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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CACTCTGCTAGCCCACAGCGCGCTCCATGGCGCCATGGCGGGGTACACCGGCTTCATCGTCGCTCCGGTCAATGGCAGACACGCCTACATCCCGTTCTATgtaagtcgagggtcttgtgcttgtgcagttgagcttcctggacatccggtcttggatcctggataaacccttctcttgttttgcag

Basic information

species Zea mays
transcript GRMZM2G132069_T01
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G132069_T01 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os01g09570.1 (Oryza sativa), 5'ss of exon 10
CACTCTGCTAGCCCACAGCGCGCTCCATGGCGCCATGGCGGGGTACACCGGCTTCATCGTCGCTCCGGTCAATGGCAGACACGCCTACATCCCGTTCTATgtaagtcgagggtcttgtgcttgtgcagttgagcttcc-tggaca------tccggtcttggatcctggata--aacccttctcttgttttgcag---------------------------
||| |||||||| |||||||| ||||| |||||||||||||||||||||||||||| |||||| |||||||| ||||| ||||| || ||||||||||| ||||||| ||     | |  ||      |  | |||   ||  ||      | | ||  |  |  |  || |  |||| |   ||  |  |   |                           
CACCCTGCTAGCTCACAGCGCCCTCCACGGCGCCATGGCGGGGTACACCGGCTTCACCGTCGCGCCGGTCAACGGCAGGCACGCGTATATCCCGTTCTACgtaagtccagaacactctttttcaatgatcaatctttagtgttcagttcagttcagttcttcacaccagacatcaaccatatcctgataatctggacactgaaactccggcgatttctacag
















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|149085166|gb|EE174669.2|EE174669
EST:     GCTTCATCGTCGCTCCGGTCAATGGCAGACACGCCTACATCCCGTTCTAT                         AGGATCACCGAGAAGCAGAACAAGGTGGTGATCACGGACCGGATGTGGGCG
genomic: GCTTCATCGTCGCTCCGGTCAATGGCAGACACGCCTACATCCCGTTCTATgtaagtcgag ... tgttttgcagAGGATCACCGAGAAGCAGAACAAGGTGGTGATCACGGACCGGATGTGGGCG
EST: gi|74235449|gb|DT643363.1|DT643363
EST:     GCTTCATCGTCGCTCCGGTCAATGGCAGACACGCCTACATCCCGTTCTAT                         AGGATCACCGAGAAGCAGAACAAGGTGGTGATCACGGACCGGATGTGGGCG
genomic: GCTTCATCGTCGCTCCGGTCAATGGCAGACACGCCTACATCCCGTTCTATgtaagtcgag ... tgttttgcagAGGATCACCGAGAAGCAGAACAAGGTGGTGATCACGGACCGGATGTGGGCG
EST: gi|45847889|gb|CN071832.1|CN071832
EST:     GCTTCATCGTCGCTCCGGTCAATGGCAGACACGCCTACATCCCGTTCTAT                         AGGATCACCGAGAAGCAGAACAAGGTGGTGATCACGGACCGGATGTGGGCG
genomic: GCTTCATCGTCGCTCCGGTCAATGGCAGACACGCCTACATCCCGTTCTATgtaagtcgag ... tgttttgcagAGGATCACCGAGAAGCAGAACAAGGTGGTGATCACGGACCGGATGTGGGCG
EST: gi|84969698|gb|DW468127.1|DW468127
EST:     GCTTCATCGTCGCTCCGGTCAATGGCAGACACGCCTACATCCCGTTCTAT                         AGGATCACCGAGAAGCAGAACAAGGTGGTGATCACGGACCGGATGTGGGCG
genomic: GCTTCATCGTCGCTCCGGTCAATGGCAGACACGCCTACATCCCGTTCTATgtaagtcgag ... tgttttgcagAGGATCACCGAGAAGCAGAACAAGGTGGTGATCACGGACCGGATGTGGGCG
EST: gi|78076659|gb|DV505093.1|DV505093
EST:     GCTTCATCGTCGCTCCGGTCAATGGCAGACACGCCTACATCCCGTTCTAT                         AGGATCACCGAGAAGCAGAACAAGGTGGTGATCACGGACCGGATGTGGGCG
genomic: GCTTCATCGTCGCTCCGGTCAATGGCAGACACGCCTACATCCCGTTCTATgtaagtcgag ... tgttttgcagAGGATCACCGAGAAGCAGAACAAGGTGGTGATCACGGACCGGATGTGGGCG
EST: gi|78023653|gb|DV492040.1|DV492040
EST:     GCTTCATCGTCGCTCCGGTCAATGGCAGACACGCCTACATCCCGTTCTAT                         AGGATCACCGAGAAGCAGAACAAGGTGGTGATCACGGACCGGATGTGGGCG
genomic: GCTTCATCGTCGCTCCGGTCAATGGCAGACACGCCTACATCCCGTTCTATgtaagtcgag ... tgttttgcagAGGATCACCGAGAAGCAGAACAAGGTGGTGATCACGGACCGGATGTGGGCG
EST: gi|78088953|gb|DV517346.1|DV517346
EST:     GCTTCATCGTCGCTCCGGTCAATGGCAGACACGCCTACATCCCGTTCTAT                         AGGATCACCGAGAAGCAGAACAAGGTGGTGATCACGGACCGGATGTGGGCG
genomic: GCTTCATCGTCGCTCCGGTCAATGGCAGACACGCCTACATCCCGTTCTATgtaagtcgag ... tgttttgcagAGGATCACCGAGAAGCAGAACAAGGTGGTGATCACGGACCGGATGTGGGCG
EST: gi|74233713|gb|DT641627.1|DT641627
EST:     GCTTCATCGTCGCTCCGGTCAATGGCAGACACGCCTACATCCCGTTCTAT                         AGGATCACCGAGAAGCAGAACAAGGTGGTGATCACGGACCGGATGTGGGCG
genomic: GCTTCATCGTCGCTCCGGTCAATGGCAGACACGCCTACATCCCGTTCTATgtaagtcgag ... tgttttgcagAGGATCACCGAGAAGCAGAACAAGGTGGTGATCACGGACCGGATGTGGGCG
EST: gi|15082833|gb|BI389517.1|BI389517
EST:     GCTTCATCGTCGCTCCGGTCAATGGCAGACACGCCTACATCCCGTTCTAT                         AGGATCACCGAGAAGCAGAACAAGGTGGTGATCACGGACCGGATGTGGGCG
genomic: GCTTCATCGTCGCTCCGGTCAATGGCAGACACGCCTACATCCCGTTCTATgtaagtcgag ... tgttttgcagAGGATCACCGAGAAGCAGAACAAGGTGGTGATCACGGACCGGATGTGGGCG
EST: gi|6021914|gb|AW066842.1|AW066842
EST:     GCTTCATCGTCGCTCCGGTCAATGGCAGACACGCCTACATCCCGTTCTAT                         AGGATCACCGAGGAAGCCAGAACAAGGGTGGTGATCACGGACCGGATGTGG
genomic: GCTTCATCGTCGCTCCGGTCAATGGCAGACACGCCTACATCCCGTTCTATgtaagtcgag ... tgttttgcagAGGATCACCGA-GAAG-CAGAACAA-GGTGGTGATCACGGACCGGATGTGG
EST: gi|28982496|gb|BQ538192.2|BQ538192
EST:     GCTTCATCGTCGCTCCGGTCAATGGCAGACACGCCTACATCCCGTTCTAT                         AGGATCACCGAGAAGCAGAACAAGGTGGTGATCACGGACCGGATGTGGGCG
genomic: GCTTCATCGTCGCTCCGGTCAATGGCAGACACGCCTACATCCCGTTCTATgtaagtcgag ... tgttttgcagAGGATCACCGAGAAGCAGAACAAGGTGGTGATCACGGACCGGATGTGGGCG
EST: gi|71315899|gb|DR794637.1|DR794637
EST:     GCTTCATCGTCGCTCCGGTCAATGGCAGACACGCCTACATCCCGTTCTAT                         AGGATCACCGAGAAGCAGAACAAGGTGGTGATCACGGACCGGATGTGGGCG
genomic: GCTTCATCGTCGCTCCGGTCAATGGCAGACACGCCTACATCCCGTTCTATgtaagtcgag ... tgttttgcagAGGATCACCGAGAAGCAGAACAAGGTGGTGATCACGGACCGGATGTGGGCG
EST: gi|89248830|gb|DY620616.1|DY620616
EST:     GCTTCATCGTCGCTCCGGTCAATGGCAGACACGCCTACATCCCGTTCTAT                         AGGATCACCGAGAAGCAGAACAAGGTGGTGATCACGGACCGGATGTGGGCG
genomic: GCTTCATCGTCGCTCCGGTCAATGGCAGACACGCCTACATCCCGTTCTATgtaagtcgag ... tgttttgcagAGGATCACCGAGAAGCAGAACAAGGTGGTGATCACGGACCGGATGTGGGCG

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), 28 (downstream exon)
Score: 5

CACTCTGCTAGCCCACAGCGCGCTCCATGGCGCCATGGCGGGGTACACCGGCTTCATCGTCGCTCCGGTCAATGGCAGACACGCCTACATCCCGTTCTATgtaagtcgag ... tgttttgcagAGGATCACCGAGAAGCAGAACAAGGTGGTGATCACGGACCGGATGTGGGCGAGGGTGCTGTGCTCGACGAACCAGCCCTGCTTCCTGAGCCACGAGGACG


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 40

CACTCTGCTAGCCCACAGCGCGCTCCATGGCGCCATGGCGGGGTACACCGGCTTCATCGTCGCTCCGGTCAATGGCAGACACGCCTACATCCCGTTCTATgtaagtcgag ... tgttttgcagAGGATCACCGAGAAGCAGAACAAGGTGGTGATCACGGACCGGATGTGGGCGAGGGTGCTGTGCTCGACGAACCAGCCCTGCTTCCTGAGCCACGAGGACG


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 68

CACTCTGCTAGCCCACAGCGCGCTCCATGGCGCCATGGCGGGGTACACCGGCTTCATCGTCGCTCCGGTCAATGGCAGACACGCCTACATCCCGTTCTATgtaagtcgag ... tgttttgcagAGGATCACCGAGAAGCAGAACAAGGTGGTGATCACGGACCGGATGTGGGCGAGGGTGCTGTGCTCGACGAACCAGCCCTGCTTCCTGAGCCACGAGGACG


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 40

CACTCTGCTAGCCCACAGCGCGCTCCATGGCGCCATGGCGGGGTACACCGGCTTCATCGTCGCTCCGGTCAATGGCAGACACGCCTACATCCCGTTCTATgtaagtcgag ... tgttttgcagAGGATCACCGAGAAGCAGAACAAGGTGGTGATCACGGACCGGATGTGGGCGAGGGTGCTGTGCTCGACGAACCAGCCCTGCTTCCTGAGCCACGAGGACG