|18648816|gb|BM497635.1|BM497635
EST:     TTCGAGTATAAATCAGCTACTGGCAGCTTTGTACCAGATCGTATAGCAGT                         CATATATTAGATAGCTTTGGTTTTCGGAAGCAGCATTTCCCCCTACATGCG
genomic: TTCGAGTATAAATCAGCTACTGGCAGCTTTGTACCAGATCGTATAGCAGTgtaagaacac ... tctaatccagCATATATTAGATAGCTTTGGTTTTCGGAAGCAGCATTTCCCCCTACATGCG
EST: gi|18649546|gb|BM498365.1|BM498365
EST:     TCGAGTATAAATCAGCTACTGGCAGGTTTGGAACCAGATCGTATAGCAGT                         CATATATTAGATAGCTTTGGTTTTCGGAAGCAGCATTTCCCCCTACATGCG
genomic: TCGAGTATAAATCAGCTACTGGCAGCTTT-GTACCAGATCGTATAGCAGTgtaagaacac ... tctaatccagCATATATTAGATAGCTTTGGTTTTCGGAAGCAGCATTTCCCCCTACATGCG
EST: gi|18649399|gb|BM498218.1|BM498218
EST:     TTCGAGTATAAATCAGCTACTGGCAGCTTTGTACCAGATCGTATAGCAGT                         CATATATTAGATAGCTTTGGTTTTCGGAAGCAGCATTTCCCCCTACATGCG
genomic: TTCGAGTATAAATCAGCTACTGGCAGCTTTGTACCAGATCGTATAGCAGTgtaagaacac ... tctaatccagCATATATTAGATAGCTTTGGTTTTCGGAAGCAGCATTTCCCCCTACATGCG
EST: gi|18649290|gb|BM498109.1|BM498109
EST:     TTCGAGTATAAATCAGCTACTGGCAGCTTTGTACCAGATCGTATAGCAGC                         CATATATTAGATAGCTTTGGTTTTCGGAAGCTGCTTTTCCCCCTACATGCG
genomic: TTCGAGTATAAATCAGCTACTGGCAGCTTTGTACCAGATCGTATAGCAGTgtaagaacac ... tctaatccagCATATATTAGATAGCTTTGGTTTTCGGAAGCAGCATTTCCCCCTACATGCG

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 1 RNA-Seqlibrary.


Block sizes: 14 (upstream exon), 36 (downstream exon)
Score: 4

GTAGCTATACAAAGCTTGATTCTGTCAATGCTGAGGATTTCTTCTGCCGCTTCGAGTATAAATCAGCTACTGGCAGCTTTGTACCAGATCGTATAGCAGTgtaagaacac ... tctaatccagCATATATTAGATAGCTTTGGTTTTCGGAAGCAGCATTTCCCCCTACATGCGACCCAATTAGATTGCTTATTGGTACTCGGGTTGGACAAGGATTAATAGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagtctgattctttaacttgtgcaatgtgttaatctcctgctacctctaatccagCATATATTAGATAGCTTTGGTTTTCGGAAGCAGCATTTCCCCCTACATGCGACCCAATTAGATTGCTTATTGGTACTCGGGTTGGACAAGGATTAATAGG
                                            ctctaat  putative branch site (score: 4)
                                 tctcctgctacctct  CT-rich tract
       attctttaa  TA-rich tract