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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atgaccattgaacaattaatttcaatgttaagtggatgcacaaaaacatgttttttacttttaatcatttcgatgctcatgatctgaacacatatttcagGATTCAGAGTTACTAGAACAGATAGACCGAGATGTAAAGCGAACACATCCTGATATTTCATTTTTCTCATCAAAGTCTAACCAG

Basic information

species Zea mays
transcript GRMZM2G122935_T01
intron # 4
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|78110295|gb|DV528710.1|DV528710
EST:     AGCATCCTTTAAGCTCTGGTAAATCTAGCCTGTGGAACCAATATTTTCAG                         GATTCAGAGTTACTAGAACAGATAGACCGAGATGTAAAGCGAACACATCCT
genomic: AGCATCCTTTAAGCTCTGGTAAATCTAGCCTGTGGAACCAATATTTTCAGgtactgttct ... catatttcagGATTCAGAGTTACTAGAACAGATAGACCGAGATGTAAAGCGAACACATCCT
EST: gi|76017397|gb|DT944567.1|DT944567
EST:     AGCATCCTTTAAGCTCTGGTAAATCTAGCCTGTGGAACCAATATTTTCAG                         GATTCAGAGTTACTAGAACAGATAGACCGAGATGTAAAGCGAACACATCCT
genomic: AGCATCCTTTAAGCTCTGGTAAATCTAGCCTGTGGAACCAATATTTTCAGgtactgttct ... catatttcagGATTCAGAGTTACTAGAACAGATAGACCGAGATGTAAAGCGAACACATCCT

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: 48 (upstream exon), 48 (downstream exon)
Score: 72

AAGTATTGAGAGGATTGGCTTTCTTTCGAGATTCGAAGTTACTAATGAAGAGCATCCTTTAAGCTCTGGTAAATCTAGCCTGTGGAACCAATATTTTCAGgtactgttct ... catatttcagGATTCAGAGTTACTAGAACAGATAGACCGAGATGTAAAGCGAACACATCCTGATATTTCATTTTTCTCATCAAAGTCTAACCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 80

AAGTATTGAGAGGATTGGCTTTCTTTCGAGATTCGAAGTTACTAATGAAGAGCATCCTTTAAGCTCTGGTAAATCTAGCCTGTGGAACCAATATTTTCAGgtactgttct ... catatttcagGATTCAGAGTTACTAGAACAGATAGACCGAGATGTAAAGCGAACACATCCTGATATTTCATTTTTCTCATCAAAGTCTAACCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 65

AAGTATTGAGAGGATTGGCTTTCTTTCGAGATTCGAAGTTACTAATGAAGAGCATCCTTTAAGCTCTGGTAAATCTAGCCTGTGGAACCAATATTTTCAGgtactgttct ... catatttcagGATTCAGAGTTACTAGAACAGATAGACCGAGATGTAAAGCGAACACATCCTGATATTTCATTTTTCTCATCAAAGTCTAACCAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 49

AAGTATTGAGAGGATTGGCTTTCTTTCGAGATTCGAAGTTACTAATGAAGAGCATCCTTTAAGCTCTGGTAAATCTAGCCTGTGGAACCAATATTTTCAGgtactgttct ... catatttcagGATTCAGAGTTACTAGAACAGATAGACCGAGATGTAAAGCGAACACATCCTGATATTTCATTTTTCTCATCAAAGTCTAACCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acatgttttttacttttaatcatttcgatgctcatgatctgaacacatatttcagGATTCAGAGTTACTAGAACAGATAGACCGAGATGTAAAGCGAACACATCCTGATATTTCATTTTTCTCATCAAAGTCTAACCAG
             ttttaat  putative branch site (score: 49)
     ttttttacttttaatc  TA-rich tract