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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacaatccttcacatcacatgtgacctttctccttgagtattctctccacaagcgcatttttacggatgtgccttcttattgacgcctttgaccatatactgtaccagCTGAGAGGTTTCGAGTTTGCTAAAGCGGTTACTCTTGTTGCTGAGCCGTTCACATTGGATAATGGCCTTCTCACCCCAACATTCAAG

Basic information

species Zea mays
transcript GRMZM2G059381_T01
intron # 21
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|60399365|gb|DN232179.1|DN232179
EST:     CAACAGCTGCTGTCCTGGCTGATATGGATTCCATTGCGAAGGAAGCACAG                         CTGAGAGGTTTCGAGTTTGCTAAAGCGGTTACTCTTGTTGCTGAGCCGTTC
genomic: CAACAGCTGCTGTCCTGGCTGATATGGATTCCATTGCGAAGGAAGCACAGgtacaatcct ... actgtaccagCTGAGAGGTTTCGAGTTTGCTAAAGCGGTTACTCTTGTTGCTGAGCCGTTC
EST: gi|60395514|gb|DN228384.1|DN228384
EST:     CAACAGCTGCTGTCCTGGCTGATATGGATTCCATTGCGAAGGAAGCACAG                         CTGAGAGGTTTCGAGTTTGCTAAAGCGGTTACTCTTGTTGCTGAGCCATTC
genomic: CAACAGCTGCTGTCCTGGCTGATATGGATTCCATTGCGAAGGAAGCACAGgtacaatcct ... actgtaccagCTGAGAGGTTTCGAGTTTGCTAAAGCGGTTACTCTTGTTGCTGAGCCGTTC
EST: gi|93283329|gb|EB675593.1|EB675593
EST:     CAACAGCTGCTGTCCTGGCTGATATGGATTCCATTGCGAAGGAAGCACAG                         CTGAGAGGTTTCGAGTTTGCTAAAGCGGTTACTCTTGTTGCTGAGCCGTTC
genomic: CAACAGCTGCTGTCCTGGCTGATATGGATTCCATTGCGAAGGAAGCACAGgtacaatcct ... actgtaccagCTGAGAGGTTTCGAGTTTGCTAAAGCGGTTACTCTTGTTGCTGAGCCGTTC

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: 100

TACGAGGACTTGAGACAGCTCTGTGCTGATCCTAGAGCAACAGCTGCTGTCCTGGCTGATATGGATTCCATTGCGAAGGAAGCACAGgtacaatcct ... actgtaccagCTGAGAGGTTTCGAGTTTGCTAAAGCGGTTACTCTTGTTGCTGAGCCGTTCACATTGGATAATGGCCTTCTCACCCCAACATTCAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 274

TACGAGGACTTGAGACAGCTCTGTGCTGATCCTAGAGCAACAGCTGCTGTCCTGGCTGATATGGATTCCATTGCGAAGGAAGCACAGgtacaatcct ... actgtaccagCTGAGAGGTTTCGAGTTTGCTAAAGCGGTTACTCTTGTTGCTGAGCCGTTCACATTGGATAATGGCCTTCTCACCCCAACATTCAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 79

TACGAGGACTTGAGACAGCTCTGTGCTGATCCTAGAGCAACAGCTGCTGTCCTGGCTGATATGGATTCCATTGCGAAGGAAGCACAGgtacaatcct ... actgtaccagCTGAGAGGTTTCGAGTTTGCTAAAGCGGTTACTCTTGTTGCTGAGCCGTTCACATTGGATAATGGCCTTCTCACCCCAACATTCAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 295

TACGAGGACTTGAGACAGCTCTGTGCTGATCCTAGAGCAACAGCTGCTGTCCTGGCTGATATGGATTCCATTGCGAAGGAAGCACAGgtacaatcct ... actgtaccagCTGAGAGGTTTCGAGTTTGCTAAAGCGGTTACTCTTGTTGCTGAGCCGTTCACATTGGATAATGGCCTTCTCACCCCAACATTCAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgcatttttacggatgtgccttcttattgacgcctttgaccatatactgtaccagCTGAGAGGTTTCGAGTTTGCTAAAGCGGTTACTCTTGTTGCTGAGCCGTTCACATTGGATAATGGCCTTCTCACCCCAACATTCAAG
                    ttcttatt  TA-rich tract