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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaccgccctcacctcctcggttccgccggtcgattagggttcgagtcagtgtagtcgcccatcagtcgcgctggaagcttgttagctttgttatttgagctccccactctgtgttcgtcgacccccctctggatcccgcctatccggcgtggtctcacgaattagtatgtgggttcacagGTCGACAGCCGCAGCCAGTCCGCCGGGAAGCGCGCGCGCACCGACG

Basic information

species Zea mays
transcript GRMZM2G134770_T03
intron # 1
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|89756650|gb|DY686607.1|DY686607
EST:     GTTCGCCCGCCGCCGCCGCCTCCGGTTCATCGCCAGCTATGTCTTCTCAG                         GTCGACAGCCGCAGCCA
genomic: GTTCGCCCGCCGCCGCCGCCACCGGTTCATCGCCAGCTATGTCTTCTCAGgtaccgccct ... gggttcacagGTCGACAGCCGCAGCCA
EST: gi|211157322|gb|FK993534.1|FK993534
EST:     AGCTATGTCTTCTCAG                         GTCGACAGCCGCAGCCAGTCCGCCGGGAAGCGCGCGCGCACCGACG
genomic: AGCTATGTCTTCTCAGgtaccgccct ... gggttcacagGTCGACAGCCGCAGCCAGTCCGCCGGGAAGCGCGCGCGCACCGACG
EST: gi|94480167|gb|EB709125.1|EB709125
EST:     CCGCCGCCGCCACCGGTTCATCGCCAGCTATGTCTTCTCAG                         GTCGACAGCCGCAGCCAGTCCGCCGGGAAGCGCGCGCGCACCGACG
genomic: CCGCCGCCGCCACCGGTTCATCGCCAGCTATGTCTTCTCAGgtaccgccct ... gggttcacagGTCGACAGCCGCAGCCAGTCCGCCGGGAAGCGCGCGCGCACCGACG

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), 46 (downstream exon)
Score: 94

GTCTGCGCTTGTCCCTCCCGTTCCAAGGAGCACGTGCTTCTCGCCGCGCCGTTCGCCCGCCGCCGCCGCCACCGGTTCATCGCCAGCTATGTCTTCTCAGgtaccgccct ... gggttcacagGTCGACAGCCGCAGCCAGTCCGCCGGGAAGCGCGCGCGCACCGACG


Block sizes: 47 (upstream exon), 45 (downstream exon)
Score: 17

GTCTGCGCTTGTCCCTCCCGTTCCAAGGAGCACGTGCTTCTCGCCGCGCCGTTCGCCCGCCGCCGCCGCCACCGGTTCATCGCCAGCTATGTCTTCTCAGgtaccgccct ... gggttcacagGTCGACAGCCGCAGCCAGTCCGCCGGGAAGCGCGCGCGCACCGACG


Block sizes: 44 (upstream exon), 30 (downstream exon)
Score: 14

GTCTGCGCTTGTCCCTCCCGTTCCAAGGAGCACGTGCTTCTCGCCGCGCCGTTCGCCCGCCGCCGCCGCCACCGGTTCATCGCCAGCTATGTCTTCTCAGgtaccgccct ... gggttcacagGTCGACAGCCGCAGCCAGTCCGCCGGGAAGCGCGCGCGCACCGACG


Block sizes: 45 (upstream exon), 46 (downstream exon)
Score: 34

GTCTGCGCTTGTCCCTCCCGTTCCAAGGAGCACGTGCTTCTCGCCGCGCCGTTCGCCCGCCGCCGCCGCCACCGGTTCATCGCCAGCTATGTCTTCTCAGgtaccgccct ... gggttcacagGTCGACAGCCGCAGCCAGTCCGCCGGGAAGCGCGCGCGCACCGACG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cctctggatcccgcctatccggcgtggtctcacgaattagtatgtgggttcacagGTCGACAGCCGCAGCCAGTCCGCCGGGAAGCGCGCGCGCACCGACG
                          gtctcac  putative branch site (score: 34)
                                  aattagtat  TA-rich tract