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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacccataacttttctgcttatgcaacaattcaaaatggttcaacagttgtattgtgctctttgaacaaatattctaactggtctctcttttcagCCTCTTGGTTGAGGAGATAGATTTGGGAGATGGCAATGTGCATCAAGTTGTTAGTGGGCTTGCCAAGTTCTTCAGCCCAGAGGAACTTGTT

Basic information

species Oryza sativa
transcript LOC_Os01g60660.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g60660.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G166345_T01 (Zea mays), 3'ss of exon 6
--------------------------------------gtacccataacttttctgcttatgcaacaattcaaaatggt-tcaacagttgtattgtgctctttgaacaaatattctaactggtctctcttttcagCCTCTTGGTTGAGGAGATAGATTTGGGAGATGGCAATGTGCATCAAGTTGTTAGTGGGCTTGCCAAGTTCTTCAGCCCAGAGGAACTTGTT
                                       | | |   | |||    ||| ||||||| ||  || |  | |||    || | || |  | ||  | | ||  |||| | || |  |      |||||| || |||||||||||||||||||||||||| ||||||| ||||||||||||||| ||||| ||||  | ||||||||| || |||  |
acaggtgctgtattttcactcttctgcaacacttagaatttctctgtattttcactcttctgcaacacttagaatttctctcagtgcttatgttatagtattcaacctaacgttctgattgatgaccgac--cagccttttagttgaggagatagatttgggagatggtaatgtgcgtcaaGTTGTTAGTGGTCTTGCAAAGTATTGCAGCCCAGATGATCTTACT

upper sequence: LOC_Os01g60660.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G166345_T02 (Zea mays), 3'ss of exon 6
----------------------------------gtacccataacttttctgcttatgcaacaattcaaaatggt-tcaacagttgtattgtgctctttgaacaaatattctaactggtctctcttttcagCCTCTTGGTTGAGGAGATAGATTTGGGAGATGGCAATGTGCATCAAGTTGTTAGTGGGCTTGCCAAGTTCTTCAGCCCAGAGGAACTTGTT
                                   | | |   | |||    ||| ||||||| ||  || |  | |||    || | || |  | ||  | | ||  |||| | || |  |      |||||| || |||||||||||||||||||||||||| ||||||| ||||||||||||||| ||||| ||||  | ||||||||| || |||  |
gtgctgtattttcactcttctgcaacacttagaatttctctgtattttcactcttctgcaacacttagaatttctctcagtgcttatgttatagtattcaacctaacgttctgattgatgaccgac--cagCCTTTTAGTTGAGGAGATAGATTTGGGAGATGGTAATGTGCGTCAAGTTGTTAGTGGTCTTGCAAAGTATTGCAGCCCAGATGATCTTACT
















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|86418870|gb|CI053671.1|CI053671
EST:     AAAGCATGGAAGCACCCATCTGCTGACAG                         CCTCTTGGTTGAGGAGATAGATTTGGGAGATGGCAATGTGCATCAAGTTGT
genomic: AAAGCATGGAAGCACCCATCTGCTGACAGgtacccataa ... ctcttttcagCCTCTTGGTTGAGGAGATAGATTTGGGAGATGGCAATGTGCATCAAGTTGT
EST: gi|29672822|gb|CB669097.1|CB669097
EST:     ATACAGGTTGGCCTTATTCGCAAAGCATGGAAGCACCCATCTGCTGACAG                         CCTCTTGGTTGAGGAGATAGATTTGGGAGATGGCAATGTGCATCAAGTTGT
genomic: ATACAGGTTGGCCTTATTCGCAAAGCATGGAAGCACCCATCTGCTGACAGgtacccataa ... ctcttttcagCCTCTTGGTTGAGGAGATAGATTTGGGAGATGGCAATGTGCATCAAGTTGT
EST: gi|29642064|gb|CB647071.1|CB647071
EST:     ATACAGGTTGGCCTTATTCGCAAAGCATGGAAGCACCCATCTGCTGACAG                         CCTCTTGGTTGAGGAGATAGATTTGGGAGATGGCAATGTGCATCAAGTTGT
genomic: ATACAGGTTGGCCTTATTCGCAAAGCATGGAAGCACCCATCTGCTGACAGgtacccataa ... ctcttttcagCCTCTTGGTTGAGGAGATAGATTTGGGAGATGGCAATGTGCATCAAGTTGT
EST: gi|29642108|gb|CB647115.1|CB647115
EST:     ATACAGGTTGGCCTTATTCGCAAAGCATGGAAGCACCCATCTGCTGACAG                         CCTCTTGGTTGAGGAGATAGATTTGGGAGATGGCAATGTGCATCAAGTTGT
genomic: ATACAGGTTGGCCTTATTCGCAAAGCATGGAAGCACCCATCTGCTGACAGgtacccataa ... ctcttttcagCCTCTTGGTTGAGGAGATAGATTTGGGAGATGGCAATGTGCATCAAGTTGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcaacagttgtattgtgctctttgaacaaatattctaactggtctctcttttcagCCTCTTGGTTGAGGAGATAGATTTGGGAGATGGCAATGTGCATCAAGTTGTTAGTGGGCTTGCCAAGTTCTTCAGCCCAGAGGAACTTGTT
                                ttctaac  putative branch site (score: 1)
                                      ctggtctctcttttc  CT-rich tract
                    tttgaacaaatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacccataacttttctgcttatgcaacaattcaaaatggttcaacagttgtattgtgctctttgaacaaatattctaactggtctctcttttcagCCTCTTGGTTGAGGAGATAGATTTGGGAGATGGCAATGTGCATCAAGTTGTTAGTGGGCTTGCCAAGTTCTTCAGCCCAGAGGAACTTGTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA