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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcagctaactaaattttgtgcaagtatatttagttgagatttgagaataccacatcaacacttatgcaatgttttttcgtcttgcctacctttggtgcagATACAATCTTCGGTCTATATCCTCATCAGCTACTGAAGTTGTTAAG

Basic information

species Oryza sativa
transcript LOC_Os07g06980.1
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g06980.1 (Oryza sativa), 3'ss of exon 14
lower sequence: GRMZM2G107309_T05 (Zea mays), 3'ss of exon 14
tcagctaactaaattttgtgcaagtatatttagttgagatttgagaataccacatcaacacttatgcaatgttttttcgtcttgcctacctt-tggtgcagATACAATCTTCGGTCTATATCCTCATCAGCTACTGAAGTTGTTAAG
  |   |   |||| |  | |    |||    ||   |   |  |           ||   |   |     |  |      | |  |   || |  | |||||||||||| ||||| ||||||||||||||||||||||||||||||
-tattgacaaaaatatcttactctaataagcggtctggtggtaggctctttttgagaaagttcccggttaatactcaaaaatcgtttgtgttgtcctacagATACAATCTCCGGTCGATATCCTCATCAGCTACTGAAGTTGTTAAG
















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|86498642|gb|CI141275.1|CI141275
EST:     ATGCTAACTGCTTGTTCACAGGGAAAATTGTTGGTTAAACTTGAGGGAGG                         AAACAATCTTCGGTCTAAATCCTCATCAGCTACTGAAGTTGTTAAG
genomic: ATGCTAACTGCTTGTTCACAGGGAAAATTGTTGGTTATACTTGAGGGAGGgtaggtaccc ... tttggtgcagATACAATCTTCGGTCTATATCCTCATCAGCTACTGAAGTTGTTAAG
EST: gi|58586909|gb|CF985217.1|CF985217
EST:     ATGCTAACTGCTTGTTCACAGGGAAAATTGTTGGTTATACTTGAGGGAGG                         ATACAATCTTCGGTCTATATCCTCATCAGCTACTGAAGTTGTTAAG
genomic: ATGCTAACTGCTTGTTCACAGGGAAAATTGTTGGTTATACTTGAGGGAGGgtaggtaccc ... tttggtgcagATACAATCTTCGGTCTATATCCTCATCAGCTACTGAAGTTGTTAAG
EST: gi|58681336|gb|CK070023.1|CK070023
EST:     ATACTTGAGGGAGG                         ATACAATCTTCGGTCTATATCCTCATCAGCTACTGAAGTTGTTAAG
genomic: ATACTTGAGGGAGGgtaggtaccc ... tttggtgcagATACAATCTTCGGTCTATATCCTCATCAGCTACTGAAGTTGTTAAG
EST: gi|29644494|gb|CB649501.1|CB649501
EST:     ATGCTAACTGCTTGTTCACAGGGAAAATTGTTGGTTATACTTGAGGGAGG                         ATACAATCTTCGGTCTATATCCTCATCAGCTACTGAAGTTGTTAAG
genomic: ATGCTAACTGCTTGTTCACAGGGAAAATTGTTGGTTATACTTGAGGGAGGgtaggtaccc ... tttggtgcagATACAATCTTCGGTCTATATCCTCATCAGCTACTGAAGTTGTTAAG
EST: gi|58665950|gb|CK054636.1|CK054636
EST:     ATGCTAACTGCTTGTTCACAGGGAAAATTGTTGGTTATACTTGAGGGAGG                         ATACAATCTTCGGTCTATA
genomic: ATGCTAACTGCTTGTTCACAGGGAAAATTGTTGGTTATACTTGAGGGAGGgtaggtaccc ... tttggtgcagATACAATCTTCGGTCTATA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aataccacatcaacacttatgcaatgttttttcgtcttgcctacctttggtgcagATACAATCTTCGGTCTATATCCTCATCAGCTACTGAAGTTGTTAAG
                          ttttttcgtcttgcct  CT-rich tract
                      aatgtttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcagctaactaaattttgtgcaagtatatttagttgagatttgagaataccacatcaacacttatgcaatgttttttcgtcttgcctacctttggtgcagATACAATCTTCGGTCTATATCCTCATCAGCTACTGAAGTTGTTAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG