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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgatgtaaaactttaatccattggtttagtatatgaaagaacaatgttctacatagcacccatcagatgactgttttggttgttttatttgtacagatcatcttcctaactacttttctgttacttctacatgttttagGCATTTTACCCTGTTCAATCCTGATTCCTGGACTGTTCTTTGTCCCTGAATCCCCAAGGTGGTTG

Basic information

species Zea mays
transcript GRMZM2G097768_T01
intron # 7
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|21390663|gb|BQ528712.1|BQ528712
EST:     TGCCTATTTGTTTGGCATGTTTGTTCCCTGGAGAATTCTTGCTGTTCTAG                         GCATTTTACCCTGTTCAATCCTGATTCCTGGACTGTTCTTTGTCCCTGAAT
genomic: TGCCTATTTGTTTGGCATGTTTGTTCCCTGGAGAATTCTTGCTGTTCTAGgtatgatgta ... catgttttagGCATTTTACCCTGTTCAATCCTGATTCCTGGACTGTTCTTTGTCCCTGAAT
EST: gi|71772625|gb|DR970553.1|DR970553
EST:     TGCCTATTTGTTTGGCATGTTTGTTCCCTGGAGAATTCTTGCTGTTCTAG                         GCATTTTACCCTGTTCAATCCTGATTCCTGGACTGTTCTTTGTCCCTGAAT
genomic: TGCCTATTTGTTTGGCATGTTTGTTCCCTGGAGAATTCTTGCTGTTCTAGgtatgatgta ... catgttttagGCATTTTACCCTGTTCAATCCTGATTCCTGGACTGTTCTTTGTCCCTGAAT

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: 147

CTCTCCGTCACGATTGGTATATTGCTTGCCTATTTGTTTGGCATGTTTGTTCCCTGGAGAATTCTTGCTGTTCTAGgtatgatgta ... catgttttagGCATTTTACCCTGTTCAATCCTGATTCCTGGACTGTTCTTTGTCCCTGAATCCCCAAGGTGGTTG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 238

CTCTCCGTCACGATTGGTATATTGCTTGCCTATTTGTTTGGCATGTTTGTTCCCTGGAGAATTCTTGCTGTTCTAGgtatgatgta ... catgttttagGCATTTTACCCTGTTCAATCCTGATTCCTGGACTGTTCTTTGTCCCTGAATCCCCAAGGTGGTTG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 172

CTCTCCGTCACGATTGGTATATTGCTTGCCTATTTGTTTGGCATGTTTGTTCCCTGGAGAATTCTTGCTGTTCTAGgtatgatgta ... catgttttagGCATTTTACCCTGTTCAATCCTGATTCCTGGACTGTTCTTTGTCCCTGAATCCCCAAGGTGGTTG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 148

CTCTCCGTCACGATTGGTATATTGCTTGCCTATTTGTTTGGCATGTTTGTTCCCTGGAGAATTCTTGCTGTTCTAGgtatgatgta ... catgttttagGCATTTTACCCTGTTCAATCCTGATTCCTGGACTGTTCTTTGTCCCTGAATCCCCAAGGTGGTTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttatttgtacagatcatcttcctaactacttttctgttacttctacatgttttagGCATTTTACCCTGTTCAATCCTGATTCCTGGACTGTTCTTTGTCCCTGAATCCCCAAGGTGGTTG
                   tcctaac  putative branch site (score: 148)
                                       cttctac  putative PPT
                                              atgtttta  TA-rich tract