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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGCTTCATGCTTTTGCAACCGAAGGTGCACATTGTGCTAGAGTTCGTGAAGTCCTGAATTCCTCTGATgtgagtaacttcccactgcaatacaagttacagaaccctatgaaattggaaactatatttgtgatcatgacaagtgattcaccaaacagaaaatggcaaacaaatgctggactgaaaaaaaacattcctttttatgtag

Basic information

species Zea mays
transcript GRMZM2G001895_T01
intron # 15
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G001895_T01 (Zea mays), 5'ss of exon 15
lower sequence: LOC_Os10g42439.1 (Oryza sativa), 5'ss of exon 21
GTGCTTCATGCTTTTGCAACCGAAGGTGCACATTGTGCTAGAGTTCGTGAAGTCCTGAATTCCTCTGATgtgagtaacttcccactgcaatacaagttacagaaccctatgaaattggaaactatatttgtgatcatgacaagtgatt-caccaaacagaaaatggcaaacaaatgctggactgaaaaaaaacattcctttttatgtag
|||||||||||||||||||| ||||| ||||| ||||||| |||||||||| | |||||||| |||||||| |||||||| |   ||   |      |   ||   ||  | | ||   |     | ||| |||||| | |||| |   ||| |||  |||||||   |  | | | ||     || || ||  |    |||  |    
GTGCTTCATGCTTTTGCAACGGAAGGCGCACACTGTGCTAAAGTTCGTGAAATTCTGAATTCTTCTGATgtaagtaacttactgatgagttcatccatctcgagtactccgtagttcatattcgaagttgggatcattagaagtaacagcactaaat-gaaaatgagcactagacg-tgagtaaaataacaatgtgttctttcttag--
















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|109637212|gb|EC590757.1|EC590757
EST:     CCGAAGGTGCACATTGTGCTAGAGTTCGTGAAGTCCTGAATTCCTCTGAT                         GTATGGAGTGCTTACAAAGACCAGAAGCACGACCTTTTCCTTCCATCCAAT
genomic: CCGAAGGTGCACATTGTGCTAGAGTTCGTGAAGTCCTGAATTCCTCTGATgtgagtaact ... ttttatgtagGTATGGAGTGCTTACAAAGACCAGAAGCACGACCTTTTCCTTCCATCCAAT
EST: gi|16927351|gb|BM080420.1|BM080420
EST:     CCGAAGGTGCACATTGTGCTAGAGTTCGTGAAGTCCTGAATTCCTCTGAT                         GTATGGAGTGCTTACAAAGACCAGAAGCACGACCTTTTCCTTCCATCCAAT
genomic: CCGAAGGTGCACATTGTGCTAGAGTTCGTGAAGTCCTGAATTCCTCTGATgtgagtaact ... ttttatgtagGTATGGAGTGCTTACAAAGACCAGAAGCACGACCTTTTCCTTCCATCCAAT
EST: gi|6012267|gb|AW061809.1|AW061809
EST:     CCGAAGGTGCACATTGTGCTAGAGTTCGTGAAGTCCTGAATTCCTCTGAT                         GTATGGAGTGCTTACAAAGACCAGAAGCACGACCT
genomic: CCGAAGGTGCACATTGTGCTAGAGTTCGTGAAGTCCTGAATTCCTCTGATgtgagtaact ... ttttatgtagGTATGGAGTGCTTACAAAGACCAGAAGCACGACCT
EST: gi|5919503|gb|AW054600.1|AW054600
EST:     AGAGTTCGTGAAGTCCTGAATTCCTCTGAT                         GTATGGAGTGCTTACAAAGACCAGAAGCNCGACCTTTTCCTTCCATCCAAT
genomic: AGAGTTCGTGAAGTCCTGAATTCCTCTGATgtgagtaact ... ttttatgtagGTATGGAGTGCTTACAAAGACCAGAAGCACGACCTTTTCCTTCCATCCAAT
EST: gi|71596430|gb|DR907181.1|DR907181
EST:     CCGAAGGTGCACATTGTGCTAGAGTTCGTGAAGTCCTGAATTCCTCTGAT                         GTATGGAGTGCTTACAAAGACCAGAAGCACGACCTTTTCCTTCCATCCAAT
genomic: CCGAAGGTGCACATTGTGCTAGAGTTCGTGAAGTCCTGAATTCCTCTGATgtgagtaact ... ttttatgtagGTATGGAGTGCTTACAAAGACCAGAAGCACGACCTTTTCCTTCCATCCAAT
EST: gi|32919339|gb|CF024151.1|CF024151
EST:     TGAATTCCTCTGAT                         GTATGGAGTGCTTACAAAGACCAGAAGCACGACCTTTTCCTTCCATCCAAT
genomic: TGAATTCCTCTGATgtgagtaact ... ttttatgtagGTATGGAGTGCTTACAAAGACCAGAAGCACGACCTTTTCCTTCCATCCAAT
EST: gi|89761888|gb|DY689721.1|DY689721
EST:     CCGAAGGTGCACATTGTGCTAGAGTTCGTGAAGTCCTGAATTCCTCTGAT                         GTATGGAGTGCTTACAAAGACCAGAAGCACGACCTTTTCCTTCCATCCAAT
genomic: CCGAAGGTGCACATTGTGCTAGAGTTCGTGAAGTCCTGAATTCCTCTGATgtgagtaact ... ttttatgtagGTATGGAGTGCTTACAAAGACCAGAAGCACGACCTTTTCCTTCCATCCAAT

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), 45 (downstream exon)
Score: 178

GTGCTTCATGCTTTTGCAACCGAAGGTGCACATTGTGCTAGAGTTCGTGAAGTCCTGAATTCCTCTGATgtgagtaact ... ttttatgtagGTATGGAGTGCTTACAAAGACCAGAAGCACGACCTTTTCCTTCCATCCAATGCACAATCTTCTGCTGCTGGAATTGCTGGGCTCATTGAGAGCTCATCAT


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 127

GTGCTTCATGCTTTTGCAACCGAAGGTGCACATTGTGCTAGAGTTCGTGAAGTCCTGAATTCCTCTGATgtgagtaact ... ttttatgtagGTATGGAGTGCTTACAAAGACCAGAAGCACGACCTTTTCCTTCCATCCAATGCACAATCTTCTGCTGCTGGAATTGCTGGGCTCATTGAGAGCTCATCAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 303

GTGCTTCATGCTTTTGCAACCGAAGGTGCACATTGTGCTAGAGTTCGTGAAGTCCTGAATTCCTCTGATgtgagtaact ... ttttatgtagGTATGGAGTGCTTACAAAGACCAGAAGCACGACCTTTTCCTTCCATCCAATGCACAATCTTCTGCTGCTGGAATTGCTGGGCTCATTGAGAGCTCATCAT


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 250

GTGCTTCATGCTTTTGCAACCGAAGGTGCACATTGTGCTAGAGTTCGTGAAGTCCTGAATTCCTCTGATgtgagtaact ... ttttatgtagGTATGGAGTGCTTACAAAGACCAGAAGCACGACCTTTTCCTTCCATCCAATGCACAATCTTCTGCTGCTGGAATTGCTGGGCTCATTGAGAGCTCATCAT