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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaacttctagatttgacttttcttctgtaagtcttccagataccagttttgacatgactcattgatttctctgccagGTATGACCTCAATGTTGATCTCTTAGATGTTCATGCTGATAAGAGTACATTTCATCGTTTTGACAAGTTCAATCTGAAATATAATCCATGTGGTCAATCT

Basic information

species Zea mays
transcript GRMZM2G134396_T03
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G134396_T02 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os07g49270.1 (Oryza sativa), 3'ss of exon 9
-----gtaacttctagatttgacttttcttctgtaagtcttccagatac--cagttttgacatgactca--ttgatttctctgccagGTATGACCTCAATGTTGATCTCTTAGATGTTCATGCTGATAAGAGTACATTTCATCGTTTTGACAAGTTCAATCTGAAATATAATCCATGTGGTCAATCT
       || ||||  || |||   ||||    |   ||||     ||    | |||| |  | ||     ||     ||||||||| ||||||||||||||||||||||||||||| ||||| ||||| |||||||| ||||| ||||||||||||||| |||| |||||||| ||||| ||||| 
gtaactgaaattctttatgtgatggttctgtcatgtatcttttgattaagatattttttaactaacctgcttttgccactctgccagTTATGACCTCAATGTTGATCTCTTAGATGTGCATGCCGATAAAAGTACATTCCATCGCTTTGACAAGTTCAATTTGAAGTATAATCCTTGTGGCCAATCC

upper sequence: GRMZM2G134396_T02 (Zea mays), 3'ss of exon 8
lower sequence: PP1S168_82V6.1 (Physcomitrella patens), 3'ss of exon 8
-----------gtaact-tctagatttgacttttcttctgtaagtcttccagataccagttttg---acatgactcattgatttc---tctgc----cagGTATGACCTCAATGTTGATCTCTTAGATGTTCATGCTGATAAGAGTACATTTCATCGTTTTGACAAGTTCAATCTGAAATATAATCCATGTGGTCAATCT
            ||| | | |   |||   |||| |  | ||   |||  | ||     |  ||   |  |  |    || | |    ||||     ||| || ||||| ||||| ||  |  | |||||||||||||| || | ||| ||||||||||| ||||||||||| |||||||| ||||| ||||| ||   |
gctttcgtcttctaattatttttgtttcctttttatagtataccactttgaaatgattttcatgtatatctaccgtgctggtcttgtgtctgaattgcagTTACGACCTTAATGTGGACTTGCTGGATGTTCATGCTGACAAAAATACGTTTCATCGTTTCGACAAGTTCAACCTGAAATACAATCCTTGTGGCCAGAGT

upper sequence: GRMZM2G134396_T02 (Zea mays), 3'ss of exon 8
lower sequence: PP1S77_89V6.1 (Physcomitrella patens), 3'ss of exon 8
--------------gtaacttctagatttgac--ttttcttctgtaagtcttccagata-ccagttttgaca-tgactcattgatttctctgc----cagGTATGACCTCAATGTTGATCTCTTAGATGTTCATGCTGATAAGAGTACATTTCATCGTTTTGACAAGTTCAATCTGAAATATAATCCATGTGGTCAATCT
               |   | | | ||   ||  |||| | |  |||  ||   |  |    | |      | ||  |   |  ||| | | |    ||| ||||| |||||||| ||| |  | ||||| |||||||| |||| ||||||||| || || |||||||||||  |||| |||||||| ||||| ||   |
tcaatttgtaaatcatttttccaaaataacacatttttataccttaatgctgttaagtggttaatgcgtgtactgtattggtattttgtgtacatttcagTTATGATCTCAATGTCGATTTGCTGGATGTCCATGCTGACAAGAATACATTTCACCGATTCGACAAGTTCAACTTGAAGTATAATCCTTGTGGCCAGAGT

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|71772853|gb|DR970776.1|DR970776
EST:     GGGACCTATTTGACTCTTAAGGAGGTTTTTGAGAGTTTGGATTTGACAGG                         GTATGACCTCAATGTTGATCTCTTAGATGTTCATGCTGATAAGAGTACATT
genomic: GGGACCTATTTGACTCTTAAGGAGGTTTTTGAGAGTTTGGATTTGACAGGgtaacttcta ... tctctgccagGTATGACCTCAATGTTGATCTCTTAGATGTTCATGCTGATAAGAGTACATT
EST: gi|32929645|gb|CF034457.1|CF034457
EST:     GGAACCTATTTGACTCTTAAGGAGGTTTTTGAGAGTTTGGATTTGACAGG                         GTATGACCTCAATGTTGATCTCTTAGATGTTCATGCTGATAAGAGT
genomic: GGGACCTATTTGACTCTTAAGGAGGTTTTTGAGAGTTTGGATTTGACAGGgtaacttcta ... tctctgccagGTATGACCTCAATGTTGATCTCTTAGATGTTCATGCTGATAAGAGT
EST: gi|32863100|gb|CF002782.1|CF002782
EST:     GGAACCTATTTGACTCTTAAGGAGGTTTTTGAGAGTTTGGATTTGACAGG                         GTATGACCTCAATGTTGATCTCTTAGATGTTCATGCTGATAAGAGTACATT
genomic: GGGACCTATTTGACTCTTAAGGAGGTTTTTGAGAGTTTGGATTTGACAGGgtaacttcta ... tctctgccagGTATGACCTCAATGTTGATCTCTTAGATGTTCATGCTGATAAGAGTACATT

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: 170

GTTGTAATCTTTAGAGATGGGACCTATTTGACTCTTAAGGAGGTTTTTGAGAGTTTGGATTTGACAGGgtaacttcta ... tctctgccagGTATGACCTCAATGTTGATCTCTTAGATGTTCATGCTGATAAGAGTACATTTCATCGTTTTGACAAGTTCAATCTGAAATATAATCCATGTGGTCAATCT


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 168

GTTGTAATCTTTAGAGATGGGACCTATTTGACTCTTAAGGAGGTTTTTGAGAGTTTGGATTTGACAGGgtaacttcta ... tctctgccagGTATGACCTCAATGTTGATCTCTTAGATGTTCATGCTGATAAGAGTACATTTCATCGTTTTGACAAGTTCAATCTGAAATATAATCCATGTGGTCAATCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 300

GTTGTAATCTTTAGAGATGGGACCTATTTGACTCTTAAGGAGGTTTTTGAGAGTTTGGATTTGACAGGgtaacttcta ... tctctgccagGTATGACCTCAATGTTGATCTCTTAGATGTTCATGCTGATAAGAGTACATTTCATCGTTTTGACAAGTTCAATCTGAAATATAATCCATGTGGTCAATCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 163

GTTGTAATCTTTAGAGATGGGACCTATTTGACTCTTAAGGAGGTTTTTGAGAGTTTGGATTTGACAGGgtaacttcta ... tctctgccagGTATGACCTCAATGTTGATCTCTTAGATGTTCATGCTGATAAGAGTACATTTCATCGTTTTGACAAGTTCAATCTGAAATATAATCCATGTGGTCAATCT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctgtaagtcttccagataccagttttgacatgactcattgatttctctgccagGTATGACCTCAATGTTGATCTCTTAGATGTTCATGCTGATAAGAGTACATTTCATCGTTTTGACAAGTTCAATCTGAAATATAATCCATGTGGTCAATCT
                                           tttctctgcc  CT-rich tract
                                      attgattt  TA-rich tract