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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgtagagacatgaccttattcacatcatcactattttgggtgctaatgtgatgctgtttagttaatctatcctggagtaacaaatttgttattttcgcagGTCTACAGTGACTTGACTGTCGATTACTTCAAGATGTTCCTGCTAAATGTTCCAGCAGCAGTTTTAGCTCTGACACT

Basic information

species Oryza sativa
transcript LOC_Os08g41460.6
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g41460.8 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM5G885392_T01 (Zea mays), 3'ss of exon 4
--tgtagagacatgacc-ttattcacatcatcactattttgggtgctaatgtgatgctgtttagttaatctatcctggagtaacaaatttgttatttt-cgcagGTCTACAGTGACTTGACTGTCGATTACTTCAAGATGTTCCTGCTAAATGTTCCAGCAGCAGTTTTAGCTCTGACACT
  | |    | || ||  ||||| | ||       | ||    |||  | || |      || |  ||   || ||| | |     || ||  |||||  |||||||||||||||||||||||| || ||||| |||||||| || ||||||||||| ||||| ||| |||||||| ||||
tatatgacaaaattactattattaaaatggaattcaattcctatgcgtaagtaaattgagttggagaaga-attctgaactt---tatatggaattttgtgcagGTCTACAGTGACTTGACTGTTGACTACTTGAAGATGTTGCTCCTAAATGTTCCCGCAGCTGTTGTAGCTCTGGCACT
















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|29625905|gb|CB630916.1|CB630916
EST:     GAAGTGAAATCGTACAAGAAGGTCCAAGATGCAGTCTTCGAAGTCGAAAG                         GTCTACAGTGACTTGACTGTCGATTACTTCAAGATGTTCCTGCTAAATGTT
genomic: GAAGTGAAATCGTACAAGAAGGTCCAAGATGCAGTCTTCGAAGTCGAAAGgttgggattg ... attttcgcagGTCTACAGTGACTTGACTGTCGATTACTTCAAGATGTTCCTGCTAAATGTT
EST: gi|29683116|gb|CB679391.1|CB679391
EST:     GAAGTGAAATCGTACAAGAAGGTCCAAGATGCAGTCTTCGAAGTCGAAAG                         GTCTACAGTGACTTGACTGTCGATTACTTCAAGATGTTCCTGCTAAATGTT
genomic: GAAGTGAAATCGTACAAGAAGGTCCAAGATGCAGTCTTCGAAGTCGAAAGgttgggattg ... attttcgcagGTCTACAGTGACTTGACTGTCGATTACTTCAAGATGTTCCTGCTAAATGTT
EST: gi|58595312|gb|CF993620.1|CF993620
EST:     GAAGTGAAATCGTACAAGAAGGTCCAAGATGCAGTCTTCGAAGTCGAAAG                         GTCTACAGTGACTTGACTGTCGATTACTTCAAGATGTTCCTGCTAAATGTT
genomic: GAAGTGAAATCGTACAAGAAGGTCCAAGATGCAGTCTTCGAAGTCGAAAGgttgggattg ... attttcgcagGTCTACAGTGACTTGACTGTCGATTACTTCAAGATGTTCCTGCTAAATGTT
EST: gi|29684942|gb|CB681217.1|CB681217
EST:     GAAGTGAAATCGTACAAGAAGGTCCAAGATGCAGTCTTCGAAGTCGAAAG                         GTCTACAGTGACTTGACTGTCGATTACTTCAAGATGTTCCTGCTAAATGTT
genomic: GAAGTGAAATCGTACAAGAAGGTCCAAGATGCAGTCTTCGAAGTCGAAAGgttgggattg ... attttcgcagGTCTACAGTGACTTGACTGTCGATTACTTCAAGATGTTCCTGCTAAATGTT
EST: gi|38474705|gb|CF958838.1|CF958838
EST:     GAAGTGAAATCGTACAAGAAGGTCCAAGATGCAGTCTTCGAAGTCGAAAG                         GTCTACAGTGACTTGACTGTCGATTACTTCAAGATGTTCCTGCTAAATGTT
genomic: GAAGTGAAATCGTACAAGAAGGTCCAAGATGCAGTCTTCGAAGTCGAAAGgttgggattg ... attttcgcagGTCTACAGTGACTTGACTGTCGATTACTTCAAGATGTTCCTGCTAAATGTT
EST: gi|87029164|gb|CI276432.1|CI276432
EST:     GTGAAATCGTACAAGAAGGTCCAAGATGCAGTCTTCGAAGTCGAAAG                         GTCTACAGTGACTTGACTGTCGATTACTTCAAGATGTTCCTGCTAAATGTT
genomic: GTGAAATCGTACAAGAAGGTCCAAGATGCAGTCTTCGAAGTCGAAAGgttgggattg ... attttcgcagGTCTACAGTGACTTGACTGTCGATTACTTCAAGATGTTCCTGCTAAATGTT
EST: gi|29662553|gb|CB658828.1|CB658828
EST:     GAAGTGAAATCGTACAAGAAGGTCCAAGATGCAGTCTTCGAAGTCGAAAG                         GTCTACAGTGACTTGACTGTCGATTACTTCAAGATGTTCCTGCTAAATGTT
genomic: GAAGTGAAATCGTACAAGAAGGTCCAAGATGCAGTCTTCGAAGTCGAAAGgttgggattg ... attttcgcagGTCTACAGTGACTTGACTGTCGATTACTTCAAGATGTTCCTGCTAAATGTT
EST: gi|29683115|gb|CB679390.1|CB679390
EST:     GAAGTGAAATCGTACAAGAAGGTCCAAGATGCAGTCTTCGAAGTCGAAAG                         GTCTACAGTGACTTGACTGTCGATTACTTCAAGATGTTCCTGCTAAATGTT
genomic: GAAGTGAAATCGTACAAGAAGGTCCAAGATGCAGTCTTCGAAGTCGAAAGgttgggattg ... attttcgcagGTCTACAGTGACTTGACTGTCGATTACTTCAAGATGTTCCTGCTAAATGTT
EST: gi|25806680|gb|CA762641.1|CA762641
EST:     GGTCCAAGATGCAGTCTTCGAAGTCGAAAG                         GTCTACAGTGACTTGACTGTCGATTACTTCAAGATGTTCCTGCTAAATGTT
genomic: GGTCCAAGATGCAGTCTTCGAAGTCGAAAGgttgggattg ... attttcgcagGTCTACAGTGACTTGACTGTCGATTACTTCAAGATGTTCCTGCTAAATGTT
EST: gi|29663222|gb|CB659497.1|CB659497
EST:     GAAGTGAAATCGTACAAGAAGGTCCAAGATGCAGTCTTCGAAGTCGAAAG                         GTCTACAGTGACTTGACTGTCGATTACTTCAAGATGTTCCTGCTAAATGTT
genomic: GAAGTGAAATCGTACAAGAAGGTCCAAGATGCAGTCTTCGAAGTCGAAAGgttgggattg ... attttcgcagGTCTACAGTGACTTGACTGTCGATTACTTCAAGATGTTCCTGCTAAATGTT
EST: gi|163920678|gb|EG710011.1|EG710011
EST:     GAAGTGAAATCGTACAAGAAGGTCCAAGATGCAGTCTTCGAAGTCGAAAG                         GTCTACAGTGACTTGACTGTCGATTACTTCAAGATGTTCCTGCTAAATGTT
genomic: GAAGTGAAATCGTACAAGAAGGTCCAAGATGCAGTCTTCGAAGTCGAAAGgttgggattg ... attttcgcagGTCTACAGTGACTTGACTGTCGATTACTTCAAGATGTTCCTGCTAAATGTT
EST: gi|29615644|gb|CB620656.1|CB620656
EST:     GAAGTGAAATCGTACAAGAAGGTCCAAGATGCAGTCTTCGAAGTCGAAAG                         GTCTACAGTGACTTGACTGTCGATTACTTCAAGATGTTCCTGCTAAATGTT
genomic: GAAGTGAAATCGTACAAGAAGGTCCAAGATGCAGTCTTCGAAGTCGAAAGgttgggattg ... attttcgcagGTCTACAGTGACTTGACTGTCGATTACTTCAAGATGTTCCTGCTAAATGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgtgatgctgtttagttaatctatcctggagtaacaaatttgttattttcgcagGTCTACAGTGACTTGACTGTCGATTACTTCAAGATGTTCCTGCTAAATGTTCCAGCAGCAGTTTTAGCTCTGACACT
                             gagtaac  putative branch site (score: 2)
                                           ttattttc  putative PPT
                                taacaaatttgttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgtagagacatgaccttattcacatcatcactattttgggtgctaatgtgatgctgtttagttaatctatcctggagtaacaaatttgttattttcgcagGTCTACAGTGACTTGACTGTCGATTACTTCAAGATGTTCCTGCTAAATGTTCCAGCAGCAGTTTTAGCTCTGACACT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG