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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactttctgtgctcatggcctcagcttcttgttctgattagtattgttggttagactggagttgtgaaatttgcttttgtgaatctgcagGTGGTTCTGATGGCCTTCGAGTGCCCACATTGTGGTGAGAG

Basic information

species Zea mays
transcript GRMZM2G351582_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G351582_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os08g36774.1 (Oryza sativa), 3'ss of exon 2
-----------gtactttctgtgctcatggcctcagcttcttgttctgattagtattgttggttagactggagt--tgtgaaatttgcttttgtgaatctgcagGTGGTTCTGATGGCCTTCGAGTGCCCACATTGTGGTGAGAG
            ||  |   |||| |||   |   | |   ||  |||| |  |  |  |  | |  |  |||   |||  ||||  | ||||| ||||||||||||||||||||||| ||||||||||| ||||| ||||||||
gtgagattagattagctctcgtgc-cattctcattggtggctgaactgactgctgcttgttctcattcgagagcggtgtcgaattcacgtttgtaaatctgcagGTGGTTCTGATGGCTTTCGAGTGCCCGCATTGCGGTGAGAG
















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|149027382|gb|EE046514.2|EE046514
EST:     GGCATCACGAGGCTTTTGCTGACGTTGATCCCGCACTTCCGGGAG                         GTGGTTCTGATGGCCTTCGAGTGCCCACATTGTGGTGAGAG
genomic: GGCATCACGAGGCTTTTGCTGACGTTGATCCCGCACTTCCGGGAGgtactttctg ... gaatctgcagGTGGTTCTGATGGCCTTCGAGTGCCCACATTGTGGTGAGAG
EST: gi|88755472|gb|DY539613.1|DY539613
EST:     GGCATCACGAGGCTTTTGCTGACGTTGATCCCGCACTTCCGGGAG                         GTGGTTCTGATGGCCTTCGAGTGCCCACATTGTGGTGAGAG
genomic: GGCATCACGAGGCTTTTGCTGACGTTGATCCCGCACTTCCGGGAGgtactttctg ... gaatctgcagGTGGTTCTGATGGCCTTCGAGTGCCCACATTGTGGTGAGAG
EST: gi|149058050|gb|EE156735.2|EE156735
EST:     GGCATCACGAGGCTTTTGCTGACGTTGATCCCGCACTTCCGGGAG                         GTGGTTCTGATGGCCTTCGAGTGCCCACATTGTGGTGAGAG
genomic: GGCATCACGAGGCTTTTGCTGACGTTGATCCCGCACTTCCGGGAGgtactttctg ... gaatctgcagGTGGTTCTGATGGCCTTCGAGTGCCCACATTGTGGTGAGAG
EST: gi|87152120|gb|DY396909.1|DY396909
EST:     GGCATCACGAGGCTTTTGCTGACGTTGATCCCGCACTTCCGGGAG                         GTGGTTCTGATGGCCTTCGAGTGCCCACATTGTGGTGAGAG
genomic: GGCATCACGAGGCTTTTGCTGACGTTGATCCCGCACTTCCGGGAGgtactttctg ... gaatctgcagGTGGTTCTGATGGCCTTCGAGTGCCCACATTGTGGTGAGAG
EST: gi|211353775|gb|FL303049.1|FL303049
EST:     GGCATCACGAGGCTTTTGCTGACGTTGATCCCGCACTTCCGGGAG                         GTGGTTCTGATGGCCTTCGAGTGCCCACATTGTGGTGAGAG
genomic: GGCATCACGAGGCTTTTGCTGACGTTGATCCCGCACTTCCGGGAGgtactttctg ... gaatctgcagGTGGTTCTGATGGCCTTCGAGTGCCCACATTGTGGTGAGAG
EST: gi|5740519|gb|AI948209.1|AI948209
EST:     GGCATCACGAGGCTTTTGCTGACGTTGATCCCGCACTTCCGGGAG                         GGGGNTCTGATGGCCTTCGAGTGCCCACATT
genomic: GGCATCACGAGGCTTTTGCTGACGTTGATCCCGCACTTCCGGGAGgtactttctg ... gaatctgcagGTGGTTCTGATGGCCTTCGAGTGCCCACATT
EST: gi|18450704|gb|BM428982.1|BM428982
EST:     GGCATCACGAGGCTTTTGCTGACGTTGATCCCGCACTTCCGGGAG                         GTGGTTCTGATGGCCTTCGAGTGCCCACATTGTGGTGAGAG
genomic: GGCATCACGAGGCTTTTGCTGACGTTGATCCCGCACTTCCGGGAGgtactttctg ... gaatctgcagGTGGTTCTGATGGCCTTCGAGTGCCCACATTGTGGTGAGAG
EST: gi|78022867|gb|DV491254.1|DV491254
EST:     GGCATCACGAGGCTTTTGCTGACGTTGATCCCGCACTTCCGGGAG                         GTGGTTCTGATGGCCTTCGAGTGCCCACATTGTGGTGAGAG
genomic: GGCATCACGAGGCTTTTGCTGACGTTGATCCCGCACTTCCGGGAGgtactttctg ... gaatctgcagGTGGTTCTGATGGCCTTCGAGTGCCCACATTGTGGTGAGAG
EST: gi|148996196|gb|EE035468.2|EE035468
EST:     GGCATCACGAGGCTTTTGCTGACGTTGATCCCGCACTTCCGGGAG                         GTGGTTCTGATGGCCTTCGAGTGCCCACATTGTGGTGAGAG
genomic: GGCATCACGAGGCTTTTGCTGACGTTGATCCCGCACTTCCGGGAGgtactttctg ... gaatctgcagGTGGTTCTGATGGCCTTCGAGTGCCCACATTGTGGTGAGAG

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: 47 (upstream exon), 49 (downstream exon)
Score: 327

GGCATCACGAGGCTTTTGCTGACGTTGATCCCGCACTTCCGGGAGgtactttctg ... gaatctgcagGTGGTTCTGATGGCCTTCGAGTGCCCACATTGTGGTGAGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 205

GGCATCACGAGGCTTTTGCTGACGTTGATCCCGCACTTCCGGGAGgtactttctg ... gaatctgcagGTGGTTCTGATGGCCTTCGAGTGCCCACATTGTGGTGAGAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 195

GGCATCACGAGGCTTTTGCTGACGTTGATCCCGCACTTCCGGGAGgtactttctg ... gaatctgcagGTGGTTCTGATGGCCTTCGAGTGCCCACATTGTGGTGAGAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 199

GGCATCACGAGGCTTTTGCTGACGTTGATCCCGCACTTCCGGGAGgtactttctg ... gaatctgcagGTGGTTCTGATGGCCTTCGAGTGCCCACATTGTGGTGAGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gattagtattgttggttagactggagttgtgaaatttgcttttgtgaatctgcagGTGGTTCTGATGGCCTTCGAGTGCCCACATTGTGGTGAGAG
 ttctgat  putative branch site (score: 199)
                             tgaaattt  TA-rich tract