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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...catttatggtgggtgctcttaagatttttatgcaacacttcctttctttccacaaggataatacaagacaaataacaaaagcttaatttgcattttgcagTGTCTCAAGAGCTGGGTTGAAGGCTCCTCCTAACCTTTTTGTGATGATGACAACACTGCTGGCCCGCAGCAACCGTTATCCTGAAATAGCCTTGTTTGTA

Basic information

species Oryza sativa
transcript LOC_Os10g26140.3
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g26140.3 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G444692_T03 (Zea mays), 3'ss of exon 5
--catttatggtgggtgctcttaagatttttatgc--aacacttcctttctttccacaaggataatacaagacaaataacaaaagcttaatttgcattttgcagTGTCTCAAGAGCTGGGTTGAAGGCTCCTCCTAACCTTTTTGTGATGATGACAACACTGCTGGCCCGCAGCAACCGTTATCCTGAAATAGCCTTGTTTGTA
  |  |||| |||  |||| ||  | ||| | |     |   |  |||   | |    |||| || ||| ||  |  ||   || ||   ||  |  |||||||||||||||  |||||| | ||||||||||  ||||||| |||||||| | | ||||| || || || |||||||||||  |||||||||| |||||||| 
ttctgttatagtgtatgct-ttgtgttttgtgtagtggatgttgtcttatctgctctcaggacaaaacaggatgagaaa---aaactatgttgtctatttgcagTGTCTCAAAGGCTGGGCTTAAGGCTCCTCACAACCTTTATGTGATGACGGCGACACTACTAGCTCGTAGCAACCGTTACGCTGAAATAGCATTGTTTGTG
















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|86502356|gb|CI144989.1|CI144989
EST:     ATGGCTGATCCTGCGTATCTTATTTCTATCATCATGGAGTTTCTACGAAG                         TGTCTCAAGAGCTGGGTTGAAGGCTCCTCCTAACCTTTTTGTGATGATGAC
genomic: ATGGCTGATCCTGCGTATCTTATTTCTATCATCATGGAGTTTCTACGAAGgtatttcttg ... cattttgcagTGTCTCAAGAGCTGGGTTGAAGGCTCCTCCTAACCTTTTTGTGATGATGAC
EST: gi|86477411|gb|CI120044.1|CI120044
EST:     ATCATCATGGAGTTTCTACGAAG                         TGTCTCAAGAGCTGGGTTGAAGGCTCCTCCTAACCTTTTTGTGATGATGAC
genomic: ATCATCATGGAGTTTCTACGAAGgtatttcttg ... cattttgcagTGTCTCAAGAGCTGGGTTGAAGGCTCCTCCTAACCTTTTTGTGATGATGAC
EST: gi|86482162|gb|CI124795.1|CI124795
EST:     ATCCTGCGTATCTTAGTTCTATCATCATGGAGTTTCTACGAAG                         TGTCTCAAGAGCTGGGTTGAAGGCTCCTCCTAACCTTTTTGTGATGATGAC
genomic: ATCCTGCGTATCTTATTTCTATCATCATGGAGTTTCTACGAAGgtatttcttg ... cattttgcagTGTCTCAAGAGCTGGGTTGAAGGCTCCTCCTAACCTTTTTGTGATGATGAC
EST: gi|86827328|gb|CI270972.1|CI270972
EST:     ATGGCTGATCCTGCGTATCTTATTTCTATCATCATGGAGTTTCTACGAAG                         TGTCTCAAGAGCTGGGTTGAAGGCTCCTCCTAACCTTTTTGTGATGATGAC
genomic: ATGGCTGATCCTGCGTATCTTATTTCTATCATCATGGAGTTTCTACGAAGgtatttcttg ... cattttgcagTGTCTCAAGAGCTGGGTTGAAGGCTCCTCCTAACCTTTTTGTGATGATGAC
EST: gi|29621826|gb|CB626837.1|CB626837
EST:     ATGGCTGATCCTGCGTATCTTATTTCTATCATCATGGAGTTTCTACGAAG                         TGTCTCAAGAGCTGGGTTGAAGGCTCCTCCTAACCTTTTTGTGATGATGAC
genomic: ATGGCTGATCCTGCGTATCTTATTTCTATCATCATGGAGTTTCTACGAAGgtatttcttg ... cattttgcagTGTCTCAAGAGCTGGGTTGAAGGCTCCTCCTAACCTTTTTGTGATGATGAC
EST: gi|87016317|gb|CI271728.1|CI271728
EST:     ATGGCTGATCCTGCGTATCTTATTTCTATCATCATGGAGTTTCTACGAAG                         TGTCTCAAGAGCTGGGTTGAAGGCTCCTCCTAACCTTTTTGTGATGATGAC
genomic: ATGGCTGATCCTGCGTATCTTATTTCTATCATCATGGAGTTTCTACGAAGgtatttcttg ... cattttgcagTGTCTCAAGAGCTGGGTTGAAGGCTCCTCCTAACCTTTTTGTGATGATGAC
EST: gi|86478805|gb|CI121438.1|CI121438
EST:     ATGGCTGATCCTGCGTATCTTATTTCTATCATCATGGAGTTTCTACGAAG                         TGTCTCAAGAGCTGGGTTGAAGGCTCCTCCTAACCTTTTTGTGATGATGAC
genomic: ATGGCTGATCCTGCGTATCTTATTTCTATCATCATGGAGTTTCTACGAAGgtatttcttg ... cattttgcagTGTCTCAAGAGCTGGGTTGAAGGCTCCTCCTAACCTTTTTGTGATGATGAC
EST: gi|286811|gb|D15618.1|D15618
EST:     ATGGCTGATCCTGCGTATCTTATTTCTATCATCATGGAGTTTCTACGAAG                         TGTCTCAAGAGCTGGGTTGAAGGCTCCTCCTAACCTTTTTGTGATGATGAC
genomic: ATGGCTGATCCTGCGTATCTTATTTCTATCATCATGGAGTTTCTACGAAGgtatttcttg ... cattttgcagTGTCTCAAGAGCTGGGTTGAAGGCTCCTCCTAACCTTTTTGTGATGATGAC
EST: gi|87016228|gb|CI271639.1|CI271639
EST:     CTATCATCATGGAGTTTCTACGAAG                         TGTCTCAAGAGCTGGGTTGAAGGCTCCTCCTAACCTTTTTGTGATGATGAC
genomic: CTATCATCATGGAGTTTCTACGAAGgtatttcttg ... cattttgcagTGTCTCAAGAGCTGGGTTGAAGGCTCCTCCTAACCTTTTTGTGATGATGAC
EST: gi|29630282|gb|CB635291.1|CB635291
EST:     TATTTCTATCATCATGGAGTTTCTACGAAG                         TGTCTCAAGAGCTGGGTTGAAGGCTCCTCCTAACCTTTTTGTGATGATGAC
genomic: TATTTCTATCATCATGGAGTTTCTACGAAGgtatttcttg ... cattttgcagTGTCTCAAGAGCTGGGTTGAAGGCTCCTCCTAACCTTTTTGTGATGATGAC
EST: gi|29669543|gb|CB665818.1|CB665818
EST:     ATGGCTGATCCTGCGTATCTTATTTCTATCATCATGGAGTTTCTACGAAG                         TGTCTCAAGAGCTGGGTTGAAGGCTCCTCCTAACCTTTTTGTGATGATGAC
genomic: ATGGCTGATCCTGCGTATCTTATTTCTATCATCATGGAGTTTCTACGAAGgtatttcttg ... cattttgcagTGTCTCAAGAGCTGGGTTGAAGGCTCCTCCTAACCTTTTTGTGATGATGAC
EST: gi|86437949|gb|CI119869.1|CI119869
EST:     ATGGCTGATCCTGCGTATCTTATTTCTATCATCATGGAGTTTCTACGAAG                         TGTCTCAAGAGCTGGGTTGAAGGCTCCTCCTAACCTTTTTGTGATGATGAC
genomic: ATGGCTGATCCTGCGTATCTTATTTCTATCATCATGGAGTTTCTACGAAGgtatttcttg ... cattttgcagTGTCTCAAGAGCTGGGTTGAAGGCTCCTCCTAACCTTTTTGTGATGATGAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctttccacaaggataatacaagacaaataacaaaagcttaatttgcattttgcagTGTCTCAAGAGCTGGGTTGAAGGCTCCTCCTAACCTTTTTGTGATGATGACAACACTGCTGGCCCGCAGCAACCGTTATCCTGAAATAGCCTTGTTTGTA
                                     ttaatttgcatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
catttatggtgggtgctcttaagatttttatgcaacacttcctttctttccacaaggataatacaagacaaataacaaaagcttaatttgcattttgcagTGTCTCAAGAGCTGGGTTGAAGGCTCCTCCTAACCTTTTTGTGATGATGACAACACTGCTGGCCCGCAGCAACCGTTATCCTGAAATAGCCTTGTTTGTA

- - - - - -ggtgctc
- - - - - - - - - - - - - -ttatgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -agacaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - taacaaa