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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGATTTGGTCATGGAGTTCTGCGTAAGACAGACCCACGGTATTCATGTCAAAGGGAGTTTGCCCTGAAGCATTTGCCCGAGGATCCACTTTTCCAACTGgtccgtctggaacctttctatctaattgcatttactttcttgagttcaacaattttaaaaataatattccgttgcag

Basic information

species Zea mays
transcript GRMZM2G064023_T01
intron # 17
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G064023_T01 (Zea mays), 5'ss of exon 17
lower sequence: LOC_Os02g10070.1 (Oryza sativa), 5'ss of exon 16
TGGATTTGGTCATGGAGTTCTGCGTAAGACAGACCCACGGTATTCATGTCAAAGGGAGTTTGCCCTGAAGCATTTGCCCGAGGATCCACTTTTCCAACTGgtccgtctggaacctttctatctaattgcatttactttcttgagttcaacaattttaaaaataa--tattccgttgcag
||| ||||||||||||||||| |||||||| || ||||||||| ||||||| |||||||||||  ||||| | ||||| |||||||||||||||||||||||  ||||  |  ||  ||   |   |   || | |  |      |||| |   || | |   |  ||| |  || |||
TGGCTTTGGTCATGGAGTTCTACGTAAGACCGATCCACGGTATACATGTCAGAGGGAGTTTGCTTTGAAGTACTTGCCTGAGGATCCACTTTTCCAACTGgttagtctaaattctagctgcatggctctcttcagtcccactgtctcaataggatttatatcgacctatcctctttcag

upper sequence: GRMZM2G064023_T01 (Zea mays), 5'ss of exon 17
lower sequence: LOC_Os11g33240.2 (Oryza sativa), 5'ss of exon 16
TGGATTTGGTCATGGAGTTCTGCGTAAGACAGACCCACGGTATTCATGTCAAAGGGAGTTTGCCCTGAAGCATTTGCCCGAGGATCCACTTTTCCAACTGgtccgtctggaacctttctatctaattgcatttactttcttg-agttcaacaattttaaaaataatatt-ccgttgcag----------
||| || |||||||||||||| |||||||| || ||||| ||| ||||||| |||||||||||  ||||| | ||||| |||||||||||||||||||||||  ||||  ||  | ||| || || |||||   || ||||| ||| |||| || | |     | | ||  || |  |           
TGGCTTCGGTCATGGAGTTCTACGTAAGACCGATCCACGATATACATGTCAGAGGGAGTTTGCTTTGAAGTACTTGCCTGAGGATCCACTTTTCCAACTGgttagtctaaaa--tgtctgtccaactgcatg-gctctcttgcagtccaactatctcattgggattcttatcgatctatatcctgtcag

upper sequence: GRMZM2G064023_T01 (Zea mays), 5'ss of exon 17
lower sequence: Vv13s0156g00180.t01 (Vitis vinifera), 5'ss of exon 16
TGGATTTGGTCATGGAGTTCTGCGTAAGACAGACCCACGGTATTCATGTCAAAGGGAGTTTGCCCTGAAGCATTTGCCCGAGGATCCACTTTTCCAACTGgtc--cgtctggaacctttct---atctaattgcatttactttcttgagttcaa---caattttaa----aaataatattccgttgcag
||| ||||| ||||||||| ||||||| ||||| ||| | |||   |||||||||||||||||  ||||||| ||||| || |||||||| ||||| |||||       |  | || |  |   |   ||| |  | |   || ||| |||| |   ||   || |    |  |  | | || || |||
TGGGTTTGGGCATGGAGTTTTGCGTAAAACAGATCCAAGATATATGTGTCAAAGGGAGTTTGCATTGAAGCACTTGCCTGATGATCCACTGTTCCAGCTGgttattacttaaagccctgattaaagacaatggtttgtttatttttgtgttccagttcatccttgagctgacttggtttaccattacag

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|211314254|gb|FK994154.1|FK994154
EST:     CCGAGGATCCACTTTTCCAACTG                         GTGTCCTTTTTATATGAAGTCGTACCTCCGATCCTCACTGAGCTAGGAAAG
genomic: CCGAGGATCCACTTTTCCAACTGgtccgtctgg ... tccgttgcagGTGTCCAAGTTATATGAAGTCGTACCTCCGATCCTCACTGAGCTAGGAAAG
EST: gi|6020672|gb|AW065480.1|AW065480
EST:     AAAGGGAGTTTGCCCTGAAGCATTTGCCCGAGGATCCACTTTTCCAACTG                         GTGTCCAAGTTATATGAAGTCGTACCTCCGATCCTCACTGAGCTAGGAAAG
genomic: AAAGGGAGTTTGCCCTGAAGCATTTGCCCGAGGATCCACTTTTCCAACTGgtccgtctgg ... tccgttgcagGTGTCCAAGTTATATGAAGTCGTACCTCCGATCCTCACTGAGCTAGGAAAG
EST: gi|5847106|gb|AW000185.1|AW000185
EST:     AAAGGGAGTTTGCCCTGAAGCATTTGCCCGAGGATCCACTTTTCCAACTG                         GTGTCCAAGTTATATGAAGTCGTACCTCCGATCCTCACTGAGCTAGGAAAG
genomic: AAAGGGAGTTTGCCCTGAAGCATTTGCCCGAGGATCCACTTTTCCAACTGgtccgtctgg ... tccgttgcagGTGTCCAAGTTATATGAAGTCGTACCTCCGATCCTCACTGAGCTAGGAAAG
EST: gi|67022591|gb|CO451340.1|CO451340
EST:     AAAGGGAGTTTGCCCTGAAGCATTTGCCCGAGGATCCACTTTTCCAACTG                         GTGTCCAAGTTATATGAAGTCGTACCTCCGATCCTCACTGAGCTAGGAAAG
genomic: AAAGGGAGTTTGCCCTGAAGCATTTGCCCGAGGATCCACTTTTCCAACTGgtccgtctgg ... tccgttgcagGTGTCCAAGTTATATGAAGTCGTACCTCCGATCCTCACTGAGCTAGGAAAG
EST: gi|32859372|gb|CD999053.1|CD999053
EST:     AAAGGGAGTTTGCCCTGAAGCATTTGCCCGAGGATCCACTTTTCCAACTG                         GTGTCCAAGTTATATGAAGTCGTACCTCCGATCCTCACTGAGCTAGGAAAG
genomic: AAAGGGAGTTTGCCCTGAAGCATTTGCCCGAGGATCCACTTTTCCAACTGgtccgtctgg ... tccgttgcagGTGTCCAAGTTATATGAAGTCGTACCTCCGATCCTCACTGAGCTAGGAAAG
EST: gi|71450119|gb|DR831169.1|DR831169
EST:     AAAGGGAGTTTGCCCTGAAGCATTTGCCCGAGGATCCACTTTTCCAACTG                         GTGTCCAAGTTATATGAAGTCGTACCTCCGATCCTCACTGAGCTAGGAAAG
genomic: AAAGGGAGTTTGCCCTGAAGCATTTGCCCGAGGATCCACTTTTCCAACTGgtccgtctgg ... tccgttgcagGTGTCCAAGTTATATGAAGTCGTACCTCCGATCCTCACTGAGCTAGGAAAG
EST: gi|4776524|gb|AI665527.1|AI665527
EST:     AAAGGGAGTTTGCCCTGAAGCATTTGCCCGAGGATCCACTTTTCCAACTG                         GTGTCCAAGTTATATGAAGTCGTACCTCCGATCCTCACTGAGCTAGGAAAG
genomic: AAAGGGAGTTTGCCCTGAAGCATTTGCCCGAGGATCCACTTTTCCAACTGgtccgtctgg ... tccgttgcagGTGTCCAAGTTATATGAAGTCGTACCTCCGATCCTCACTGAGCTAGGAAAG
EST: gi|76284364|gb|DV023932.1|DV023932
EST:     AAAGGGAGTTTGCCCTGAAGCATTTGCCCGAGGATCCACTTTTCCAACTG                         GTGTCCAAGTTATATGAAGTCGTACCTCCGATCCTCACTGAGCTAGGAAAG
genomic: AAAGGGAGTTTGCCCTGAAGCATTTGCCCGAGGATCCACTTTTCCAACTGgtccgtctgg ... tccgttgcagGTGTCCAAGTTATATGAAGTCGTACCTCCGATCCTCACTGAGCTAGGAAAG
EST: gi|6952534|gb|AW424602.1|AW424602
EST:     AAAGGGAGTTTGCCCTGAAGCATTTGCCCGAGGATCCACTTTTCCAACTG                         GTGTCCAAGTTATATGAAGTCGTACCTCCGATCCTCACTGAGCTAGGAAAG
genomic: AAAGGGAGTTTGCCCTGAAGCATTTGCCCGAGGATCCACTTTTCCAACTGgtccgtctgg ... tccgttgcagGTGTCCAAGTTATATGAAGTCGTACCTCCGATCCTCACTGAGCTAGGAAAG
EST: gi|31361873|gb|CD446230.1|CD446230
EST:     AAAGGGAGTTTGCCCTGAAGCATTTGCCCGAGGATCCACTTTTCCAACTG                         GTGTCCAAGTTATATGAAGTCGTACCTCCGATCCTCACTGAGCTAGGAAAG
genomic: AAAGGGAGTTTGCCCTGAAGCATTTGCCCGAGGATCCACTTTTCCAACTGgtccgtctgg ... tccgttgcagGTGTCCAAGTTATATGAAGTCGTACCTCCGATCCTCACTGAGCTAGGAAAG
EST: gi|149082724|gb|EE171942.2|EE171942
EST:     AAAGGGAGTTTGCCCTGAAGCATTTGCCCGAGGATCCACTTTTCCAACTG                         GTGTCCAAGTTATATGAAGTCGTACCTCCGATCCTCACTGAGCTAGGAAAG
genomic: AAAGGGAGTTTGCCCTGAAGCATTTGCCCGAGGATCCACTTTTCCAACTGgtccgtctgg ... tccgttgcagGTGTCCAAGTTATATGAAGTCGTACCTCCGATCCTCACTGAGCTAGGAAAG

Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGGATTTGGTCATGGAGTTCTGCGTAAGACAGACCCACGGTATTCATGTCAAAGGGAGTTTGCCCTGAAGCATTTGCCCGAGGATCCACTTTTCCAACTGgtccgtctggaacctttctatctaattgcatttactttcttgagttcaacaattttaaaaataatattccgttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT