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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCCTGAACACCTCAAAGTGGATCGATGAAGTGCGCACCGAGAGAGGTGGCGATGTGATAATCGTGCTCGTTGGCAACAAAACTGATCTTGTCGACAAGAGgtcagcatcgtgatttgagctctcaagtttctttgtaggctagattcagagaaatatacagatggtgctactgctagcttgcaagctcgtgatcatttcgccttgttctacgcag

Basic information

species Zea mays
transcript GRMZM2G128771_T01
intron # 4
splice site 5'
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|149095335|gb|EE180972.2|EE180972
EST:     GATGTGATAATCGTGCTCGTTGGCAACAAAACTGATCTTGTCGACAAGAG                         ACAAGTGTCCACAGAAGAAGGAGAGAGCAAGGCAAAAGAATTGAATGTCAT
genomic: GATGTGATAATCGTGCTCGTTGGCAACAAAACTGATCTTGTCGACAAGAGgtcagcatcg ... ttctacgcagACAAGTGTCCACAGAAGAAGGAGAGAGCAAGGCAAAAGAATTGAATGTCAT
EST: gi|37387848|gb|CF631126.1|CF631126
EST:     GATGTGATAATCGTGCTCGTTGGCAACAAAACTGATCTTGTCGACAAAAG                         ACAAGTGTCCACAGAAGAAGGAGAGAGCAAGGCAAAAGAATTGAATGTCAT
genomic: GATGTGATAATCGTGCTCGTTGGCAACAAAACTGATCTTGTCGACAAGAGgtcagcatcg ... ttctacgcagACAAGTGTCCACAGAAGAAGGAGAGAGCAAGGCAAAAGAATTGAATGTCAT
EST: gi|211492535|gb|FL462462.1|FL462462
EST:     GATGTGAAAATCGTGCTCGTTGGCAACAAAACTGATCTTGTCGACAAAAG                         ACAAGTGTCCACAGAAGAAGGAGAGAGCAAGGCAAAAGAATTGAATGTCAT
genomic: GATGTGATAATCGTGCTCGTTGGCAACAAAACTGATCTTGTCGACAAGAGgtcagcatcg ... ttctacgcagACAAGTGTCCACAGAAGAAGGAGAGAGCAAGGCAAAAGAATTGAATGTCAT
EST: gi|211435904|gb|FL357606.1|FL357606
EST:     GATGTGATAATCGTGCTCGTTGGCAACAAAACTGATCTTGTCGACAAAAG                         ACAAGTGTCCACAGAAGAAGGAGAGAGCAAGGCAAAAGAATTGAATGTCAT
genomic: GATGTGATAATCGTGCTCGTTGGCAACAAAACTGATCTTGTCGACAAGAGgtcagcatcg ... ttctacgcagACAAGTGTCCACAGAAGAAGGAGAGAGCAAGGCAAAAGAATTGAATGTCAT
EST: gi|37379915|gb|CF626729.1|CF626729
EST:     GATGTGATAATCGTGCTCGTTGGCAACAAAACTGATCTTGTCGACAAAAG                         ACAAGTGTCCACAGAAGAAGGAGAGAGCAAGGCAAAAGAATTGAATGTCAT
genomic: GATGTGATAATCGTGCTCGTTGGCAACAAAACTGATCTTGTCGACAAGAGgtcagcatcg ... ttctacgcagACAAGTGTCCACAGAAGAAGGAGAGAGCAAGGCAAAAGAATTGAATGTCAT
EST: gi|40335969|gb|CK370039.1|CK370039
EST:     GATGTGATAATCGTGCTCGTTGGCAACAAAACTGATCTTGTCGACAAAAG                         ACAAGTGTCCACAGAAGAAGGAGAGAGCAAGGCAAAAGAATTGAATGTCAT
genomic: GATGTGATAATCGTGCTCGTTGGCAACAAAACTGATCTTGTCGACAAGAGgtcagcatcg ... ttctacgcagACAAGTGTCCACAGAAGAAGGAGAGAGCAAGGCAAAAGAATTGAATGTCAT
EST: gi|211481374|gb|FL368109.1|FL368109
EST:     GATGTGATAATCGTGCTCGTTGGCAACAAAACTGATCTTGTCGACAAAAG                         ACAAGTGTCCACAGAAGAAGGAGAGAGCAAGGCAAAAGAATTGAATGTCAT
genomic: GATGTGATAATCGTGCTCGTTGGCAACAAAACTGATCTTGTCGACAAGAGgtcagcatcg ... ttctacgcagACAAGTGTCCACAGAAGAAGGAGAGAGCAAGGCAAAAGAATTGAATGTCAT
EST: gi|211492534|gb|FL462461.1|FL462461
EST:     GATGTGATAATCGTGCTCGTTGGCAACAAAACTGATCTTGTCGACAAAAG                         ACAAGTGTCCACAGAAGAAGGAGAGAGCAAGGCAAAAGAATTGAATGTCAT
genomic: GATGTGATAATCGTGCTCGTTGGCAACAAAACTGATCTTGTCGACAAGAGgtcagcatcg ... ttctacgcagACAAGTGTCCACAGAAGAAGGAGAGAGCAAGGCAAAAGAATTGAATGTCAT

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: 39 (upstream exon), 32 (downstream exon)
Score: 6

TCCTGAACACCTCAAAGTGGATCGATGAAGTGCGCACCGAGAGAGGTGGCGATGTGATAATCGTGCTCGTTGGCAACAAAACTGATCTTGTCGACAAGAGgtcagcatcg ... ttctacgcagACAAGTGTCCACAGAAGAAGGAGAGAGCAAGGCAAAAGAATTGAATGTCATGTTCATCGAGACCAGCGCGAAAGCCGGCTTCAACATCAAG


Block sizes: 27 (upstream exon), 36 (downstream exon)
Score: 4

TCCTGAACACCTCAAAGTGGATCGATGAAGTGCGCACCGAGAGAGGTGGCGATGTGATAATCGTGCTCGTTGGCAACAAAACTGATCTTGTCGACAAGAGgtcagcatcg ... ttctacgcagACAAGTGTCCACAGAAGAAGGAGAGAGCAAGGCAAAAGAATTGAATGTCATGTTCATCGAGACCAGCGCGAAAGCCGGCTTCAACATCAAG


Block sizes: 42 (upstream exon), 49 (downstream exon)
Score: 9

TCCTGAACACCTCAAAGTGGATCGATGAAGTGCGCACCGAGAGAGGTGGCGATGTGATAATCGTGCTCGTTGGCAACAAAACTGATCTTGTCGACAAGAGgtcagcatcg ... ttctacgcagACAAGTGTCCACAGAAGAAGGAGAGAGCAAGGCAAAAGAATTGAATGTCATGTTCATCGAGACCAGCGCGAAAGCCGGCTTCAACATCAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 217

TCCTGAACACCTCAAAGTGGATCGATGAAGTGCGCACCGAGAGAGGTGGCGATGTGATAATCGTGCTCGTTGGCAACAAAACTGATCTTGTCGACAAGAGgtcagcatcg ... ttctacgcagACAAGTGTCCACAGAAGAAGGAGAGAGCAAGGCAAAAGAATTGAATGTCATGTTCATCGAGACCAGCGCGAAAGCCGGCTTCAACATCAAG