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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGTTGCTCACTGCGAGAATGAACATTTTACTTACGATATCACGTCTAAGTTGAAGACCAAGTTTTTGGGAAATTCAGTGGAAATTTACCCAGTTGGAAGgtgaattattagaattgtatttgtttcttggagatctgcgtgccttaatatttttgacccatttgagctaatggaataaaatggaaaccattttgaaggctgcgttgggaccacttgtataaatcagtaaatctaacccctctaatataatttccatgtcacag

Basic information

species Zea mays
transcript GRMZM2G174644_T01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G174644_T01 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os03g16690.1 (Oryza sativa), 5'ss of exon 6
GTGTTGCTCACTGCGAGAATGAACATTTTACTTACGATATCACGTCTAAGTTGAAGACCAAGTTTTTGGGAAATTCAGTGGAAATTTACCCAGTTGGAAGgtgaattattagaattgtatttgtttc----ttggagatctgcgtgc-cttaatatttttgacccatttgagctaatggaataaaatggaaaccattttgaaggctgcgttgggaccacttgtataaatcagtaaatctaacccctctaatataatttccatgtcacag
|||  |||||||| || |||| ||||||||| || || ||||| || |||||||||||||| || ||||| || ||  ||||| |||| ||| ||||||||| | ||  |  || |||  |||||||    ||    ||   |  || ||| ||||  |  |    |||  | |  || |  | |                                                                                    
GTGCCGCTCACTGTGAAAATGCACATTTTACATATGACATCACCTCCAAGTTGAAGACCAAATTCTTGGGGAACTCTCTGGAAGTTTATCCACTTGGAAGgtaattttgtcaaactgtgattgtttcaggattatgaataaaccagctctttatatcctaaatggttttttgtttctgcatcacag-----------------------------------------------------------------------------------

upper sequence: GRMZM2G174644_T01 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA12G06690.1 (Glycine max), 5'ss of exon 6
GTGTTGCTCACTGCGAGAATGAACATTTTACTTACGATATCACGTCTAAGTTGAAGACCAAGTTTTTGGGAAATTCAGTGGAAATTTACCCAGTTGGAAGgtgaattattagaattgtatttgtttcttggagatctgcgtgccttaatatttttgacccatttgagctaatggaataaaatggaaaccattttgaaggctgcgttgggaccacttgtataaatcagtaaatctaacccctctaatataatttccatgtcacag
||| ||| ||   ||||||||| |||||||| || ||| | || || |||||||| || |||||||||||||| || || ||  ||||||| ||||||||||||   ||    |||  ||||||||  | ||  ||  | ||   ||  |||||   |   ||    || |||   |   ||     | | ||  ||  |||  |                                                           
GTGCTGCGCATGCCGAGAATGAGCATTTTACATATGATGTGACTTCAAAGTTGAAAACTAAGTTTTTGGGAAACTCTGTTGATGTTTACCCTGTTGGAAGgtgacaaat--atattacatttgtttagtagatttcctc-tgttatatcattttattcttcttgttactgatg--tttgtattcttccaagttccaactctgatt-----------------------------------------------------------

upper sequence: GRMZM2G174644_T01 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA11G14770.1 (Glycine max), 5'ss of exon 6
GTGTTGCTCACTGCGAGAATGAACATTTTACTTACGATATCACGTCTAAGTTGAAGACCAAGTTTTTGGGAAATTCAGTGGAAATTTACCCAGTTGGAAGgtgaattattagaattgtatttgtttcttggagatctgcgtgccttaatatttttgacccatttgagctaatggaataaaatggaaaccattttgaaggctgcgttgggaccacttgtataaatcagtaaatctaacccctctaatataatttccatgtcacag
||| ||| ||   ||||||||| |||||||| || ||| | || || |||||||| || ||||||||||||||||| || ||  ||||||| ||||||||||||   ||    |||| ||||||||  | ||  ||  | ||   ||   | ||   |   ||   | || ||  ||    |    |  ||||  |   |    |  |                                                        
GTGCTGCGCATGCCGAGAATGAGCATTTTACATATGATGTGACTTCAAAGTTGAAAACTAAGTTTTTGGGAAATTCTGTTGATGTTTACCCTGTTGGAAGgtgacaaat--atattgcatttgtttagtagatttcctc-tgttatatcgtcttattcttctt---gttactg--atgttgtttgtattatttcaagttccaactctg--------------------------------------------------------

upper sequence: GRMZM2G174644_T01 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA15G04210.1 (Glycine max), 5'ss of exon 6
GTGTTGCTCACTGCGAGAATGAACATTTTACTTACGATATCACGTCTAAGTTGAAGACCAAGTTTTTGGGAAATTCAGTGGAAATTTACCCAGTTGGAAGgtgaattattagaattgtatttgtttcttggagatctgcgtgccttaatatttttgacccatttgagctaatgga-ataaaatggaaaccattttgaaggctgcgttgggaccacttgtataaatcagtaaatctaacccctctaatataatttccatgtcacag
||| ||  ||    |||||||| |||||||| || ||| | || || ||||| ||||| ||||||||||||||||| || ||  ||||||| ||||||||||||   ||    |||| ||||||||  |  ||||   | |    |  |||| |      |||  |  || |     ||   |   |||  ||   |  ||| | |                                                           
GTGCTGGGCATGCTGAGAATGAGCATTTTACATATGATGTGACTTCAAAGTTAAAGACTAAGTTTTTGGGAAATTCTGTTGATGTTTACCCTGTTGGAAGgtgatcaat--acattgcatttgtttggt--agattaccttattatcctattctatttttattgtacttattttttgtatccttccaac--ttcctattgctccat-----------------------------------------------------------

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|74244334|gb|DT652248.1|DT652248
EST:     TTGAAGACCAAGTTTTTGGGAAATTCAGTGGAAATTTACCCAGTTGGAAG                         GACTCGAGTGACACTNNNNNNNTCTGGTGTCGTGTTGGATTTGGTGCCACC
genomic: TTGAAGACCAAGTTTTTGGGAAATTCAGTGGAAATTTACCCAGTTGGAAGgtgaattatt ... catgtcacagGACTCGAGTGACACTAAAAAAATCTGGTGTCGTGTTGGATTTGGTGCCACC
EST: gi|31349767|gb|CD434124.1|CD434124
EST:     TTGAAGACCAAGCTTTTGGGAAATTCAGTGGAAATTTACCCAGTTGGAAG                         GACTCGAGTGACACTNNNNNNNTCTGGTGTCGTGCTGGATTTGGTGCCACC
genomic: TTGAAGACCAAGTTTTTGGGAAATTCAGTGGAAATTTACCCAGTTGGAAGgtgaattatt ... catgtcacagGACTCGAGTGACACTAAAAAAATCTGGTGTCGTGTTGGATTTGGTGCCACC
EST: gi|211409590|gb|FL109891.1|FL109891
EST:     TTGAAGACCAAGTTTTTGGGAAATTCAGTGGAAATTTACCCAGTTGGAAG                         GACTCGAGTGACACTNNNNNNNTCTGGTGTCGTGTTGGATTTGGTGCCACC
genomic: TTGAAGACCAAGTTTTTGGGAAATTCAGTGGAAATTTACCCAGTTGGAAGgtgaattatt ... catgtcacagGACTCGAGTGACACTAAAAAAATCTGGTGTCGTGTTGGATTTGGTGCCACC
EST: gi|78025234|gb|DV493621.1|DV493621
EST:     TTGAAGACCAAGTTTTTGGGAAATTCAGTGGAAATTTACCCAGTTGGAAG                         GACTCGAGTGACACTNNNNNNNTCTGGTGTCGTGTTGGATTTGGTGCCACC
genomic: TTGAAGACCAAGTTTTTGGGAAATTCAGTGGAAATTTACCCAGTTGGAAGgtgaattatt ... catgtcacagGACTCGAGTGACACTAAAAAAATCTGGTGTCGTGTTGGATTTGGTGCCACC
EST: gi|50328677|gb|CO523803.1|CO523803
EST:     TTGAAGACCAAGTTTTTGGGAAATTCAGTGGAAATTTACCCAGTTGGAAG                         GACTCGAGTGACACTNNNNNNNTCTGGTGTCGTGTTGGATTTGGTGCCACC
genomic: TTGAAGACCAAGTTTTTGGGAAATTCAGTGGAAATTTACCCAGTTGGAAGgtgaattatt ... catgtcacagGACTCGAGTGACACTAAAAAAATCTGGTGTCGTGTTGGATTTGGTGCCACC
EST: gi|149078287|gb|EE167049.2|EE167049
EST:     TGAAGACCAAGTTTTTGGGAAATTCAGTGGAAATTTACCCCAGT-GGAAG                         GACTCGAGTGACACTAAAA
genomic: TGAAGACCAAGTTTTTGGGAAATTCAGTGGAAATTTACCC-AGTTGGAAGgtgaattatt ... catgtcacagGACTCGAGTGACACTAAAA
EST: gi|211454955|gb|FL196639.1|FL196639
EST:     TTGAAGACCAAGTTTTTGGGAAATTCAGTGGAAATTTACCCAGTTGGAAG                         GACTCGAGTGACACTNNNNNNNTCTGGTGTCGTGTTGGATTTGGTGCCACC
genomic: TTGAAGACCAAGTTTTTGGGAAATTCAGTGGAAATTTACCCAGTTGGAAGgtgaattatt ... catgtcacagGACTCGAGTGACACTAAAAAAATCTGGTGTCGTGTTGGATTTGGTGCCACC
EST: gi|94475418|gb|EB704376.1|EB704376
EST:     TTGAAGACCAAGTTTTTGGGAAATTCAGTGGAAATTTACCCAGTTGGAAG                         GACTCGAGTGACACT
genomic: TTGAAGACCAAGTTTTTGGGAAATTCAGTGGAAATTTACCCAGTTGGAAGgtgaattatt ... catgtcacagGACTCGAGTGACACT
EST: gi|148995971|gb|EE035219.2|EE035219
EST:     TTGAAGACCAAGTTTTTGGGAAATTCAGTGGAAATTTACCCAGTTGGAAG                         GACTCGAGTGACACTNNNNNNNTCTGGTGTCGTGTTGGATTTGGTGCCACC
genomic: TTGAAGACCAAGTTTTTGGGAAATTCAGTGGAAATTTACCCAGTTGGAAGgtgaattatt ... catgtcacagGACTCGAGTGACACTAAAAAAATCTGGTGTCGTGTTGGATTTGGTGCCACC
EST: gi|20507134|gb|BQ279500.1|BQ279500
EST:     TTGAAGACCAAGTTTTTGGGAAATTCAGTGGAAATTTACCCAGTTGGAAG                         GACTCGAGTGACACTAAAAAA-TCTGGTGTCGTGTTGGATTTGGTGCCACC
genomic: TTGAAGACCAAGTTTTTGGGAAATTCAGTGGAAATTTACCCAGTTGGAAGgtgaattatt ... catgtcacagGACTCGAGTGACACTAAAAAAATCTGGTGTCGTGTTGGATTTGGTGCCACC
EST: gi|76011657|gb|DT938827.1|DT938827
EST:     TTGAAGACCAAGTTTTTGGGAAATTCAGTGGAAATTTACCCAGTTGGAAG                         GACTCGAGTGACACT
genomic: TTGAAGACCAAGTTTTTGGGAAATTCAGTGGAAATTTACCCAGTTGGAAGgtgaattatt ... catgtcacagGACTCGAGTGACACT
EST: gi|71326507|gb|DR799931.1|DR799931
EST:     TTGAAGACCAAGTTTTTGGGAAAATCAGTGGAAATTTACCCAGTTGGAAG                         GACTCGAGTGACACT
genomic: TTGAAGACCAAGTTTTTGGGAAATTCAGTGGAAATTTACCCAGTTGGAAGgtgaattatt ... catgtcacagGACTCGAGTGACACT
EST: gi|5499280|gb|AI855147.1|AI855147
EST:     TTGAAGACCAAGTTTTTGGGAAATTCAGTGGAAATTTACCCAGTTGGAAG                         GACTCGAGTGACACTNNNNNNNTCTGGTGTCGTGTTGGATTTGGTGCCACC
genomic: TTGAAGACCAAGTTTTTGGGAAATTCAGTGGAAATTTACCCAGTTGGAAGgtgaattatt ... catgtcacagGACTCGAGTGACACTAAAAAAATCTGGTGTCGTGTTGGATTTGGTGCCACC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGTTGCTCACTGCGAGAATGAACATTTTACTTACGATATCACGTCTAAGTTGAAGACCAAGTTTTTGGGAAATTCAGTGGAAATTTACCCAGTTGGAAGgtgaattattagaattgtatttgtttcttggagatctgcgtgccttaatatttttgacccatttgagctaatggaataaaatggaaaccattttgaaggctgcgttgggaccacttgtataaatcagtaaatctaacccctctaatataatttccatgtcacag

- - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG