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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagttaatggcttctatttatgcctcaactattccagtcaatattctctagtttcttcaagtgtcctattttacatatttggccctgttgcccttttaaaatctgtcactctgtaaatatagccacttaatattctgatatacactgatctcctttgaagatggagctaattattcatgttcatcttccgtagGACTGCTGCTTGATTCCTGAGTCACCCTTTTATTTGGAAGGGGAGGGTGGACTATTTGAGTATATAGATAGGAGGTTGAAGGAGAACAATCACACGGTTA

Basic information

species Zea mays
transcript GRMZM5G879882_T03
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G879882_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os01g53680.1 (Oryza sativa), 3'ss of exon 10
gtgagttaatggcttctatttatgcctcaactattccagtcaatattctctagtttcttcaagtgtcctattttacatatttggccctgttgcccttttaaaatctgtcactctgtaaatatagccacttaatattctgatatacactgatctcctttgaagatggagctaattattcatgttcatcttccgtagGACTGCTGCTTGATTCCTGAGTCACCCTTTTATTTGGAAGGGGAGGGTGGACTATTTGAGTATATAGATAGGAGGTTGAAGGAGAACAATCACACGGTTA
|| ||||||||  || ||| |||| |                   |||| |||||||||| |||    |||| |   ||||              || |     | || |  |  |  |     |||| ||  |||||  |   |   ||      | | |  |     | |||     | |   |||||  |||||||||||||| |||||||||||||| |||||||||||||||||||||||||| |||||||| ||||| | ||||||||| |||||||| |||| |||||
gtaagttaatgctttatatctatgtc------------------gttctttagtttcttcgagtcaaatattctgtgtattca----------tgttctgggtgcagtaatgcattgga-----ccacctagcattcttcttctccacgaa-----tggtacctcctattcattgggtttctctgtcttctatagGACTGCTGCTTAATTCCTGAGTCACCATTTTATTTGGAAGGGGAGGGTGGACTGTTTGAGTACATAGAGAAGAGGTTGAAAGAGAACAACCACATGGTTA
















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|40334982|gb|CK369052.1|CK369052
EST:     GATTTATTGCCATGTTTGCTACTCTTGCAAGCAGAGATGTG                         GACTGCTGTTTGATTCCTGAGTCACCCTTTTATTTGGAAGGGGAGGGTGGA
genomic: GATTTATTGCCATGTATGCTACTCTTGCAAGCAGAGATGTGgtgagttaat ... tcttccgtagGACTGCTGCTTGATTCCTGAGTCACCCTTTTATTTGGAAGGGGAGGGTGGA
EST: gi|87153557|gb|DY398346.1|DY398346
EST:     GATTTATTGCCATGTATGCTACTCTTGCAAGCAGAGATGTG                         GACTGCTGTTTGATTCCTGAGTCACCCTTTTATTTGGAAGGGGAGGGTGGA
genomic: GATTTATTGCCATGTATGCTACTCTTGCAAGCAGAGATGTGgtgagttaat ... tcttccgtagGACTGCTGCTTGATTCCTGAGTCACCCTTTTATTTGGAAGGGGAGGGTGGA
EST: gi|19351112|gb|BM895644.1|BM895644
EST:     GATTTATTGCCATGTATGCTACTCTCGCAAGCAGAGATGTG                         GACTGCTGTTTGATTCCTGAGTCACCCTTT-ATTTGGAAGGGGAGGGTGGA
genomic: GATTTATTGCCATGTATGCTACTCTTGCAAGCAGAGATGTGgtgagttaat ... tcttccgtagGACTGCTGCTTGATTCCTGAGTCACCCTTTTATTTGGAAGGGGAGGGTGGA
EST: gi|108954346|gb|EC365109.1|EC365109
EST:     GATTTATTGCCATGTATGCTACTCTTGCAAGCAGAGATGTG                         GACTGCTGCTTGATTCCTGAGTCACCCTTTTATTTGGAAGGGGAGGGTGGA
genomic: GATTTATTGCCATGTATGCTACTCTTGCAAGCAGAGATGTGgtgagttaat ... tcttccgtagGACTGCTGCTTGATTCCTGAGTCACCCTTTTATTTGGAAGGGGAGGGTGGA
EST: gi|22491553|gb|BU051476.1|BU051476
EST:     GATTTTATTGCCATGTATGCTACTCTTGCAAGCAGAGATGTG                         G-CTGCTGTTTGATTCCTGAGTC-CCCTTTTATTTGGAAGGGGAGGGTGG-
genomic: GATTT-ATTGCCATGTATGCTACTCTTGCAAGCAGAGATGTGgtgagttaat ... tcttccgtagGACTGCTGCTTGATTCCTGAGTCACCCTTTTATTTGGAAGGGGAGGGTGGA
EST: gi|33942634|gb|CF349234.1|CF349234
EST:     GATTTATTGCCATGTATGCTACTCTTGCAAGCAGAGATGTG                         GACTGCTGCTTGATTCCTGAGTCACCCTTTTATTTGGAAGGGGAGGGTGGA
genomic: GATTTATTGCCATGTATGCTACTCTTGCAAGCAGAGATGTGgtgagttaat ... tcttccgtagGACTGCTGCTTGATTCCTGAGTCACCCTTTTATTTGGAAGGGGAGGGTGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatacactgatctcctttgaagatggagctaattattcatgttcatcttccgtagGACTGCTGCTTGATTCCTGAGTCACCCTTTTATTTGGAAGGGGAGGGTGGACTATTTGAGTATATAGATAGGAGGTTGAAGGAGAACAATCACACGGTTA
                          agctaat  putative branch site (score: 3)
                                         ttcatcttcc  putative PPT
                             taattattcatgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagttaatggcttctatttatgcctcaactattccagtcaatattctctagtttcttcaagtgtcctattttacatatttggccctgttgcccttttaaaatctgtcactctgtaaatatagccacttaatattctgatatacactgatctcctttgaagatggagctaattattcatgttcatcttccgtagGACTGCTGCTTGATTCCTGAGTCACCCTTTTATTTGGAAGGGGAGGGTGGACTATTTGAGTATATAGATAGGAGGTTGAAGGAGAACAATCACACGGTTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA