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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGAAAAGAATATGAATACGATGCCCCCGTGAAGTTGTTGGACAAGCATTTGCATGCAATGGCACAATCATCTGATGAGCAGCTTGTGGTGGTGTCACAGgtctctttttctatatgatgggtcatgaaaacttcaagttacatagacacatctgagcatctctatttgctctgtagcttattgtgcaattaacactaattttatttcttcatgaatcttcag

Basic information

species Zea mays
transcript GRMZM2G165969_T01
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G165969_T01 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os06g12780.1 (Oryza sativa), 5'ss of exon 6
TGGAAAAGAATATGAATACGATGCCCCCGTGAAGTTGTTGGACAAGCATTTGCATGCAATGGCACAATCATCTGATGAGCAGCTTGTGGTGGTGTCACAGgtctct--ttttctatatgatgggtcatga----aaacttcaagttacatagacacatctgagcatctctattt---gctctgtagcttattgtgcaatta-acactaattttatttc-----ttcatgaatcttcag
||||||||| ||||| || |||||||| || ||||||||||||||||| || ||||||||||| |||||| |||| |||||||||||||||||||||||||||||   || | | | |  |     |||     |   |  || | | || |  |    |       | |||||   |||  |||  ||||| |   || | |    |||||| |         | |||||| |||||
TGGAAAAGACTATGAGTATGATGCCCCTGTCAAGTTGTTGGACAAGCACTTACATGCAATGGCTCAATCACCTGACGAGCAGCTTGTGGTGGTGTCACAGgtctcaagttctttctgtactaacctatgtttttatgttataaatgagatggctaacctttcttgcttttatttagagcttggta-tttattatttcatcatatgacaattttttgaaaaaaaatgatgaattttcag
















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|32836083|gb|CD975761.1|CD975761
EST:     TGCATGCAATGGCACAATCATCTGATGAGCAGCTTGTGGTGGTGTCACAG                         GTGCTTGTGGCTGATATAAACATTGGTTACGAAGATATAGTCAACATTCAG
genomic: TGCATGCAATGGCACAATCATCTGATGAGCAGCTTGTGGTGGTGTCACAGgtctcttttt ... gaatcttcagGTGCTTGTGGCTGATATAAACATTGGTTACGAAGATATAGTCAACATTCAG
EST: gi|32834126|gb|CD973804.1|CD973804
EST:     TGCATGCAATGGCACAATCATCTGATGAGCAGCTTGTGGTGGTGTCACAG                         GTGCTTGTGGCTGATATAAACATTGGTTACGAAGATATAGTCAACATTCAG
genomic: TGCATGCAATGGCACAATCATCTGATGAGCAGCTTGTGGTGGTGTCACAGgtctcttttt ... gaatcttcagGTGCTTGTGGCTGATATAAACATTGGTTACGAAGATATAGTCAACATTCAG
EST: gi|33091610|gb|CF051604.1|CF051604
EST:     TGCATGCAATGGCACAATCATCTGATGAGCAGCTTGTGGTGGTGTCACAG                         GTGCTTGTGGCTGATATAAACATTGGTTACGAAGATATAGTCAACATTCAG
genomic: TGCATGCAATGGCACAATCATCTGATGAGCAGCTTGTGGTGGTGTCACAGgtctcttttt ... gaatcttcagGTGCTTGTGGCTGATATAAACATTGGTTACGAAGATATAGTCAACATTCAG
EST: gi|32832305|gb|CD971983.1|CD971983
EST:     TGCATGCAATGGCACAATCATCTGATGAGCAGCTTGTGGTGGTGTCACAG                         GTGCTTGTGGCTGATATAAACATTGGTTACGAAGATATAGTCAACATTCAG
genomic: TGCATGCAATGGCACAATCATCTGATGAGCAGCTTGTGGTGGTGTCACAGgtctcttttt ... gaatcttcagGTGCTTGTGGCTGATATAAACATTGGTTACGAAGATATAGTCAACATTCAG
EST: gi|32831923|gb|CD971601.1|CD971601
EST:     TGCATGCAATGGCACAATCATCTGATGAGCAGCTTGTGGTGGTGTCACAG                         GTGCTTGTGGCTGATATAAACATTGGTTACGAAGATATAGTCAACATTCAG
genomic: TGCATGCAATGGCACAATCATCTGATGAGCAGCTTGTGGTGGTGTCACAGgtctcttttt ... gaatcttcagGTGCTTGTGGCTGATATAAACATTGGTTACGAAGATATAGTCAACATTCAG
EST: gi|32832217|gb|CD971895.1|CD971895
EST:     TGCATGCAATGGCACAATCATCTGATGAGCAGCTTGTGGTGGCGTCACAG                         GTGCTTGTGGCTGATATAAACATTGGTTACGAAGATATAGTCAACATTCAG
genomic: TGCATGCAATGGCACAATCATCTGATGAGCAGCTTGTGGTGGTGTCACAGgtctcttttt ... gaatcttcagGTGCTTGTGGCTGATATAAACATTGGTTACGAAGATATAGTCAACATTCAG
EST: gi|32832159|gb|CD971837.1|CD971837
EST:     TGCATGCAATGGCACAATCATCTGATGAGCAGCTTGTGGTGGTGTCACAG                         GTGCTTGTGGCTGATATAAACATTGGTTACGAAGATATAGTCAACATTCAG
genomic: TGCATGCAATGGCACAATCATCTGATGAGCAGCTTGTGGTGGTGTCACAGgtctcttttt ... gaatcttcagGTGCTTGTGGCTGATATAAACATTGGTTACGAAGATATAGTCAACATTCAG
EST: gi|32833886|gb|CD973564.1|CD973564
EST:     TGCATGCAATGGCACAATCATCTGATGAGCAGCTTGTGGTGGTGTCACAG                         GTGCTTGTGGCTGATATAAACATTGGTTACGAAGATATAGTCAACATTCAG
genomic: TGCATGCAATGGCACAATCATCTGATGAGCAGCTTGTGGTGGTGTCACAGgtctcttttt ... gaatcttcagGTGCTTGTGGCTGATATAAACATTGGTTACGAAGATATAGTCAACATTCAG
EST: gi|32850028|gb|CD989709.1|CD989709
EST:     TGCATGCAATGGCACAATCATCTGATGAGCAGCTTGTGGTGGTGTCACAG                         GTGCTTGTGGCTGATATAAACATTGGTTACGAAGATATAGTCAACATTCAG
genomic: TGCATGCAATGGCACAATCATCTGATGAGCAGCTTGTGGTGGTGTCACAGgtctcttttt ... gaatcttcagGTGCTTGTGGCTGATATAAACATTGGTTACGAAGATATAGTCAACATTCAG
EST: gi|32832780|gb|CD972458.1|CD972458
EST:     TGCATGCAATGGCACAATCATCTGATGAGCAGCTTGTGGTGGTGTCACAG                         GTGCTTGTGGCTGATATAAACATTGGTTACGAAGATATAGTCAACATTCAG
genomic: TGCATGCAATGGCACAATCATCTGATGAGCAGCTTGTGGTGGTGTCACAGgtctcttttt ... gaatcttcagGTGCTTGTGGCTGATATAAACATTGGTTACGAAGATATAGTCAACATTCAG
EST: gi|32833979|gb|CD973657.1|CD973657
EST:     TGCATGCAATGGCACAATCATCTGATGAGCAGCTTGTGGTGGTGTCACAG                         GTGCTTGTGGCTGATATAAACATTGGTTACGAAGATATAGTCAACATTCAG
genomic: TGCATGCAATGGCACAATCATCTGATGAGCAGCTTGTGGTGGTGTCACAGgtctcttttt ... gaatcttcagGTGCTTGTGGCTGATATAAACATTGGTTACGAAGATATAGTCAACATTCAG
EST: gi|32832342|gb|CD972020.1|CD972020
EST:     TGCATGCAATGGCACAATCATCTGATGAGCAGCTTGTGGCGGTGTCACAG                         GTGCTTGTGGCTGATATAAACATTGGTT
genomic: TGCATGCAATGGCACAATCATCTGATGAGCAGCTTGTGGTGGTGTCACAGgtctcttttt ... gaatcttcagGTGCTTGTGGCTGATATAAACATTGGTT
EST: gi|32931506|gb|CF036318.1|CF036318
EST:     TGCATGCAATGGCACAACCATCTGATGAGCAGCTTGTGGTGGTGTCACAG                         GTGCTTGTGGCTGATATAAACATTGGTTACGAAGATATAGTCAACATTCAG
genomic: TGCATGCAATGGCACAATCATCTGATGAGCAGCTTGTGGTGGTGTCACAGgtctcttttt ... gaatcttcagGTGCTTGTGGCTGATATAAACATTGGTTACGAAGATATAGTCAACATTCAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGGAAAAGAATATGAATACGATGCCCCCGTGAAGTTGTTGGACAAGCATTTGCATGCAATGGCACAATCATCTGATGAGCAGCTTGTGGTGGTGTCACAGgtctctttttctatatgatgggtcatgaaaacttcaagttacatagacacatctgagcatctctatttgctctgtagcttattgtgcaattaacactaattttatttcttcatgaatcttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG