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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgcatgtgttcaccactgggaatgtggtattgctgagagtttgacatcagtggcattttctttgtataacctgtttgagtctgtattaatcaagtctgtaattggcagGATAATTGGAATAATTTGGAAAAGCCTTATGGAAGCATATTTTTAAGTATCCCTACAGTTCTTGATCCATCATTAGCTCCCGAAGGACATCATATACTTC

Basic information

species Zea mays
transcript GRMZM2G106531_T01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G106531_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os11g36440.1 (Oryza sativa), 3'ss of exon 8
gtatgcatgtgttcaccactgggaatgtggtattgctgagagtttgacatcagtggcattttctttgtataacctgtttgagtctgtattaatcaagtc-----tgtaattggcagGATAATTGGAATAATTTGGAAAAGCCTTATGGAAGCATATTTTTAAGTATCCCTACAGTTCTTGATCCATCATTAGCTCCCGAAGGACATCATATACTTC
||| | |||  | |||   |||| ||  | |||  | |  | |  |    || ||  |  ||  |   | |||  |||| ||||  || |||   | |      |  ||||| |||||| | |||  ||||||||| |||||||||||||||||||||||||||||||||||||| ||||| ||||| || |||||||||||||| ||||||||||
gtaggtatgactccactg-tgggtatcagatatcacaggcaatgggtacacaatgctaagttggt-acacaaca-gttttagtccataataacttaattctaattacaattgccagGATGACTGGGCTAATTTGGAGAAGCCTTATGGAAGCATATTTTTAAGTATCCCTACAGTGCTTGACCCATCCTTGGCTCCCGAAGGACACCATATACTTC
















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|160481285|gb|EY254207.1|EY254207
EST:     AAGCGTCAGTTCTGCCTGCTGGCACTGACTGCCACCATTTTATACTTGAG                         GATAATTGGAATAATTTGGAAAAGCCTTATGGAAGCATATTTTTAAGTATC
genomic: AAGCGTCAGTTCTGCCTGCTGGCACTGACTGCCACCATTTTATACTTGAGgtatgcatgt ... taattggcagGATAATTGGAATAATTTGGAAAAGCCTTATGGAAGCATATTTTTAAGTATC




















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), 47 (downstream exon)
Score: 25

AAAGAATTACGTTAAGGCACCATCATTCCTTTCAATTCATATGGGTGTCAAAGCGTCAGTTCTGCCTGCTGGCACTGACTGCCACCATTTTATACTTGAGgtatgcatgt ... taattggcagGATAATTGGAATAATTTGGAAAAGCCTTATGGAAGCATATTTTTAAGTATCCCTACAGTTCTTGATCCATCATTAGCTCCCGAAGGACATCATATACTTC


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 26

AAAGAATTACGTTAAGGCACCATCATTCCTTTCAATTCATATGGGTGTCAAAGCGTCAGTTCTGCCTGCTGGCACTGACTGCCACCATTTTATACTTGAGgtatgcatgt ... taattggcagGATAATTGGAATAATTTGGAAAAGCCTTATGGAAGCATATTTTTAAGTATCCCTACAGTTCTTGATCCATCATTAGCTCCCGAAGGACATCATATACTTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 29

AAAGAATTACGTTAAGGCACCATCATTCCTTTCAATTCATATGGGTGTCAAAGCGTCAGTTCTGCCTGCTGGCACTGACTGCCACCATTTTATACTTGAGgtatgcatgt ... taattggcagGATAATTGGAATAATTTGGAAAAGCCTTATGGAAGCATATTTTTAAGTATCCCTACAGTTCTTGATCCATCATTAGCTCCCGAAGGACATCATATACTTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 31

AAAGAATTACGTTAAGGCACCATCATTCCTTTCAATTCATATGGGTGTCAAAGCGTCAGTTCTGCCTGCTGGCACTGACTGCCACCATTTTATACTTGAGgtatgcatgt ... taattggcagGATAATTGGAATAATTTGGAAAAGCCTTATGGAAGCATATTTTTAAGTATCCCTACAGTTCTTGATCCATCATTAGCTCCCGAAGGACATCATATACTTC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cattttctttgtataacctgtttgagtctgtattaatcaagtctgtaattggcagGATAATTGGAATAATTTGGAAAAGCCTTATGGAAGCATATTTTTAAGTATCCCTACAGTTCTTGATCCATCATTAGCTCCCGAAGGACATCATATACTTC
                              tattaat  putative branch site (score: 31)
                              tattaatcaa  TA-rich tract