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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgttcttgttaatctaattgtccgtctgaaagatctgttcagacctgtctgggtttttgctagtacctgatatttgatattttattagatgcagACTCATCTGTGAAAACTGCATCCAAGCCATCTGGCCGCCCCTGGGATAAGATCGCTGCAAATCTGATGGCTTGTCTTATGGCTATTGTAATGTTGGTTCG

Basic information

species Zea mays
transcript GRMZM2G073571_T02
intron # 12
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|8383108|gb|BE055991.1|BE055991
EST:     TGCTACATGGAAGAGAGAGCAACCACGAAAGGCACCATCCGTGCCCCAAG                         ATGCAGACTCATCTGTGAAAACTGCATCCAAGCCATCTGGCC
genomic: TGCTACATGGAAGAGAGAGCAACCACGAAAGGCACCATCCGTGCCCCAAGgtttgttctt ... ttagatgcagA--C----TCATCTGTGAAAACTGCATCCAAGCCATCTGGCC
EST: gi|15177587|gb|BI398526.1|BI398526
EST:     TGCTACATGGAAGAGAGAGCAACCACGAAAGGCACCATCCGTGCCCCAAG                         ATGCAGACTCATCTGTGAAAACTGCATCCAAGCCATCTGGCC
genomic: TGCTACATGGAAGAGAGAGCAACCACGAAAGGCACCATCCGTGCCCCAAGgtttgttctt ... ttagatgcagA--C----TCATCTGTGAAAACTGCATCCAAGCCATCTGGCC
EST: gi|16137338|gb|BI894203.1|BI894203
EST:     TGCTACATGGAAGAGAGAGCAACCACGAAAGGCACCATCCGTGCCCCAAG                         ATGCAGACTCATCTGTGAAAACTGCATCCAAGCCATCTGGCCGCCCCTGGG
genomic: TGCTACATGGAAGAGAGAGCAACCACGAAAGGCACCATCCGTGCCCCAAGgtttgttctt ... ttagatgcagA--C----TCATCTGTGAAAACTGCATCCAAGCCATCTGGCCGCCCCTGGG
EST: gi|3172014|gb|AJ006545.1|AJ006545
EST:     TGCTACATGGAAGAGAGAGCAACCACGAAAGGCACCATTCGTGCCCCAAG                         ACTCATCTGTGAAAACTGCATCCAAGCCATCTGGCCGCCCCTGGGATAAGA
genomic: TGCTACATGGAAGAGAGAGCAACCACGAAAGGCACCATCCGTGCCCCAAGgtttgttctt ... ttagatgcagACTCATCTGTGAAAACTGCATCCAAGCCATCTGGCCGCCCCTGGGATAAGA
EST: gi|15177586|gb|BI398525.1|BI398525
EST:     TGCTACATGGAAGAGAGAGCAACCACGAAAGGCACCATCCGTGCCCCAAG                         ATGCAGACTCATCTGTGAAAACTGCATCCAAGCCATCTGGCCGCCCCTGGG
genomic: TGCTACATGGAAGAGAGAGCAACCACGAAAGGCACCATCCGTGCCCCAAGgtttgttctt ... ttagatgcagA--C----TCATCTGTGAAAACTGCATCCAAGCCATCTGGCCGCCCCTGGG
EST: gi|15188204|gb|BI417181.1|BI417181
EST:     TGCTACATGGAAGAGAGAGCAACCACGAAAGGCACCATCCGTGCCCCAAG                         ATGCAGACTCATCTGTGAAAACTGCATCCAAGCCATCTGGCCGCCCCTGGG
genomic: TGCTACATGGAAGAGAGAGCAACCACGAAAGGCACCATCCGTGCCCCAAGgtttgttctt ... ttagatgcagA--C----TCATCTGTGAAAACTGCATCCAAGCCATCTGGCCGCCCCTGGG
EST: gi|15323597|gb|BI478855.1|BI478855
EST:     TGCTACATGGAAGAGAGAGCAACCACGAAAGGCACCATCCGTGCCCCAAG                         ATGCAGACTCATCTGTGAAAACTGCATCCAAGCCATCTGGCCGCCCCTGGG
genomic: TGCTACATGGAAGAGAGAGCAACCACGAAAGGCACCATCCGTGCCCCAAGgtttgttctt ... ttagatgcagA--C----TCATCTGTGAAAACTGCATCCAAGCCATCTGGCCGCCCCTGGG
EST: gi|60401555|gb|DN234362.1|DN234362
EST:     TGCTACATGGAAGAGAGAGCAACCACGAAAGGCACCATCCGTGCCCCAAGATGCAG                    
genomic: TGCTACATGGAAGAGAGAGCAACCACGAAAGGCACCATCCGTGCCCC---A---AGgtttgttctt ... ttaga
EST: gi|15323596|gb|BI478854.1|BI478854
EST:     TGCTACATGGAAGAGAGAGCAACCACGAAAGGCACCATCCGTGCCCCAAG                         ATGCAGACTCATCTGTGAAAACTGCATCCAAGCCATCTGGCCGCCCCTGGG
genomic: TGCTACATGGAAGAGAGAGCAACCACGAAAGGCACCATCCGTGCCCCAAGgtttgttctt ... ttagatgcagA--C----TCATCTGTGAAAACTGCATCCAAGCCATCTGGCCGCCCCTGGG

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: 53

TCTACTCGTGTCCCTGAATATGATGTACCTGTTGTTGACAAGGCCGTGGATGCTACATGGAAGAGAGAGCAACCACGAAAGGCACCATCCGTGCCCCAAGgtttgttctt ... ttagatgcagACTCATCTGTGAAAACTGCATCCAAGCCATCTGGCCGCCCCTGGGATAAGATCGCTGCAAATCTGATGGCTTGTCTTATGGCTATTGTAATGTTGGTTCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 35

TCTACTCGTGTCCCTGAATATGATGTACCTGTTGTTGACAAGGCCGTGGATGCTACATGGAAGAGAGAGCAACCACGAAAGGCACCATCCGTGCCCCAAGgtttgttctt ... ttagatgcagACTCATCTGTGAAAACTGCATCCAAGCCATCTGGCCGCCCCTGGGATAAGATCGCTGCAAATCTGATGGCTTGTCTTATGGCTATTGTAATGTTGGTTCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 33

TCTACTCGTGTCCCTGAATATGATGTACCTGTTGTTGACAAGGCCGTGGATGCTACATGGAAGAGAGAGCAACCACGAAAGGCACCATCCGTGCCCCAAGgtttgttctt ... ttagatgcagACTCATCTGTGAAAACTGCATCCAAGCCATCTGGCCGCCCCTGGGATAAGATCGCTGCAAATCTGATGGCTTGTCTTATGGCTATTGTAATGTTGGTTCG


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 38

TCTACTCGTGTCCCTGAATATGATGTACCTGTTGTTGACAAGGCCGTGGATGCTACATGGAAGAGAGAGCAACCACGAAAGGCACCATCCGTGCCCCAAGgtttgttctt ... ttagatgcagACTCATCTGTGAAAACTGCATCCAAGCCATCTGGCCGCCCCTGGGATAAGATCGCTGCAAATCTGATGGCTTGTCTTATGGCTATTGTAATGTTGGTTCG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cagacctgtctgggtttttgctagtacctgatatttgatattttattagatgcagACTCATCTGTGAAAACTGCATCCAAGCCATCTGGCCGCCCCTGGGATAAGATCGCTGCAAATCTGATGGCTTGTCTTATGGCTATTGTAATGTTGGTTCG
                                        ttttatt  CT-rich tract
                            tgatatttgatatttt  TA-rich tract