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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAAACTTTAGGGCTCTTTGTACAGgtattttctctctggtctccatggcttattttctcgccagcaaccccacctgagctgatcgttcatgtccatttgttcaccatttcag

Basic information

species Zea mays
transcript GRMZM2G158237_T03
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G158237_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os09g36670.1 (Oryza sativa), 5'ss of exon 4
AAAACTTTAGGGCTCTTTGTACAGgtattttctct-ctggtctccatggcttattttctcgccagcaaccccacc--tgagctgatcgttcatgt--ccatttgttcaccatttcag
 ||| |||||||||||||||||||||||||  ||| |     || ||  ||  |      |  |   | ||  |   | |  ||||  | ||| |  |  | ||||||| ||| |||
CAAATTTTAGGGCTCTTTGTACAGgtatttcttcttcctagatctattcctgttacagctgaaattcaaccttctgttcacatgattatccatattgcactctgttcactattgcag
















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|211434807|gb|FL427281.1|FL427281
EST:     GAAAACTTTAGGGCTCTTTGTACAG                         GTGAAAAAGGTGTCGGGTCCAATGGCAAACCTCTTCACTATAAGGGAACAC
genomic: GAAAACTTTAGGGCTCTTTGTACAGgtattttctc ... accatttcagGTGAAAAAGGTGTCGGGTCCAATGGCAAACCTCTTCACTATAAGGGAACAC
EST: gi|211431653|gb|FL404571.1|FL404571
EST:     GAAAACTTTAGGGCTCTTTGTACAG                         GTGAAAAAGGTGTCGGGTCCAATGGCAAACCTCTTCACTATAAGGGAACAC
genomic: GAAAACTTTAGGGCTCTTTGTACAGgtattttctc ... accatttcagGTGAAAAAGGTGTCGGGTCCAATGGCAAACCTCTTCACTATAAGGGAACAC
EST: gi|211093050|gb|FL420421.1|FL420421
EST:     KAAAACTTTAGGGCTCTTTGTACAG                         GTGAAAAAGGTGTCGGGTCCAATGGCAAACCTCTTCACTATAAGGGAACAC
genomic: GAAAACTTTAGGGCTCTTTGTACAGgtattttctc ... accatttcagGTGAAAAAGGTGTCGGGTCCAATGGCAAACCTCTTCACTATAAGGGAACAC
EST: gi|211109670|gb|FL337450.1|FL337450
EST:     GAAAACTTTAGGGCTCTTTGTACAG                         GTGAAAAAGGTGTCGGGTCCAATGGCAAACCTCTTCACTATAAGGGAACAC
genomic: GAAAACTTTAGGGCTCTTTGTACAGgtattttctc ... accatttcagGTGAAAAAGGTGTCGGGTCCAATGGCAAACCTCTTCACTATAAGGGAACAC
EST: gi|30704819|gb|CD058611.1|CD058611
EST:     GAAAACTTTAGGGCTCTTTGTACAG                         GTGAAAAAGGTGTCGGGTCCAATGGCAAACCTCTTCACTATAAGGGAACAC
genomic: GAAAACTTTAGGGCTCTTTGTACAGgtattttctc ... accatttcagGTGAAAAAGGTGTCGGGTCCAATGGCAAACCTCTTCACTATAAGGGAACAC
EST: gi|211300966|gb|FL391501.1|FL391501
EST:     GAAAACTTTAGGGCTCTTTGTACAG                         GTGAAAAAGGTGTCGGGTCCAATGGCAAACCTCTTCACTATAAGGGAACAC
genomic: GAAAACTTTAGGGCTCTTTGTACAGgtattttctc ... accatttcagGTGAAAAAGGTGTCGGGTCCAATGGCAAACCTCTTCACTATAAGGGAACAC
EST: gi|211229694|gb|FL389659.1|FL389659
EST:     GAAAACTTTAGGGCTCTTTGTACAG                         GTGAAAAAGGTGTCGGGTCCAATGGCAAACCTCTTCACTATAAGGGAACAC
genomic: GAAAACTTTAGGGCTCTTTGTACAGgtattttctc ... accatttcagGTGAAAAAGGTGTCGGGTCCAATGGCAAACCTCTTCACTATAAGGGAACAC
EST: gi|211256545|gb|FL390498.1|FL390498
EST:     GAAAACTTTAGGGCTCTTTGTATAG                         GTGAAAAAGGTGTCGGGTCCAATGGCAAACCTCTTCACTATAAGGGAACAC
genomic: GAAAACTTTAGGGCTCTTTGTACAGgtattttctc ... accatttcagGTGAAAAAGGTGTCGGGTCCAATGGCAAACCTCTTCACTATAAGGGAACAC
EST: gi|67015837|gb|CO444586.1|CO444586
EST:     GAAAACTTTAGGGCTCTTTGTACAG                         GTGAAAAAGGTGTCGGGTCCAATGGCAAACCTCTTCACTATAAGGGAACAC
genomic: GAAAACTTTAGGGCTCTTTGTACAGgtattttctc ... accatttcagGTGAAAAAGGTGTCGGGTCCAATGGCAAACCTCTTCACTATAAGGGAACAC
EST: gi|211521053|gb|FL387965.1|FL387965
EST:     AAAACTTTTAGGGCTCTTTGTACAG                         GTGAAAAAGGTGTCGGGTCCMATGAGCAAACCTCTTCACTATAAGGGAACA
genomic: AAAACTTT-AGGGCTCTTTGTACAGgtattttctc ... accatttcagGTGAAAAAGGTGTCGGGTCCAATG-GCAAACCTCTTCACTATAAGGGAACA
EST: gi|211182577|gb|FL404772.1|FL404772
EST:     GAAAACTTTAGGGCTCTTTGTACAG                         GTGAAAAAGGTGTCGGGTCCAATGGCAAACCTCTTCACTATAAGGGAACAC
genomic: GAAAACTTTAGGGCTCTTTGTACAGgtattttctc ... accatttcagGTGAAAAAGGTGTCGGGTCCAATGGCAAACCTCTTCACTATAAGGGAACAC
EST: gi|211534860|gb|FL340389.1|FL340389
EST:     GAAAACTTTAGGGCTCTTTGTACAG                         GTGAAAAAGGTGTCGGGTCCAATGGCAAACCTCTTCACTATAAGGGAACAC
genomic: GAAAACTTTAGGGCTCTTTGTACAGgtattttctc ... accatttcagGTGAAAAAGGTGTCGGGTCCAATGGCAAACCTCTTCACTATAAGGGAACAC
EST: gi|211057736|gb|FL416996.1|FL416996
EST:     GAAAACTTTAGGGCTCTTTGTACAG                         GTGAAAAAGGTGTCGGGTCCAATGGCAAACCTCTTCACTATAAGGGAACAC
genomic: GAAAACTTTAGGGCTCTTTGTACAGgtattttctc ... accatttcagGTGAAAAAGGTGTCGGGTCCAATGGCAAACCTCTTCACTATAAGGGAACAC
EST: gi|88755062|gb|DY539203.1|DY539203
EST:     GAAAACTTTAGGGCTCTTTGTACAG                         GAGAAAAAGGTGTCGGGTCCAATGGCAAACCTCTTCACTATAAGGGAACAC
genomic: GAAAACTTTAGGGCTCTTTGTACAGgtattttctc ... accatttcagGTGAAAAAGGTGTCGGGTCCAATGGCAAACCTCTTCACTATAAGGGAACAC
EST: gi|211402954|gb|FL382690.1|FL382690
EST:     GAAAACTTTAGGGCTCTTTGTACAG                         GTGAAAAAGGTGTCGGGTCCAATTGGCAAACCTCTTCACTATAAGGGAACA
genomic: GAAAACTTTAGGGCTCTTTGTACAGgtattttctc ... accatttcagGTGAAAAAGGTGTCGGGTCCAAT-GGCAAACCTCTTCACTATAAGGGAACA
EST: gi|211194087|gb|FL377670.1|FL377670
EST:     GAAAACTTTAGGGCTCTTTGTACAG                         GTGAAAAAGGTGTCGGGTCCAATGGCAAACCTCTTCACTATAAGGGAACAC
genomic: GAAAACTTTAGGGCTCTTTGTACAGgtattttctc ... accatttcagGTGAAAAAGGTGTCGGGTCCAATGGCAAACCTCTTCACTATAAGGGAACAC
EST: gi|211373857|gb|FL385822.1|FL385822
EST:     GAAAACTTTAGGGCTCTTTGTACAG                         GTGAAAAAGGTGTCGGGTCCAATGGCAAACCTCTTCACTATAAGGGAACAC
genomic: GAAAACTTTAGGGCTCTTTGTACAGgtattttctc ... accatttcagGTGAAAAAGGTGTCGGGTCCAATGGCAAACCTCTTCACTATAAGGGAACAC
EST: gi|211211751|gb|FL376364.1|FL376364
EST:     GAAAACTTTAGGGCTCTTTGTACAG                         GTGAAAAAGGTGTCGGGTCCAATGGCAAACCTCTTCACTATAAGGGAACAC
genomic: GAAAACTTTAGGGCTCTTTGTACAGgtattttctc ... accatttcagGTGAAAAAGGTGTCGGGTCCAATGGCAAACCTCTTCACTATAAGGGAACAC
EST: gi|78080821|gb|DV509233.1|DV509233
EST:     GAAAACTTTAGGGCTCTTTGTACAG                         GTGAAAAAGGTGTCGGGTCCAATGGCAAACCTCTTCACTATAAGGGAACAC
genomic: GAAAACTTTAGGGCTCTTTGTACAGgtattttctc ... accatttcagGTGAAAAAGGTGTCGGGTCCAATGGCAAACCTCTTCACTATAAGGGAACAC
EST: gi|211061094|gb|FL320234.1|FL320234
EST:     GAAAACTTTAGGGCTCTTTGTACAG                         GTGAAAAAGGTGTCGGGTCCAATGGCAAACCTCTTCACTATAAGGGAACAC
genomic: GAAAACTTTAGGGCTCTTTGTACAGgtattttctc ... accatttcagGTGAAAAAGGTGTCGGGTCCAATGGCAAACCTCTTCACTATAAGGGAACAC
EST: gi|211341298|gb|FL394244.1|FL394244
EST:     GAAAACTTTAGGGCTCTTTGTACAG                         GTGAAAAAGGTGYCGGGYCCAATGGCAAACCTCTTCACTATAAGGGAACAC
genomic: GAAAACTTTAGGGCTCTTTGTACAGgtattttctc ... accatttcagGTGAAAAAGGTGTCGGGTCCAATGGCAAACCTCTTCACTATAAGGGAACAC
EST: gi|26558040|gb|CA830275.1|CA830275
EST:     GAAAACTTTAGGGCTCTTTGTACAG                         GTGAAAAAGGTGTCGGGTCCAATGGCAAACCTCTTCACTATAAGGGAACAC
genomic: GAAAACTTTAGGGCTCTTTGTACAGgtattttctc ... accatttcagGTGAAAAAGGTGTCGGGTCCAATGGCAAACCTCTTCACTATAAGGGAACAC
EST: gi|60346388|gb|DN213361.1|DN213361
EST:     CTCTTTGTACAG                         GTGAAAAAAGGTGTCGGGTCCAAATGGCATACCTCTTCACTATAAGGGAAC
genomic: CTCTTTGTACAGgtattttctc ... accatttcagGTG-AAAAAGGTGTCGGGTCC-AATGGCAAACCTCTTCACTATAAGGGAAC
EST: gi|76922696|gb|DV169126.1|DV169126
EST:     GAAAACTTTAGGGCTCTTTGTACAG                         GTGAAAAAGGTGTCGGGTCCAATGGCAAACCTCTTCACTATAAGGGAACAC
genomic: GAAAACTTTAGGGCTCTTTGTACAGgtattttctc ... accatttcagGTGAAAAAGGTGTCGGGTCCAATGGCAAACCTCTTCACTATAAGGGAACAC
EST: gi|91877249|gb|EB407206.1|EB407206
EST:     GAAAACTTTAGGGCTCTTTGTACAG                         GTGAAAAAGGTGTCGGGTCCAATGGCAAACCTCTTCACTATAAGGGAACAC
genomic: GAAAACTTTAGGGCTCTTTGTACAGgtattttctc ... accatttcagGTGAAAAAGGTGTCGGGTCCAATGGCAAACCTCTTCACTATAAGGGAACAC
EST: gi|76922694|gb|DV169125.1|DV169125
EST:     AAAACAG-TGAAAACTTTAAGGGCTCTTTGTACAG                         GTGAAAAAGGTGTCGGGTTCAATGGCAAACCTCTTCACTATAAGGGAACAC
genomic: AAAACAGTTGAAAACTTT-AGGGCTCTTTGTACAGgtattttctc ... accatttcagGTGAAAAAGGTGTCGGGTCCAATGGCAAACCTCTTCACTATAAGGGAACAC
EST: gi|31355561|gb|CD439918.1|CD439918
EST:     GAAAACTTTAGGGCTCTTTGTACAG                         GTGAAAAAGGTGTCGGGTCCAATGGCAAACCTCTTCACTATAAGGGAACAC
genomic: GAAAACTTTAGGGCTCTTTGTACAGgtattttctc ... accatttcagGTGAAAAAGGTGTCGGGTCCAATGGCAAACCTCTTCACTATAAGGGAACAC
EST: gi|211076170|gb|FL369895.1|FL369895
EST:     GAAAACTTTAGGGCTCTTTGTACAG                         GTGAAAAAGGTGTCGGGTCCAATGGCAAACCTCTTCACTATAAGGGAACAC
genomic: GAAAACTTTAGGGCTCTTTGTACAGgtattttctc ... accatttcagGTGAAAAAGGTGTCGGGTCCAATGGCAAACCTCTTCACTATAAGGGAACAC
EST: gi|21843567|gb|BQ704148.1|BQ704148
EST:     GAAAACTTTAGGGCTCTTTGTACAG                         GTGAAAAAGGTGTCGGGTCCAATGGCAAACCTCTTCACTATAAGGGAACAC
genomic: GAAAACTTTAGGGCTCTTTGTACAGgtattttctc ... accatttcagGTGAAAAAGGTGTCGGGTCCAATGGCAAACCTCTTCACTATAAGGGAACAC
EST: gi|211163731|gb|FL337956.1|FL337956
EST:     GAAAACTTTAGGGCTCTTTGTACAG                         GTGAAAAAGGTGTCGGGTCCAATGGCAAACCTCTTCACTATAAGGGAACAC
genomic: GAAAACTTTAGGGCTCTTTGTACAGgtattttctc ... accatttcagGTGAAAAAGGTGTCGGGTCCAATGGCAAACCTCTTCACTATAAGGGAACAC

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: 24 (upstream exon), 48 (downstream exon)
Score: 127

AAAACTTTAGGGCTCTTTGTACAGgtattttctc ... accatttcagGTGAAAAAGGTGTCGGGTCCAATGGCAAACCTCTTCACTATAAGGGAACACCATTCCATCGTATTATCCCTGGCTTCATGATTCAGGGCGGTGACATAGT


Block sizes: 24 (upstream exon), 48 (downstream exon)
Score: 134

AAAACTTTAGGGCTCTTTGTACAGgtattttctc ... accatttcagGTGAAAAAGGTGTCGGGTCCAATGGCAAACCTCTTCACTATAAGGGAACACCATTCCATCGTATTATCCCTGGCTTCATGATTCAGGGCGGTGACATAGT


Block sizes: 24 (upstream exon), 47 (downstream exon)
Score: 126

AAAACTTTAGGGCTCTTTGTACAGgtattttctc ... accatttcagGTGAAAAAGGTGTCGGGTCCAATGGCAAACCTCTTCACTATAAGGGAACACCATTCCATCGTATTATCCCTGGCTTCATGATTCAGGGCGGTGACATAGT


Block sizes: 24 (upstream exon), 48 (downstream exon)
Score: 115

AAAACTTTAGGGCTCTTTGTACAGgtattttctc ... accatttcagGTGAAAAAGGTGTCGGGTCCAATGGCAAACCTCTTCACTATAAGGGAACACCATTCCATCGTATTATCCCTGGCTTCATGATTCAGGGCGGTGACATAGT