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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cacatttctggaccttgtgtgtcacggtaatcagttctgcattattcatagttatgcttctagtttgttgttttgacaaatggcatgctttctccttcagGCTTACGATTTCACTCGAATATTGAGCTCCTTTTATTTCAAGGGCTACACTTTACTGACAAAAATACAGCGCATCGAATGGAACAATAG

Basic information

species Zea mays
transcript GRMZM2G016184_T01
intron # 2
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|211370346|gb|FL342982.1|FL342982
EST:     CACTAGTTCCGTACACCTCTGTGCTCATTGGCATTGTCCTCTGCAAGATG                         GCTTACGATTTCACTCGAATATTGAGCTCCTTTTATTTCAAGGGCTACACT
genomic: CACTAGTTCCGTACACCTCTGTGCTCATTGGCATTGTCCTCTGCAAGATGgtaggttgat ... tctccttcagGCTTACGATTTCACTCGAATATTGAGCTCCTTTTATTTCAAGGGCTACACT
EST: gi|211446537|gb|FL323006.1|FL323006
EST:     CACTAGTTCCGTACACCTCTGTGCTCATTGGCATTGTCCTCTGCAAGATG                         GCTTACGATTTCACTCGAATATT
genomic: CACTAGTTCCGTACACCTCTGTGCTCATTGGCATTGTCCTCTGCAAGATGgtaggttgat ... tctccttcagGCTTACGATTTCACTCGAATATT
EST: gi|211367569|gb|FL335348.1|FL335348
EST:     CACTAGTTCCGTWCACCTCTGTGCTCATTGGCATTGTCCTYTGCAAGATG                         GCTTACGATTTCACTCGAATATTGAGCTCC
genomic: CACTAGTTCCGTACACCTCTGTGCTCATTGGCATTGTCCTCTGCAAGATGgtaggttgat ... tctccttcagGCTTACGATTTCACTCGAATATTGAGCTCC
EST: gi|211235414|gb|FL352706.1|FL352706
EST:     ACTAGTTCCGTACACCTCTGTGCTCATTTGGCATTGTCCTCTGCAAGATG                         GCTTTACGATTTCACTCG
genomic: ACTAGTTCCGTACACCTCTGTGCTCATT-GGCATTGTCCTCTGCAAGATGgtaggttgat ... tctccttcagGCTT-ACGATTTCACTCG
EST: gi|211154538|gb|FL360790.1|FL360790
EST:     CACTAGTTCCGTACACCTCTGTGCTCATTGGCATTGTCCTCTGCAAGATG                         GCTTACGATTTCACTCGAATATTGAGCTCCTTTTATTTCAAGGGCTACACT
genomic: CACTAGTTCCGTACACCTCTGTGCTCATTGGCATTGTCCTCTGCAAGATGgtaggttgat ... tctccttcagGCTTACGATTTCACTCGAATATTGAGCTCCTTTTATTTCAAGGGCTACACT

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), 49 (downstream exon)
Score: 109

TTACAAGTATCAAGCTCAGGCCTTGATGAGGGACTATCTGCTAGCTGATCCACTAGTTCCGTACACCTCTGTGCTCATTGGCATTGTCCTCTGCAAGATGgtaggttgat ... tctccttcagGCTTACGATTTCACTCGAATATTGAGCTCCTTTTATTTCAAGGGCTACACTTTACTGACAAAAATACAGCGCATCGAATGGAACAATAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 90

TTACAAGTATCAAGCTCAGGCCTTGATGAGGGACTATCTGCTAGCTGATCCACTAGTTCCGTACACCTCTGTGCTCATTGGCATTGTCCTCTGCAAGATGgtaggttgat ... tctccttcagGCTTACGATTTCACTCGAATATTGAGCTCCTTTTATTTCAAGGGCTACACTTTACTGACAAAAATACAGCGCATCGAATGGAACAATAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 45

TTACAAGTATCAAGCTCAGGCCTTGATGAGGGACTATCTGCTAGCTGATCCACTAGTTCCGTACACCTCTGTGCTCATTGGCATTGTCCTCTGCAAGATGgtaggttgat ... tctccttcagGCTTACGATTTCACTCGAATATTGAGCTCCTTTTATTTCAAGGGCTACACTTTACTGACAAAAATACAGCGCATCGAATGGAACAATAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 112

TTACAAGTATCAAGCTCAGGCCTTGATGAGGGACTATCTGCTAGCTGATCCACTAGTTCCGTACACCTCTGTGCTCATTGGCATTGTCCTCTGCAAGATGgtaggttgat ... tctccttcagGCTTACGATTTCACTCGAATATTGAGCTCCTTTTATTTCAAGGGCTACACTTTACTGACAAAAATACAGCGCATCGAATGGAACAATAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcatagttatgcttctagtttgttgttttgacaaatggcatgctttctccttcagGCTTACGATTTCACTCGAATATTGAGCTCCTTTTATTTCAAGGGCTACACTTTACTGACAAAAATACAGCGCATCGAATGGAACAATAG
                         ttttgac  putative branch site (score: 112)
                                      catgctttctccttc  putative PPT
                      ttgtttt  TA-rich tract