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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcggtaacctttgcattgttttggctgatctcttctctttaatctctgtgttaaaccaatatcgtattttctgatgcagCATTATTCAGAGTTGCCTGATATCAAGCGTGTCATTGTAAATACTCATGCCATTGAGCCCCAG

Basic information

species Zea mays
transcript GRMZM2G057576_T02
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 15
lower sequence: LOC_Os12g01390.1 (Oryza sativa), 3'ss of exon 17
gtcggtaacctttgcattgttttggctga--tctcttctctttaatctctgtgttaaaccaatatcgtattttctgatgcagCATTATTCAGAGTTGCCTGATATCAAGCGTGTCATTGTAAATACTCATGCCATTGAGCCCCAG
||| ||| |||||   ||||||||| | |  | | || |  ||   || | |||| ||  || ||  |||| |  ||||||||||||  |||| || || ||||||||||||||||| || ||||| |||||||||||||| |||
gtcagta-cctttttgttgttttggtttacttttttttttctttgcctgtctgtttaattaacattatattgt--gatgcagCATTACACAGAATTACCAGATATCAAGCGTGTCATGGTGAATACCCATGCCATTGAGCCACAG

upper sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 15
lower sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 17
gtcggtaacctttgcattgttttggctga-tctcttctctttaatctctgtgttaaaccaatatcgtattttctgatgcagCATTATTCAGAGTTGCCTGATATCAAGCGTGTCATTGTAAATACTCATGCCATTGAGCCCCAG
||| ||| |||||   ||||||||| | | | | || |  ||   || | |||| ||  || ||  |||| |  ||||||||||||  |||| || || ||||||||||||||||| || ||||| |||||||||||||| |||
gtcagta-cctttttgttgttttggtttactttttttttctttgcctgtctgtttaattaacattatattgt--gatgcagCATTACACAGAATTACCAGATATCAAGCGTGTCATGGTGAATACCCATGCCATTGAGCCACAG

upper sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 15
lower sequence: GLYMA01G38580.1 (Glycine max), 3'ss of exon 17
-gtcggtaacctttgcattgttttggc----tgatctcttctctttaatctctgtgttaaaccaatatcgtattttctgatgcagCATTATTCAGAGTTGCCTGATATCAAGCGTGTCATTGTAAATACTCATGCCATTGAGCCCCAG
  ||  |     ||   || |  || |    | ||    |||  |||   | | | || ||||      |||| ||    ||||||||||| | ||||||||||| ||||| ||||||||||| ||||| |||||||||||||| |||
gttctttgcttcttaagttctgatgacagtataatgatctcttgttagaatatttcttgaaccgtgtctgtatatt---gtgcagCATTATACTGAGTTGCCTGACATCAAACGTGTCATTGTGAATACACATGCCATTGAGCCACAG

upper sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 15
lower sequence: GLYMA18G02960.1 (Glycine max), 3'ss of exon 16
------gtcggtaacctttgcattgttttggctgatctcttctcttta------atctctgtgttaaaccaatatcgtattttctgatgcagCATTATTCAGAGTTGCCTGATATCAAGCGTGTCATTGTAAATACTCATGCCATTGAGCCCCAG
             |  | ||  || || |  ||| | |  |   || |      | |  | | ||  ||  ||  |    ||| || ||||||||||  |||||||||| ||||| || ||||| ||||||||||| ||||| |||||||| |||
gtaatgactcaccaaatgtgttttattattactggttttcttatttaacccaaaagccttctcttttactgattacactatttttggtgcagCATTACACAGAGTTGCCAGATATAAAACGTGTGATTGTAAATACACATGCAATTGAGCCACAG

upper sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 15
lower sequence: GLYMA11G06720.1 (Glycine max), 3'ss of exon 17
-gtcggtaacctttgcattgttttggctg----atctcttctctttaatctctgtgttaaaccaatatcgtattttctgatgcagCATTATTCAGAGTTGCCTGATATCAAGCGTGTCATTGTAAATACTCATGCCATTGAGCCCCAG
  ||  |     ||   || |  || |||    || |  ||| ||||   | | | || ||||      || | ||    ||||||||||| | ||||||||||| ||||| ||||||||||| ||||| |||||||||||||| |||
gttctttgcttcttaagttctgatgactgtataatgttctctttttagaatatttcttgaaccttgtctgtgtatt---gtgcagCATTATACTGAGTTGCCTGACATCAAACGTGTCATTGTGAATACACATGCCATTGAGCCACAG

upper sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 15
lower sequence: GLYMA14G37510.1 (Glycine max), 3'ss of exon 15
gtcggtaacctttgcattgtt--ttggctgatctcttctctttaatctctgtgttaaaccaatatcgtatttt-ctgatgcagCATTATTCAGAGTTGCCTGATATCAAGCGTGTCATTGTAAATACTCATGCCATTGAGCCCCAG
||   |  | | |    |  |   || ||| | | |  | |   |    | | || ||||  | | || | || ||  ||||||||||||| ||||||||||| ||||| ||||||||||| ||||| |||||||| || || |||
gttctttgcttctattcttatgactgactgttatttcttgtcagaataatttcttgaacct-tcttgtgtgttgcttgtgcagCATTATTCCGAGTTGCCTGACATCAAACGTGTCATTGTGAATACACATGCCATCGAACCGCAG

upper sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 15
lower sequence: GLYMA11G35460.1 (Glycine max), 3'ss of exon 16
------gtcggtaacctttgcattgttttggctgatctcttctctttaatc------tctgtgttaaaccaatatcgtattttctgatgcagCATTATTCAGAGTTGCCTGATATCAAGCGTGTCATTGTAAATACTCATGCCATTGAGCCCCAG
             |  | ||  || || |  ||| | |  |   || |  |        | | ||  |   ||  | |  ||| || ||||||||||  |||||||||| ||||| || ||||| ||||||||||| ||||| |||||||| |||
gtaatgactcaccaaatgtgttttattcttactggttttcttatttaacccaaaggccttctcttttattgattacattatttttggtgcagCATTACACAGAGTTGCCAGATATAAAACGTGTAATTGTAAATACACATGCAATTGAGCCACAG

upper sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 15
lower sequence: GLYMA02G39360.1 (Glycine max), 3'ss of exon 17
gtcggtaacctttgcattgttttggctgatc----tcttctctttaatctctgtgttaaaccaatatcgtatttt-ctgatgcagCATTATTCAGAGTTGCCTGATATCAAGCGTGTCATTGTAAATACTCATGCCATTGAGCCCCAG
||   |  | |||  ||| || || ||||      | |  | |   |    | | || ||||  | | || | || || |||||||||||||| || |||||||| ||||| ||||||||||| ||||| |||||||| || || |||
gttctttgctttt--attcttatgactgactgtaatttcttgtcagaataatttcttgaacct-tcttgtgtgttgcttatgcagCATTATTCCGAATTGCCTGACATCAAACGTGTCATTGTGAATACACATGCCATCGAACCACAG

upper sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 15
lower sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 17
-------gtcggtaacctttgcattgttttgg--ctgatctcttctctttaatctctgtgttaaaccaatatcgtattttctgatgcagCATTATTCAGAGTTGCCTGATATCAAGCGTGTCATTGTAAATACTCATGCCATTGAGCCCCAG
        ||  |  | | |  | | || | |  || ||   |    |||  | ||     |||     | || | ||   |  |||||||||| |||||||| ||||||||||| ||||| ||||| || || ||||| |||||||| |||
gtttttgctcaatgtcttctttaatattcttggcctaatagatgtatttttttttcccctctaacttcgtttccttttgctttgtgcagCATTACTCAGAGTTACCTGATATCAAACGTGTAATTGTGAACACACATGCTATTGAGCCACAG

upper sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 15
lower sequence: Vv13s0067g01290.t01 (Vitis vinifera), 3'ss of exon 17
--gtcggtaacctttgca--ttgttttggctgatctctt--ctctttaatctctgtgttaaaccaatatcgtatttt-----------------ctgatgcagCATTATTCAGAGTTGCCTGATATCAAGCGTGTCATTGTAAATACTCATGCCATTGAGCCCCAG
  |    |     |||||  |  ||||   | || | ||  || ||| ||   |   | |||  |||      | ||                  |  ||||||||||| | |||||||| ||||| || || |||||||| ||||| ||||| |||||||| |||
gtgaaattggttcttgcaattcattttattttattttttaccttttttattgttacatgaaattaattatacgtcttggttaaaacacttatattttgtgcagCATTATACTGAGTTGCCAGATATAAAACGCGTCATTGTGAATACACATGCAATTGAGCCACAG

upper sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 15
lower sequence: Vv06s0004g06860.t01 (Vitis vinifera), 3'ss of exon 17
--------gtcggtaacctttgcattgttttggctgatctcttc--tctttaatctctgtgttaaaccaatatcgtattttctgatgcagCATTATTCAGAGTTGCCTGATATCAAGCGTGTCATTGTAAATACTCATGCCATTGAGCCCCAG
        ||   | ||  |   |||| |     | || ||      |||| ||   | | ||  |  ||     |  | ||| |||||||||||| | || ||||| |||||||| ||||||||||| || || |||||||||||||| |||
gtataatggtttctcactatctgattgatgaactttatttcacagacctttgattgtt-tcttggattaaatgattcatctcttatgcagCATTATACTGAATTGCCCGATATCAAACGTGTCATTGTGAACACACATGCCATTGAGCCACAG

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|16137384|gb|BI894249.1|BI894249
EST:     GTATTGCTCAGCTCTGTGAAAAGGCTGGATTATACTTGCGTGCCCTCCAG                         CATTATTCAGAGTTGCCTGATATCAAGCGTGTCATTGTAAATACTCATGCC
genomic: GTATTGCTCAGCTCTGTGAAAAGGCTGGATTATACTTGCGTGCCCTCCAGgtcggtaacc ... tctgatgcagCATTATTCAGAGTTGCCTGATATCAAGCGTGTCATTGTAAATACTCATGCC
EST: gi|18384990|gb|BM418189.1|BM418189
EST:     GTATTGCTCAGCTCTGTGAAAAGGCTGGATTATACTTGCGTGCCCTCCAG                         CATTATTCAGAGTTGCCTGATATCAAGCGTGTCATTGTAAATACTCATGCC
genomic: GTATTGCTCAGCTCTGTGAAAAGGCTGGATTATACTTGCGTGCCCTCCAGgtcggtaacc ... tctgatgcagCATTATTCAGAGTTGCCTGATATCAAGCGTGTCATTGTAAATACTCATGCC
EST: gi|15188223|gb|BI417200.1|BI417200
EST:     GTATTGCTCAGCTCTGTGAAAAGGCTGGATTATACTTGCGTGCCCTCCAG                         CATTATTCAGAGTTGCCTGATATCAAGCGTGTCATTGTAAATACTCATGCC
genomic: GTATTGCTCAGCTCTGTGAAAAGGCTGGATTATACTTGCGTGCCCTCCAGgtcggtaacc ... tctgatgcagCATTATTCAGAGTTGCCTGATATCAAGCGTGTCATTGTAAATACTCATGCC
EST: gi|18385023|gb|BM418222.1|BM418222
EST:     GTATTGCTCAGCTCTGTGAAAAGGCTGGATTATACTTGCGTGCCCACCAG                         CATTATTCAGAGTTGCCTGATATCAAGCGTGTCATTGTAAATACTCATGCC
genomic: GTATTGCTCAGCTCTGTGAAAAGGCTGGATTATACTTGCGTGCCCTCCAGgtcggtaacc ... tctgatgcagCATTATTCAGAGTTGCCTGATATCAAGCGTGTCATTGTAAATACTCATGCC
EST: gi|22489541|gb|BU049464.1|BU049464
EST:     GGCTGGATTATACTTGCGTGCCCTCCAG                         CATTATTCAGAGTTGCCTGATATCAAGCGTGTCATTGTAAATACTCATGCC
genomic: GGCTGGATTATACTTGCGTGCCCTCCAGgtcggtaacc ... tctgatgcagCATTATTCAGAGTTGCCTGATATCAAGCGTGTCATTGTAAATACTCATGCC
EST: gi|18053133|gb|BM318791.1|BM318791
EST:     GTATTGCTCAGCTCTGTGAAAAGGCTGGATTATACTTGCGTGCCCTCCAG                         CATTATTCAGAGTTGCCTGATATCAAGCGTGTCATTGTAAATACTTATGCC
genomic: GTATTGCTCAGCTCTGTGAAAAGGCTGGATTATACTTGCGTGCCCTCCAGgtcggtaacc ... tctgatgcagCATTATTCAGAGTTGCCTGATATCAAGCGTGTCATTGTAAATACTCATGCC
EST: gi|15313673|gb|BI478897.1|BI478897
EST:     GTATTGCTCAGCTCTGTGAAAAGGCTGGATTATACTTGCGTGCCCTCCAG                         CATTATTCAGAGTTGCCTGATATCAAGCGTGTCATTGTAAATACTCATGCC
genomic: GTATTGCTCAGCTCTGTGAAAAGGCTGGATTATACTTGCGTGCCCTCCAGgtcggtaacc ... tctgatgcagCATTATTCAGAGTTGCCTGATATCAAGCGTGTCATTGTAAATACTCATGCC
EST: gi|15313671|gb|BI478896.1|BI478896
EST:     GTATTGCTCAGCTCTGTGAAAAGGCTGGATTATACTTGCGTGCCCTCCAG                         CATTATTCAGAGTTGCCTGATATCAAGCGTGTCATTGTAAATACTCATGCC
genomic: GTATTGCTCAGCTCTGTGAAAAGGCTGGATTATACTTGCGTGCCCTCCAGgtcggtaacc ... tctgatgcagCATTATTCAGAGTTGCCTGATATCAAGCGTGTCATTGTAAATACTCATGCC
EST: gi|15177612|gb|BI398551.1|BI398551
EST:     GTATTGCTCAGCTCTGTGAAAAGGCTGGATTATACTTGCGTGCCCTCCAG                         CATTATTCAGAGTTGCCTGATATCAAGCGTGTCATTGTAAATACTCATGCC
genomic: GTATTGCTCAGCTCTGTGAAAAGGCTGGATTATACTTGCGTGCCCTCCAGgtcggtaacc ... tctgatgcagCATTATTCAGAGTTGCCTGATATCAAGCGTGTCATTGTAAATACTCATGCC
EST: gi|88758497|gb|DY542866.1|DY542866
EST:     GTATTGCTCAGCTCTGTGAAAAGGCTGGATTATACTTGCGTGCCCTCCAG                         CATTATTCAGAGTTGCCTGATATCAAGCGTGTCATTGTAAATACTCATGCC
genomic: GTATTGCTCAGCTCTGTGAAAAGGCTGGATTATACTTGCGTGCCCTCCAGgtcggtaacc ... tctgatgcagCATTATTCAGAGTTGCCTGATATCAAGCGTGTCATTGTAAATACTCATGCC
EST: gi|32929052|gb|CF033864.1|CF033864
EST:     CGTGCCCTCCAG                         CATTATTCAGAGTTGCCTGATATCAAGCGTGTCATTGTAAATACTCATGCC
genomic: CGTGCCCTCCAGgtcggtaacc ... tctgatgcagCATTATTCAGAGTTGCCTGATATCAAGCGTGTCATTGTAAATACTCATGCC

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: 44 (upstream exon), 49 (downstream exon)
Score: 149

TGCAGATGCCATTCTTGCGAATGGTATGTTCAGTCATTATGACCGTCCTCGTATTGCTCAGCTCTGTGAAAAGGCTGGATTATACTTGCGTGCCCTCCAGgtcggtaacc ... tctgatgcagCATTATTCAGAGTTGCCTGATATCAAGCGTGTCATTGTAAATACTCATGCCATTGAGCCCCAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 118

TGCAGATGCCATTCTTGCGAATGGTATGTTCAGTCATTATGACCGTCCTCGTATTGCTCAGCTCTGTGAAAAGGCTGGATTATACTTGCGTGCCCTCCAGgtcggtaacc ... tctgatgcagCATTATTCAGAGTTGCCTGATATCAAGCGTGTCATTGTAAATACTCATGCCATTGAGCCCCAG


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 80

TGCAGATGCCATTCTTGCGAATGGTATGTTCAGTCATTATGACCGTCCTCGTATTGCTCAGCTCTGTGAAAAGGCTGGATTATACTTGCGTGCCCTCCAGgtcggtaacc ... tctgatgcagCATTATTCAGAGTTGCCTGATATCAAGCGTGTCATTGTAAATACTCATGCCATTGAGCCCCAG


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 178

TGCAGATGCCATTCTTGCGAATGGTATGTTCAGTCATTATGACCGTCCTCGTATTGCTCAGCTCTGTGAAAAGGCTGGATTATACTTGCGTGCCCTCCAGgtcggtaacc ... tctgatgcagCATTATTCAGAGTTGCCTGATATCAAGCGTGTCATTGTAAATACTCATGCCATTGAGCCCCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgatctcttctctttaatctctgtgttaaaccaatatcgtattttctgatgcagCATTATTCAGAGTTGCCTGATATCAAGCGTGTCATTGTAAATACTCATGCCATTGAGCCCCAG
                                            ttctgat  putative branch site (score: 178)
                                        tattttct  CT-rich tract
           tctttaat  TA-rich tract