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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATCTTCTTCACTGGGTCCTCCGCTGCTTCTAGTCACGCATCTAAATCCGGAGTTGCCAGCATTCGCTTGAGGTGCCGGACCACAGCACACCATCATGCAGgtgggtagtactggattatctctcttgattggttggcgcgtgatctgtattctatatgctgcggtactagaaattttcatttggttaaaaatggagaact...

Basic information

species Zea mays
transcript GRMZM2G121942_T03
intron # 2
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|211191930|gb|FL276018.1|FL276018
EST:     AGTTGCCAGCATTCGCTTGAGGTGCCGGACCACAGCACACCATCATGCAG                         GCTAGCGATAGGTTCAACATAAACTCTCAGCTTGAGCATCTTCAAGCCAAA
genomic: AGTTGCCAGCATTCGCTTGAGGTGCCGGACCACAGCACACCATCATGCAGgtgggtagta ... tatttgaaagGCTAGCGATAGGTTCAACATAAACTCTCAGCTTGAGCATCTTCAAGCCAAA
EST: gi|211194324|gb|FL276026.1|FL276026
EST:     AGTTGCCAGCATTCGCTTGAGGTGCCGGACCACAGCACACCATCATGCAG                         GCTAGCGATAGGTTCAACATAAACTCTCAGCTTGAGCATCTTCAAGCCAAA
genomic: AGTTGCCAGCATTCGCTTGAGGTGCCGGACCACAGCACACCATCATGCAGgtgggtagta ... tatttgaaagGCTAGCGATAGGTTCAACATAAACTCTCAGCTTGAGCATCTTCAAGCCAAA
EST: gi|211191923|gb|FL276011.1|FL276011
EST:     AGTTGCCAGCATTCGCTTGAGGTGCCGGACCACAGCACACCATCATGCAG                         GCTAGCGATAGGTTCAACATAAACTCTCAGCTTGAGCATCTTCAAGCCAAA
genomic: AGTTGCCAGCATTCGCTTGAGGTGCCGGACCACAGCACACCATCATGCAGgtgggtagta ... tatttgaaagGCTAGCGATAGGTTCAACATAAACTCTCAGCTTGAGCATCTTCAAGCCAAA
EST: gi|211191934|gb|FL276022.1|FL276022
EST:     AGTTGCCAGCATTCGCTTGAGGTGCCGGACCACAGCACACCATCATGCAG                         -C--G--ATAGGTTCAACATAAACTCTCAGCTTGAGCATCTTCAAGCCAAA
genomic: AGTTGCCAGCATTCGCTTGAGGTGCCGGACCACAGCACACCATCATGCAGgtgggtagta ... tatttgaaagGCTAGCGATAGGTTCAACATAAACTCTCAGCTTGAGCATCTTCAAGCCAAA
EST: gi|211194323|gb|FL276025.1|FL276025
EST:     AGTTGCCAGCATTCGCTTGAGGTGCCGGACCACAGCACACCATCATGCAG                         GCTAGCGATAGGTTCAACATAAACTCTCAGCTTGAGCATCTTCAAGCCAAA
genomic: AGTTGCCAGCATTCGCTTGAGGTGCCGGACCACAGCACACCATCATGCAGgtgggtagta ... tatttgaaagGCTAGCGATAGGTTCAACATAAACTCTCAGCTTGAGCATCTTCAAGCCAAA
EST: gi|211191922|gb|FL276010.1|FL276010
EST:     AGTTGCCAGCATTCGCTTGAGGTGCCGGACCACAGCACACCATCATGCAG                         GCTAGCGATAGGTTCAACATAAACTCTCAGCTTGAGCATCTTCAAGCCAAA
genomic: AGTTGCCAGCATTCGCTTGAGGTGCCGGACCACAGCACACCATCATGCAGgtgggtagta ... tatttgaaagGCTAGCGATAGGTTCAACATAAACTCTCAGCTTGAGCATCTTCAAGCCAAA
EST: gi|211359713|gb|FL342921.1|FL342921
EST:     AGTTGCCAGCATTCGCTTGAGGTGCCTGA-CAAAGCACACCATCATGCAG                         GCTAGCGATAGGTTCAACATAAACTCTCAGCTTGAGCATCTTCAAGCCAAA
genomic: AGTTGCCAGCATTCGCTTGAGGTGCCGGACCACAGCACACCATCATGCAGgtgggtagta ... tatttgaaagGCTAGCGATAGGTTCAACATAAACTCTCAGCTTGAGCATCTTCAAGCCAAA
EST: gi|211194325|gb|FL276027.1|FL276027
EST:     AGTTGCCAGCATTCGCTTGAGGTGCCGGACCACAGCACACCATCATGCAG                         GCTAGCGATAGGTTCAACATAAACTCTCAGCTTGAGCATCTTCAAGCCAAA
genomic: AGTTGCCAGCATTCGCTTGAGGTGCCGGACCACAGCACACCATCATGCAGgtgggtagta ... tatttgaaagGCTAGCGATAGGTTCAACATAAACTCTCAGCTTGAGCATCTTCAAGCCAAA
EST: gi|211088952|gb|FL225885.1|FL225885
EST:     AGTTGCCAGCATTCGCTTGAGGTGCCGGACCACAGCACACCATCATGCAG                         GCTAGCGATAGGTTCAACATAAACTCTCAGCTTGAGCATCTTCAAGCCAAA
genomic: AGTTGCCAGCATTCGCTTGAGGTGCCGGACCACAGCACACCATCATGCAGgtgggtagta ... tatttgaaagGCTAGCGATAGGTTCAACATAAACTCTCAGCTTGAGCATCTTCAAGCCAAA
EST: gi|211191933|gb|FL276021.1|FL276021
EST:     AGTTGCCAGCATTCGCTTGAGGTGCCGGACCACAGCACACCATCATGCAG                         GCTAGCGATAGGTTTCAACATAAACTCTCAGCTTGAGCATCTTCAAGCCAA
genomic: AGTTGCCAGCATTCGCTTGAGGTGCCGGACCACAGCACACCATCATGCAGgtgggtagta ... tatttgaaagGCTAGCGATAGGTT-CAACATAAACTCTCAGCTTGAGCATCTTCAAGCCAA
EST: gi|211191925|gb|FL276013.1|FL276013
EST:     AGTTGCCAGCATTCGCTTGAGGTGCCGGACCACAGCACACCATCATGCAG                         GCTAGCGATAGGTTCAACATAAACTCTCAGCTTGAGCATCTTCAAGCCAAA
genomic: AGTTGCCAGCATTCGCTTGAGGTGCCGGACCACAGCACACCATCATGCAGgtgggtagta ... tatttgaaagGCTAGCGATAGGTTCAACATAAACTCTCAGCTTGAGCATCTTCAAGCCAAA
EST: gi|211191928|gb|FL276016.1|FL276016
EST:     AGTTGCCAGCATTCGCTTGAGGTGCCGGACCACAGCACACCATCATGCAG                         GCTAGCGATAGGTTCAACATAAACTCTCAGCTTGAGCATCTTCAAGCCAAA
genomic: AGTTGCCAGCATTCGCTTGAGGTGCCGGACCACAGCACACCATCATGCAGgtgggtagta ... tatttgaaagGCTAGCGATAGGTTCAACATAAACTCTCAGCTTGAGCATCTTCAAGCCAAA
EST: gi|37387079|gb|CF630732.1|CF630732
EST:     AGTTGCCAGCATTCGCTTGAGGTGCCGGACCACAGCACACCATCATGCAG                         GCTAGCGATAGGTTCAACATAAACTCTCAGCTTGAGCATCTTCAAGCCAAA
genomic: AGTTGCCAGCATTCGCTTGAGGTGCCGGACCACAGCACACCATCATGCAGgtgggtagta ... tatttgaaagGCTAGCGATAGGTTCAACATAAACTCTCAGCTTGAGCATCTTCAAGCCAAA
EST: gi|211191926|gb|FL276014.1|FL276014
EST:     AGTTGCCAGCATTCGCTTGAGGTGCCGGACCACAGCACACCATCATGCAG                         GCTAGCGATAGGTTCAACATAAACTCTCAGCTTGAGCATCTTCAAGCCAAA
genomic: AGTTGCCAGCATTCGCTTGAGGTGCCGGACCACAGCACACCATCATGCAGgtgggtagta ... tatttgaaagGCTAGCGATAGGTTCAACATAAACTCTCAGCTTGAGCATCTTCAAGCCAAA
EST: gi|211194322|gb|FL276024.1|FL276024
EST:     AGTTGCCAGCATTCGCTTGAGGTGCCGGACCACAGCACACCATCATGCAG                         GCTAGCGATAGGTTCAACATAAACTCTCAGCTTGAGCATCTTCAAGCCAAA
genomic: AGTTGCCAGCATTCGCTTGAGGTGCCGGACCACAGCACACCATCATGCAGgtgggtagta ... tatttgaaagGCTAGCGATAGGTTCAACATAAACTCTCAGCTTGAGCATCTTCAAGCCAAA

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), 49 (downstream exon)
Score: 602

ATCTTCTTCACTGGGTCCTCCGCTGCTTCTAGTCACGCATCTAAATCCGGAGTTGCCAGCATTCGCTTGAGGTGCCGGACCACAGCACACCATCATGCAGgtgggtagta ... tatttgaaagGCTAGCGATAGGTTCAACATAAACTCTCAGCTTGAGCATCTTCAAGCCAAATATGTTGGTACAGGGCATGCTGATTTGTCTAGATT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 577

ATCTTCTTCACTGGGTCCTCCGCTGCTTCTAGTCACGCATCTAAATCCGGAGTTGCCAGCATTCGCTTGAGGTGCCGGACCACAGCACACCATCATGCAGgtgggtagta ... tatttgaaagGCTAGCGATAGGTTCAACATAAACTCTCAGCTTGAGCATCTTCAAGCCAAATATGTTGGTACAGGGCATGCTGATTTGTCTAGATT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 438

ATCTTCTTCACTGGGTCCTCCGCTGCTTCTAGTCACGCATCTAAATCCGGAGTTGCCAGCATTCGCTTGAGGTGCCGGACCACAGCACACCATCATGCAGgtgggtagta ... tatttgaaagGCTAGCGATAGGTTCAACATAAACTCTCAGCTTGAGCATCTTCAAGCCAAATATGTTGGTACAGGGCATGCTGATTTGTCTAGATT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 475

ATCTTCTTCACTGGGTCCTCCGCTGCTTCTAGTCACGCATCTAAATCCGGAGTTGCCAGCATTCGCTTGAGGTGCCGGACCACAGCACACCATCATGCAGgtgggtagta ... tatttgaaagGCTAGCGATAGGTTCAACATAAACTCTCAGCTTGAGCATCTTCAAGCCAAATATGTTGGTACAGGGCATGCTGATTTGTCTAGATT