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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGAATGCTGATATTGTAGGAACATCCACTCTGCATTCTGCATCTCTACCAAAACAGGAATCGTCAACAGCTACATCCAAGAGTTATACTTTTAGAGAAGgttttgttaactattcttcattattacttaatgtattgagttattttttctctcaaggtatgattttgcttccag

Basic information

species Zea mays
transcript GRMZM2G126453_T01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G126453_T01 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os11g43970.1 (Oryza sativa), 5'ss of exon 10
GTGAATGCTGATATTGTAGGAACATCCACTCTGCATTCTGCATCTCTACCAAAACAGGAATCGTCAACAGCTACATCCAAGAGTTATACTTTTAGAGAAGgttt--tgtta----actat-tcttcattattacttaat-gtattgagttat--tttttctctcaaggtatgattttgcttccag-----
||| |||||||||| || || ||||| |||||||||||||||||| | || ||||||||||| |||||||||||||||||||| ||||||||||||||||||||  |  ||    | ||| ||||  ||||   |  ||  | || |  |||  | |   |  |     |||| |   || |||      
GTGCATGCTGATATCGTGGGTACATCGACTCTGCATTCTGCATCTTTGCCCAAACAGGAATCATCAACAGCTACATCCAAGAGCTATACTTTTAGAGAAGgttttctactatgatattatctcttgtttatcgatagatcattttcaactatgctatacttacccgaacatgactgcactgccattgtag
















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|22489619|gb|BU049542.1|BU049542
EST:     GAAACAGGAATCGTCAACAGCTACATCCAAGAGTTATACTTTTAGAGAAG                         GTGATAGGGTGCGTTATGTGGGTCCAGCTCAACCATGCTCGTTGTCACAAA
genomic: AAAACAGGAATCGTCAACAGCTACATCCAAGAGTTATACTTTTAGAGAAGgttttgttaa ... ttgcttccagGTGATAGGGTGCGTTATGTGGGTCCAGCTCAACCATGCTCGTTGTCACAAA
EST: gi|67031399|gb|CO460148.1|CO460148
EST:     AAAACAGGAATCGTCAACAGCTACATCCAAGAGTTATACTTTTAGAGAAG                         GTGATAGGGTGCGTTATGTGGGTCCAGCTCAACCATGCTCGTTGTCACAAA
genomic: AAAACAGGAATCGTCAACAGCTACATCCAAGAGTTATACTTTTAGAGAAGgttttgttaa ... ttgcttccagGTGATAGGGTGCGTTATGTGGGTCCAGCTCAACCATGCTCGTTGTCACAAA
EST: gi|87152375|gb|DY397164.1|DY397164
EST:     GAAACAGGAATCGTCAACAGCTACATCCAAGAGTTATACTTTTAGAGAAG                         GTGATAGGGTGCGTTATGTGGGTCCAGCTCAACCATGCTCGTTGTCACAAA
genomic: AAAACAGGAATCGTCAACAGCTACATCCAAGAGTTATACTTTTAGAGAAGgttttgttaa ... ttgcttccagGTGATAGGGTGCGTTATGTGGGTCCAGCTCAACCATGCTCGTTGTCACAAA
EST: gi|18384327|gb|BM417526.1|BM417526
EST:     GAAACAGGAATCGTCAACAGCTACATCCAAGAGTTATACTTTTAGAGAAG                         GTGATAGGGTGCGTTATGTGGGTCCAGCTCAACCATGCTCGTTGTCACAAA
genomic: AAAACAGGAATCGTCAACAGCTACATCCAAGAGTTATACTTTTAGAGAAGgttttgttaa ... ttgcttccagGTGATAGGGTGCGTTATGTGGGTCCAGCTCAACCATGCTCGTTGTCACAAA

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), 48 (downstream exon)
Score: 216

GTGAATGCTGATATTGTAGGAACATCCACTCTGCATTCTGCATCTCTACCAAAACAGGAATCGTCAACAGCTACATCCAAGAGTTATACTTTTAGAGAAGgttttgttaa ... ttgcttccagGTGATAGGGTGCGTTATGTGGGTCCAGCTCAACCATGCTCGTTGTCACAAAG


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

GTGAATGCTGATATTGTAGGAACATCCACTCTGCATTCTGCATCTCTACCAAAACAGGAATCGTCAACAGCTACATCCAAGAGTTATACTTTTAGAGAAGgttttgttaa ... ttgcttccagGTGATAGGGTGCGTTATGTGGGTCCAGCTCAACCATGCTCGTTGTCACAAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 168

GTGAATGCTGATATTGTAGGAACATCCACTCTGCATTCTGCATCTCTACCAAAACAGGAATCGTCAACAGCTACATCCAAGAGTTATACTTTTAGAGAAGgttttgttaa ... ttgcttccagGTGATAGGGTGCGTTATGTGGGTCCAGCTCAACCATGCTCGTTGTCACAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 179

GTGAATGCTGATATTGTAGGAACATCCACTCTGCATTCTGCATCTCTACCAAAACAGGAATCGTCAACAGCTACATCCAAGAGTTATACTTTTAGAGAAGgttttgttaa ... ttgcttccagGTGATAGGGTGCGTTATGTGGGTCCAGCTCAACCATGCTCGTTGTCACAAAG