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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAAAAAAAAGGCATTTTATACGGCAGCATTCTCTGGTTTGGCTGAACCACTAGGAGTGGTTGCTGTAGgtatgctaattcctgaaccctcctattgtaattgtgtccttcagacgcaaactagatccaaagctatctatgatatggtaccttatttagcactgatgttatttcggttactgcag

Basic information

species Zea mays
transcript GRMZM2G050484_T01
intron # 9
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|88749903|gb|DY534044.1|DY534044
EST:     AACATACCAGAGGGGGTTGCTGTAGCTCTTCCAATCTATTTTGCTACCAAAAG
genomic: AACATACCAGAGGGGGTTGCTGTAGCTCTTCCAATCTATTTTGCTACCAAAAG
EST: gi|78115522|gb|DV533910.1|DV533910
EST:     TACGGCAGCATTCTTTGGTTTGGCTGAACCACTAGGAGTGGTTGCTGTAG                         CTTTGTTGTTTCCAAGCAGTTTGAATCCTGACATTCTTGAAGGCCTACTTG
genomic: TACGGCAGCATTCTCTGGTTTGGCTGAACCACTAGGAGTGGTTGCTGTAGgtatgctaat ... gttactgcagCTTTGTTGTTTCCAAGCAGTTTGAATCCTGACATTCTTGAAGGCCTACTTG
EST: gi|18164662|gb|BM334501.1|BM334501
EST:     CCACTAGGAGTGGTTGCTGTAG                         CTTTGTTGTTTCCAAGCAGTTTGAATCCTGACATTCTTGAAGGCCTACTTG
genomic: CCACTAGGAGTGGTTGCTGTAGgtatgctaat ... gttactgcagCTTTGTTGTTTCCAAGCAGTTTGAATCCTGACATTCTTGAAGGCCTACTTG
EST: gi|101385255|gb|EB814673.1|EB814673
EST:     AACATACCAGAGGGGGTTGCTGTAGCTCTTCCAATCTATTTTGCTACCAAAAG
genomic: AACATACCAGAGGGGGTTGCTGTAGCTCTTCCAATCTATTTTGCTACCAAAAG
EST: gi|18178000|gb|BM379210.1|BM379210
EST:     TACGGCAGCATTCTCTGGTTTGGCTGAACCACTAGGAGTGGTTGCTGTAG                         CTTTGTTGTTTCCAAGCAGTTTGAATCCTGACATTCTTGAAGGCCTACTTG
genomic: TACGGCAGCATTCTCTGGTTTGGCTGAACCACTAGGAGTGGTTGCTGTAGgtatgctaat ... gttactgcagCTTTGTTGTTTCCAAGCAGTTTGAATCCTGACATTCTTGAAGGCCTACTTG
EST: gi|71308419|gb|DR790442.1|DR790442
EST:     AACATACCAGAGGGGGTTGCTGTAGCTCTTCCAATCTATTTTGCTACCAAAAG
genomic: AACATACCAGAGGGGGTTGCTGTAGCTCTTCCAATCTATTTTGCTACCAAAAG
EST: gi|76288875|gb|DV028443.1|DV028443
EST:     AACATACCAGAGGGGGTTGCTGTAGCTCTTCCAATCTATTTTGCTACCAAAAG
genomic: AACATACCAGAGGGGGTTGCTGTAGCTCTTCCAATCTATTTTGCTACCAAAAG
EST: gi|166572571|gb|EG286519.1|EG286519
EST:     TACGGCAGCATTCTCTGGTTTGGCTGAACCACTAGGAGTGGTTGCTGTAG                         CTTTGTTGTTTCCAAGCAGTTTGAATCCTGACATTCTTGAAGGCC
genomic: TACGGCAGCATTCTCTGGTTTGGCTGAACCACTAGGAGTGGTTGCTGTAGgtatgctaat ... gttactgcagCTTTGTTGTTTCCAAGCAGTTTGAATCCTGACATTCTTGAAGGCC
EST: gi|50324963|gb|CO520089.1|CO520089
EST:     AACATACCAGAGGGGGTTGCTGTAGCTCTTCCAATCTATTTTGCTACCAAAAG
genomic: AACATACCAGAGGGGGTTGCTGTAGCTCTTCCAATCTATTTTGCTACCAAAAG
EST: gi|71300310|gb|DR786224.1|DR786224
EST:     AACATACCAGAGGGGGTTGCTGTAGCTCTTCCAATCTATTTTGCTACCAAAAG
genomic: AACATACCAGAGGGGGTTGCTGTAGCTCTTCCAATCTATTTTGCTACCAAAAG
EST: gi|89762575|gb|DY690101.1|DY690101
EST:     AACATACCAGAGGGGGTTGCTGTAGCTCTTCCAATCTATTTTGCTACCAAAAG
genomic: AACATACCAGAGGGGGTTGCTGTAGCTCTTCCAATCTATTTTGCTACCAAAAG
EST: gi|71446246|gb|DR827296.1|DR827296
EST:     AACATACCAGAGGGGGTTGCTGTAGCTCTTCCAATCTATTTTGCTACCAAAAG
genomic: AACATACCAGAGGGGGTTGCTGTAGCTCTTCCAATCTATTTTGCTACCAAAAG
EST: gi|91052253|gb|EB162671.1|EB162671
EST:     AACATACCAGAGGGGGTTGCTGTAGCTCTTCCAATCTATTTTGCTACCAAAAG
genomic: AACATACCAGAGGGGGTTGCTGTAGCTCTTCCAATCTATTTTGCTACCAAAAG

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: 49 (upstream exon), 45 (downstream exon)
Score: 27

CAAAAAAAAGGCATTTTATACGGCAGCATTCTCTGGTTTGGCTGAACCACTAGGAGTGGTTGCTGTAGgtatgctaat ... gttactgcagCTTTGTTGTTTCCAAGCAGTTTGAATCCTGACATTCTTGAAGGCCTACTTGGATCTG


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

CAAAAAAAAGGCATTTTATACGGCAGCATTCTCTGGTTTGGCTGAACCACTAGGAGTGGTTGCTGTAGgtatgctaat ... gttactgcagCTTTGTTGTTTCCAAGCAGTTTGAATCCTGACATTCTTGAAGGCCTACTTGGATCTG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 82

CAAAAAAAAGGCATTTTATACGGCAGCATTCTCTGGTTTGGCTGAACCACTAGGAGTGGTTGCTGTAGgtatgctaat ... gttactgcagCTTTGTTGTTTCCAAGCAGTTTGAATCCTGACATTCTTGAAGGCCTACTTGGATCTG


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 67

CAAAAAAAAGGCATTTTATACGGCAGCATTCTCTGGTTTGGCTGAACCACTAGGAGTGGTTGCTGTAGgtatgctaat ... gttactgcagCTTTGTTGTTTCCAAGCAGTTTGAATCCTGACATTCTTGAAGGCCTACTTGGATCTG