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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcagggtcgccatctcatccgcatcgcatcctcatggagttggttgctcgacgacgccttctcttctttcttacccagacggcacttcatcccgttcccgtgcgcagGTGGTGGCGCTGTGCCAGGCTCCGTTCCTCCTCGATGACCCCAATGTCGGCCTCATGTTCCCGCCCGATGCCATCGTGCGGGCCAAGCGCTATCTCGCCA

Basic information

species Zea mays
transcript GRMZM5G840582_T02
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G840582_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os07g01760.1 (Oryza sativa), 3'ss of exon 1
gtcagggtcgccatctcatccgcatcgcatcctcatggagttggttgctcgacgacgccttctcttctttcttacccagacggcacttcatcccgttcccgtgcgcagGTGGTGGCGCTGTGCCAGGCTCCGTTCCTCCTCGATGACCCCAATGTCGGCCTCATGTTCCCGCCCGATGCCATCGTGCGGGCCAAGCGCTATCTCGCCA
                        || |  |  |      ||  ||  ||  | ||  ||  |    |   |      ||   | |   || | |||    || |||||| ||||||||||||||||| || ||||| |||||||| ||||| |||||||| || |||||  |||| ||||||| ||||||||||| ||| |||||||
-----------------------gtcactactcctctttctttcttcttcctctactactagtagattcgatcgatt-gatttctccctattctgttgtgttgtgcagGTTGTGGCGCTGTGCCAGGCCCCCTTCCTGCTCGATGATCCCAACGTCGGCCTTATCTTCCCCGCCGACGCCATCGCGCGGGCCAAGCACTACCTCGCCA
















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|148974504|gb|EE025287.2|EE025287
EST:     TCGGCAACCCGCACGCCCTCGGCCAGAAGCCGCTCACCTTCCCGCGCCAG                         GTGGTGGCGCTGTGCCAGGCTCCGTTCCTCCTCGATGACCCCAATGTCGGC
genomic: TCGGCAACCCGCACGCCCTCGGCCAGAAGCCGCTCACCTTCCCGCGCCAGgtcagggtcg ... ccgtgcgcagGTGGTGGCGCTGTGCCAGGCTCCGTTCCTCCTCGATGACCCCAATGTCGGC
EST: gi|148974460|gb|EE025239.2|EE025239
EST:     TCGGCAACCCGCACGCCCTCGGCCAGAAGCCGCTCACCTTCCCGCGCCAG                         GTGGTGGCGCTGTGCCAGGCTCCGTTCCTCCTCGATGACCCCAATGTCGGC
genomic: TCGGCAACCCGCACGCCCTCGGCCAGAAGCCGCTCACCTTCCCGCGCCAGgtcagggtcg ... ccgtgcgcagGTGGTGGCGCTGTGCCAGGCTCCGTTCCTCCTCGATGACCCCAATGTCGGC
EST: gi|149026983|gb|EE046321.2|EE046321
EST:     TCGGCAACCCGCACGCCCTCGGCCAGAAGCCGCTCACCTTCCCGCGCCAG                         GTGGTGGCGCTGTGCCAGGCTCCGTTCCTCCTCGATGACCCCAATGTCGGC
genomic: TCGGCAACCCGCACGCCCTCGGCCAGAAGCCGCTCACCTTCCCGCGCCAGgtcagggtcg ... ccgtgcgcagGTGGTGGCGCTGTGCCAGGCTCCGTTCCTCCTCGATGACCCCAATGTCGGC
EST: gi|211033758|gb|FL005921.1|FL005921
EST:     TCGGCAACCCGCACGCCCTCGGCCAGAAGCCGCTCACCTTCCCGCGCCAG                         GTGGTGGCGCTGTGCCAGGCTCCGTTCCTCCTCGATGACCCCAATGTCGGC
genomic: TCGGCAACCCGCACGCCCTCGGCCAGAAGCCGCTCACCTTCCCGCGCCAGgtcagggtcg ... ccgtgcgcagGTGGTGGCGCTGTGCCAGGCTCCGTTCCTCCTCGATGACCCCAATGTCGGC
EST: gi|148940269|gb|EC885045.2|EC885045
EST:     TCGGCAACCCGCACGCCCTCGGCCAGAAGCCGCTCACCTTCCCGCGCCAG                         GTGGTGGCGCTGTGCCAGGCTCCGTTCCTCCTCGATGACCCCAATGTCGGC
genomic: TCGGCAACCCGCACGCCCTCGGCCAGAAGCCGCTCACCTTCCCGCGCCAGgtcagggtcg ... ccgtgcgcagGTGGTGGCGCTGTGCCAGGCTCCGTTCCTCCTCGATGACCCCAATGTCGGC
EST: gi|149070661|gb|EE159075.2|EE159075
EST:     TCGGCAACCCGCACGCCCTCGGCCAGAAGCCGCTCACCTTCCCGCGCCAG                         GTGGTGGCGCTGTGCCAGGCTCCGTTCCTCCTCGATGACCCCAATGTCGGC
genomic: TCGGCAACCCGCACGCCCTCGGCCAGAAGCCGCTCACCTTCCCGCGCCAGgtcagggtcg ... ccgtgcgcagGTGGTGGCGCTGTGCCAGGCTCCGTTCCTCCTCGATGACCCCAATGTCGGC
EST: gi|91048303|gb|EB158721.1|EB158721
EST:     TCGGCAACCCGCACGCCCTCGGCCAGAAGCCGCTCACCTTCCCGCGCCAG                         GTGGTGGCGCTGTGCCAGGCTCCGTTCCTCCTCGATGACCCCAATGTCGGC
genomic: TCGGCAACCCGCACGCCCTCGGCCAGAAGCCGCTCACCTTCCCGCGCCAGgtcagggtcg ... ccgtgcgcagGTGGTGGCGCTGTGCCAGGCTCCGTTCCTCCTCGATGACCCCAATGTCGGC
EST: gi|78112476|gb|DV530870.1|DV530870
EST:     TCGGCAACCCGCACGCCCTCGGCCAGAAGCCGCTCACCTTCCCGCGCCAG                         GTGGTGGCGCTGTGCCAGGCTCCGTTCCTCCTCGATGACCCCAATGTCGGC
genomic: TCGGCAACCCGCACGCCCTCGGCCAGAAGCCGCTCACCTTCCCGCGCCAGgtcagggtcg ... ccgtgcgcagGTGGTGGCGCTGTGCCAGGCTCCGTTCCTCCTCGATGACCCCAATGTCGGC
EST: gi|211033757|gb|FL005920.1|FL005920
EST:     TCGGCAACCCGCACGCCCTCGGCCAGAAGCCGCTCACCTTCCCGCGCCAG                         GTGGTGGCGCTGTGCCAGGCTCCGTTCCTCCTCGATGACCCCAATGTCGGC
genomic: TCGGCAACCCGCACGCCCTCGGCCAGAAGCCGCTCACCTTCCCGCGCCAGgtcagggtcg ... ccgtgcgcagGTGGTGGCGCTGTGCCAGGCTCCGTTCCTCCTCGATGACCCCAATGTCGGC
EST: gi|149041122|gb|EE046896.2|EE046896
EST:     TCGGCAACCCGCACGCCCTCGGCCAGAAGCCGCTCACCTTCCCGCGCCAG                         GTGGTGGCGCTGTGCCAGGCTCCGTTCCTCCTCGATGACCCCAATGTCGGC
genomic: TCGGCAACCCGCACGCCCTCGGCCAGAAGCCGCTCACCTTCCCGCGCCAGgtcagggtcg ... ccgtgcgcagGTGGTGGCGCTGTGCCAGGCTCCGTTCCTCCTCGATGACCCCAATGTCGGC

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: 34

CCGCGCCTCCCAGCTCCAGAAGGAGGGCAAGAAGATCATCTTCACCAACGTCGGCAACCCGCACGCCCTCGGCCAGAAGCCGCTCACCTTCCCGCGCCAGgtcagggtcg ... ccgtgcgcagGTGGTGGCGCTGTGCCAGGCTCCGTTCCTCCTCGATGACCCCAATGTCGGCCTCATGTTCCCGCCCGATGCCATCGTGCGGGCCAAGCGCTATCTCGCCA


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 138

CCGCGCCTCCCAGCTCCAGAAGGAGGGCAAGAAGATCATCTTCACCAACGTCGGCAACCCGCACGCCCTCGGCCAGAAGCCGCTCACCTTCCCGCGCCAGgtcagggtcg ... ccgtgcgcagGTGGTGGCGCTGTGCCAGGCTCCGTTCCTCCTCGATGACCCCAATGTCGGCCTCATGTTCCCGCCCGATGCCATCGTGCGGGCCAAGCGCTATCTCGCCA


Block sizes: 44 (upstream exon), 43 (downstream exon)
Score: 8

CCGCGCCTCCCAGCTCCAGAAGGAGGGCAAGAAGATCATCTTCACCAACGTCGGCAACCCGCACGCCCTCGGCCAGAAGCCGCTCACCTTCCCGCGCCAGgtcagggtcg ... ccgtgcgcagGTGGTGGCGCTGTGCCAGGCTCCGTTCCTCCTCGATGACCCCAATGTCGGCCTCATGTTCCCGCCCGATGCCATCGTGCGGGCCAAGCGCTATCTCGCCA


Block sizes: 48 (upstream exon), 46 (downstream exon)
Score: 45

CCGCGCCTCCCAGCTCCAGAAGGAGGGCAAGAAGATCATCTTCACCAACGTCGGCAACCCGCACGCCCTCGGCCAGAAGCCGCTCACCTTCCCGCGCCAGgtcagggtcg ... ccgtgcgcagGTGGTGGCGCTGTGCCAGGCTCCGTTCCTCCTCGATGACCCCAATGTCGGCCTCATGTTCCCGCCCGATGCCATCGTGCGGGCCAAGCGCTATCTCGCCA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gacgccttctcttctttcttacccagacggcacttcatcccgttcccgtgcgcagGTGGTGGCGCTGTGCCAGGCTCCGTTCCTCCTCGATGACCCCAATGTCGGCCTCATGTTCCCGCCCGATGCCATCGTGCGGGCCAAGCGCTATCTCGCCA
               ttcttac  putative branch site (score: 45)
                                cttcatcccgttccc  putative PPT
              tttctta  TA-rich tract