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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGCAAATGTCATGCTAGGTGGTAAAAGACACAGCCTGGGAATGTCATTTTATGAGCCAACTGTAGTAGGGAATGTCAGCAATGATATGCTTCTTTTCAGgtaaagtttacagttagaccttctaatcttaacaatttcaaccagaccttgttgtagtgcatagaatctactttcacgtgcgagtaaatggtctaatattgaggaattgtctgacacttcatagttgttaacatctttttttcatttcag

Basic information

species Zea mays
transcript GRMZM2G119482_T01
intron # 16
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G119482_T01 (Zea mays), 5'ss of exon 16
lower sequence: LOC_Os02g07760.1 (Oryza sativa), 5'ss of exon 16
GAGCAAATGTCATGCTAGGTGGTAAAAGACACAGCCTGGGAATGTCATTTTATGAGCCAACTGTAGTAGGGAATGTCAGCAATGATATGCTTCTTTTCAGgtaaagtttacagttagaccttctaatcttaacaatttcaaccagaccttgttgtagtgcatagaatctactttcacgtgcgagtaaatggtctaatattgaggaattgtctgacact----tcatagttgttaacatctttttttcatttcag
|||||||  ||||||| ||||||||||| |||||||| || |||||||| ||||||||||||||||||||||| |||||||||||||||||||||||||||||  ||| | |                     ||||   |   |||||| || |||||||||   | ||| ||||  |||||  ||||| || |  |||||| |||| | |||||      |  |||||  |||||      |||   |||||
GAGCAAACATCATGCTTGGTGGTAAAAGGCACAGCCTTGGGATGTCATTCTATGAGCCAACTGTAGTAGGGAACGTCAGCAATGATATGCTTCTTTTCAGgtagggttcaaa---------------------aattgtgatttgaccttattttagtgcatatgctttaccttca--tgcgaagaaatgttcaatcattgagaaattctttgacatccttgttctagtttctaacaatcacatttggcttcag

upper sequence: GRMZM2G119482_T01 (Zea mays), 5'ss of exon 16
lower sequence: Vv19s0085g00880.t01 (Vitis vinifera), 5'ss of exon 16
GAGCAAATGTCATGCTAGGTGGTAAAAGACACAGCCTGGGAATGTCATTTTATGAGCCAACTGTAGTAGGGAATGTCAGCAATGATATGCTTCTTTTCAGgtaaagtttacagttagaccttctaatcttaacaatttcaaccagaccttgttgtagtgcatagaatctactttcacgtgcgagtaaatggtctaatattgaggaattgtctgacacttcatagttgttaacatctttttttcatttcag
||||||| ||| | || || |||||||||||||| ||||||||| | || ||||||||||| ||| | ||  |  |||  ||||| |||||| ||   ||||||| | |  ||| | || |  | ||   || ||||      ||     | |  | |   || |||  | ||    |||  |    |   || || |   |  ||                                            
GAGCAAAAGTCCTTCTTGGGGGTAAAAGACACAGTCTGGGAATGACCTTCTATGAGCCAACGGTAATTGGTGACATCAAGAATGACATGCTTATTGCGAGgtaaactct--agtca-acatgtttattccaaaaattctgctaag-----gataca-tatgtataattaaattgttggtgttatatgactatcaaaaaaaaaaaaaaaa-----------------------------------------
















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|149008263|gb|EE040415.2|EE040415
EST:     TATGAGCCAACTGTAGTAGGGAATGTCAGCAATGATATGCTTCTTTTCAG                         AGAAGAAGTTTTTGGTCCAGTTGCACCCCTTATCCCGTTCAAAACTGAGGA
genomic: TATGAGCCAACTGTAGTAGGGAATGTCAGCAATGATATGCTTCTTTTCAGgtaaagttta ... ttcatttcagAGAAGAAGTTTTTGGTCCAGTTGCACCCCTTATACCGTTCAAAACTGAGGA
EST: gi|78179569|gb|DV549942.1|DV549942
EST:     TATGAGCCAACTGTAGTAGGGAATGTCAGCAATGATATGCTTCTTTTCAG                         AGAAGAAGTTTTTGGTCCAGTTGCACCCCTTATACCGTTCAAAACTGAGGA
genomic: TATGAGCCAACTGTAGTAGGGAATGTCAGCAATGATATGCTTCTTTTCAGgtaaagttta ... ttcatttcagAGAAGAAGTTTTTGGTCCAGTTGCACCCCTTATACCGTTCAAAACTGAGGA
EST: gi|5608478|gb|AI902055.1|AI902055
EST:     TATGAGCCAACTGTAGTAGGGAATGTCAGCAATGATATGCTTCTTTTCAG                         AGAAGAAGTTTTTGGTCCAGTTGCACCCCTTATACCGTTCAAAACTGAGGA
genomic: TATGAGCCAACTGTAGTAGGGAATGTCAGCAATGATATGCTTCTTTTCAGgtaaagttta ... ttcatttcagAGAAGAAGTTTTTGGTCCAGTTGCACCCCTTATACCGTTCAAAACTGAGGA
EST: gi|6827661|gb|AW331304.1|AW331304
EST:     TATGAGCCAACTGTAGTAGGGAATGTCAGCAATGATATGCTTCTTTTCAG                         AGAAGAAGTTTTTGGTCCAGTTGCACCCCTTATACCGTTCAAAACTGAGGA
genomic: TATGAGCCAACTGTAGTAGGGAATGTCAGCAATGATATGCTTCTTTTCAGgtaaagttta ... ttcatttcagAGAAGAAGTTTTTGGTCCAGTTGCACCCCTTATACCGTTCAAAACTGAGGA
EST: gi|76921993|gb|DV168796.1|DV168796
EST:     TATGAGCCAACTGTAGTAGGGAATGTCAGCAATGATATGCTTCTTTTCAG                         AGAAGAAGTTTTTGGTCCAGTTGCACCCCTTATACCGTTCAAAACTGAGGA
genomic: TATGAGCCAACTGTAGTAGGGAATGTCAGCAATGATATGCTTCTTTTCAGgtaaagttta ... ttcatttcagAGAAGAAGTTTTTGGTCCAGTTGCACCCCTTATACCGTTCAAAACTGAGGA
EST: gi|76286305|gb|DV025873.1|DV025873
EST:     TATGAGCCAACTGTAGTAGGGAATGTCAGCAATGATATGCTTCTTTTCAG                         AGAAGAAGTTTTTGGTCCAGTTGCACCCCTTATACCGTTCAAAACTGAGGA
genomic: TATGAGCCAACTGTAGTAGGGAATGTCAGCAATGATATGCTTCTTTTCAGgtaaagttta ... ttcatttcagAGAAGAAGTTTTTGGTCCAGTTGCACCCCTTATACCGTTCAAAACTGAGGA
EST: gi|60348461|gb|DN215434.1|DN215434
EST:     TATGAGCCAACTGTAGTAGGGAATGTCAGCAATGATATGCTTCTTTTCAG                         AGAAGAAGTTTTTGGTCCAGTTGCACCCCTTATACCGTTCAAAACTGAGGA
genomic: TATGAGCCAACTGTAGTAGGGAATGTCAGCAATGATATGCTTCTTTTCAGgtaaagttta ... ttcatttcagAGAAGAAGTTTTTGGTCCAGTTGCACCCCTTATACCGTTCAAAACTGAGGA
EST: gi|60341947|gb|DN208920.1|DN208920
EST:     TATGAGCCAACTGTAGTAGGGAATGTCAGCAATGATATGCTTCTTTTCAG                         AGAAGAAGTTTTTGGTCCAGTTGCACCCCTTATACCGTTCAAAACTGAGGA
genomic: TATGAGCCAACTGTAGTAGGGAATGTCAGCAATGATATGCTTCTTTTCAGgtaaagttta ... ttcatttcagAGAAGAAGTTTTTGGTCCAGTTGCACCCCTTATACCGTTCAAAACTGAGGA

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: 45 (upstream exon), 49 (downstream exon)
Score: 185

GAGCAAATGTCATGCTAGGTGGTAAAAGACACAGCCTGGGAATGTCATTTTATGAGCCAACTGTAGTAGGGAATGTCAGCAATGATATGCTTCTTTTCAGgtaaagttta ... ttcatttcagAGAAGAAGTTTTTGGTCCAGTTGCACCCCTTATACCGTTCAAAACTGAGGAAGAAGCAGTTCATATGGCCAACGATACAAACGCAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 258

GAGCAAATGTCATGCTAGGTGGTAAAAGACACAGCCTGGGAATGTCATTTTATGAGCCAACTGTAGTAGGGAATGTCAGCAATGATATGCTTCTTTTCAGgtaaagttta ... ttcatttcagAGAAGAAGTTTTTGGTCCAGTTGCACCCCTTATACCGTTCAAAACTGAGGAAGAAGCAGTTCATATGGCCAACGATACAAACGCAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 180

GAGCAAATGTCATGCTAGGTGGTAAAAGACACAGCCTGGGAATGTCATTTTATGAGCCAACTGTAGTAGGGAATGTCAGCAATGATATGCTTCTTTTCAGgtaaagttta ... ttcatttcagAGAAGAAGTTTTTGGTCCAGTTGCACCCCTTATACCGTTCAAAACTGAGGAAGAAGCAGTTCATATGGCCAACGATACAAACGCAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 290

GAGCAAATGTCATGCTAGGTGGTAAAAGACACAGCCTGGGAATGTCATTTTATGAGCCAACTGTAGTAGGGAATGTCAGCAATGATATGCTTCTTTTCAGgtaaagttta ... ttcatttcagAGAAGAAGTTTTTGGTCCAGTTGCACCCCTTATACCGTTCAAAACTGAGGAAGAAGCAGTTCATATGGCCAACGATACAAACGCAG