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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttaagatccctgaatacctcagcttgatttttttctttataagacccttgttgtctaaatggtgtatttccttttacagCTCATAGTGCTGTTGTATTGAAAGCTGAGAGCACGGCCGACAAAGTTGAGTGGGTAAATAAGATACGGGCTGTAATTCAAAGCAAAGGGGGATCATTCAA

Basic information

species Oryza sativa
transcript LOC_Os06g13820.1
intron # 17
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g13820.1 (Oryza sativa), 3'ss of exon 17
lower sequence: GRMZM5G811223_T01 (Zea mays), 3'ss of exon 5
gtta-agatccctgaatacctcagctt---gattt---ttttctttataagacccttgttgtctaaatggtgtatttcctt-----ttacagCTCATAGTGCTGTTGTATTGAAAGCTGAGAGCACGGCCGACAAAGTTGAGTGGGTAAATAAGATACGGGCTGTAATTCAAAGCAAAGGGGGATCATTCAA
|||  | | ||   |||    |||| |   || ||   ||| ||| ||    |  || || | || ||  |    | | ||     || ||||||| ||||||||| | || || |||||||||| | | ||||| ||||||||||| ||||||||    ||||| ||||| ||||||||||| || |||||
gttgtataccctcaaatcgtacagcctatggagttatatttgcttcatggttctgtttttttttatataattctctgctttaatatttgcagCTCACAGTGCTGTTCTGTTAAAGGCTGAGAGCATGCCTGACAAGGTTGAGTGGGTGAATAAGATCAAAGCTGTTATTCAGAGCAAAGGGGGTTCTTTCAA

upper sequence: LOC_Os06g13820.1 (Oryza sativa), 3'ss of exon 17
lower sequence: GRMZM2G157462_T01 (Zea mays), 3'ss of exon 17
gttaagat--ccctgaatacctcagctt---gattt---ttttctttataagacccttgttgtctaaatggt-gtatttccttttacagCTCATAGTGCTGTTGTATTGAAAGCTGAGAGCACGGCCGACAAAGTTGAGTGGGTAAATAAGATACGGGCTGTAATTCAAAGCAAAGGGGGATCATTCAA
||| | ||  || |||||    ||||||   || ||   ||| |||| |    |  || || | ||| |  | |  ||   |||| ||||||| ||||||||||| || || |||||||||| ||||||||| ||||||||||||||||||||    ||||| ||||| ||||||||||| || |||||
gttgatatacccttgaatcgtacagcttatggagttgtatttgctttgtgtttctgtttttttataattctttgctttaaattttgcagCTCACAGTGCTGTTGTGTTAAAGGCTGAGAGCATGGCCGACAAGGTTGAGTGGGTAAATAAGATCAAAGCTGTTATTCAGAGCAAAGGGGGTTCTTTCAA
















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|325493116|gb|JG457640.1|JG457640
EST:     TCTCGTCTTTAAGATAACTAACAGGGTTGCCTACAAAACAGTTCTAAAAG                         CTCATAGTGCTGTTGTATTGAAAGCTGAGAGCACGGCCGACAAAGTTGAGT
genomic: TCTCGTCTTTAAGATAACTAACAGGGTTGCCTACAAAACAGTTCTAAAAGgttaagatcc ... ccttttacagCTCATAGTGCTGTTGTATTGAAAGCTGAGAGCACGGCCGACAAAGTTGAGT
EST: gi|29614012|gb|CB619025.1|CB619025
EST:     TCTCGTCTTTAAGATAACTAACAGGGTTGCCTACAAAACAGTTCTAAAAG                         CTCATAGTGCTGTTGTATTGAAAGCTGAGAGCACGGCCGACAAAGTTGAGT
genomic: TCTCGTCTTTAAGATAACTAACAGGGTTGCCTACAAAACAGTTCTAAAAGgttaagatcc ... ccttttacagCTCATAGTGCTGTTGTATTGAAAGCTGAGAGCACGGCCGACAAAGTTGAGT
EST: gi|29657562|gb|CB653837.1|CB653837
EST:     TCTCGTCTTTAAGATAACTAACAGGGTTGCCTACAAAACAGTTCTAAAAG                         CTCATAGTGCTGTTGTATTGAAAGCTGAGAGCACGGCCGACAAAGTTGAGT
genomic: TCTCGTCTTTAAGATAACTAACAGGGTTGCCTACAAAACAGTTCTAAAAGgttaagatcc ... ccttttacagCTCATAGTGCTGTTGTATTGAAAGCTGAGAGCACGGCCGACAAAGTTGAGT
EST: gi|58652777|gb|CK041457.1|CK041457
EST:     TCTCGTCTTTAAGATAAGTAACAGGGTTGCCTACAAAACAGTTCTAAAAG                         CTCATAGTGCTGTTGTATTGAAAGCTGAGAGCACGGCCGACAAAGTTGAGT
genomic: TCTCGTCTTTAAGATAACTAACAGGGTTGCCTACAAAACAGTTCTAAAAGgttaagatcc ... ccttttacagCTCATAGTGCTGTTGTATTGAAAGCTGAGAGCACGGCCGACAAAGTTGAGT
EST: gi|33795777|gb|CF323758.1|CF323758
EST:     TCTCGTCTTTAAGATAACTAACAGGGTTGCCTACAAAACAGTTCTAAAAG                         CTCATAGTGCTGTTGTATTGAAAGCTGAGAGCACGGCCGACAAAGTTGAGT
genomic: TCTCGTCTTTAAGATAACTAACAGGGTTGCCTACAAAACAGTTCTAAAAGgttaagatcc ... ccttttacagCTCATAGTGCTGTTGTATTGAAAGCTGAGAGCACGGCCGACAAAGTTGAGT
EST: gi|58679703|gb|CK068390.1|CK068390
EST:     TCTCGTCTTTAAGATAACTAACAGGGTTGCCTACAAAACAGTTCTAAAAG                         CTCATAGTGCTGTTGTATTGAAAGCTGAGAGCACGGCCGACAAAGTTGAGT
genomic: TCTCGTCTTTAAGATAACTAACAGGGTTGCCTACAAAACAGTTCTAAAAGgttaagatcc ... ccttttacagCTCATAGTGCTGTTGTATTGAAAGCTGAGAGCACGGCCGACAAAGTTGAGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgatttttttctttataagacccttgttgtctaaatggtgtatttccttttacagCTCATAGTGCTGTTGTATTGAAAGCTGAGAGCACGGCCGACAAAGTTGAGTGGGTAAATAAGATACGGGCTGTAATTCAAAGCAAAGGGGGATCATTCAA
                            gtctaaa  putative branch site (score: 3)
                                        tatttcctttt  putative PPT
     tttttctttataaga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttaagatccctgaatacctcagcttgatttttttctttataagacccttgttgtctaaatggtgtatttccttttacagCTCATAGTGCTGTTGTATTGAAAGCTGAGAGCACGGCCGACAAAGTTGAGTGGGTAAATAAGATACGGGCTGTAATTCAAAGCAAAGGGGGATCATTCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG