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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATGCAGAAGAATGCTGGACACAGTTGGTGTATACGCTTTCTCAAACTCTTACCTCAGATTCAAGgtaacctgtttgttgtcaaaatgtcaactaatggctcttcaccttgtaaccatttatatttatcgtattatctttgtcttccctgtaatttttatggcaatgtttggctactttgcctaaaattatttgcctactttttttttctatag

Basic information

species Zea mays
transcript GRMZM2G017086_T04
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G017086_T01 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os01g36930.1 (Oryza sativa), 5'ss of exon 8
GATGCAGAAGAATGCTGGACACAGTTGGTGTATACGCTTTCTCAAACTCTTACCTCAGATTCAAGgtaacctgtt--------------------tgttgtcaaaatgtcaactaatggctcttcaccttgtaa---ccatttatatttatcgtattatctttgtcttccctgtaatttt-----tatggcaatgtttggctactttgcctaaaattatttgcctactttttttttctatag
|||||||||||||||||||| || ||||||||||| ||||||||||||||||| |||||  ||||||||  | ||                    |  | |  || |||  | | |||  | ||  ||| |  |    |     |      |   ||  |||| || ||||| |   | |      |  | | ||||||||| ||  || ||  |||  ||| ||  |||  |         
GATGCAGAAGAATGCTGGACCCAATTGGTGTATACACTTTCTCAAACTCTTACATCAGAAACAAGgtaatttattgcagttattcacctaacagctcatatgcaattgtggagtgatgtttgttttcctggggatgctcccccctccccccccccttccctttttcctccctctctctctgagtacacagtagtgtttggctgctccgcttaccatt--ttgtcttttttggtag-------
















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|32934266|gb|CF039078.1|CF039078
EST:     TGGACACAGTTGGTGTATACGCTTTCTCAAACTCTTACCTCAGATTCAAG                         TGAATCTGCAGCTCTTCCGATGAAGCAACTATTTGGGATAGATCTCGTGAG
genomic: TGGACACAGTTGGTGTATACGCTTTCTCAAACTCTTACCTCAGATTCAAGgtaacctgtt ... ttttctatagTGAATCTGCAGCTCTTCCGATGAAGCAACTATTTGGGATAGATCTCGTGAG
EST: gi|241994792|gb|GR421145.1|GR421145
EST:     TGGACACAGTTGGTGTATACGCTTTCTCAAACTCTTACCTCAGATTCAAG                         TGAATCTGCAGCTCTTCCGATGAAGCAACTATTTGGGATAGATCTCGTGAG
genomic: TGGACACAGTTGGTGTATACGCTTTCTCAAACTCTTACCTCAGATTCAAGgtaacctgtt ... ttttctatagTGAATCTGCAGCTCTTCCGATGAAGCAACTATTTGGGATAGATCTCGTGAG
EST: gi|32932531|gb|CF037343.1|CF037343
EST:     TGGACACAGTTGGTGTATACGCTTTCTCAAACTCTTACCTCAGATTCAAG                         TGAATCTGCAGCTCTTCCGATGAAGCAACTATTTGGGATAGATCTCGTGAG
genomic: TGGACACAGTTGGTGTATACGCTTTCTCAAACTCTTACCTCAGATTCAAGgtaacctgtt ... ttttctatagTGAATCTGCAGCTCTTCCGATGAAGCAACTATTTGGGATAGATCTCGTGAG
EST: gi|211437528|gb|FK975648.1|FK975648
EST:     TGGACACAGTTGGTGTATACGCTTTCTCAAACTCTTACCTCAGATTCAAG                         TGAATCTGCAGCTCTTCCGATGAAGCAACTATTTGGGATAGATCTCGTGAG
genomic: TGGACACAGTTGGTGTATACGCTTTCTCAAACTCTTACCTCAGATTCAAGgtaacctgtt ... ttttctatagTGAATCTGCAGCTCTTCCGATGAAGCAACTATTTGGGATAGATCTCGTGAG
EST: gi|32863109|gb|CF002791.1|CF002791
EST:     TGGACACAGTTGGTGTATACGCTTTCTCAAACTCTTACCTCAGATTCAAG                         TGAATCTGCAGCTCTTCCGATGAAGCAACTATTTGGGATAGATCTCGTGAG
genomic: TGGACACAGTTGGTGTATACGCTTTCTCAAACTCTTACCTCAGATTCAAGgtaacctgtt ... ttttctatagTGAATCTGCAGCTCTTCCGATGAAGCAACTATTTGGGATAGATCTCGTGAG
EST: gi|32930082|gb|CF034894.1|CF034894
EST:     TGGACACAGTTGGTGTATACGCTTTCTCAAACTCTTACCTCAGATTCAAG                         TGAATCTGCAGCTCTTCCGATGAAGCAACTATTTGGGATAGATCTCGTGAG
genomic: TGGACACAGTTGGTGTATACGCTTTCTCAAACTCTTACCTCAGATTCAAGgtaacctgtt ... ttttctatagTGAATCTGCAGCTCTTCCGATGAAGCAACTATTTGGGATAGATCTCGTGAG
EST: gi|32945380|gb|CF050199.1|CF050199
EST:     TGGACACAGTTGGTGTATACGCTTTCTCAAACTCTTACCTCAGATTCAAG                         TGAATCTGCAGCTCTTCCGATGAAGCAACTATTTGGGATAGATCTCGTGAG
genomic: TGGACACAGTTGGTGTATACGCTTTCTCAAACTCTTACCTCAGATTCAAGgtaacctgtt ... ttttctatagTGAATCTGCAGCTCTTCCGATGAAGCAACTATTTGGGATAGATCTCGTGAG
EST: gi|32866635|gb|CF006317.1|CF006317
EST:     TGGACACAGTTGGTGTATACGCTTTCTCAAACTCTTACCTCAGATTCAAG                         TGAATCTGCAGCTCTTCCGATGAAGCAACTATTTGGGATAGATCTCGTGAG
genomic: TGGACACAGTTGGTGTATACGCTTTCTCAAACTCTTACCTCAGATTCAAGgtaacctgtt ... ttttctatagTGAATCTGCAGCTCTTCCGATGAAGCAACTATTTGGGATAGATCTCGTGAG
EST: gi|32911302|gb|CF016114.1|CF016114
EST:     TGGACACAGTTGGTGTATACGCTTTCTCAAACTCTTACCTCAGATTCAAG                         TGAATCTGCAGCTCTTCCGATGAAGCAACTATTTGGGATAGATCTCGTGAG
genomic: TGGACACAGTTGGTGTATACGCTTTCTCAAACTCTTACCTCAGATTCAAGgtaacctgtt ... ttttctatagTGAATCTGCAGCTCTTCCGATGAAGCAACTATTTGGGATAGATCTCGTGAG
EST: gi|32932473|gb|CF037285.1|CF037285
EST:     TGGACACAGTTGGTGTATACGCTTTCTCAAACTCTTACCTCAGATTCAAG                         TGAATCTGCAGCTCTTCCGATGAAGCAACTATTTGGGATAGATCTCGTGAG
genomic: TGGACACAGTTGGTGTATACGCTTTCTCAAACTCTTACCTCAGATTCAAGgtaacctgtt ... ttttctatagTGAATCTGCAGCTCTTCCGATGAAGCAACTATTTGGGATAGATCTCGTGAG
EST: gi|74240015|gb|DT647929.1|DT647929
EST:     TGGACACAGTTGGTGTATACGCTTTCTCAAACTCTTACCTCAGATTCCAG                         TGAATCTGCAGCTCTTCCGATGAAGCAACTATTTGGGATAGATCTCGTGAG
genomic: TGGACACAGTTGGTGTATACGCTTTCTCAAACTCTTACCTCAGATTCAAGgtaacctgtt ... ttttctatagTGAATCTGCAGCTCTTCCGATGAAGCAACTATTTGGGATAGATCTCGTGAG
EST: gi|32931528|gb|CF036340.1|CF036340
EST:     TGGACACAGTTGGTGTATACGCTTTCTCAAACTCTTACCTCAGATTCAAG                         TGAATCTGCAGCTCTTCCGATGAAGCAACTATTTGGGATAGACCTCGTGAG
genomic: TGGACACAGTTGGTGTATACGCTTTCTCAAACTCTTACCTCAGATTCAAGgtaacctgtt ... ttttctatagTGAATCTGCAGCTCTTCCGATGAAGCAACTATTTGGGATAGATCTCGTGAG
EST: gi|67017287|gb|CO446036.1|CO446036
EST:     TGGACACAGTTGGTGTATACGCTTTCTCAAACTCTTACCTCAGATTCAAG                         TGAATCTGCAGCTCTTCCGATGAAGCAACTATTTGGGATAGATCTCGTGAG
genomic: TGGACACAGTTGGTGTATACGCTTTCTCAAACTCTTACCTCAGATTCAAGgtaacctgtt ... ttttctatagTGAATCTGCAGCTCTTCCGATGAAGCAACTATTTGGGATAGATCTCGTGAG
EST: gi|50332356|gb|CO527482.1|CO527482
EST:     TGGACACAGTTGGTGTATACGCTTTCTCAAACTCTTACCTCAGATTCAAG                         TGAATCTGCAGCTCTTCCGATGAAGCAACTATTTGGGATAGATCTCGTGAG
genomic: TGGACACAGTTGGTGTATACGCTTTCTCAAACTCTTACCTCAGATTCAAGgtaacctgtt ... ttttctatagTGAATCTGCAGCTCTTCCGATGAAGCAACTATTTGGGATAGATCTCGTGAG

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: 47 (upstream exon), 47 (downstream exon)
Score: 220

GATGCAGAAGAATGCTGGACACAGTTGGTGTATACGCTTTCTCAAACTCTTACCTCAGATTCAAGgtaacctgtt ... ttttctatagTGAATCTGCAGCTCTTCCGATGAAGCAACTATTTGGGATAGATCTCGTGAGCAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 204

GATGCAGAAGAATGCTGGACACAGTTGGTGTATACGCTTTCTCAAACTCTTACCTCAGATTCAAGgtaacctgtt ... ttttctatagTGAATCTGCAGCTCTTCCGATGAAGCAACTATTTGGGATAGATCTCGTGAGCAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 201

GATGCAGAAGAATGCTGGACACAGTTGGTGTATACGCTTTCTCAAACTCTTACCTCAGATTCAAGgtaacctgtt ... ttttctatagTGAATCTGCAGCTCTTCCGATGAAGCAACTATTTGGGATAGATCTCGTGAGCAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 194

GATGCAGAAGAATGCTGGACACAGTTGGTGTATACGCTTTCTCAAACTCTTACCTCAGATTCAAGgtaacctgtt ... ttttctatagTGAATCTGCAGCTCTTCCGATGAAGCAACTATTTGGGATAGATCTCGTGAGCAG