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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtaggtccacctttgatccatcatgctctatagcattatgataatttgtggtgtatttcttatttctgacattgtttttcatctttgtgggtaaattactttttgttgcctgctgccaaattcttctagACGATCTGCCTCTTTGGG

Basic information

species Zea mays
transcript GRMZM2G420310_T01
intron # 3
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|60351142|gb|DN218115.1|DN218115
EST:     GCAGTTTGCTGATGCCATTGAAAGCTCATATTGGTTTGAATTTTTTATAG                         ACGATCTGCCTCTTTGGG
genomic: GCAGTTTGCTGATGCCATTGAAAGCTCATATTGGTTTGAATTTTTTATAGgtatgtaggt ... attcttctagACGATCTGCCTCTTTGGG
EST: gi|211318943|gb|FL142494.1|FL142494
EST:     GCAGTTTGCTGATGCCATTGAAAGCTCATATTGGTTTGAATTTTTTATAG                         ACGATCTGCCTCTTTGGG
genomic: GCAGTTTGCTGATGCCATTGAAAGCTCATATTGGTTTGAATTTTTTATAGgtatgtaggt ... attcttctagACGATCTGCCTCTTTGGG
EST: gi|160481321|gb|EY254485.1|EY254485
EST:     GCAGTTTGCTGATGCCATTGAAAGCTCATATTGGTTTGAATTTTTTATAG                         ACGATCTGCCTCTTTGGG
genomic: GCAGTTTGCTGATGCCATTGAAAGCTCATATTGGTTTGAATTTTTTATAGgtatgtaggt ... attcttctagACGATCTGCCTCTTTGGG
EST: gi|78079180|gb|DV507592.1|DV507592
EST:     GCAGTTTGCTGATGCCATTGAAAGCTCATATTGGTTTGAATTTTTTATAG                         ACGATCTGCCTCTTTGGG
genomic: GCAGTTTGCTGATGCCATTGAAAGCTCATATTGGTTTGAATTTTTTATAGgtatgtaggt ... attcttctagACGATCTGCCTCTTTGGG
EST: gi|31356502|gb|CD440859.1|CD440859
EST:     GCAGTTTGCTGATGCCATTGAAAGCTCATATTGGTTTGAATTTTTTATAG                         ACGATCTGCCTCTTTGGG
genomic: GCAGTTTGCTGATGCCATTGAAAGCTCATATTGGTTTGAATTTTTTATAGgtatgtaggt ... attcttctagACGATCTGCCTCTTTGGG
EST: gi|71766500|gb|DR964437.1|DR964437
EST:     GCAGTTTGCTGATGCCATTGAAAGCTCATATTGGTTTGAATTTTTTATAG                         ACGATCTGCCTCTTTGGG
genomic: GCAGTTTGCTGATGCCATTGAAAGCTCATATTGGTTTGAATTTTTTATAGgtatgtaggt ... attcttctagACGATCTGCCTCTTTGGG
EST: gi|89249564|gb|DY621350.1|DY621350
EST:     GCAGTTTGCTGATGCCATTGAAAGCTCATATTGGTTTGAATTTTTTATAG                         ACGATCTGCCTCTTTGGG
genomic: GCAGTTTGCTGATGCCATTGAAAGCTCATATTGGTTTGAATTTTTTATAGgtatgtaggt ... attcttctagACGATCTGCCTCTTTGGG
EST: gi|160481319|gb|EY254483.1|EY254483
EST:     GCAGTTTGCTGATGCCATTGAAAGCTCATATTGGTTTGAATTTTTTATAG                         ACGATCTGCCTCTTTGGG
genomic: GCAGTTTGCTGATGCCATTGAAAGCTCATATTGGTTTGAATTTTTTATAGgtatgtaggt ... attcttctagACGATCTGCCTCTTTGGG
EST: gi|29130633|gb|CB381337.1|CB381337
EST:     GCAGTTTGCTGATGCCATTGAAAGCTCATATTGGTTTGAATTTTTTATAG                         ACGATCTGNCTCTTTGGG
genomic: GCAGTTTGCTGATGCCATTGAAAGCTCATATTGGTTTGAATTTTTTATAGgtatgtaggt ... attcttctagACGATCTGCCTCTTTGGG

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), 18 (downstream exon)
Score: 176

GTGGAGAAGGGCTTCATTTGTACACTTGAGCTAGATGCTAAAAAGGTCCAGCAGTTTGCTGATGCCATTGAAAGCTCATATTGGTTTGAATTTTTTATAGgtatgtaggt ... attcttctagACGATCTGCCTCTTTGGG


Block sizes: 47 (upstream exon), 18 (downstream exon)
Score: 203

GTGGAGAAGGGCTTCATTTGTACACTTGAGCTAGATGCTAAAAAGGTCCAGCAGTTTGCTGATGCCATTGAAAGCTCATATTGGTTTGAATTTTTTATAGgtatgtaggt ... attcttctagACGATCTGCCTCTTTGGG


Block sizes: 48 (upstream exon), 18 (downstream exon)
Score: 238

GTGGAGAAGGGCTTCATTTGTACACTTGAGCTAGATGCTAAAAAGGTCCAGCAGTTTGCTGATGCCATTGAAAGCTCATATTGGTTTGAATTTTTTATAGgtatgtaggt ... attcttctagACGATCTGCCTCTTTGGG


Block sizes: 48 (upstream exon), 18 (downstream exon)
Score: 346

GTGGAGAAGGGCTTCATTTGTACACTTGAGCTAGATGCTAAAAAGGTCCAGCAGTTTGCTGATGCCATTGAAAGCTCATATTGGTTTGAATTTTTTATAGgtatgtaggt ... attcttctagACGATCTGCCTCTTTGGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttttcatctttgtgggtaaattactttttgttgcctgctgccaaattcttctagACGATCTGCCTCTTTGGG
                                              ttcttct  CT-rich tract
                 taaattactttttgtt  TA-rich tract