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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACATGCAGTCTCTGACTCCCTAGTAAGATACAAAGCTATGCGGATGCTTCGTGGAAATGAGTCCGCCCTTTTCCTTTCACTATGCCAGGCATTCATCGAGgtttgtttagttttccatgatagaccagtggttttgaatctgataagagaacataacttgctacaacacacatgaaatgaaaccaaatgactcagtcttacccgtaaagcctaaattgtaaataaacagtaaacatttgtctttagacgtagggagagttcacatcttggttttccatatcag

Basic information

species Zea mays
transcript GRMZM2G006781_T01
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G006781_T02 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os12g35290.1 (Oryza sativa), 5'ss of exon 11
ACATGCAGTCTCTGACTCCCTAGTAAGATACAAAGCTATGCGGATGCTTCGTGGAAATGAGTCCGCCCTTTTCCTTTCACTATGCCAGGCATTCATCGAGgtttgtttagttttccatgatagaccagtggttttgaatctgataagagaacataacttgctacaacacacatgaaatgaaaccaaatgactcagtcttacccgta-aagcctaaattgtaaataaacagtaaacatttgtctttagacgtagggagagttcacatcttggttttccatatcag
||| || || |||||||||||||| |||||||| || ||||||||||| ||||||||||||||| | |||||||||||||| ||||||||||| || |||||  |    |   ||   || | |  |||  |||||  ||  ||              | ||  |||| | |  |    |||  |  ||||   ||  |     || |  |||| |     | || | | |||   ||| || |   |                                    
ACAAGCCGTTTCTGACTCCCTAGTCAGATACAATGCCATGCGGATGCTGCGTGGAAATGAGTCCTCTCTTTTCCTTTCACTTTGCCAGGCATTTATTGAGgtaag---gggcctctg-gaaaaaggagtatttttg--tccaat--------------tcctcaaacaaataatattccaaatta--tgaccaggtggtgtttctatacacctagagaaggattacatattaa---tttatcctcgcag-----------------------------------
















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|24767774|gb|CA402910.1|CA402910
EST:     GTGGAAATGAGTCCGCCCTTTTCCTTTCACTATGCCAGGCATTCATCGAG                         GTTGCATATCCTTATTGTGCCGCATGTTTTGGCCGATGCTACCCAAACGGG
genomic: GTGGAAATGAGTCCGCCCTTTTCCTTTCACTATGCCAGGCATTCATCGAGgtttgtttag ... tccatatcagGTTGCATATCCTTATTGTGCCGCATGTTTTGGCCGATGCTACCCAAACGGG
EST: gi|31360458|gb|CD444815.1|CD444815
EST:     GTGGAAATGAGTCCGCCCTTTTCCTTTCACTATGCCAGGCATTCATCGAG                         GTTGCATATCCTTATTGTGCCGCATGTTTTGGCCGATGCTACCCAAACGGG
genomic: GTGGAAATGAGTCCGCCCTTTTCCTTTCACTATGCCAGGCATTCATCGAGgtttgtttag ... tccatatcagGTTGCATATCCTTATTGTGCCGCATGTTTTGGCCGATGCTACCCAAACGGG
EST: gi|76018822|gb|DT945992.1|DT945992
EST:     GTGGAAATGAGTCCGCCCTTTTCCTTTCACTATGCCAGGCATTCATCGAG                         GTTGCATATCCTTATTGTGCCGCATGTTTTGGCCGATGCTACCCAAACGGG
genomic: GTGGAAATGAGTCCGCCCTTTTCCTTTCACTATGCCAGGCATTCATCGAGgtttgtttag ... tccatatcagGTTGCATATCCTTATTGTGCCGCATGTTTTGGCCGATGCTACCCAAACGGG
EST: gi|32837856|gb|CD977534.1|CD977534
EST:     GTGGAAATGAGTCCGCCCTTTTCCTTTCACTATGCCAGACATTCATCGAG                         GTTGCATATCCTTATTGTGCCGCATGTTTTGGCCGATGCTACCCGGACGGG
genomic: GTGGAAATGAGTCCGCCCTTTTCCTTTCACTATGCCAGGCATTCATCGAGgtttgtttag ... tccatatcagGTTGCATATCCTTATTGTGCCGCATGTTTTGGCCGATGCTACCCAAACGGG
EST: gi|32839358|gb|CD979039.1|CD979039
EST:     GTGGAAATGAGTCCGCCCTTTTCCTTTCACTATGCCAGACATTCATCGAG                         GTTGCATATCCTTATTGTGCCGCATGTTTTGGCCGATGCTACCCTGACGGG
genomic: GTGGAAATGAGTCCGCCCTTTTCCTTTCACTATGCCAGGCATTCATCGAGgtttgtttag ... tccatatcagGTTGCATATCCTTATTGTGCCGCATGTTTTGGCCGATGCTACCCAAACGGG
EST: gi|32836515|gb|CD976193.1|CD976193
EST:     GTGGAAATGAGTCCGCCCTTTTCCTTTCACTATGCCAGACATTCATCGAG                         GTTGCATATCCTTATTGTGCCGCATGTTTTGGCCGATGCTACCCGGACGGG
genomic: GTGGAAATGAGTCCGCCCTTTTCCTTTCACTATGCCAGGCATTCATCGAGgtttgtttag ... tccatatcagGTTGCATATCCTTATTGTGCCGCATGTTTTGGCCGATGCTACCCAAACGGG
EST: gi|60347978|gb|DN214951.1|DN214951
EST:     GTGGAAATGAGTCCGCCCTTTTCCTTTCACTATGCCAGGCATTCATCGAG                         GTTGCATATCCTTATTGTGCCGCATGTTTTGGCCGATGCTACCCAAACGGG
genomic: GTGGAAATGAGTCCGCCCTTTTCCTTTCACTATGCCAGGCATTCATCGAGgtttgtttag ... tccatatcagGTTGCATATCCTTATTGTGCCGCATGTTTTGGCCGATGCTACCCAAACGGG
EST: gi|110202470|gb|EC884367.1|EC884367
EST:     GGGGAAATGAGTCCGCCCTTTTCCTTTCACTATGCCAGGCATTCATCGAG                         GTTGCATATCCTTATTGTGGCCGCATGTTTTGGCCGATGCTACCCAAACGG
genomic: GTGGAAATGAGTCCGCCCTTTTCCTTTCACTATGCCAGGCATTCATCGAGgtttgtttag ... tccatatcagGTTGCATATCCTTATTGT-GCCGCATGTTTTGGCCGATGCTACCCAAACGG
EST: gi|83278283|gb|DV942291.1|DV942291
EST:     GTGGAAATGAGTCCGCCCTTTTCCTTTCACTATGCCAGGCATTCATCGAG                         GTTGCATATCCTTATTGTGCCGCATGTTTTGGCCGATGCTACCCAAACGGG
genomic: GTGGAAATGAGTCCGCCCTTTTCCTTTCACTATGCCAGGCATTCATCGAGgtttgtttag ... tccatatcagGTTGCATATCCTTATTGTGCCGCATGTTTTGGCCGATGCTACCCAAACGGG
EST: gi|32836806|gb|CD976484.1|CD976484
EST:     GTGGAAATGAGTCCGCCCTTTTCCTTTCACTATGCCAGACATTCATCGAG                         GTTGCATATCCTTATTGTGCCGCATGTTTTGGCCGATGCTACCCGGACGGG
genomic: GTGGAAATGAGTCCGCCCTTTTCCTTTCACTATGCCAGGCATTCATCGAGgtttgtttag ... tccatatcagGTTGCATATCCTTATTGTGCCGCATGTTTTGGCCGATGCTACCCAAACGGG
EST: gi|211402668|gb|FL477442.1|FL477442
EST:     GTGGAAATGAGTCCGCCCTTTTCCTTTCACTATGCCAGGCATTCATCGAG                         GTTGCATATCCTTATTGTGCCGCATGTTTTGGCCGATGCTACCCAAACGGG
genomic: GTGGAAATGAGTCCGCCCTTTTCCTTTCACTATGCCAGGCATTCATCGAGgtttgtttag ... tccatatcagGTTGCATATCCTTATTGTGCCGCATGTTTTGGCCGATGCTACCCAAACGGG
EST: gi|32794424|gb|CD946660.1|CD946660
EST:     GTGGAAATGAGTCCGCCCTTTTCCTTTCACTATGCCAGGCATTCATCGAG                         GTTGCATATCCTTATTGTGCCGCATGTTTTGGCCGATGCTACCCAAACGGG
genomic: GTGGAAATGAGTCCGCCCTTTTCCTTTCACTATGCCAGGCATTCATCGAGgtttgtttag ... tccatatcagGTTGCATATCCTTATTGTGCCGCATGTTTTGGCCGATGCTACCCAAACGGG
EST: gi|148999330|gb|EE036266.2|EE036266
EST:     ATGAGTCCGCCCTTTTTCCTTTTCACTATGCCAGGCATTCATCGAG                         GTTGCATATCCTTATTGTGCCGCATGTTTTGGCCGATGCTACCCAAACGGG
genomic: ATGAGTCCGCCC-TTTTCC-TTTCACTATGCCAGGCATTCATCGAGgtttgtttag ... tccatatcagGTTGCATATCCTTATTGTGCCGCATGTTTTGGCCGATGCTACCCAAACGGG
EST: gi|32827025|gb|CD966703.1|CD966703
EST:     GTGGAAATGAGTCCGCCCTTTTCCTTTCACTATGCCAGACATTCATCGAG                         GTTGCATATCCTTATTGTGCCGCATGTTTTGGCCGATGCTACCCGGACGGG
genomic: GTGGAAATGAGTCCGCCCTTTTCCTTTCACTATGCCAGGCATTCATCGAGgtttgtttag ... tccatatcagGTTGCATATCCTTATTGTGCCGCATGTTTTGGCCGATGCTACCCAAACGGG
EST: gi|71316956|gb|DR795162.1|DR795162
EST:     GTGGAAATGAGTCCGCCCTTTTCCTTTCACTATGCCAGGCATTCATCGAG                         GTTGCATATCCTTATTGTGCCGCATGTTTTGGCCGATGCTACCCAAACGGG
genomic: GTGGAAATGAGTCCGCCCTTTTCCTTTCACTATGCCAGGCATTCATCGAGgtttgtttag ... tccatatcagGTTGCATATCCTTATTGTGCCGCATGTTTTGGCCGATGCTACCCAAACGGG

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: 49 (upstream exon), 44 (downstream exon)
Score: 28

ACATGCAGTCTCTGACTCCCTAGTAAGATACAAAGCTATGCGGATGCTTCGTGGAAATGAGTCCGCCCTTTTCCTTTCACTATGCCAGGCATTCATCGAGgtttgtttag ... tccatatcagGTTGCATATCCTTATTGTGCCGCATGTTTTGGCCGATGCTACCCAAACGGGGCAACATTGATCTCAGAGCGTCAAGGCACATTTGACGCTGTCCGTCAGC


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 45

ACATGCAGTCTCTGACTCCCTAGTAAGATACAAAGCTATGCGGATGCTTCGTGGAAATGAGTCCGCCCTTTTCCTTTCACTATGCCAGGCATTCATCGAGgtttgtttag ... tccatatcagGTTGCATATCCTTATTGTGCCGCATGTTTTGGCCGATGCTACCCAAACGGGGCAACATTGATCTCAGAGCGTCAAGGCACATTTGACGCTGTCCGTCAGC


Block sizes: 41 (upstream exon), 42 (downstream exon)
Score: 17

ACATGCAGTCTCTGACTCCCTAGTAAGATACAAAGCTATGCGGATGCTTCGTGGAAATGAGTCCGCCCTTTTCCTTTCACTATGCCAGGCATTCATCGAGgtttgtttag ... tccatatcagGTTGCATATCCTTATTGTGCCGCATGTTTTGGCCGATGCTACCCAAACGGGGCAACATTGATCTCAGAGCGTCAAGGCACATTTGACGCTGTCCGTCAGC


Block sizes: 47 (upstream exon), 47 (downstream exon)
Score: 54

ACATGCAGTCTCTGACTCCCTAGTAAGATACAAAGCTATGCGGATGCTTCGTGGAAATGAGTCCGCCCTTTTCCTTTCACTATGCCAGGCATTCATCGAGgtttgtttag ... tccatatcagGTTGCATATCCTTATTGTGCCGCATGTTTTGGCCGATGCTACCCAAACGGGGCAACATTGATCTCAGAGCGTCAAGGCACATTTGACGCTGTCCGTCAGC