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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAAGGAAACTTGCAGTCTACCATCTGAATCGAGTTATGCTGATAAATCATCATCTGAACCTCCAAGTTCTACTCCATTAAGCGACCCCATCAACAATAAGgttagcatattacagccatctatgagaaagtaaagattgtttacaatcattttgttgctgttgttctgttacctctcttctttcccgtggaattgtgatgtatctcgaaggaagaaaataacatgaatccttattgtttccacaatgtgctccggtag

Basic information

species Zea mays
transcript GRMZM2G106931_T01
intron # 16
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G106931_T01 (Zea mays), 5'ss of exon 16
lower sequence: LOC_Os02g47120.1 (Oryza sativa), 5'ss of exon 16
AAAGGAAACTTGCAGTCTACCATCTGAATCGAGTTATGCTGATAAATCATCATCTGAACCTCCAAGTTCTACTCCATTAAGCGACCCCATCAACAATAAGgttagcatattacagccatctatgagaaagtaaagattgtttacaatcattt-------tgttgctgttgttctgttacctctcttctttcccgtg-gaattgtgatgta---------tctcgaa----ggaagaaaataacatga--------atccttattgtttccacaatgtgctccggtag
 || ||  | |    |||  |  | || || ||  |  ||||   |||  |||||||||||||||| ||||||||||| || || |||||||||||||||||   ||||||   || || | | |           || | || | ||  ||       ||||   ||| |  |||||  |   | ||   |  |  | ||    |  ||         |||||||    |  |||||  ||||| |        ||||| |  ||||   || | ||| | | |||
TAAAGAGGCCTCATCTCTGACTCCCGATTCAAGCAACACTGAACGATCGACATCTGAACCTCCAAGCTCTACTCCATTGAGTGATCCCATCAACAATAAGgtggacatattctggctatatctcatgtttattctgttttgtatagtccattaagaagatgttatagttctcttgttagtttgttactgcacgatacggatcagaacatacacccggattctcgaaatcagatagaaagcaacataatatgctcaatcctcaccgtttattcattatgccctg-tag
















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|18170893|gb|BM340733.1|BM340733
EST:     CATCTGAACCTCCAAGTTCTACTCCATTAAGCGACCCCATCAACAATAAG                         GTGCATTTGCTCAGAACCATGCTTCAATGGGAGGAGCAAGTTCGTCGTGGC
genomic: CATCTGAACCTCCAAGTTCTACTCCATTAAGCGACCCCATCAACAATAAGgttagcatat ... gctccggtagGTGCATTTGCTCAGAACCATGCTTCAATGGGAGGAGCAAGTTCGTCGTGGC
EST: gi|18173772|gb|BM349160.1|BM349160
EST:     CATCTGAACCTCCAAGTTCTACTCCATTAAGCGACCCCATCAACAATAAG                         GTGCATTTGCTCAGAACCATGCTTCAATGGGAGGAGCAAGTTCGTCGTGGC
genomic: CATCTGAACCTCCAAGTTCTACTCCATTAAGCGACCCCATCAACAATAAGgttagcatat ... gctccggtagGTGCATTTGCTCAGAACCATGCTTCAATGGGAGGAGCAAGTTCGTCGTGGC
EST: gi|18163883|gb|BM333722.1|BM333722
EST:     CATCTGAACCTCCAAGTTCTACTCCATTAAGCGACCCCATCAACAATAAG                         GTGCATTTGCTCAGAACCATGCTTCAATGGGAGGAGCAAGTTCGTCGTGGC
genomic: CATCTGAACCTCCAAGTTCTACTCCATTAAGCGACCCCATCAACAATAAGgttagcatat ... gctccggtagGTGCATTTGCTCAGAACCATGCTTCAATGGGAGGAGCAAGTTCGTCGTGGC
EST: gi|18166093|gb|BM335932.1|BM335932
EST:     CATCTGAACCTCCAAGTTCTACTCCATTAAGCGACCCCATCAACAATAAG                         GTGCATTTGCTCAGAACCATGCTTCAATGGGAGGAGCAAGTTCGTCGTGGC
genomic: CATCTGAACCTCCAAGTTCTACTCCATTAAGCGACCCCATCAACAATAAGgttagcatat ... gctccggtagGTGCATTTGCTCAGAACCATGCTTCAATGGGAGGAGCAAGTTCGTCGTGGC
EST: gi|211217076|gb|FL154222.1|FL154222
EST:     CATCTGAACCTCCAAGTTCTACTCCATTAAGCGACCCCATCAACAATAAG                         GTGCATTTGCTCAGAACCATGCTTCAATGGGAGGAGCAAGTTCGTCGTGGC
genomic: CATCTGAACCTCCAAGTTCTACTCCATTAAGCGACCCCATCAACAATAAGgttagcatat ... gctccggtagGTGCATTTGCTCAGAACCATGCTTCAATGGGAGGAGCAAGTTCGTCGTGGC
EST: gi|24934420|gb|CA452638.1|CA452638
EST:     CATCTGACCCTCCAAGTTCTACTCCATTAAGCGACCCCATCAACAATAAG                         GTGCATTTGCTCAGAACCATGCTTCAATGGGAGGAGCAAGTTCGCCGTGGC
genomic: CATCTGAACCTCCAAGTTCTACTCCATTAAGCGACCCCATCAACAATAAGgttagcatat ... gctccggtagGTGCATTTGCTCAGAACCATGCTTCAATGGGAGGAGCAAGTTCGTCGTGGC
EST: gi|31359063|gb|CD443420.1|CD443420
EST:     CATCTGAACCTCCAAGTTCTACTCCATTAAGCGACCCCATCAACAATAAG                         GTGCATTTGCTCAGAACCATGCTTCAATGGGAGGAGNCA-GTTCGCCGTGG
genomic: CATCTGAACCTCCAAGTTCTACTCCATTAAGCGACCCCATCAACAATAAGgttagcatat ... gctccggtagGTGCATTTGCTCAGAACCATGCTTCAATGGGAGGAG-CAAGTTCGTCGTGG

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

AAAGGAAACTTGCAGTCTACCATCTGAATCGAGTTATGCTGATAAATCATCATCTGAACCTCCAAGTTCTACTCCATTAAGCGACCCCATCAACAATAAGgttagcatat ... gctccggtagGTGCATTTGCTCAGAACCATGCTTCAATGGGAGGAGCAAGTTCGTCGTGGCGCATCTTTGGCAGAGAAAAGTCTCAGTGCAAGCATCTGCACAAAGGCAA


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 54

AAAGGAAACTTGCAGTCTACCATCTGAATCGAGTTATGCTGATAAATCATCATCTGAACCTCCAAGTTCTACTCCATTAAGCGACCCCATCAACAATAAGgttagcatat ... gctccggtagGTGCATTTGCTCAGAACCATGCTTCAATGGGAGGAGCAAGTTCGTCGTGGCGCATCTTTGGCAGAGAAAAGTCTCAGTGCAAGCATCTGCACAAAGGCAA


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

AAAGGAAACTTGCAGTCTACCATCTGAATCGAGTTATGCTGATAAATCATCATCTGAACCTCCAAGTTCTACTCCATTAAGCGACCCCATCAACAATAAGgttagcatat ... gctccggtagGTGCATTTGCTCAGAACCATGCTTCAATGGGAGGAGCAAGTTCGTCGTGGCGCATCTTTGGCAGAGAAAAGTCTCAGTGCAAGCATCTGCACAAAGGCAA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 35

AAAGGAAACTTGCAGTCTACCATCTGAATCGAGTTATGCTGATAAATCATCATCTGAACCTCCAAGTTCTACTCCATTAAGCGACCCCATCAACAATAAGgttagcatat ... gctccggtagGTGCATTTGCTCAGAACCATGCTTCAATGGGAGGAGCAAGTTCGTCGTGGCGCATCTTTGGCAGAGAAAAGTCTCAGTGCAAGCATCTGCACAAAGGCAA