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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatcctctctcaatgttatgccgtgcactcgttctctcaatgtccaggaaaagaaagttatgatatagtcaatgttcttcttcttcctagtcttgtatgtgcttcttggtcactttgagtttgcttgttatgtgtaaacagGAAGAGGAAATCGCCAGATTACATGCAAAACTTAGTCAAACGGAAATTCATGCTACCAGTTTGATCTCGAGGCTTGAG

Basic information

species Zea mays
transcript GRMZM2G098129_T01
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|60353496|gb|DN220469.1|DN220469
EST:     AGAGGGAAGATGCTTTGAGGTCAGAGCTTGCTAACCAGCTATCTGAGAAG                         GAAGAGGAAATCGCCGAGATTACATGCAAAACTTAGTCAAACGGAAATTCA
genomic: AGAGGGAAGATGCTTTGAGGTCAGAGCTTGCTAACCAGCTATCTGAGAAGgtaatcctct ... gtgtaaacagGAAGAGGAAATCGCC-AGATTACATGCAAAACTTAGTCAAACGGAAATTCA
EST: gi|21843270|gb|BQ703851.1|BQ703851
EST:     AGAGGGAAGATGCTTTGAGGTCAGAGCTTGCTAACCAGCTATCTGAGAAG                         GAAGAGGAAATCGCCAGATTACATGCAAAACTTAGTCAAACGGAAATTCAT
genomic: AGAGGGAAGATGCTTTGAGGTCAGAGCTTGCTAACCAGCTATCTGAGAAGgtaatcctct ... gtgtaaacagGAAGAGGAAATCGCCAGATTACATGCAAAACTTAGTCAAACGGAAATTCAT
EST: gi|211025429|gb|FL195732.1|FL195732
EST:     AGAGGGAAGATGCTTTGAGGTCAGAGCTTGCTAACCAGCTATCTGAGAAG                         GAAGAGGAAATCGCCAGATTACATGCAAAACTTAGTCAAACGGAAATTCAT
genomic: AGAGGGAAGATGCTTTGAGGTCAGAGCTTGCTAACCAGCTATCTGAGAAGgtaatcctct ... gtgtaaacagGAAGAGGAAATCGCCAGATTACATGCAAAACTTAGTCAAACGGAAATTCAT
EST: gi|26557892|gb|CA830127.1|CA830127
EST:     AGAGGGAAGATGCTTTGAGGTCAGAGCTTGCTAACCAGCTATCTGAGAAG                         GAAGAGGAAATCGCCAGATTACATGCAAAACTTAGTCAAACGGAAATTCAT
genomic: AGAGGGAAGATGCTTTGAGGTCAGAGCTTGCTAACCAGCTATCTGAGAAGgtaatcctct ... gtgtaaacagGAAGAGGAAATCGCCAGATTACATGCAAAACTTAGTCAAACGGAAATTCAT

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: 48 (upstream exon), 49 (downstream exon)
Score: 87

TCTGCAGAGAGCGGCTGTAGCACAGGAACGCACAAATAAGAAAGTGCAAGAGAGGGAAGATGCTTTGAGGTCAGAGCTTGCTAACCAGCTATCTGAGAAGgtaatcctct ... gtgtaaacagGAAGAGGAAATCGCCAGATTACATGCAAAACTTAGTCAAACGGAAATTCATGCTACCAGTTTGATCTCGAGGCTTGAG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 32

TCTGCAGAGAGCGGCTGTAGCACAGGAACGCACAAATAAGAAAGTGCAAGAGAGGGAAGATGCTTTGAGGTCAGAGCTTGCTAACCAGCTATCTGAGAAGgtaatcctct ... gtgtaaacagGAAGAGGAAATCGCCAGATTACATGCAAAACTTAGTCAAACGGAAATTCATGCTACCAGTTTGATCTCGAGGCTTGAG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 14

TCTGCAGAGAGCGGCTGTAGCACAGGAACGCACAAATAAGAAAGTGCAAGAGAGGGAAGATGCTTTGAGGTCAGAGCTTGCTAACCAGCTATCTGAGAAGgtaatcctct ... gtgtaaacagGAAGAGGAAATCGCCAGATTACATGCAAAACTTAGTCAAACGGAAATTCATGCTACCAGTTTGATCTCGAGGCTTGAG


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 21

TCTGCAGAGAGCGGCTGTAGCACAGGAACGCACAAATAAGAAAGTGCAAGAGAGGGAAGATGCTTTGAGGTCAGAGCTTGCTAACCAGCTATCTGAGAAGgtaatcctct ... gtgtaaacagGAAGAGGAAATCGCCAGATTACATGCAAAACTTAGTCAAACGGAAATTCATGCTACCAGTTTGATCTCGAGGCTTGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctagtcttgtatgtgcttcttggtcactttgagtttgcttgttatgtgtaaacagGAAGAGGAAATCGCCAGATTACATGCAAAACTTAGTCAAACGGAAATTCATGCTACCAGTTTGATCTCGAGGCTTGAG
                                      ttgttat  TA-rich tract