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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgacctccctccctctccctagatctgcgcgcgaaggcgcgacgacggtgagtcacgctgctgatctgctcctactctcgctcgcggcagGTACACGAAGATGGGGTTCGCGGGGAACGTGGAGCCCTGCTTCATCACCCCCACTGTCGTCGCCGTCAACGATTCCTTTTCCGGTTCAGGCCAGCCGGCG

Basic information

species Zea mays
transcript GRMZM2G092459_T02
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G092459_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os02g38340.1 (Oryza sativa), 3'ss of exon 1
-----gtacgacctccctccctctccctagatctgcgcgcgaag-gcgcg-acgacggtgagtc--acgctgctgatctgctcctactctcgctcgcg-gcagGTACACGAAGATGGGGTTCGCGGGGAACGTGGAGCCCTGCTTCATCACCCCCACTGTCGTCGCCGTCAACGATTCCTTTTCCGGTTCAGGCCAG--CCGGCG
        |   ||| ||| ||||  | ||||||||||||| || ||| |  |  ||| || ||  | || | ||||  |       |  ||| |||| ||||||||||||||||||||||||| |||||||||||||||||||||||||||||||| |||||||||||||||||  ||||  ||||  ||| ||||  ||  | 
gtaagcctccctctctctctctctttccagatctgcgcgcggagagcgtgcgccgcggcgaatctgaggcgggtgatgagaatggg-tggcgcgcgcgcgcagGTACACGAAGATGGGGTTCGCCGGGAACGTGGAGCCCTGCTTCATCACCCCCACCGTCGTCGCCGTCAACGACACCTTCGCCGGC-CAGACCAGGGCCAAC-

upper sequence: GRMZM2G092459_T02 (Zea mays), 3'ss of exon 1
lower sequence: PP1S85_160V6.1 (Physcomitrella patens), 3'ss of exon 1
------gtacgacctccctccctctccctagatctgcgcgcgaaggcgcgac--gacggtgagtcacgctgctgatctgctcctactctcgctcgcggcagGTACACGAAGATGGGGTTCGCGGGGAACGTGGAGCCCTGCTTCATCACCCCCACTGTCGTCGCCGTCAACGATTCCTTTTCCGGTTCAGGCCAGCCGGCG-
        |   | ||  |     ||   |||  ||         || | |   |||||    |   ||     ||    ||  ||           | ||||| ||||||||||| ||||| ||||| ||||||||||| || || |  || || || || ||  |||| || |||||||  ||  ||| |    |     
gtctttaaagatcgtctttaaagatcgtgagacatggtatttgtagctcaatttgacggcatattgagcc-tacatagaatctcacgacatgaatatgtagGTATACGAAGATGGGATTCGCAGGGAATGTGGAGCCCTGTTTTATTATTCCTACAGTAGTGGCACTCAATGAGTCCTTTTTGGGC-CAGTCGGCTCCAAAG
















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|71448010|gb|DR829060.1|DR829060
EST:     GCCATGGACGCCTTGTCCCGCCCCGCTGTTGTCATCGACAACGGCACCGG                         GTACACTAAGATGGGGTTCGCGGGGAACGTGGAGCCCTGCTTCATCACCCC
genomic: GCCATGGACGCCTTGTCCCGCCCCGCTGTTGTCATCGACAACGGCACCGGgtacgacctc ... ctcgcggcagGTACACGAAGATGGGGTTCGCGGGGAACGTGGAGCCCTGCTTCATCACCCC
EST: gi|78093378|gb|DV521752.1|DV521752
EST:     GCCATGGACGCCTTGTCCCGCCCCGCTGTTGTCATCGACAACGGCACCGG                         GTACACGAAGATGGGGTTCGCGGGGAACGTGGAGCCCTGCTTCATCACCCC
genomic: GCCATGGACGCCTTGTCCCGCCCCGCTGTTGTCATCGACAACGGCACCGGgtacgacctc ... ctcgcggcagGTACACGAAGATGGGGTTCGCGGGGAACGTGGAGCCCTGCTTCATCACCCC
EST: gi|50332359|gb|CO527485.1|CO527485
EST:     GCCATGGACGCCTTGTCCCGCCCCGCTGTTGTCATCGACAACGGCACCGG                         GTACACGAAGATGGGGTTCGCGGGGAACGTGGAGCCCTGCTTCATCACCCC
genomic: GCCATGGACGCCTTGTCCCGCCCCGCTGTTGTCATCGACAACGGCACCGGgtacgacctc ... ctcgcggcagGTACACGAAGATGGGGTTCGCGGGGAACGTGGAGCCCTGCTTCATCACCCC
EST: gi|71448011|gb|DR829061.1|DR829061
EST:     GCCATGGACGCCTTGTCCCGCCCCGCTGTTGTCATCGACAACGGCACCGG                         GTACACGAAGATGGGGTTCGCGGGGAACGTGGAGCCCTGCTTCATCACCCC
genomic: GCCATGGACGCCTTGTCCCGCCCCGCTGTTGTCATCGACAACGGCACCGGgtacgacctc ... ctcgcggcagGTACACGAAGATGGGGTTCGCGGGGAACGTGGAGCCCTGCTTCATCACCCC
EST: gi|71304657|gb|DR788445.1|DR788445
EST:     GCCATGGACGCCTTGTCCCGCCCCGCTGTTGTCATCGACAACGGCACCGG                         GTACACGAAGATGGGGTTCGCGGGGAACGTGGAGCCCTGCTTCATCACCCC
genomic: GCCATGGACGCCTTGTCCCGCCCCGCTGTTGTCATCGACAACGGCACCGGgtacgacctc ... ctcgcggcagGTACACGAAGATGGGGTTCGCGGGGAACGTGGAGCCCTGCTTCATCACCCC
EST: gi|50332366|gb|CO527492.1|CO527492
EST:     GCCATGGACGCCTTGTCCCGCCCCGCTGTTGTCATCGACAACGGCACCGG                         GTACACGAAGATGGGGTTCGCGGGGAACGTGGAGCCCTGCTTCATCACCCC
genomic: GCCATGGACGCCTTGTCCCGCCCCGCTGTTGTCATCGACAACGGCACCGGgtacgacctc ... ctcgcggcagGTACACGAAGATGGGGTTCGCGGGGAACGTGGAGCCCTGCTTCATCACCCC

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), 48 (downstream exon)
Score: 94

GCCTCTCCAATTGCCACCGCCACTGACGAGCGACCACACGCTTGGCGCCCGCCATGGACGCCTTGTCCCGCCCCGCTGTTGTCATCGACAACGGCACCGGgtacgacctc ... ctcgcggcagGTACACGAAGATGGGGTTCGCGGGGAACGTGGAGCCCTGCTTCATCACCCCCACTGTCGTCGCCGTCAACGATTCCTTTTCCGGTTCAGGCCAGCCGGCG


Block sizes: 39 (upstream exon), 49 (downstream exon)
Score: 41

GCCTCTCCAATTGCCACCGCCACTGACGAGCGACCACACGCTTGGCGCCCGCCATGGACGCCTTGTCCCGCCCCGCTGTTGTCATCGACAACGGCACCGGgtacgacctc ... ctcgcggcagGTACACGAAGATGGGGTTCGCGGGGAACGTGGAGCCCTGCTTCATCACCCCCACTGTCGTCGCCGTCAACGATTCCTTTTCCGGTTCAGGCCAGCCGGCG


Block sizes: 39 (upstream exon), 48 (downstream exon)
Score: 34

GCCTCTCCAATTGCCACCGCCACTGACGAGCGACCACACGCTTGGCGCCCGCCATGGACGCCTTGTCCCGCCCCGCTGTTGTCATCGACAACGGCACCGGgtacgacctc ... ctcgcggcagGTACACGAAGATGGGGTTCGCGGGGAACGTGGAGCCCTGCTTCATCACCCCCACTGTCGTCGCCGTCAACGATTCCTTTTCCGGTTCAGGCCAGCCGGCG


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 86

GCCTCTCCAATTGCCACCGCCACTGACGAGCGACCACACGCTTGGCGCCCGCCATGGACGCCTTGTCCCGCCCCGCTGTTGTCATCGACAACGGCACCGGgtacgacctc ... ctcgcggcagGTACACGAAGATGGGGTTCGCGGGGAACGTGGAGCCCTGCTTCATCACCCCCACTGTCGTCGCCGTCAACGATTCCTTTTCCGGTTCAGGCCAGCCGGCG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggcgcgacgacggtgagtcacgctgctgatctgctcctactctcgctcgcggcagGTACACGAAGATGGGGTTCGCGGGGAACGTGGAGCCCTGCTTCATCACCCCCACTGTCGTCGCCGTCAACGATTCCTTTTCCGGTTCAGGCCAGCCGGCG
                       tgctgat  putative branch site (score: 86)
                                 ctcctactctcgctc  putative PPT