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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCACTTGGACTCTGCTAATTCCATTGAGGAGAAGGACAAGATCATTGAGATAACAGGACTCCAGAACTTGGCCAAGTCATTATCTACACAACATTGTGgtaagttttcagtgctatggattgcttaaattgcaggcagagaaactgagtttgctttaacttttcaagtaaaataagttcagagaaactaaacttgtct...

Basic information

species Zea mays
transcript GRMZM2G300651_T02
intron # 3
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|76925580|gb|DV170489.1|DV170489
EST:     GATAACAGGACTCCAGAACTTGGCCAAGTCATTATCTACACAACATTGTG                         ACACGCGCAGCGATAGATCATCAGCGCGCGGTTCTAGACTTCACTGGCATG
genomic: GATAACAGGACTCCAGAACTTGGCCAAGTCATTATCTACACAACATTGTGgtaagttttc ... acttgtacagACACGCGCAGCGATAGATCATCAGCGCGCGGTTCTAGACTTCACTGGCATG
EST: gi|71326679|gb|DR799997.1|DR799997
EST:     GATAACAGGACTCCAGAACTTGGCCAAGTCATTATCTACACAACATTGTG                         ACACGCGCAGCGATAGATCATCAGCGCGCGGTTCTAGACTTCACTGGCATG
genomic: GATAACAGGACTCCAGAACTTGGCCAAGTCATTATCTACACAACATTGTGgtaagttttc ... acttgtacagACACGCGCAGCGATAGATCATCAGCGCGCGGTTCTAGACTTCACTGGCATG
EST: gi|71447562|gb|DR828612.1|DR828612
EST:     GATAACAGGACTCCAGAACTTGGCCAAGTCATTATCTACACAACATTGTG                         ACACGCGCAGCGATAGATCATCAGCGCGCGGTTCTAGACTTCGCTGGCATG
genomic: GATAACAGGACTCCAGAACTTGGCCAAGTCATTATCTACACAACATTGTGgtaagttttc ... acttgtacagACACGCGCAGCGATAGATCATCAGCGCGCGGTTCTAGACTTCACTGGCATG
EST: gi|78113498|gb|DV531889.1|DV531889
EST:     GATAACAGGACTCCAGAACTTGGCCAAGTCATTATCTACACAACATTGTG                         ACACGCGCAGCGATAGATCATCAGCGCGCGGTTCTAGACTTCACTGGCATG
genomic: GATAACAGGACTCCAGAACTTGGCCAAGTCATTATCTACACAACATTGTGgtaagttttc ... acttgtacagACACGCGCAGCGATAGATCATCAGCGCGCGGTTCTAGACTTCACTGGCATG
EST: gi|78104008|gb|DV522426.1|DV522426
EST:     GATAACAGGACTCCAGAACTTGGCCAAGTCATTATCTACACAACATTGTG                         ACACGCGCAGCGATAGATCATCAGCGCGCGGTTCTAGACTTCACTGGCATG
genomic: GATAACAGGACTCCAGAACTTGGCCAAGTCATTATCTACACAACATTGTGgtaagttttc ... acttgtacagACACGCGCAGCGATAGATCATCAGCGCGCGGTTCTAGACTTCACTGGCATG

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: 41 (upstream exon), 31 (downstream exon)
Score: 17

GCACTTGGACTCTGCTAATTCCATTGAGGAGAAGGACAAGATCATTGAGATAACAGGACTCCAGAACTTGGCCAAGTCATTATCTACACAACATTGTGgtaagttttc ... acttgtacagACACGCGCAGCGATAGATCATCAGCGCGCGGTTCTAGACTTCACTGGCATGAGTTCATTGCGACCAACCAGCCTCTTCGTGAGTATTGCGACGCTTCCAG


Block sizes: 44 (upstream exon), 46 (downstream exon)
Score: 15

GCACTTGGACTCTGCTAATTCCATTGAGGAGAAGGACAAGATCATTGAGATAACAGGACTCCAGAACTTGGCCAAGTCATTATCTACACAACATTGTGgtaagttttc ... acttgtacagACACGCGCAGCGATAGATCATCAGCGCGCGGTTCTAGACTTCACTGGCATGAGTTCATTGCGACCAACCAGCCTCTTCGTGAGTATTGCGACGCTTCCAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 21

GCACTTGGACTCTGCTAATTCCATTGAGGAGAAGGACAAGATCATTGAGATAACAGGACTCCAGAACTTGGCCAAGTCATTATCTACACAACATTGTGgtaagttttc ... acttgtacagACACGCGCAGCGATAGATCATCAGCGCGCGGTTCTAGACTTCACTGGCATGAGTTCATTGCGACCAACCAGCCTCTTCGTGAGTATTGCGACGCTTCCAG


Block sizes: 41 (upstream exon), 26 (downstream exon)
Score: 26

GCACTTGGACTCTGCTAATTCCATTGAGGAGAAGGACAAGATCATTGAGATAACAGGACTCCAGAACTTGGCCAAGTCATTATCTACACAACATTGTGgtaagttttc ... acttgtacagACACGCGCAGCGATAGATCATCAGCGCGCGGTTCTAGACTTCACTGGCATGAGTTCATTGCGACCAACCAGCCTCTTCGTGAGTATTGCGACGCTTCCAG