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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatgagaaatttggttcataaacattccctgtctatccataatattccattcattgatatgctagttgtcaatattttttgcagATATGAAATCCCACCACTCGAAACTATTCAAAAAGGATAAATATTTTTTCATTTCAAATACG

Basic information

species Zea mays
transcript GRMZM5G845878_T01
intron # 1
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|18165281|gb|BM335120.1|BM335120
EST:     AAATGAAGTTATTATTTGGAAGGCAGCATTATTCTCATACCATATTCCAG                         ATATGAAATCCCACCACTCGAAACTATTCAAAAAGGATAAATATTTTTTCA
genomic: AAATGAAGTTATTATTTGGAAGGCAGCATTATTCTCATACCATATTCCAGgtaatgagaa ... ttttttgcagATATGAAATCCCACCACTCGAAACTATTCAAAAAGGATAAATATTTTTTCA
EST: gi|60341451|gb|DN208424.1|DN208424
EST:     AAATGAAGTTATTATTTGGAAGGCAGCATTATTCTCATACCATATTCCAG                         ATATGAAATCCCACCACTCGAAACTATTCAAAAAGGATAAATATTTTTTCA
genomic: AAATGAAGTTATTATTTGGAAGGCAGCATTATTCTCATACCATATTCCAGgtaatgagaa ... ttttttgcagATATGAAATCCCACCACTCGAAACTATTCAAAAAGGATAAATATTTTTTCA
EST: gi|18166666|gb|BM336505.1|BM336505
EST:     AAATGGAGTTATTATTTGGAAGGCAGCATTATTCTCATACCATATTCCAG                         ATATGAAATCCCACCACTCGAAACTATTCAAAAAGGATAAATATTTTTTCA
genomic: AAATGAAGTTATTATTTGGAAGGCAGCATTATTCTCATACCATATTCCAGgtaatgagaa ... ttttttgcagATATGAAATCCCACCACTCGAAACTATTCAAAAAGGATAAATATTTTTTCA
EST: gi|16379085|gb|BI992744.1|BI992744
EST:     AAATGAAGTTATTATTTGGAAGGCAGCATTATTCTCATGCCATATTCCAG                         ATATGAAATCCCACCACTCGGAACTATTCAAAAAGGATAAATATTTTTTCA
genomic: AAATGAAGTTATTATTTGGAAGGCAGCATTATTCTCATACCATATTCCAGgtaatgagaa ... ttttttgcagATATGAAATCCCACCACTCGAAACTATTCAAAAAGGATAAATATTTTTTCA
EST: gi|7162323|gb|AW519930.1|AW519930
EST:     AAATGAAGTTATTATTTGGAAGGCAGCATTATTCTCATACCATATTCCAG                         ATATGAAATCCCACCACTCGAAACTATTCAAAAAGGATAAATANNNNNNNC
genomic: AAATGAAGTTATTATTTGGAAGGCAGCATTATTCTCATACCATATTCCAGgtaatgagaa ... ttttttgcagATATGAAATCCCACCACTCGAAACTATTCAAAAAGGATAAATATTTTTT-C
EST: gi|13381999|gb|BG458674.1|BG458674
EST:     AAATGAAGTTATTATTTGGAAGGCAGCATTATTCTCATACCATATTCCAG                         ATATGAAATCCCACCACTCGGGACTATTCAAAAAGGATAAATATTTTTTCA
genomic: AAATGAAGTTATTATTTGGAAGGCAGCATTATTCTCATACCATATTCCAGgtaatgagaa ... ttttttgcagATATGAAATCCCACCACTCGAAACTATTCAAAAAGGATAAATATTTTTTCA

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: 40 (upstream exon), 46 (downstream exon)
Score: 23

CATTAGTACCCAAAAGAAAATTGTCATGGATCTCCAATTCAAATGTACTGAAATGAAGTTATTATTTGGAAGGCAGCATTATTCTCATACCATATTCCAGgtaatgagaa ... ttttttgcagATATGAAATCCCACCACTCGAAACTATTCAAAAAGGATAAATATTTTTTCATTTCAAATACG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 128

CATTAGTACCCAAAAGAAAATTGTCATGGATCTCCAATTCAAATGTACTGAAATGAAGTTATTATTTGGAAGGCAGCATTATTCTCATACCATATTCCAGgtaatgagaa ... ttttttgcagATATGAAATCCCACCACTCGAAACTATTCAAAAAGGATAAATATTTTTTCATTTCAAATACG


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 70

CATTAGTACCCAAAAGAAAATTGTCATGGATCTCCAATTCAAATGTACTGAAATGAAGTTATTATTTGGAAGGCAGCATTATTCTCATACCATATTCCAGgtaatgagaa ... ttttttgcagATATGAAATCCCACCACTCGAAACTATTCAAAAAGGATAAATATTTTTTCATTTCAAATACG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtctatccataatattccattcattgatatgctagttgtcaatattttttgcagATATGAAATCCCACCACTCGAAACTATTCAAAAAGGATAAATATTTTTTCATTTCAAATACG
                      cattgat  putative branch site (score: 70)
                                           tatttttt  putative PPT
                                    ttgtcaatatttttt  TA-rich tract