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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgtgctgtacactctgaaatgcatctacattatgcctttggaagcactatgctcctgagctaaccactgacagatcaaaattttgctttccgcagTTTCTGACCTGGAGATGCTCTTTGGGAGGCTATGGACACAATGCCAGGAGTGCCAAGGATCTCTGCACCAGGACGTTCTCTGCACAAG

Basic information

species Zea mays
transcript GRMZM2G115245_T01
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G115245_T01 (Zea mays), 3'ss of exon 12
lower sequence: LOC_Os11g08330.1 (Oryza sativa), 3'ss of exon 28
gtacgtgctgtacactctgaaatgcatctacattatgcctttggaagcactatgctcctgagctaaccactgacagatcaaaattttgctttccgcagTTTCTGACCTGGAGATGCTCTTTGGGAGGCTATGGACACAATGCCAGGAGTGCCAAGGATCTCTGCACCAGGACGTTCTCTGCACAAG
               |  || ||       || || |  |||    |  ||     | |    | |  |||| | ||   || | ||    || ||||||||||| ||||||||||||||||||||||| ||||| || ||||||||||||||||| || || || ||||||||||||||||||||
--------------gtacgatatatcctctcaataagggtttactgggtctcctggcgt---ttgattactggctgaattaa-tgttaacgtctgcagTTTCTGAGCTGGAGATGCTCTTTGGGAGGCTCTGGACGCAGTGCCAGGAGTGCCAAGGCTCCCTTCATCAGGACGTTCTCTGCACAAG

upper sequence: GRMZM2G115245_T01 (Zea mays), 3'ss of exon 12
lower sequence: GLYMA04G38800.2 (Glycine max), 3'ss of exon 12
----gtacgtgctgtacactctgaaatgcatctacattatgcctttggaagcactatgctcctgagctaaccactgacagatcaaa---attttgcttt--ccgcagTTTCTGACCTGGAGATGCTCTTTGGGAGGCTATGGACACAATGCCAGGAGTGCCAAGGATCTCTGCACCAGGACGTTCTCTGCACAAG
    | |  |  ||  | |||||  |    || | || ||    ||| |  |   ||| | |  ||||      |    ||| |||    |  || | |  | ||||| ||||| ||||||||||| ||||||||| | |||||||| || |||||||||||||| || || || ||||| ||||||||||||||
gtaggcatctcttgagctctctgttaaatttcca-atcattttgttgta--ctgcatggttcc-agctgtgttttattggataaaacaagtggtggtgtggctgcagTGTCTGAGCTGGAGATGCTTTTTGGGAGGTTGTGGACACAGTGTCAGGAGTGCCAAGGTTCACTTCATCAGGATGTTCTCTGCACAAG

upper sequence: GRMZM2G115245_T01 (Zea mays), 3'ss of exon 12
lower sequence: GLYMA06G16110.2 (Glycine max), 3'ss of exon 28
----gtacgtgctgtacactctgaaatgcatctacattatgcctttggaagcactatgctcctgag--ctaaccactgacagatcaaaattttgcttt--ccgcagTTTCTGACCTGGAGATGCTCTTTGGGAGGCTATGGACACAATGCCAGGAGTGCCAAGGATCTCTGCACCAGGACGTTCTCTGCACAAG
    | |  |  ||  | |||||       || | ||  |    ||| |     |  | ||| ||    |    | ||    |   || |  || | |  | ||||| ||||| ||||||||||| ||||||||| | |||||||| || |||||||||||||| || || || ||||| ||||||||||| ||
gtaggcatctcttgagctctctgttcaatttcca-atcgttttgttgtactggatg-gttccagatgtttttttattggataaaacaagtggtggtgtgactgcagTGTCTGAGCTGGAGATGCTTTTTGGGAGGTTGTGGACACAGTGTCAGGAGTGCCAAGGTTCACTTCATCAGGATGTTCTCTGCACCAG

upper sequence: GRMZM2G115245_T01 (Zea mays), 3'ss of exon 12
lower sequence: AT5G63960.2 (Arabidopsis thaliana), 3'ss of exon 28
gtacgtgctgtacactctgaaatgcatctacattatgcctttggaagcactatgctcctgagctaaccactgacagatcaaaattttgct---ttccgcagTTTCTGACCTGGAGATGCTCTTTGGGAGGCTATGGACACAATGCCAGGAGTGCCAAGGATCTCTGCACCAGGACGTTCTCTGCACAAG
                      |       | || | || ||     |  ||  ||| |      | |  | | |  | | | ||| | |   ||   ||||  |||| || ||   | | ||||||||||| |||||||| ||||||||||| ||||| ||||| || || || ||  | ||||| ||
---------------------gtatgctgccgtttttcccttt---cctatagactctttgatatatctataaaatttgatactttcgttgtgttattcagTGGCTGAGCTTGAAGAGGTTTTTGGGAGGCTGTGGACACAGTGCCAGGAGTGTCAAGGCTCTCTTCATCAAGATGTCTTGTGCACCAG

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|17921941|gb|BM259592.1|BM259592
EST:     ACATTGCAAGGGAAGAGAAGCAGAGTTGTACTGCAAAACAGTAGCAAATG                         TTTCTGACCTGGAGATGCTCTTTGGGAGGCTATGGACACAATGCCAGGAGT
genomic: ACATTGCAAGGGAAGAGAAGCAGAGTTGTACTGCAAAACAGTAGCAAATGgtacgtgctg ... ctttccgcagTTTCTGACCTGGAGATGCTCTTTGGGAGGCTATGGACACAATGCCAGGAGT
EST: gi|101399027|gb|EB821386.1|EB821386
EST:     ACATTGCAAGGGAAGAGAAGCAGAGTTGTACTGCAAAACAGTAGCAAATG                         TTTCTGACCTGGAGATGCTCTTTGGGAGGCTATGGACACAATGCCAGGAGT
genomic: ACATTGCAAGGGAAGAGAAGCAGAGTTGTACTGCAAAACAGTAGCAAATGgtacgtgctg ... ctttccgcagTTTCTGACCTGGAGATGCTCTTTGGGAGGCTATGGACACAATGCCAGGAGT
EST: gi|17921796|gb|BM259447.1|BM259447
EST:     ACATTGCATGGGAAGAGAAGCAGAGTTGTACTGCAAAACAGTAGCAAATG                         TTTCTGACCTGGAGATGCTCTTTGGGAGGCTATGGACACAATGCCAGGAGT
genomic: ACATTGCAAGGGAAGAGAAGCAGAGTTGTACTGCAAAACAGTAGCAAATGgtacgtgctg ... ctttccgcagTTTCTGACCTGGAGATGCTCTTTGGGAGGCTATGGACACAATGCCAGGAGT
EST: gi|211441104|gb|FL033100.1|FL033100
EST:     ACATTGCAAGGGAAGAGAAGCAGAGTTGTACTGCAAAACAGTAGCAAATG                         TTTCTGACCTGGAGATGCTCTTTGGGAGGCTATGGACACAATGCCAGGAGT
genomic: ACATTGCAAGGGAAGAGAAGCAGAGTTGTACTGCAAAACAGTAGCAAATGgtacgtgctg ... ctttccgcagTTTCTGACCTGGAGATGCTCTTTGGGAGGCTATGGACACAATGCCAGGAGT
EST: gi|17921470|gb|BM259121.1|BM259121
EST:     AGAAGCAGAG-TGTACTGCAAAACAGTAGCAAATG                         TTTCTGACCTGGAGATGCTCTTTGGGAGGCTATGGACACAATGCCAGGAGT
genomic: AGAAGCAGAGTTGTACTGCAAAACAGTAGCAAATGgtacgtgctg ... ctttccgcagTTTCTGACCTGGAGATGCTCTTTGGGAGGCTATGGACACAATGCCAGGAGT
EST: gi|17921753|gb|BM259404.1|BM259404
EST:     ACATTGCAAGGGAAGAGAAGCAGAGTTGTACTGCAAAACAGTAGCAAATG                         TTTCTGACCTGGAGATGCTCTTTGGGAGGCTATGGACACAATGCCTGGAGT
genomic: ACATTGCAAGGGAAGAGAAGCAGAGTTGTACTGCAAAACAGTAGCAAATGgtacgtgctg ... ctttccgcagTTTCTGACCTGGAGATGCTCTTTGGGAGGCTATGGACACAATGCCAGGAGT

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), 48 (downstream exon)
Score: 379

TGGTGCCAGTCAGACACTTTGCTCACATTGCAAGGGAAGAGAAGCAGAGTTGTACTGCAAAACAGTAGCAAATGgtacgtgctg ... ctttccgcagTTTCTGACCTGGAGATGCTCTTTGGGAGGCTATGGACACAATGCCAGGAGTGCCAAGGATCTCTGCACCAGGACGTTCTCTGCACAAG


Block sizes: 44 (upstream exon), 42 (downstream exon)
Score: 81

TGGTGCCAGTCAGACACTTTGCTCACATTGCAAGGGAAGAGAAGCAGAGTTGTACTGCAAAACAGTAGCAAATGgtacgtgctg ... ctttccgcagTTTCTGACCTGGAGATGCTCTTTGGGAGGCTATGGACACAATGCCAGGAGTGCCAAGGATCTCTGCACCAGGACGTTCTCTGCACAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 77

TGGTGCCAGTCAGACACTTTGCTCACATTGCAAGGGAAGAGAAGCAGAGTTGTACTGCAAAACAGTAGCAAATGgtacgtgctg ... ctttccgcagTTTCTGACCTGGAGATGCTCTTTGGGAGGCTATGGACACAATGCCAGGAGTGCCAAGGATCTCTGCACCAGGACGTTCTCTGCACAAG


Block sizes: 48 (upstream exon), 45 (downstream exon)
Score: 69

TGGTGCCAGTCAGACACTTTGCTCACATTGCAAGGGAAGAGAAGCAGAGTTGTACTGCAAAACAGTAGCAAATGgtacgtgctg ... ctttccgcagTTTCTGACCTGGAGATGCTCTTTGGGAGGCTATGGACACAATGCCAGGAGTGCCAAGGATCTCTGCACCAGGACGTTCTCTGCACAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaagcactatgctcctgagctaaccactgacagatcaaaattttgctttccgcagTTTCTGACCTGGAGATGCTCTTTGGGAGGCTATGGACACAATGCCAGGAGTGCCAAGGATCTCTGCACCAGGACGTTCTCTGCACAAG
                        cactgac  putative branch site (score: 69)
                                        ttttgctttcc  putative PPT
                                 atcaaaatttt  TA-rich tract