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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttttattagatacgtcaagcataaatagactgcgaacttgtaacagtgttggcacgtactgcacatatgctcgttgctgacataatctattctacaacagGTCGTAATGATTGATGGTCGTGAAATTGGTGACGGGAAAATAGGTCCGGTCACAAGACAAATCCAGAATGCATACAAAGTCATAACTGCAGGTTCTGGAG

Basic information

species Oryza sativa
transcript LOC_Os03g24460.3
intron # 17
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g24460.3 (Oryza sativa), 3'ss of exon 17
lower sequence: GRMZM2G108416_T01 (Zea mays), 3'ss of exon 18
ttttattagatacgtcaagcataaatagactgcgaacttgtaacagtgttggcac---gtactgcacatat-gctcgttgctgacataatctattctacaacagGTCGTAATGATTGATGGTCGTGAAATTGGTGACGGGAAAATAGGTCCGGTCACAAGACAAATCCAGAATGCATACAAAGTCATAACTGCAGGTTCTGGAG
  |  ||| | | |  ||  |      ||     | |    ||| | | | ||||    || |   | ||| |||   |||||| | | | |  | |||| ||||| |||||||||||||| |||||||| || ||||||||||| ||||| ||||| |||||||||||||| ||||||||  || | || |||||    ||||
--tagttaaaaatg--aactagcggacgataaatatccgaaaacggaggtagcacccaatagttgtcgtattgctgaatgctgaaacattttgctttacatcagGTTGTAATGATTGATGGACGTGAAATCGGCGACGGGAAAATTGGTCCAGTCACTAGACAAATCCAGAAGGCATACAAGATCCTGACAGCAGGGCAAGGAG
















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|89187323|gb|CI047390.1|CI047390
EST:     GTATGGACTACTGGAACGATGGGTGAAATCACACCG                         GTCGTAATGATTGATGGTCGTGAAATTGGTGACGGGAAAATAGGTCCGGTC
genomic: GTATGGACTACTGGAACGATGGGTGAAATCACACCGgtgagtttac ... tctacaacagGTCGTAATGATTGATGGTCGTGAAATTGGTGACGGGAAAATAGGTCCGGTC
EST: gi|88278817|gb|CI397621.1|CI397621
EST:     GTATGGACTACTGGAACGATGGGTGAAATCACACCG                         GTCGTAATGATTGATGGTCGTGAAATTGGTGACGGGAAAATAGGTCCGGTC
genomic: GTATGGACTACTGGAACGATGGGTGAAATCACACCGgtgagtttac ... tctacaacagGTCGTAATGATTGATGGTCGTGAAATTGGTGACGGGAAAATAGGTCCGGTC
EST: gi|88542896|gb|CI472254.1|CI472254
EST:     GTATGGACTACTGGAACGATGGGTGAAATCACACCG                         GTCGTAATGATTGATGGTCGTGAAATTGGTGACGGGAAAATAGGTCCGGTC
genomic: GTATGGACTACTGGAACGATGGGTGAAATCACACCGgtgagtttac ... tctacaacagGTCGTAATGATTGATGGTCGTGAAATTGGTGACGGGAAAATAGGTCCGGTC
EST: gi|86869013|gb|CI335580.1|CI335580
EST:     GTATGGACTACTGGAACGATGGGTGAAATCACACCG                         GTCGTAATGATTGATGGTCGTGAAATTGGTGACGGGAAAATAGGTCCGGTC
genomic: GTATGGACTACTGGAACGATGGGTGAAATCACACCGgtgagtttac ... tctacaacagGTCGTAATGATTGATGGTCGTGAAATTGGTGACGGGAAAATAGGTCCGGTC
EST: gi|88535830|gb|CI465539.1|CI465539
EST:     ACGAGGTATGGACTACTGGAACGATGGGTGAAATCACACCG                         GTCGTAATGATTGATGGTCGTGAAATTGGTGACGGGAAAATAGGTCCGGTC
genomic: ACGAGGTATGGACTACTGGAACGATGGGTGAAATCACACCGgtgagtttac ... tctacaacagGTCGTAATGATTGATGGTCGTGAAATTGGTGACGGGAAAATAGGTCCGGTC
EST: gi|88534447|gb|CI463170.1|CI463170
EST:     ATGGGTGAAATCACACCG                         GTCGTAATGATTGATGGTCGTGAAATTGGTGACGGGAAAATAGGTCCGGTC
genomic: ATGGGTGAAATCACACCGgtgagtttac ... tctacaacagGTCGTAATGATTGATGGTCGTGAAATTGGTGACGGGAAAATAGGTCCGGTC
EST: gi|88551445|gb|CI481502.1|CI481502
EST:     GATGGGTG-AATCACACCG                         GTCGTAATGATTGATGGTCGTGAAATTGGTGACGGGAAAATAGGTCCGGTC
genomic: GATGGGTGAAATCACACCGgtgagtttac ... tctacaacagGTCGTAATGATTGATGGTCGTGAAATTGGTGACGGGAAAATAGGTCCGGTC
EST: gi|88828489|gb|CI073359.1|CI073359
EST:     GTATGGACTACTGGAACGATGGGTGGAATCACACCG                         GTCGTAATGATTGATGGTCGTGAAATTGGTGACGGGAAAATAGGTCCGGTC
genomic: GTATGGACTACTGGAACGATGGGTGAAATCACACCGgtgagtttac ... tctacaacagGTCGTAATGATTGATGGTCGTGAAATTGGTGACGGGAAAATAGGTCCGGTC
EST: gi|88541711|gb|CI470997.1|CI470997
EST:     ACTACTGGAACGATGGGTGAAATCACACCG                         GTCGTAATGATTGATGGTCGTGAAATTGGTGACGGGAAAATAGGTCCGGTC
genomic: ACTACTGGAACGATGGGTGAAATCACACCGgtgagtttac ... tctacaacagGTCGTAATGATTGATGGTCGTGAAATTGGTGACGGGAAAATAGGTCCGGTC
EST: gi|88554540|gb|CI484730.1|CI484730
EST:     GGTGAAATCACACCG                         GTCGTAATGATTGATGGTCGTGAAATTGGTGACGGGAAAATAGGTCCGGTC
genomic: GGTGAAATCACACCGgtgagtttac ... tctacaacagGTCGTAATGATTGATGGTCGTGAAATTGGTGACGGGAAAATAGGTCCGGTC
EST: gi|88523685|gb|CI451533.1|CI451533
EST:     TGGGTGAAATCACACCG                         GTCGTAATGATTGATGGTCGTGAAATTGGTGACGGGAAAATAGGTCCGGTC
genomic: TGGGTGAAATCACACCGgtgagtttac ... tctacaacagGTCGTAATGATTGATGGTCGTGAAATTGGTGACGGGAAAATAGGTCCGGTC
EST: gi|88527970|gb|CI456170.1|CI456170
EST:     GGAACGATGGGTGAAATCACACCG                         GTCGTAATGATTGATGGTCGTGAAATTGGTGACGGGAAAATAGGTCCGGTC
genomic: GGAACGATGGGTGAAATCACACCGgtgagtttac ... tctacaacagGTCGTAATGATTGATGGTCGTGAAATTGGTGACGGGAAAATAGGTCCGGTC
EST: gi|88957211|gb|CI095197.1|CI095197
EST:     GTATGGACTACTGGAACGATGGGTGAAATCACACCG                         GTCGTAATGATTGATGGTCGTGAAATTGGTGACGGGAAAATAGGTCCGGTC
genomic: GTATGGACTACTGGAACGATGGGTGAAATCACACCGgtgagtttac ... tctacaacagGTCGTAATGATTGATGGTCGTGAAATTGGTGACGGGAAAATAGGTCCGGTC
EST: gi|88263285|gb|CI367059.1|CI367059
EST:     GTATGGACTACTGGAACGATGGGTGAAATCACACCG                         CTCGTAATGATTGATGTTCGTGAAATTGGTGACGGGAAAATAGGTCCGGTC
genomic: GTATGGACTACTGGAACGATGGGTGAAATCACACCGgtgagtttac ... tctacaacagGTCGTAATGATTGATGGTCGTGAAATTGGTGACGGGAAAATAGGTCCGGTC
EST: gi|88437450|gb|CI528809.1|CI528809
EST:     GTATGGACTACTGGAACGATGGGTGAAATCACACCG                         GTCGTAATGATTGATGGTCGTGAAATTGGTGACGGGAAAATAGGTCCGGTC
genomic: GTATGGACTACTGGAACGATGGGTGAAATCACACCGgtgagtttac ... tctacaacagGTCGTAATGATTGATGGTCGTGAAATTGGTGACGGGAAAATAGGTCCGGTC
EST: gi|88958377|gb|CI095895.1|CI095895
EST:     GTATGGACTACTGGAACGATGGGTGAAATCACACCG                         GTCGTAATGATTGATGGTCGTGAAATTGGTGACGGGAAAATAGGTCCGGTC
genomic: GTATGGACTACTGGAACGATGGGTGAAATCACACCGgtgagtttac ... tctacaacagGTCGTAATGATTGATGGTCGTGAAATTGGTGACGGGAAAATAGGTCCGGTC
EST: gi|88525458|gb|CI453913.1|CI453913
EST:     GTATGGACTACTGGAACGATGGGTGAAATCACACCG                         GTCGTAATGATTGATGGTCGTGAAATTGGTGACGGGAAAATAGGTCCGGTC
genomic: GTATGGACTACTGGAACGATGGGTGAAATCACACCGgtgagtttac ... tctacaacagGTCGTAATGATTGATGGTCGTGAAATTGGTGACGGGAAAATAGGTCCGGTC
EST: gi|88545773|gb|CI475357.1|CI475357
EST:     AGGTATGGACTACTGGAACGATGGGTGAAATCACACCG                         GTCGTAATGATTGATGGTCGTGAAATTGGTGACGGGAAAATAGGTCCGGTC
genomic: AGGTATGGACTACTGGAACGATGGGTGAAATCACACCGgtgagtttac ... tctacaacagGTCGTAATGATTGATGGTCGTGAAATTGGTGACGGGAAAATAGGTCCGGTC
EST: gi|88531544|gb|CI460026.1|CI460026
EST:     GTATGGACTACTGGAACGATGGGTGAAATCACACCG                         GTCGTAATGATTGATGGTCGTGAAATTGGTGACGGGAAAATAGGTCCGGTC
genomic: GTATGGACTACTGGAACGATGGGTGAAATCACACCGgtgagtttac ... tctacaacagGTCGTAATGATTGATGGTCGTGAAATTGGTGACGGGAAAATAGGTCCGGTC
EST: gi|86433061|gb|CI093404.1|CI093404
EST:     GTATGGACTACTGGAACGATGGGTGAAATCACACCG                         GTCGTAATGATTGATGGTCGTGAAATTGGTGACGGGAAAATAGGTCCGGTC
genomic: GTATGGACTACTGGAACGATGGGTGAAATCACACCGgtgagtttac ... tctacaacagGTCGTAATGATTGATGGTCGTGAAATTGGTGACGGGAAAATAGGTCCGGTC
EST: gi|88525507|gb|CI453967.1|CI453967
EST:     ACGATGGGTGAAATCACACCG                         GTCGTAATGATTGATGGTCGTGAAATTGGTGACGGGAAAATAGGTCCGGTC
genomic: ACGATGGGTGAAATCACACCGgtgagtttac ... tctacaacagGTCGTAATGATTGATGGTCGTGAAATTGGTGACGGGAAAATAGGTCCGGTC
EST: gi|88542096|gb|CI471404.1|CI471404
EST:     TATGGACTACTGGAACGATGGGTGAAATCACACCG                         GTCGTAATGATTGATGGTCGTGAAATTGGTGACGGGAAAATAGGTCCGGTC
genomic: TATGGACTACTGGAACGATGGGTGAAATCACACCGgtgagtttac ... tctacaacagGTCGTAATGATTGATGGTCGTGAAATTGGTGACGGGAAAATAGGTCCGGTC
EST: gi|86426440|gb|CI071537.1|CI071537
EST:     GTATGGACTACTGGAACGATGGGTGAAATCACACCG                         GTCGTAATGATTGATGGTCGTGATATTGGTGACGGGAAAATAGGTCCGGTC
genomic: GTATGGACTACTGGAACGATGGGTGAAATCACACCGgtgagtttac ... tctacaacagGTCGTAATGATTGATGGTCGTGAAATTGGTGACGGGAAAATAGGTCCGGTC
EST: gi|88539468|gb|CI469423.1|CI469423
EST:     TGGGTGAAATCACACCG                         GTCGTAATGATTGATGGTCGTGAAATTGGTGACGGGAAAATAGGTCCGGTC
genomic: TGGGTGAAATCACACCGgtgagtttac ... tctacaacagGTCGTAATGATTGATGGTCGTGAAATTGGTGACGGGAAAATAGGTCCGGTC
EST: gi|88543623|gb|CI473647.1|CI473647
EST:     TGCAGACGAGGTATGGACTACTGGAACGATGGGTGAAATCACACCG                         GTCGTAATGATTGATGGTCGTGAAATTGGTGACGGGAAAATAGGTCCGGTC
genomic: TGCAGACGAGGTATGGACTACTGGAACGATGGGTGAAATCACACCGgtgagtttac ... tctacaacagGTCGTAATGATTGATGGTCGTGAAATTGGTGACGGGAAAATAGGTCCGGTC
EST: gi|88556968|gb|CI487334.1|CI487334
EST:     CTGGAACGATGGGTGAAATCACACCG                         TTCGTAATGATTGATGGTCGTGAAATTGGTGACGGGAAAATAGGTCCGGTC
genomic: CTGGAACGATGGGTGAAATCACACCGgtgagtttac ... tctacaacagGTCGTAATGATTGATGGTCGTGAAATTGGTGACGGGAAAATAGGTCCGGTC
EST: gi|88541495|gb|CI470767.1|CI470767
EST:     GTATGGACTACTGGAACGATGGGTGAAATCACACCG                         GTCGTAATGATTGATGGTCGTGAAATTGGTGACGGGAAAATAGGTCCGGTC
genomic: GTATGGACTACTGGAACGATGGGTGAAATCACACCGgtgagtttac ... tctacaacagGTCGTAATGATTGATGGTCGTGAAATTGGTGACGGGAAAATAGGTCCGGTC
EST: gi|88536060|gb|CI465783.1|CI465783
EST:     GACGAGGTATGGACTACTGGAACGATGGGTGAAATCACACCG                         GTCGTAATGATTGATGGTCGTGAAATTGGTGACGGGAAAATAGGTCCGGTC
genomic: GACGAGGTATGGACTACTGGAACGATGGGTGAAATCACACCGgtgagtttac ... tctacaacagGTCGTAATGATTGATGGTCGTGAAATTGGTGACGGGAAAATAGGTCCGGTC
EST: gi|88278792|gb|CI397596.1|CI397596
EST:     GTATGGACTACTGGAACGATGGGTGAAATCACACCG                         GTCGTAATGATTGATGGTCGTGAAATTGGTGACGGGAAAATAGGTCCGGTC
genomic: GTATGGACTACTGGAACGATGGGTGAAATCACACCGgtgagtttac ... tctacaacagGTCGTAATGATTGATGGTCGTGAAATTGGTGACGGGAAAATAGGTCCGGTC
EST: gi|88548475|gb|CI476851.1|CI476851
EST:     GTATGGACTACTGGAACGATGGGTGAAATCACACCG                         GTCGTAATGATTGATGGTCGTGAAATTGGTGACGGGAAAATAGGTCCGGTC
genomic: GTATGGACTACTGGAACGATGGGTGAAATCACACCGgtgagtttac ... tctacaacagGTCGTAATGATTGATGGTCGTGAAATTGGTGACGGGAAAATAGGTCCGGTC
EST: gi|88964563|gb|CI069911.1|CI069911
EST:     GTATGGACTACTGGAACGATGGGTGAAATCACACCG                         GTCGTAATGATTGATGGTCGTGAAATTGGTGACGGGAAAATAGGTCCGGTC
genomic: GTATGGACTACTGGAACGATGGGTGAAATCACACCGgtgagtttac ... tctacaacagGTCGTAATGATTGATGGTCGTGAAATTGGTGACGGGAAAATAGGTCCGGTC
EST: gi|88551624|gb|CI481698.1|CI481698
EST:     CGATGGGTGAAATCACACCG                         GTCGTAATGATTGATGGTCGTGAAATTGGTGACGGGAAAATAGGTCCGGTC
genomic: CGATGGGTGAAATCACACCGgtgagtttac ... tctacaacagGTCGTAATGATTGATGGTCGTGAAATTGGTGACGGGAAAATAGGTCCGGTC
EST: gi|88482389|gb|CI419660.1|CI419660
EST:     GGAACGATGGGTGAAATCACACCG                         GTCGTAATGATTGATGGTCGTNAAATTGGTGACGGGAAAATAGGTCCGGTC
genomic: GGAACGATGGGTGAAATCACACCGgtgagtttac ... tctacaacagGTCGTAATGATTGATGGTCGTGAAATTGGTGACGGGAAAATAGGTCCGGTC
EST: gi|88536166|gb|CI465895.1|CI465895
EST:     CTACTGGAACGATGGGTGAAATCACACCG                         GTCGTAATGATTGATGTTCGTGAAATTGGTGACGGGAAAATAGGTCCGGTC
genomic: CTACTGGAACGATGGGTGAAATCACACCGgtgagtttac ... tctacaacagGTCGTAATGATTGATGGTCGTGAAATTGGTGACGGGAAAATAGGTCCGGTC
EST: gi|88548070|gb|CI476983.1|CI476983
EST:     TACTGGAACGATGGGTGAAATCACACCG                         GTCGTAATGATTGATGGTCGTGAAATTGGTGACGGGAAAATAGGTCCGGTC
genomic: TACTGGAACGATGGGTGAAATCACACCGgtgagtttac ... tctacaacagGTCGTAATGATTGATGGTCGTGAAATTGGTGACGGGAAAATAGGTCCGGTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgttggcacgtactgcacatatgctcgttgctgacataatctattctacaacagGTCGTAATGATTGATGGTCGTGAAATTGGTGACGGGAAAATAGGTCCGGTCACAAGACAAATCCAGAATGCATACAAAGTCATAACTGCAGGTTCTGGAG
                             tgctgac  putative branch site (score: 2)
                                        tctattct  putative PPT
                                    ataatctatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttttattagatacgtcaagcataaatagactgcgaacttgtaacagtgttggcacgtactgcacatatgctcgttgctgacataatctattctacaacagGTCGTAATGATTGATGGTCGTGAAATTGGTGACGGGAAAATAGGTCCGGTCACAAGACAAATCCAGAATGCATACAAAGTCATAACTGCAGGTTCTGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG