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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgagaaatcctccttgcttttccttggtttgtctgcccttgggtactgtcatgttgagatggcattgcattacaagttgtgttcacttggcatggtaattttcttattatattcgtgtgatttatttcagGTTGGTGCAGAACCAGCACCTCAGGCTGGAGTAGTGTCAGCAGACATTGGGTTCAAGGATATGACTAGCCACTGCGAAGCCCTGACGATTGGGAAACAGC

Basic information

species Zea mays
transcript GRMZM2G431573_T02
intron # 9
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|87154279|gb|DY399068.1|DY399068
EST:     CTTCTATACCTGCATCAGATCTTCTGAGTATCGATCAGCTTCTTGAAACG                         GTTGGTGCAGAACCAGCACCTCAGGCTGGAGTAGTGTCAGCAGACATTGGG
genomic: CTTCTATACCTGCATCAGATCTTCTGAGTATCGATCAGCTTCTTGAAACGgtatgagaaa ... tttatttcagGTTGGTGCAGAACCAGCACCTCAGGCTGGAGTAGTGTCAGCAGACATTGGG
EST: gi|32869573|gb|CF009255.1|CF009255
EST:     CTTCTATACCTGCATCAGATCTTCTGAGTATCGATCAGCTTCTTGAAACG                         GTTGGTGCAGAACCAGCACCTCAGGCTGGAGTAGTGTCAGCAGACATTGGG
genomic: CTTCTATACCTGCATCAGATCTTCTGAGTATCGATCAGCTTCTTGAAACGgtatgagaaa ... tttatttcagGTTGGTGCAGAACCAGCACCTCAGGCTGGAGTAGTGTCAGCAGACATTGGG
EST: gi|21390345|gb|BQ528394.1|BQ528394
EST:     CTTCTATACCTGCATCAGATCTTCTGAGTATCGATCAGCTTCTTGAAACG                         GTTGGTGCAGAACCAGCACCTCAGGCTGGAGTAGTGTCAGCAGACATTGGG
genomic: CTTCTATACCTGCATCAGATCTTCTGAGTATCGATCAGCTTCTTGAAACGgtatgagaaa ... tttatttcagGTTGGTGCAGAACCAGCACCTCAGGCTGGAGTAGTGTCAGCAGACATTGGG
EST: gi|21329900|gb|BQ485281.1|BQ485281
EST:     CTTCTATACCTGCATCAGATCTTCTGAGTATCGATCAGCTTCTTGAAACG                         GTTGGTGCAGAACCAGCACCTCAGGCTGGAGTAGTGTCAGCAGACATTGGG
genomic: CTTCTATACCTGCATCAGATCTTCTGAGTATCGATCAGCTTCTTGAAACGgtatgagaaa ... tttatttcagGTTGGTGCAGAACCAGCACCTCAGGCTGGAGTAGTGTCAGCAGACATTGGG

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 3 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 11

TGACCATGATGCTTTTGGGGAAGCTTCAGAAAGCGCAGAAGCTTCCGCATCTTCTATACCTGCATCAGATCTTCTGAGTATCGATCAGCTTCTTGAAACGgtatgagaaa ... tttatttcagGTTGGTGCAGAACCAGCACCTCAGGCTGGAGTAGTGTCAGCAGACATTGGGTTCAAGGATATGACTAGCCACTGCGAAGCCCTGACGATTGGGAAACAGC


Block sizes: 49 (upstream exon), 18 (downstream exon)
Score: 2

TGACCATGATGCTTTTGGGGAAGCTTCAGAAAGCGCAGAAGCTTCCGCATCTTCTATACCTGCATCAGATCTTCTGAGTATCGATCAGCTTCTTGAAACGgtatgagaaa ... tttatttcagGTTGGTGCAGAACCAGCACCTCAGGCTGGAGTAGTGTCAGCAGACATTGGGTTCAAGGATATGACTAGCCACTGCGAAGCCCTGACGATTGGGAAACAGC


Block sizes: 49 (upstream exon), 39 (downstream exon)
Score: 24

TGACCATGATGCTTTTGGGGAAGCTTCAGAAAGCGCAGAAGCTTCCGCATCTTCTATACCTGCATCAGATCTTCTGAGTATCGATCAGCTTCTTGAAACGgtatgagaaa ... tttatttcagGTTGGTGCAGAACCAGCACCTCAGGCTGGAGTAGTGTCAGCAGACATTGGGTTCAAGGATATGACTAGCCACTGCGAAGCCCTGACGATTGGGAAACAGC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttgtgttcacttggcatggtaattttcttattatattcgtgtgatttatttcagGTTGGTGCAGAACCAGCACCTCAGGCTGGAGTAGTGTCAGCAGACATTGGGTTCAAGGATATGACTAGCCACTGCGAAGCCCTGACGATTGGGAAACAGC
                                             tttatttc  CT-rich tract
                atggtaattttcttat  TA-rich tract