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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgttttcacagttctttaattcttccgttcagaagtcttggcaccacttggttccaacactagcttttcacctcacgtttcttctgcaccatgcagACTTTGGACGAGATACCACTTGACGCAGAGGCAGTAGAGAGGGGTGGATACTCCCTGGATTCTGATGCGATTGGTCTGCCAAGGGCCCATGGGCTTTCTT

Basic information

species Zea mays
transcript GRMZM2G129155_T01
intron # 19
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|5847452|gb|AW000531.1|AW000531
EST:     AGAGGAAGCAGATACGTGAAAATCTCAAGGTCCTTCAACAAGCTTACAAA                         ACTTTGGACGAGATACCACTTGACGCAGAGGCAGTAGAGAGGGGTGGATAC
genomic: AGAGGAAGCAGATACGTGAAAATCTCAAGGTCCTTCAACAAGCTTACAAAgtacgttttc ... caccatgcagACTTTGGACGAGATACCACTTGACGCAGAGGCAGTAGAGAGGGGTGGATAC
EST: gi|211024339|gb|FL478389.1|FL478389
EST:     AGAGGAAGCAGATACGTGAAAATCTCAAGGTCCTTCAACAAGCTTACAAA                         ACTTTGGACGAGATACCACTTGACGCAGAGGCAGTAGAGAGGGGTGGATAC
genomic: AGAGGAAGCAGATACGTGAAAATCTCAAGGTCCTTCAACAAGCTTACAAAgtacgttttc ... caccatgcagACTTTGGACGAGATACCACTTGACGCAGAGGCAGTAGAGAGGGGTGGATAC
EST: gi|33100316|gb|CF060276.1|CF060276
EST:     TCTCAAGGTCCTTCAACAAGCTTACAAA                         ACTTTGGACGAGATACCACTTGACGCAGAGGCAGTAGAGAGGGGTGGATAC
genomic: TCTCAAGGTCCTTCAACAAGCTTACAAAgtacgttttc ... caccatgcagACTTTGGACGAGATACCACTTGACGCAGAGGCAGTAGAGAGGGGTGGATAC
EST: gi|5895668|gb|AW036914.1|AW036914
EST:     AGAGGAAGCAGATACGTGAAAATCTCAAGGTCCTTCAACAAGCTTACAAA                         ACTTTGGACGAGATACCACTTGACGCAGAGGCAGTAGAGAGGGGTGGATAC
genomic: AGAGGAAGCAGATACGTGAAAATCTCAAGGTCCTTCAACAAGCTTACAAAgtacgttttc ... caccatgcagACTTTGGACGAGATACCACTTGACGCAGAGGCAGTAGAGAGGGGTGGATAC
EST: gi|88758145|gb|DY542286.1|DY542286
EST:     AGAGGAAGCAGATACGTGAAAATCTCAAGGTCCTTCAACAAGCTTACAAA                         ACTTTGGACGAGATACCACTTGACGCAGAGGCAGTAGAGAGGGGTGGATAC
genomic: AGAGGAAGCAGATACGTGAAAATCTCAAGGTCCTTCAACAAGCTTACAAAgtacgttttc ... caccatgcagACTTTGGACGAGATACCACTTGACGCAGAGGCAGTAGAGAGGGGTGGATAC
EST: gi|33097482|gb|CF057442.1|CF057442
EST:     AGAGGAAGCAGATACGTGAAAATCTCAAGGTCCTTCAACAAGCTTACAAA                         ACTTTGGACGAGATACCACTTGACGCAGAGGCAGTAGAGAGGGGTGGATAC
genomic: AGAGGAAGCAGATACGTGAAAATCTCAAGGTCCTTCAACAAGCTTACAAAgtacgttttc ... caccatgcagACTTTGGACGAGATACCACTTGACGCAGAGGCAGTAGAGAGGGGTGGATAC
EST: gi|32828402|gb|CD968080.1|CD968080
EST:     AGAGGAAGCAGATACGTGAAAATCTCAAGGTCCTTCAACAAGCTTACAAA                         ACTTTGGACGAGATACCACTTGACGCAGAGGCAGTAGAGAGGGGTGGATAC
genomic: AGAGGAAGCAGATACGTGAAAATCTCAAGGTCCTTCAACAAGCTTACAAAgtacgttttc ... caccatgcagACTTTGGACGAGATACCACTTGACGCAGAGGCAGTAGAGAGGGGTGGATAC
EST: gi|71448926|gb|DR829976.1|DR829976
EST:     ACAAGCTTACAAA                         ACTTTGGACGAGATACCACTTGACGCAGAGGCAGTAGAGAGGGGTGGATAC
genomic: ACAAGCTTACAAAgtacgttttc ... caccatgcagACTTTGGACGAGATACCACTTGACGCAGAGGCAGTAGAGAGGGGTGGATAC

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: 71

AGATGATCTTTTGGAAGACTTGCTCAAAGAACCTGATGAGATAACCATAAAGAGGAAGCAGATACGTGAAAATCTCAAGGTCCTTCAACAAGCTTACAAAgtacgttttc ... caccatgcagACTTTGGACGAGATACCACTTGACGCAGAGGCAGTAGAGAGGGGTGGATACTCCCTGGATTCTGATGCGATTGGTCTGCCAAGGGCCCATGGGCTTTCTT


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 105

AGATGATCTTTTGGAAGACTTGCTCAAAGAACCTGATGAGATAACCATAAAGAGGAAGCAGATACGTGAAAATCTCAAGGTCCTTCAACAAGCTTACAAAgtacgttttc ... caccatgcagACTTTGGACGAGATACCACTTGACGCAGAGGCAGTAGAGAGGGGTGGATACTCCCTGGATTCTGATGCGATTGGTCTGCCAAGGGCCCATGGGCTTTCTT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 128

AGATGATCTTTTGGAAGACTTGCTCAAAGAACCTGATGAGATAACCATAAAGAGGAAGCAGATACGTGAAAATCTCAAGGTCCTTCAACAAGCTTACAAAgtacgttttc ... caccatgcagACTTTGGACGAGATACCACTTGACGCAGAGGCAGTAGAGAGGGGTGGATACTCCCTGGATTCTGATGCGATTGGTCTGCCAAGGGCCCATGGGCTTTCTT


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 109

AGATGATCTTTTGGAAGACTTGCTCAAAGAACCTGATGAGATAACCATAAAGAGGAAGCAGATACGTGAAAATCTCAAGGTCCTTCAACAAGCTTACAAAgtacgttttc ... caccatgcagACTTTGGACGAGATACCACTTGACGCAGAGGCAGTAGAGAGGGGTGGATACTCCCTGGATTCTGATGCGATTGGTCTGCCAAGGGCCCATGGGCTTTCTT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caccacttggttccaacactagcttttcacctcacgtttcttctgcaccatgcagACTTTGGACGAGATACCACTTGACGCAGAGGCAGTAGAGAGGGGTGGATACTCCCTGGATTCTGATGCGATTGGTCTGCCAAGGGCCCATGGGCTTTCTT
                            acctcac  putative branch site (score: 109)
                                    tttcttctgc  CT-rich tract