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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTCAACGTCCCGGATCTCCGCGTCGGCACCCTCGACTCGCTCCTCGCGCTCAGTGACGACCTCGTCAAGgttccccgcacgatctcgatcccctctcccctctccagctgccccggggcactagcctctgattccgtgccatcgtgtgtttgtctctatatgtatacccgcag

Basic information

species Zea mays
transcript GRMZM2G128995_T06
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G128995_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os05g51530.1 (Oryza sativa), 5'ss of exon 2
TTCAACGTCCCGGATCTCCGCGTCGGCACCCTCGACTCGCTCCTCGCGCTCAGTGACGACCTCGTCAAGgttccccgcacgatctcgatcccctctcccctctccagctgccccggggcactagcctctgattccgtgccatcgtgtgtttgtctctatatgtatacccgcag
||||||||||| ||||||||||||||||| |||||||| |||||||| ||||| ||||| |||||||||||  |||     |||||  || | |||||||  ||  | |  |||  | | |    |||| |  |  | || |  | |   || | ||   || |         
TTCAACGTCCCCGATCTCCGCGTCGGCACGCTCGACTCCCTCCTCGCCCTCAGCGACGATCTCGTCAAGgtaaccc-----atctct-tctcttctccccgatctcgatctcccttgccccccagctctcacgcgattcc-tattattcctgccgctgc-tgcag--------

upper sequence: GRMZM2G128995_T01 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA16G26220.1 (Glycine max), 5'ss of exon 2
TTCAACGTCCCGGATCTCCGCGTCGGCACCCTCGACTCGCTCCTCGCGCTCAGTGACGACCTCGTCAAGgttccccgcacgat-ctcgatcccctctcccctctccagctgccccggggcactagcctctgattccgtgccatcgtgtgtttgtctctatatgt-atacccgcag--------------------------------------------------------------
|||||  ||||  ||||||| ||||| ||||| ||||| |||||| | ||||| ||||| |||||||||||    || || || | | ||| |          | || |     ||  ||  |  | |   |||  |    || | |  |   | |   |||||  |  | |||                                                               
TTCAATATCCCCAATCTCCGGGTCGGAACCCTAGACTCCCTCCTCTCCCTCAGCGACGATCTCGTCAAGgta---cgtacaattcccaatcacacgaaaaacattcaccgttttcgttgcgatc-cttgatattgtggaaaattgcggataaatgtggttatgttgtggctgcaattgcgccttgtttgtttattggtttcattttgcttgatctgtttgtgtgtgtgtgtgtgcag
















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|211136925|gb|FL422189.1|FL422189
EST:     GCGTCGGCACCCTCGACTCGCTCCTCGCGCTCAGTGACGACCTCGTCAAG                         TCCAATGTCTTCGTGGAGGGCGTGTCACACAAGATCCGGAGGCAGATCGAG
genomic: GCGTCGGCACCCTCGACTCGCTCCTCGCGCTCAGTGACGACCTCGTCAAGgttccccgca ... atacccgcagTCCAATGTCTTCGTGGAGGGCGTGTCACACAAGATCCGGAGGCAGATCGAG
EST: gi|211377201|gb|FL412470.1|FL412470
EST:     GCGTCGGCACCCTCGACTCGCTCCTCGCGCTCAGTGACGACCTCGTCAAG                         TCCAATGTCTTCG
genomic: GCGTCGGCACCCTCGACTCGCTCCTCGCGCTCAGTGACGACCTCGTCAAGgttccccgca ... atacccgcagTCCAATGTCTTCG
EST: gi|211539519|gb|FL409049.1|FL409049
EST:     GCGTCGGCACCCTCGACTCGCTCCTCGCGCTCAGTGACGACCTCGTCAAG                         TCCAATGYCTTCGTGGAGGGCGTGTCACACAAGATCCGGAGGCAGATCGAG
genomic: GCGTCGGCACCCTCGACTCGCTCCTCGCGCTCAGTGACGACCTCGTCAAGgttccccgca ... atacccgcagTCCAATGTCTTCGTGGAGGGCGTGTCACACAAGATCCGGAGGCAGATCGAG
EST: gi|211363177|gb|FL385284.1|FL385284
EST:     GCGTCGGCACCCTCGACTCGCTCCTCGCGCTCAGTGACGACCTCGTCAAG                         TCCAATGTCTTCGTGGAGGGCGTGTCACACAAGATCCGGAGGCAGATCGAG
genomic: GCGTCGGCACCCTCGACTCGCTCCTCGCGCTCAGTGACGACCTCGTCAAGgttccccgca ... atacccgcagTCCAATGTCTTCGTGGAGGGCGTGTCACACAAGATCCGGAGGCAGATCGAG
EST: gi|211441636|gb|FL403705.1|FL403705
EST:     GCGTCGGCACCCTCGACTCGCTCCTCGCGCTCAGTGACGACCTCGTCAAG                         TCCAATGTCTTCGTGGAGGGCGTGTCACACAAGATCCGGAG-CAGATCGAG
genomic: GCGTCGGCACCCTCGACTCGCTCCTCGCGCTCAGTGACGACCTCGTCAAGgttccccgca ... atacccgcagTCCAATGTCTTCGTGGAGGGCGTGTCACACAAGATCCGGAGGCAGATCGAG
EST: gi|211202638|gb|FL424402.1|FL424402
EST:     GCGTCGGCACCCTCGACTCGCTCCTCGCGCTCAGTGACGACCTCGTCAAG                         TCCAATGTCTTCGTGGAGGGCGTGTCACACAAGATCCGGAG-CAGATCGAG
genomic: GCGTCGGCACCCTCGACTCGCTCCTCGCGCTCAGTGACGACCTCGTCAAGgttccccgca ... atacccgcagTCCAATGTCTTCGTGGAGGGCGTGTCACACAAGATCCGGAGGCAGATCGAG
EST: gi|211247493|gb|FL399189.1|FL399189
EST:     GCGTCGGCACCCTCGACTCGCTCCTCGCGCTCAGTGACGACCTCGTCAAG                         TCCAATGTCTTCGTGGAGGGCGTGTCACACAA
genomic: GCGTCGGCACCCTCGACTCGCTCCTCGCGCTCAGTGACGACCTCGTCAAGgttccccgca ... atacccgcagTCCAATGTCTTCGTGGAGGGCGTGTCACACAA
EST: gi|211504705|gb|FL413781.1|FL413781
EST:     GCGTCGGCACCCTCGACTCGCTCCTCGCGCTCAGTGACGANCTCGTCWAG                         TCCAATGTCTTCGTGGAGGGCGTGTCACACAAGATCCGGAGGCMGATCGAG
genomic: GCGTCGGCACCCTCGACTCGCTCCTCGCGCTCAGTGACGACCTCGTCAAGgttccccgca ... atacccgcagTCCAATGTCTTCGTGGAGGGCGTGTCACACAAGATCCGGAGGCAGATCGAG
EST: gi|149102700|gb|EE288050.2|EE288050
EST:     GCGTCGGCACCCTCGACTCGCTCCTCGCGCTCAGTGACGACCTCGTCAAG                         TCCAATGTCTTCGTGGAGGGCGTGTCACACAAGATCCGGAGGCAGATCGAG
genomic: GCGTCGGCACCCTCGACTCGCTCCTCGCGCTCAGTGACGACCTCGTCAAGgttccccgca ... atacccgcagTCCAATGTCTTCGTGGAGGGCGTGTCACACAAGATCCGGAGGCAGATCGAG
EST: gi|15312764|gb|BI478361.1|BI478361
EST:     GCGTCGGCACCCTCGACTCGCTCCTCGCGCTCAGTGACGACCTCGTCAAG                         TCCAATGTCTTCGTGGAGGGCGTGTCACACAAGATCCGGAGGCAGATCGAG
genomic: GCGTCGGCACCCTCGACTCGCTCCTCGCGCTCAGTGACGACCTCGTCAAGgttccccgca ... atacccgcagTCCAATGTCTTCGTGGAGGGCGTGTCACACAAGATCCGGAGGCAGATCGAG
EST: gi|211264685|gb|FL426671.1|FL426671
EST:     GCGTCGGCACCCTCGACTCGCTCCTCGCGCTCAGTGACGACCTCGTCAAG                         TCCAATGTCTTCGTGGAGGGCGTGTCACACAAGATCCGGAGGCAGATCGAG
genomic: GCGTCGGCACCCTCGACTCGCTCCTCGCGCTCAGTGACGACCTCGTCAAGgttccccgca ... atacccgcagTCCAATGTCTTCGTGGAGGGCGTGTCACACAAGATCCGGAGGCAGATCGAG
EST: gi|211217327|gb|FL397497.1|FL397497
EST:     GCGTCGGCACCCTCGACTCGCTCCTCGCGCTCAGTGACGACCTCGTCAAG                         TCCAATGTCTTCGTGGAGGGCGTGTCACACAAGATCCGGAG-CAGATCGAG
genomic: GCGTCGGCACCCTCGACTCGCTCCTCGCGCTCAGTGACGACCTCGTCAAGgttccccgca ... atacccgcagTCCAATGTCTTCGTGGAGGGCGTGTCACACAAGATCCGGAGGCAGATCGAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTCAACGTCCCGGATCTCCGCGTCGGCACCCTCGACTCGCTCCTCGCGCTCAGTGACGACCTCGTCAAGgttccccgcacgatctcgatcccctctcccctctccagctgccccggggcactagcctctgattccgtgccatcgtgtgtttgtctctatatgtatacccgcag

- - - - - - - - - - - - - - - - - - -  CTCCTC