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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAATTCCCTGCATCCAGACCGTTTGGTATCAAGTACAAGTTTCACTTAGAGgtaagtgggacttgtttttcgttaatatatgccttgtatttcgtttaaaggatcgttgatcttgtcactaatttttaatagtcttttggatttaaatatc...

Basic information

species Zea mays
transcript GRMZM2G042398_T01
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G042398_T01 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os08g08200.2 (Oryza sativa), 5'ss of exon 9
AAATTCCCTGCATCCAGACCGTTTGGTATCAAGTACAAGTTTCACTTAGAGgtaagtggg-acttgtttttcgttaatatatgcctt--gtat-ttcgtttaaaggatcgttgatcttgtcactaatttttaatagtcttttggatttaaatatc
|||||||| ||||||||||| || |||||||| ||||||||||||||||||||||| |   |||  |  || || |  || |  |||  || | |   | || ||| |  || |||||  ||||  ||| |  ||||   ||  |||  | ||  
AAATTCCCCGCATCCAGACCTTTCGGTATCAAATACAAGTTTCACTTAGAGgtaagggattactcataatttgtaatcatgttgctttagtgtgtgtttctatagggtgatttatcttagcacttgtttct--tagttgctttaatt-gagtac-

upper sequence: GRMZM2G042398_T01 (Zea mays), 5'ss of exon 10
lower sequence: Vv19s0014g04740.t01 (Vitis vinifera), 5'ss of exon 9
AAATTCCCTGCATCCAGACCGTTTGGTATCAAGTACAAGTTTCACTTAGAGgtaagtgggacttgtttttcgttaatatatg-ccttgtatttcgtttaaaggatcgttgatcttgtcactaattttta-atagtcttttgg-atttaaatatc
|||||     | || || || |||||||||||||||||||| ||| |||||||||       ||    ||| ||| ||||   |||| |  |   |||    | | | |  | ||   ||| | |  |    | | | ||    |||| ||   
AAATTTAAAACTTCTAGTCCCTTTGGTATCAAGTACAAGTTCCACCTAGAGgtaatgttctattaaacttctttattataaatccttttgctaattttggttggttggtatttttcagactgaatgatgtgcactatgttaatgtttagat---
















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|166478805|gb|EG300577.1|EG300577
EST:     ATTCCCTGCATCCAGACCGTTTGGTATCAAGTACAAGTTTCAACTTAGAG                         GATGCTGTTGATTGCCCAGAATGGGTTGTTCCATTCCATCTCTTCAAATT
genomic: ATTCCCTGCATCCAGACCGTTTGGTATCAAGTACAAGTTTC-ACTTAGAGgtaagtggga ... caacatgcagGATGCTGTTGATTGCCCAGAATGGGTTGTTCCATTCCATCTCTTCAAATT
EST: gi|16925826|gb|BM078894.1|BM078894
EST:     AATTCCCTGCATCCAGACCGTTTGGTATCAAGTACAAGTTTCACTTAGAG                         GATGCTGTTGATTGCCCAGAATGGGTTGTTCCATTCCATCTCTTCAAATTA
genomic: AATTCCCTGCATCCAGACCGTTTGGTATCAAGTACAAGTTTCACTTAGAGgtaagtggga ... caacatgcagGATGCTGTTGATTGCCCAGAATGGGTTGTTCCATTCCATCTCTTCAAATTA
EST: gi|32937233|gb|CF042052.1|CF042052
EST:     AATTCCCTGCATCCAGACCGTTTGGTATCAAGTACAAGTTTCACTTAGAG                         GATGCTGTTGATTGCCCAGAATGGGTTGTTCCATTCCATCTCTTCAAATTA
genomic: AATTCCCTGCATCCAGACCGTTTGGTATCAAGTACAAGTTTCACTTAGAGgtaagtggga ... caacatgcagGATGCTGTTGATTGCCCAGAATGGGTTGTTCCATTCCATCTCTTCAAATTA
EST: gi|211031439|gb|FL127271.1|FL127271
EST:     AATTCCCTGCTTCCAGACCGTTTGGTATCAAGTACAAGTTTCACTTAGAG                         GATGCTGTTGATTGCCCAGAATGGGTTGTTCCATTCCATCTCTTCAAATTA
genomic: AATTCCCTGCATCCAGACCGTTTGGTATCAAGTACAAGTTTCACTTAGAGgtaagtggga ... caacatgcagGATGCTGTTGATTGCCCAGAATGGGTTGTTCCATTCCATCTCTTCAAATTA
EST: gi|18165055|gb|BM334900.1|BM334900
EST:     CTGCATCCAGACCGTTTGGTATCAAGTACAAGTTTCACTTAGAG                         GATGCTGTTGATTGCCCAGAATGGGTTGTTCCATTCCATCTCTTCAAATTA
genomic: CTGCATCCAGACCGTTTGGTATCAAGTACAAGTTTCACTTAGAGgtaagtggga ... caacatgcagGATGCTGTTGATTGCCCAGAATGGGTTGTTCCATTCCATCTCTTCAAATTA
EST: gi|60395442|gb|DN228312.1|DN228312
EST:     AATTCCCTGCATCCAGACCGTTTGGTATCAAGTACAAGTTTCACTTAGAG                         GATGCTGTTGATTGCCCAGAATGGGTTGTTCCATTCCATCTCTTCAAATTA
genomic: AATTCCCTGCATCCAGACCGTTTGGTATCAAGTACAAGTTTCACTTAGAGgtaagtggga ... caacatgcagGATGCTGTTGATTGCCCAGAATGGGTTGTTCCATTCCATCTCTTCAAATTA
EST: gi|211475864|gb|FL467329.1|FL467329
EST:     AATTCCCTGCATCCAGACCGTTTGGTATCAAGTACAAGTTTCACTTAGAG                         GATGCTGTTGATTGCCCAGAATGGGTTGTTCCATTCCATCTCTTCAAATTA
genomic: AATTCCCTGCATCCAGACCGTTTGGTATCAAGTACAAGTTTCACTTAGAGgtaagtggga ... caacatgcagGATGCTGTTGATTGCCCAGAATGGGTTGTTCCATTCCATCTCTTCAAATTA
EST: gi|18164178|gb|BM334017.1|BM334017
EST:     AATTCCCTGCATCCAGACCGTTTGGTATCAAGTACAAGTTTCACTTAGAG                         GATGCTGTTGATTGCCCAGAATGGGTTGTTCCATTCCATCTCTTCAAATTA
genomic: AATTCCCTGCATCCAGACCGTTTGGTATCAAGTACAAGTTTCACTTAGAGgtaagtggga ... caacatgcagGATGCTGTTGATTGCCCAGAATGGGTTGTTCCATTCCATCTCTTCAAATTA

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), 47 (downstream exon)
Score: 144

AAATTCCCTGCATCCAGACCGTTTGGTATCAAGTACAAGTTTCACTTAGAGgtaagtggga ... caacatgcagGATGCTGTTGATTGCCCAGAATGGGTTGTTCCATTCCATCTCTTCAAATTATTGGCAGAGGAG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 118

AAATTCCCTGCATCCAGACCGTTTGGTATCAAGTACAAGTTTCACTTAGAGgtaagtggga ... caacatgcagGATGCTGTTGATTGCCCAGAATGGGTTGTTCCATTCCATCTCTTCAAATTATTGGCAGAGGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 126

AAATTCCCTGCATCCAGACCGTTTGGTATCAAGTACAAGTTTCACTTAGAGgtaagtggga ... caacatgcagGATGCTGTTGATTGCCCAGAATGGGTTGTTCCATTCCATCTCTTCAAATTATTGGCAGAGGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 206

AAATTCCCTGCATCCAGACCGTTTGGTATCAAGTACAAGTTTCACTTAGAGgtaagtggga ... caacatgcagGATGCTGTTGATTGCCCAGAATGGGTTGTTCCATTCCATCTCTTCAAATTATTGGCAGAGGAG