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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgccgcccgtacgtcagaataatgcagtagcaggcagcagcagcaggcctaataattactaataaacctttgcagGGCGGGTCGGGGCTGGTGCAGGGCGTGAGGTTCTCGAACATCCAGGTCACGGAGGTGCAGACGCCCATCATGATAGACCAGTTCTACTGCGACAGGGCGA

Basic information

species Zea mays
transcript GRMZM2G002034_T02
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|6538974|gb|AW225113.1|AW225113
EST:     ATGTCAAGATGTTCAGGACAACGACGGGTGTCAGAATCAAGACATGGCAG                         GGCGGGTCGGGGCTGGTGCAGGGCGTGAGGTTCTCGAACATCCAGGTCACG
genomic: ATGTCAAGATGTTCAGGACAACGACGGGTGTCAGAATCAAGACATGGCAGgtacgccgcc ... acctttgcagGGCGGGTCGGGGCTGGTGCAGGGCGTGAGGTTCTCGAACATCCAGGTCACG
EST: gi|71760132|gb|DR958069.1|DR958069
EST:     ATGTCAAGATGTTCAGGACAACGACGGGTGTCAGAATCAAGACATGGCAG                         GGCGGGTCGGGGCTGGTGCAGGGCGTGAGGTTCTCGAACATCCAGGTCACG
genomic: ATGTCAAGATGTTCAGGACAACGACGGGTGTCAGAATCAAGACATGGCAGgtacgccgcc ... acctttgcagGGCGGGTCGGGGCTGGTGCAGGGCGTGAGGTTCTCGAACATCCAGGTCACG
EST: gi|89763933|gb|DY690920.1|DY690920
EST:     GACGGGTGTCAGAATCAAGACATGGCAG                         GGCGGGTCGGGGCTGGTGCAGGGCGTGAGGTTCTCGAACATCCAGGTCACG
genomic: GACGGGTGTCAGAATCAAGACATGGCAGgtacgccgcc ... acctttgcagGGCGGGTCGGGGCTGGTGCAGGGCGTGAGGTTCTCGAACATCCAGGTCACG
EST: gi|94475995|gb|EB704953.1|EB704953
EST:     ATGTCAAGATGTTCAGGACAACGACGGGTGTCAGAATCAAGACATGGCAG                         GGCGGGTCGGGGCTGGTGCAGGGCGTGAGGTTCTCGAACATCCAGGTCACG
genomic: ATGTCAAGATGTTCAGGACAACGACGGGTGTCAGAATCAAGACATGGCAGgtacgccgcc ... acctttgcagGGCGGGTCGGGGCTGGTGCAGGGCGTGAGGTTCTCGAACATCCAGGTCACG
EST: gi|37384129|gb|CF629114.1|CF629114
EST:     ATGTCAAGATGTTCAGGACAACGACGGGTGTCAGAATCAAGACATGGCAG                         GGCGGGTCGGGGCTGGTGCAGGGCGTGAGGTTCTCGAACATCCAGGTCACG
genomic: ATGTCAAGATGTTCAGGACAACGACGGGTGTCAGAATCAAGACATGGCAGgtacgccgcc ... acctttgcagGGCGGGTCGGGGCTGGTGCAGGGCGTGAGGTTCTCGAACATCCAGGTCACG
EST: gi|74238758|gb|DT646672.1|DT646672
EST:     CAGAATCAAGACATGGCAG                         GGCGGGTCGGGGCTGGTGCAGGGCGTGAGGTTCTCGAACATCCAGGTCACG
genomic: CAGAATCAAGACATGGCAGgtacgccgcc ... acctttgcagGGCGGGTCGGGGCTGGTGCAGGGCGTGAGGTTCTCGAACATCCAGGTCACG
EST: gi|76285053|gb|DV024621.1|DV024621
EST:     ATGTCAAGATGTTCAGGACAACGACGGGTGTCAGAATCAAGACATGGCAG                         GGCGGGTCGGGGCTGGTGCAGGGCGTGAGGTTCTCGAACATCCAGGTCACG
genomic: ATGTCAAGATGTTCAGGACAACGACGGGTGTCAGAATCAAGACATGGCAGgtacgccgcc ... acctttgcagGGCGGGTCGGGGCTGGTGCAGGGCGTGAGGTTCTCGAACATCCAGGTCACG
EST: gi|88748834|gb|DY532975.1|DY532975
EST:     ATGTCAAGATGTTCAGGACAACGACGGGTGTCAGAATCAAGACATGGCAG                         GGCGGGTCGGGGCTGGTGCAGGGCGTGAGGTTCTCGAACATCCAGGTCACG
genomic: ATGTCAAGATGTTCAGGACAACGACGGGTGTCAGAATCAAGACATGGCAGgtacgccgcc ... acctttgcagGGCGGGTCGGGGCTGGTGCAGGGCGTGAGGTTCTCGAACATCCAGGTCACG
EST: gi|71430589|gb|DR811639.1|DR811639
EST:     ATGTCAAGATGTTCAGGACAACGACGGGTGTCAGAATCAAGACATGGCAG                         GGCGGGTCGGGGCTGGTGCAGGGCGTGAGGTTCTCGAACATCCAGGTCACG
genomic: ATGTCAAGATGTTCAGGACAACGACGGGTGTCAGAATCAAGACATGGCAGgtacgccgcc ... acctttgcagGGCGGGTCGGGGCTGGTGCAGGGCGTGAGGTTCTCGAACATCCAGGTCACG
EST: gi|149067463|gb|EE157671.2|EE157671
EST:     ATGTCAAGATGTTCAGGACAACGACGGGTGTCAGAATCAAGACATGGCAG                         GGCGGGTCGGGGCTGGTGCAGGGCGTGAGGTTCTCGAACATCCAGGTCACG
genomic: ATGTCAAGATGTTCAGGACAACGACGGGTGTCAGAATCAAGACATGGCAGgtacgccgcc ... acctttgcagGGCGGGTCGGGGCTGGTGCAGGGCGTGAGGTTCTCGAACATCCAGGTCACG

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), 21 (downstream exon)
Score: 3

TCTAGGGAGGTTCAACACGAAGGCGTGCGTGTCCAACGTCACCGTACGAGATGTCAAGATGTTCAGGACAACGACGGGTGTCAGAATCAAGACATGGCAGgtacgccgcc ... acctttgcagGGCGGGTCGGGGCTGGTGCAGGGCGTGAGGTTCTCGAACATCCAGGTCACGGAGGTGCAGACGCCCATCATGATAGACCAGTTCTACTGCGACAGGGCGA


Block sizes: 35 (upstream exon), 15 (downstream exon)
Score: 4

TCTAGGGAGGTTCAACACGAAGGCGTGCGTGTCCAACGTCACCGTACGAGATGTCAAGATGTTCAGGACAACGACGGGTGTCAGAATCAAGACATGGCAGgtacgccgcc ... acctttgcagGGCGGGTCGGGGCTGGTGCAGGGCGTGAGGTTCTCGAACATCCAGGTCACGGAGGTGCAGACGCCCATCATGATAGACCAGTTCTACTGCGACAGGGCGA


Block sizes: 45 (upstream exon), 41 (downstream exon)
Score: 5

TCTAGGGAGGTTCAACACGAAGGCGTGCGTGTCCAACGTCACCGTACGAGATGTCAAGATGTTCAGGACAACGACGGGTGTCAGAATCAAGACATGGCAGgtacgccgcc ... acctttgcagGGCGGGTCGGGGCTGGTGCAGGGCGTGAGGTTCTCGAACATCCAGGTCACGGAGGTGCAGACGCCCATCATGATAGACCAGTTCTACTGCGACAGGGCGA


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 10

TCTAGGGAGGTTCAACACGAAGGCGTGCGTGTCCAACGTCACCGTACGAGATGTCAAGATGTTCAGGACAACGACGGGTGTCAGAATCAAGACATGGCAGgtacgccgcc ... acctttgcagGGCGGGTCGGGGCTGGTGCAGGGCGTGAGGTTCTCGAACATCCAGGTCACGGAGGTGCAGACGCCCATCATGATAGACCAGTTCTACTGCGACAGGGCGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatgcagtagcaggcagcagcagcaggcctaataattactaataaacctttgcagGGCGGGTCGGGGCTGGTGCAGGGCGTGAGGTTCTCGAACATCCAGGTCACGGAGGTGCAGACGCCCATCATGATAGACCAGTTCTACTGCGACAGGGCGA
                                    tactaat  putative branch site (score: 10)
                                              cctttgc  putative PPT
                             taataattactaataa  TA-rich tract