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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgttcttgttaatctaattgtccgtctgaaagatctgttcagacctgtctgggtttttgctagtacctgatatttgatattttattagATGCAGACTCATCTGTGAAAACTGCATCCAAGCCATCTGGCCGCCCCTGGGATAAGATCGCTGCAAATCTGATGGCTTGTCTTATGGCTATTGTAATGTT

Basic information

species Zea mays
transcript GRMZM2G073571_T03
intron # 9
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|22543321|gb|BU093759.1|BU093759
EST:     TGCTACATGGAAGAGAGAGCAACCACGAAAGGCACCATTCGTGCCCCAAG                         ATGCAGACTCATCTGTGAAAACTGCATCCAAGCCATCTGGCCGCCCCTGGG
genomic: TGCTACATGGAAGAGAGAGCAACCACGAAAGGCACCATCCGTGCCCCAAGgtttgttctt ... attttattagATGCAGACTCATCTGTGAAAACTGCATCCAAGCCATCTGGCCGCCCCTGGG
EST: gi|16137339|gb|BI894204.1|BI894204
EST:     TGCTACATGGAAGAGAGAGCAACCACGAAAGGCACCATCCGTGCCCCAAG                         ATGCAGACTCATCTGTGAAAACTGCATCCAAGCCATCTGGCCGCCCCTGGG
genomic: TGCTACATGGAAGAGAGAGCAACCACGAAAGGCACCATCCGTGCCCCAAGgtttgttctt ... attttattagATGCAGACTCATCTGTGAAAACTGCATCCAAGCCATCTGGCCGCCCCTGGG
EST: gi|15188204|gb|BI417181.1|BI417181
EST:     TGCTACATGGAAGAGAGAGCAACCACGAAAGGCACCATCCGTGCCCCAAG                         ATGCAGACTCATCTGTGAAAACTGCATCCAAGCCATCTGGCCGCCCCTGGG
genomic: TGCTACATGGAAGAGAGAGCAACCACGAAAGGCACCATCCGTGCCCCAAGgtttgttctt ... attttattagATGCAGACTCATCTGTGAAAACTGCATCCAAGCCATCTGGCCGCCCCTGGG
EST: gi|15323596|gb|BI478854.1|BI478854
EST:     TGCTACATGGAAGAGAGAGCAACCACGAAAGGCACCATCCGTGCCCCAAG                         ATGCAGACTCATCTGTGAAAACTGCATCCAAGCCATCTGGCCGCCCCTGGG
genomic: TGCTACATGGAAGAGAGAGCAACCACGAAAGGCACCATCCGTGCCCCAAGgtttgttctt ... attttattagATGCAGACTCATCTGTGAAAACTGCATCCAAGCCATCTGGCCGCCCCTGGG
EST: gi|15177586|gb|BI398525.1|BI398525
EST:     TGCTACATGGAAGAGAGAGCAACCACGAAAGGCACCATCCGTGCCCCAAG                         ATGCAGACTCATCTGTGAAAACTGCATCCAAGCCATCTGGCCGCCCCTGGG
genomic: TGCTACATGGAAGAGAGAGCAACCACGAAAGGCACCATCCGTGCCCCAAGgtttgttctt ... attttattagATGCAGACTCATCTGTGAAAACTGCATCCAAGCCATCTGGCCGCCCCTGGG
EST: gi|16137338|gb|BI894203.1|BI894203
EST:     TGCTACATGGAAGAGAGAGCAACCACGAAAGGCACCATCCGTGCCCCAAG                         ATGCAGACTCATCTGTGAAAACTGCATCCAAGCCATCTGGCCGCCCCTGGG
genomic: TGCTACATGGAAGAGAGAGCAACCACGAAAGGCACCATCCGTGCCCCAAGgtttgttctt ... attttattagATGCAGACTCATCTGTGAAAACTGCATCCAAGCCATCTGGCCGCCCCTGGG

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), 47 (downstream exon)
Score: 154

TCTACTCGTGTCCCTGAATATGATGTACCTGTTGTTGACAAGGCCGTGGATGCTACATGGAAGAGAGAGCAACCACGAAAGGCACCATCCGTGCCCCAAGgtttgttctt ... attttattagATGCAGACTCATCTGTGAAAACTGCATCCAAGCCATCTGGCCGCCCCTGGGATAAGATCGCTGCAAATCTGATGGCTTGTCTTATGGCTATTGTAATGTT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 83

TCTACTCGTGTCCCTGAATATGATGTACCTGTTGTTGACAAGGCCGTGGATGCTACATGGAAGAGAGAGCAACCACGAAAGGCACCATCCGTGCCCCAAGgtttgttctt ... attttattagATGCAGACTCATCTGTGAAAACTGCATCCAAGCCATCTGGCCGCCCCTGGGATAAGATCGCTGCAAATCTGATGGCTTGTCTTATGGCTATTGTAATGTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 154

TCTACTCGTGTCCCTGAATATGATGTACCTGTTGTTGACAAGGCCGTGGATGCTACATGGAAGAGAGAGCAACCACGAAAGGCACCATCCGTGCCCCAAGgtttgttctt ... attttattagATGCAGACTCATCTGTGAAAACTGCATCCAAGCCATCTGGCCGCCCCTGGGATAAGATCGCTGCAAATCTGATGGCTTGTCTTATGGCTATTGTAATGTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 111

TCTACTCGTGTCCCTGAATATGATGTACCTGTTGTTGACAAGGCCGTGGATGCTACATGGAAGAGAGAGCAACCACGAAAGGCACCATCCGTGCCCCAAGgtttgttctt ... attttattagATGCAGACTCATCTGTGAAAACTGCATCCAAGCCATCTGGCCGCCCCTGGGATAAGATCGCTGCAAATCTGATGGCTTGTCTTATGGCTATTGTAATGTT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctgttcagacctgtctgggtttttgctagtacctgatatttgatattttattagATGCAGACTCATCTGTGAAAACTGCATCCAAGCCATCTGGCCGCCCCTGGGATAAGATCGCTGCAAATCTGATGGCTTGTCTTATGGCTATTGTAATGTT
                                              ttttatt  CT-rich tract
                                  tgatatttgatatttt  TA-rich tract