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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatattgtgcgtactaggtgtgctacgcaggaaagtagaaatgagaaatatccatgacatattggtgttgcattttcagGGCGGCACCTTCACTGTATCAAATTTGGGAGGTCCCTTCGGAATTAAACAATTCTGCGCCATCATAAATCCTCCCCAGTCAGCAATTTTGGCCATTGGTT

Basic information

species Zea mays
transcript GRMZM2G015132_T01
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G015132_T01 (Zea mays), 3'ss of exon 15
lower sequence: LOC_Os02g01500.1 (Oryza sativa), 3'ss of exon 16
gtatattgtgcgtactaggtgtgctacgcaggaaagtagaaatgagaaatatccatgacatattggtgttgcattttcagGGCGGCACCTTCACTGTATCAAATTTGGGAGGTCCCTTCGGAATTAAACAATTCTGCGCCATCATAAATCCTCCCCAGTCAGCAATTTTGGCCATTGGTT
|||||| |  || |   |||     |   | | | |    ||    |  | ||| ||| |  |   || ||| ||||||||| ||||| |||||  |||||||  | |||||||| |||||||| ||||||||||| ||||||||||||||||| ||||||||||| |||||||||||| 
gtatatggatcgcat--ggtagctaatataagcatgagacaacatcatttttccttgaaaattc--tggtgc-ttttcagGGAGGCACATTCACCATATCAAACCTAGGAGGTCCTTTCGGAATCAAACAATTCTGTGCCATCATAAATCCTCCTCAGTCAGCAATCTTGGCCATTGGTA

upper sequence: GRMZM2G015132_T01 (Zea mays), 3'ss of exon 15
lower sequence: LOC_Os07g22720.2 (Oryza sativa), 3'ss of exon 16
gtatattg--tgcgtactaggtgtgctacgcaggaaagtagaaatgagaaatatccatgaca-tattggtgttgcattttcagGGCGGCACCTTCACTGTATCAAATTTGGGAGGTCCCTTCGGAATTAAACAATTCTGCGCCATCATAAATCCTCCCCAGTCAGCAATTTTGGCCATTGGTT
|||||| |  ||  |  ||| |    |  ||| ||||     ||    |  | ||||||| |   ||  ||| |  ||||||||| ||||| |||||  ||||||| ||||||||||| || |||||||| ||||| || ||||||||||||||||| ||||| ||||| |||||||||||||
gtatatggattgtatggtagttaatttttgcatgaaac----aacagcatttttccatgagaacttttatgtggtgttttcagGGAGGCACATTCACCATATCAAACTTGGGAGGTCCTTTTGGAATTAAGCAATTTTGTGCCATCATAAATCCTCCTCAGTCGGCAATCTTGGCCATTGGTT
















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|29576885|gb|CB616997.1|CB616997
EST:     AGTTGGCTCAAAAAGCAAGAGATAATAGCCTAAAACCAGCAGATTACGAG                         GGCGGCACCTTCACTGTATCAAATTTGGGAGGTCCCTTCGGAATTAAACAA
genomic: AGTTGGCTCAAAAAGCAAGAGATAATAGCCTAAAACCAGCAGATTACGAGgtatattgtg ... gcattttcagGGCGGCACCTTCACTGTATCAAATTTGGGAGGTCCCTTCGGAATTAAACAA
EST: gi|71761137|gb|DR959074.1|DR959074
EST:     AGTTGGCTCAAAAAGCAAGAGATAATAGCCTAAAACCAGCAGATTACGAG                         GGCGGCACCTTCACTGTATCAAATTTGGGAGGTCCCTTCGGAATTAAACAA
genomic: AGTTGGCTCAAAAAGCAAGAGATAATAGCCTAAAACCAGCAGATTACGAGgtatattgtg ... gcattttcagGGCGGCACCTTCACTGTATCAAATTTGGGAGGTCCCTTCGGAATTAAACAA
EST: gi|76932163|gb|DV172956.1|DV172956
EST:     AGTTGGCTCAAAAAGCAAGAGATAATAGCCTAAAACCAGCAGATTACGAG                         GGCGGCACCTTCACTGTATCAAATTTGGGAGGTCCCTTCGGAATTAAACAA
genomic: AGTTGGCTCAAAAAGCAAGAGATAATAGCCTAAAACCAGCAGATTACGAGgtatattgtg ... gcattttcagGGCGGCACCTTCACTGTATCAAATTTGGGAGGTCCCTTCGGAATTAAACAA
EST: gi|71333154|gb|DR803611.1|DR803611
EST:     AGTTGGCTCAAAAAGCAAGAGATAATAGCCTAAAACCAGCAGATTACGAG                         GGCGGCACCTTCACTGTATCAAATTTGGGAGGTCCCTTCGGAATTAAACAA
genomic: AGTTGGCTCAAAAAGCAAGAGATAATAGCCTAAAACCAGCAGATTACGAGgtatattgtg ... gcattttcagGGCGGCACCTTCACTGTATCAAATTTGGGAGGTCCCTTCGGAATTAAACAA
EST: gi|211011840|gb|FL066266.1|FL066266
EST:     AGTTGGCTCAAAAAGCAAGAGATAATAGCCTAAAACCAGCAGATTACGAG                         GGCGGCACCTTCACTGTATCAAATTTGGGAGGTCCCTTCGGAATTAAACAA
genomic: AGTTGGCTCAAAAAGCAAGAGATAATAGCCTAAAACCAGCAGATTACGAGgtatattgtg ... gcattttcagGGCGGCACCTTCACTGTATCAAATTTGGGAGGTCCCTTCGGAATTAAACAA
EST: gi|78091151|gb|DV519525.1|DV519525
EST:     AGTTGGCTCAAAAAGCAAGAGATAATAGCCTAAAACCAGCAGATTACGAG                         GGCGGCACCTTCACTGTATCAAATTTGGGAGGTCCCTTCGGAATTAAACAA
genomic: AGTTGGCTCAAAAAGCAAGAGATAATAGCCTAAAACCAGCAGATTACGAGgtatattgtg ... gcattttcagGGCGGCACCTTCACTGTATCAAATTTGGGAGGTCCCTTCGGAATTAAACAA

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: 41 (upstream exon), 49 (downstream exon)
Score: 123

GATGCAGACAAGAAGGGACTCGGTGCAATTGCTGAGGAGGTGAAGCAGTTGGCTCAAAAAGCAAGAGATAATAGCCTAAAACCAGCAGATTACGAGgtatattgtg ... gcattttcagGGCGGCACCTTCACTGTATCAAATTTGGGAGGTCCCTTCGGAATTAAACAATTCTGCGCCATCATAAATCCTCCCCAGTCAGCAATTTTGGCCATTGGTT


Block sizes: 41 (upstream exon), 49 (downstream exon)
Score: 255

GATGCAGACAAGAAGGGACTCGGTGCAATTGCTGAGGAGGTGAAGCAGTTGGCTCAAAAAGCAAGAGATAATAGCCTAAAACCAGCAGATTACGAGgtatattgtg ... gcattttcagGGCGGCACCTTCACTGTATCAAATTTGGGAGGTCCCTTCGGAATTAAACAATTCTGCGCCATCATAAATCCTCCCCAGTCAGCAATTTTGGCCATTGGTT


Block sizes: 41 (upstream exon), 49 (downstream exon)
Score: 158

GATGCAGACAAGAAGGGACTCGGTGCAATTGCTGAGGAGGTGAAGCAGTTGGCTCAAAAAGCAAGAGATAATAGCCTAAAACCAGCAGATTACGAGgtatattgtg ... gcattttcagGGCGGCACCTTCACTGTATCAAATTTGGGAGGTCCCTTCGGAATTAAACAATTCTGCGCCATCATAAATCCTCCCCAGTCAGCAATTTTGGCCATTGGTT


Block sizes: 41 (upstream exon), 47 (downstream exon)
Score: 174

GATGCAGACAAGAAGGGACTCGGTGCAATTGCTGAGGAGGTGAAGCAGTTGGCTCAAAAAGCAAGAGATAATAGCCTAAAACCAGCAGATTACGAGgtatattgtg ... gcattttcagGGCGGCACCTTCACTGTATCAAATTTGGGAGGTCCCTTCGGAATTAAACAATTCTGCGCCATCATAAATCCTCCCCAGTCAGCAATTTTGGCCATTGGTT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acgcaggaaagtagaaatgagaaatatccatgacatattggtgttgcattttcagGGCGGCACCTTCACTGTATCAAATTTGGGAGGTCCCTTCGGAATTAAACAATTCTGCGCCATCATAAATCCTCCCCAGTCAGCAATTTTGGCCATTGGTT
                                              cattttc  CT-rich tract
                   agaaatat  TA-rich tract