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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CATCAACTCCGCCGTCGGCTCCCTCCTCGTCAGCTTCACCGTCTACATCATCCCGGCGCTGGCGCACATGATCACGTTCCGGTCCGCAACAGCCCGTGAGgtagtatattttattactcccatgcatgcactacttttattaatacgttttattacccaatgctttttttttacttcatcgatgaaagctacctagctac...

Basic information

species Zea mays
transcript GRMZM2G149481_T04
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G149481_T04 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os03g14080.1 (Oryza sativa), 5'ss of exon 6
CATCAACTCCGCCGTCGGCTCCCTCCTCGTCAGCTTCACCGTCTACATCATCCCGGCGCTGGCGCACATGATCACGTTCCGGTCCGCAACAGCCCGTGAGgta--gtatattttattactcccatgcatgcacta--cttttattaatacgttttattacccaatgctttttttttacttcatcgatgaaagctacctagctac
|||||||||||||||||||||||||||||||||||||||||||||||||||||| || || |||||||||||||| ||||| |||||    || |||||||||  ||| |  |  |  |  |  |  |  ||||   ||||| ||   || ||||  |   || |  | |  |   | || |    || | |  || |   |  
CATCAACTCCGCCGTCGGCTCCCTCCTCGTCAGCTTCACCGTCTACATCATCCCCGCCCTCGCGCACATGATCACCTTCCGCTCCGCGCACGCTCGTGAGgtatagtaaaaatcttggcatctttttaatcactgcgctttttttttaaccttttggt-ttcacttttatcatgcgagtttactagtgtagg--acttgcatg-

upper sequence: GRMZM2G149481_T04 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA12G03490.1 (Glycine max), 5'ss of exon 7
CATCAACTCCGCCGTCGGCTCCCTCCTCGTCAGCTTCACCGTCTACATCATCCCGGCGCTGGCGCACATGATCACGTTCCGGTCCGCAACAGCCCGTGAGgtagtatattttattactcccatgcatgcactacttttattaatacgtttt--attaccc-aatgctttttttttacttcatcgatgaaagctacctagctac
|||||||||| |||| ||||| ||||| |||||||||||||| ||||| ||||| || || || |||||  |||| |||   ||  |  | ||| |  |||||  |||| | ||   |    || || ||  | | |  |   ||| |     | |||   ||    | | |    | |  | ||   ||  |   |   |  
CATCAACTCCACCGTTGGCTCTCTCCTTGTCAGCTTCACCGTTTACATTATCCCCGCCCTCGCCCACATCTTCACCTTCAAATCACCCTCTGCCAGACAGgtaccatatat-atagttattttgtat-caaaattgtcctacgtacctcacggactactttaacatatatatccctcctactagacttaaattggttccttc-

upper sequence: GRMZM2G149481_T04 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA06G00690.1 (Glycine max), 5'ss of exon 7
CATCAACTCCGCCGTCGGCTCCCTCCTCGTCAGCTTCACCGTCTACATCATCCCGGCGCTGGCGCACATGATCACGTTCCGGTCCGCAACAGCCCGTGAGgtagtatattttattactcccatgcatgcactacttttattaatacgttttattacccaatgctttttttttacttcatcgatgaaagctacctagctac---
|||||||||| |||| || || || || |||||||||||||| ||||||||||| || || || |||||| |||| |||   ||  |  | |||||  ||||| ||||||    ||     || ||  |        |  ||  | ||   ||||   |||    |      |        |      |||| | || |    
CATCAACTCCACCGTTGGATCTCTACTTGTCAGCTTCACCGTTTACATCATCCCCGCCCTCGCCCACATGTTCACCTTCAAATCACCCTCTGCCCGACAGgtactatattcctatatattaattcaacccaagtgcatgctacaaagt--aattaattaattgcgtacaaaaaaaatgctaactcggactac-tcgcaattca

upper sequence: GRMZM2G149481_T04 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA04G00640.1 (Glycine max), 5'ss of exon 7
CATCAACTCCGCCGTCGGCTCCCTCCTCGTCAGCTTCACCGTCTACATCATCCCGGCGCTGGCGCACATGATCACGTTCCGGTCCGCAACAGCCCGTGAGgtagtatattttattactcccatgcatgcactacttttattaatacgttttattacccaatgctttttttttacttcatcgatgaaagctacctagctac---
|||||||||| |||| || || || || |||||||||||||| ||||||||||| || || || |||||| |||| |||   ||  |  | |||||   ||||   || | ||||     ||| ||  | | | ||| |||   ||  ||||  |   || |||       | |   |   || ||   | | |   |     
CATCAACTCCACCGTTGGATCTCTTCTTGTCAGCTTCACCGTTTACATCATCCCCGCCCTCGCCCACATGTTCACCTTCAAATCACCCGCTGCCCGACGGgta-cgtactatattcaattcattca-acccaattttaattttaactatttacaaag-aaagctagaacagttcgagaaaaataaagtatgcatgcatgtggg

upper sequence: GRMZM2G149481_T04 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA11G11310.1 (Glycine max), 5'ss of exon 7
CATCAACTCCGCCGTCGGCTCCCTCCTCGTCAGCTTCACCGTCTACATCATCCCGGCGCTGGCGCACATGATCACGTTCCGGTCCGCAACAGCCCGTGAGgtagtatattttattactcccatgcatgcactacttttatta-atacgttttattacccaatgctttttttttacttcatcgatgaaagctacctagctac---
|||||||||| |||| ||||| ||||| |||||||||||||| ||||||||||| || || || |||||  |||| ||| | ||  |  |  || |  ||||| ||||| | ||  |  | || |||   || | || |||| |||  ||  | |  | |||   ||  ||  |  |  |   | ||    |  ||  ||    
CATCAACTCCACCGTTGGCTCTCTCCTTGTCAGCTTCACCGTTTACATCATCCCCGCCCTCGCCCACATCTTCACCTTCAGATCACCCTCTTCCAGACAGgtattatatat-atcgcatc-attcat-ttcttccttcattatatatattacactgtctaatttattccttcaatatacttagtaaacatcaa-tacttatttt

upper sequence: GRMZM2G149481_T04 (Zea mays), 5'ss of exon 5
lower sequence: EFJ21839 (Selaginella moellendorffii), 5'ss of exon 7
CATCAACTCCGCCGTCGGCTCCCTCCTCGTCAGCTTCACCGTCTACATCATCCCGGCGCTGGCGCACATGATCACGTTCCGGTCCGCAACAGCCCGTGAGgtagtatattttattactcccatgcatgcactacttttattaatacgttttattacccaatgctttttttttacttcatcgatgaaagctacctagctac
 ||||||||||| |||||  | |||||||||| |||||| ||||| ||||||||  |||| || |||||||||||||   |  | ||    ||| | | ||||   |  |     | || | |   |     | || |   | | |   ||        |          | |  | ||   |      |   |  ||| 
AATCAACTCCGCGGTCGGGGCGCTCCTCGTCACCTTCACTGTCTATATCATCCCCTCGCTCGCACACATGATCACGTATAGAACAGCCTTCGCCAGGGCGgtaagtttctcgcaaaatctcgtttttctggaagttcttccactcctcgtttccttttgagtgccggagatgagattatttttcttgcttgtttctctag

upper sequence: GRMZM2G149481_T04 (Zea mays), 5'ss of exon 5
lower sequence: EFJ18760 (Selaginella moellendorffii), 5'ss of exon 7
CATCAACTCCGCCGTCGGCTCCCTCCTCGTCAGCTTCACCGTCTACATCATCCCGGCGCTGGCGCACATGATCACGTTCCGGTCCGCAACAGCCCGTGAGgta-------gtatattttattactcccatgcatgcactacttttattaatacgt--tttattacc--caatgctttttttttacttcatcgatgaaagctacctagctac---------------------------------
 || ||||||||||| ||||| || ||||||| |||||| ||||||||||| ||    || || || ||| |||| ||| || | ||    || || ||||||         ||  |||   |||  |   | || || | | | |  ||   ||   |   |||     || |||||  | |  |  |  | | | | |      | |                                   
TATAAACTCCGCCGTGGGCTCTCTACTCGTCACCTTCACAGTCTACATCATTCCTTGCCTCGCACATATGCTCACTTTCAGGACTGCCTTTGCACGAGAGgtacgtacttaaatgcttttccactttctctcgtggacgaatct-acgaacttgtagctagctactgttcatccttttcgtgtgttctagtgttcacatcaggactgatggatcgatccttggttttttttgtttgtcaaacag

upper sequence: GRMZM2G149481_T04 (Zea mays), 5'ss of exon 5
lower sequence: EFJ34222 (Selaginella moellendorffii), 5'ss of exon 7
CATCAACTCCGCCGTCGGCTCCCTCCTCGTCAGCTTCACCGTCTACATCATCCCGGCGCTGGCGCACATGATCACGTTCCGGTCCGCAACAGCCCGTGAGgtagtatattt------tattactcccatgcatgcactacttttattaatacgttttattacccaatgctttttttttacttcatcgatgaaagctacctagctac
 ||||||||||| |||||  | |||||||||| |||||| ||||| ||||||||  |||| || |||||||||||||   |  | ||    ||| | | ||||   |  |       | |   |    || | |  || |   |  |  |    |||     |||| | |    ||||  ||| | | |     || |  ||    
AATCAACTCCGCGGTCGGGGCGCTCCTCGTCACCTTCACTGTCTATATCATCCCCTCGCTCGCACACATGATCACGTATAGAACAGCCTTCGCCAGGGCGgtaagtttctcgcaaaatctcgtttttctggaagttcttccactgctcgtttcctttgagtgccaaagatgagattttttttc-ttgcttgtttct-ctgag----

upper sequence: GRMZM2G149481_T04 (Zea mays), 5'ss of exon 5
lower sequence: EFJ36050 (Selaginella moellendorffii), 5'ss of exon 7
CATCAACTCCGCCGTCGGCTCCCTCCTCGTCAGCTTCACCGTCTACATCATCCCGGCGCTGGCGCACATGATCACGTTCCGGTCCGCAACAGCCCGTGAGgta-------gtatattttattactcccatgcatgcactacttttattaatacgt--tttattacc--caatgctttttttttacttcatcgatgaaagctacctagctac---------------------------------
 || ||||||||||| ||||| || ||||||| |||||| ||||||||||| ||    || || || ||| |||| ||| || | ||    || || ||||||         ||  |||   |||      | || || | | | |  ||   ||   |   |||     || |||||  | |  |  |  | | | | |      | |                                   
TATAAACTCCGCCGTGGGCTCTCTACTCGTCACCTTCACAGTCTACATCATTCCTTGCCTCGCACATATGCTCACTTTCAGGACTGCCTTTGCACGAGAGgtacgcacttaaatgcttttccactttatctcgtggacgaatct-acgaacttgtagctagctactgttcatccttttcgtgtgttctagtgttcacatcaggactgatggatcgatccttggttttttttgtttgtcaaacag

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|20208310|gb|BQ134399.1|BQ134399
EST:     TCCCGGCGCTGGCGCACATGATCACGTTCCGGTCCGCAACAGCCCGTGAG                         AACGCGATGGAGCCGCCGCCGCGGCTGCTGGGGCGTTGGACGGGCGCGTAC
genomic: TCCCGGCGCTGGCGCACATGATCACGTTCCGGTCCGCAACAGCCCGTGAGgtagtatatt ... cgcggtgcagAACGCGATGGAGCCGCCGCCGCGGCTGCTGGGGCGTTGGACGGGCGCGTAC
EST: gi|88746179|gb|DY530320.1|DY530320
EST:     TCCCGGCGCTGGCGCACATGATCACGTTCCGGTCCGCAACACCCCGTGAG                         AACGCTATGGACCCGCCGCCGCGGCTGCTGGGGCGTTGGACGGGCGCGTAC
genomic: TCCCGGCGCTGGCGCACATGATCACGTTCCGGTCCGCAACAGCCCGTGAGgtagtatatt ... cgcggtgcagAACGCGATGGAGCCGCCGCCGCGGCTGCTGGGGCGTTGGACGGGCGCGTAC
EST: gi|93283638|gb|EB675902.1|EB675902
EST:     TCCCGGCGCTGGCGCACATGATCACGTTCCGGTCCGCAACAGCCCGTGAG                         AACGCGATGGAGCCGCCGCCGCGGCTGCTGGGGCGTTGGACGGGCGCGTAC
genomic: TCCCGGCGCTGGCGCACATGATCACGTTCCGGTCCGCAACAGCCCGTGAGgtagtatatt ... cgcggtgcagAACGCGATGGAGCCGCCGCCGCGGCTGCTGGGGCGTTGGACGGGCGCGTAC