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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacatccacatctccattgagccaaaaatattttacgtgtattttcatgtttccacacaagaacagaaaggggctaaaatatttttcctttttgtcagGATTGTTGCTTGATCCCAGAATCACCGTTCTATTTGGAAGGCGAAGGCGGACTTTTTAGATACATAGAAAAACGTTTGAAGGACAATGGTCATATGGTTA

Basic information

species Zea mays
transcript GRMZM2G443985_T02
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G443985_T04 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os06g05860.1 (Oryza sativa), 3'ss of exon 10
gtacatccacatctccattgagccaaaaatattt-tacgtgt-attttcatgtttccacacaagaacagaaag-----------------gggctaaaatatttttcct---ttttgtcagGATTGTTGCTTGATCCCAGAATCACCGTTCTATTTGGAAGGCGAAGGCGGACTTTTTAGATACATAGAAAAACGTTTGAAGGACAATGGTCATATGGTTA
|||  | ||||||||  |  |||  |||| |||| ||  | | ||||   || ||  ||  || || |    |                 | | | | | | ||||  |   ||||||||||||||||||||||| ||||| ||||| |||||| ||||||| ||||| || |||||||||||  | ||||| ||| ||||||| ||||||||||||||||
gtatgttcacatctctgtcaagctgaaaacatttatatatatcatttctgtgattttactaaaaaaaaaggggtttaattttctccaattgaggtgagaaactttttttatattttgtcagGATTGTTGCTTGATTCCAGAGTCACCTTTCTATCTGGAAGGTGAAGGTGGCCTTTTTAGATATTTGGAAAAGCGTCTGAAGGAGAATGGTCATATGGTTA
















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|32938375|gb|CF043194.1|CF043194
EST:     GTTTTATTGCACATTATGCTACTCTGGCTAGCAGGGACGTG                         GATTGTTGCTTGATCCCAGAATCACCGTTCTATTTGGAAGGCGAAGGCGGA
genomic: GTTTTATTGCACATTATGCTACTCTGGCTAGCAGGGACGTGgtacatccac ... tttttgtcagGATTGTTGCTTGATCCCAGAATCACCGTTCTATTTGGAAGGCGAAGGCGGA
EST: gi|6095550|gb|AW120217.1|AW120217
EST:     GGCTAGCAGGGACGTG                         GATTGTTGCTTGATCCCAGAATCACCGTTCTATTTGGAAGGCGAAGGCGGA
genomic: GGCTAGCAGGGACGTGgtacatccac ... tttttgtcagGATTGTTGCTTGATCCCAGAATCACCGTTCTATTTGGAAGGCGAAGGCGGA
EST: gi|32938968|gb|CF043787.1|CF043787
EST:     GTTTTATTGCACATTATGCTACTCTGGCTAGCAGGGACGTG                         GATTGTTGCTTGATCCCAGAATCACCGTTCTATTTGGAAGGCGAAGGCGGA
genomic: GTTTTATTGCACATTATGCTACTCTGGCTAGCAGGGACGTGgtacatccac ... tttttgtcagGATTGTTGCTTGATCCCAGAATCACCGTTCTATTTGGAAGGCGAAGGCGGA
EST: gi|488227|gb|T18808.1|T18808
EST:     GTTTTATTGCACATTATGCTACTCTGGCTAGCAGGGACGTG                         GATTGTTGCTTGATCCCAGAATCACCGTTCTATTTGGAAGGCGAAGGCG-A
genomic: GTTTTATTGCACATTATGCTACTCTGGCTAGCAGGGACGTGgtacatccac ... tttttgtcagGATTGTTGCTTGATCCCAGAATCACCGTTCTATTTGGAAGGCGAAGGCGGA
EST: gi|32939806|gb|CF044625.1|CF044625
EST:     GTTTTATTGCACATTATGCTACTCTGGCTAGCAGGGACGTG                         GATTGTTACTTGATCCCAGAATCACCGTTCTATTTGGAAGGCGAAGGCGGA
genomic: GTTTTATTGCACATTATGCTACTCTGGCTAGCAGGGACGTGgtacatccac ... tttttgtcagGATTGTTGCTTGATCCCAGAATCACCGTTCTATTTGGAAGGCGAAGGCGGA
EST: gi|32939493|gb|CF044312.1|CF044312
EST:     GTTTTATTGCACATTATGCTACTCTGGCTAGCAGGGACGTG                         GATTGTTGCTTGATCCCAGAATCACCGTTCTATTTGGAAGGCGAAGGCGGA
genomic: GTTTTATTGCACATTATGCTACTCTGGCTAGCAGGGACGTGgtacatccac ... tttttgtcagGATTGTTGCTTGATCCCAGAATCACCGTTCTATTTGGAAGGCGAAGGCGGA
EST: gi|76921243|gb|DV168509.1|DV168509
EST:     GTTTTATTGCACATTATGCTACTCTGGCTAGCAGGGACGTG                         GATTGTTGCTTGATCCCAGAATCACCGTTCTATTTGGAAGGCGAAGGCGGA
genomic: GTTTTATTGCACATTATGCTACTCTGGCTAGCAGGGACGTGgtacatccac ... tttttgtcagGATTGTTGCTTGATCCCAGAATCACCGTTCTATTTGGAAGGCGAAGGCGGA
EST: gi|211132969|gb|FL170874.1|FL170874
EST:     GTTTTATTGCACATTATGCTACTCTGGCTAGCAGGGACGTG                         GATTGTTGCTTGATCCCAGAATCACCATTCTA
genomic: GTTTTATTGCACATTATGCTACTCTGGCTAGCAGGGACGTGgtacatccac ... tttttgtcagGATTGTTGCTTGATCCCAGAATCACCGTTCTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcatgtttccacacaagaacagaaaggggctaaaatatttttcctttttgtcagGATTGTTGCTTGATCCCAGAATCACCGTTCTATTTGGAAGGCGAAGGCGGACTTTTTAGATACATAGAAAAACGTTTGAAGGACAATGGTCATATGGTTA
                            ggctaaa  putative branch site (score: 3)
                                    tatttttcctttttgt  CT-rich tract
                               taaaatatttttcctt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacatccacatctccattgagccaaaaatattttacgtgtattttcatgtttccacacaagaacagaaaggggctaaaatatttttcctttttgtcagGATTGTTGCTTGATCCCAGAATCACCGTTCTATTTGGAAGGCGAAGGCGGACTTTTTAGATACATAGAAAAACGTTTGAAGGACAATGGTCATATGGTTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG