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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgatgttgtaatcaacattttttttgttctaaatttgtttgaagttgttccgacaaagtacatatactttgtttactcagaggaactcttggctgataatttgttacacacagttaacaattaaaaccatatatcactaattcccatattcacacttttaaagCCAGGAGAGTCACTAAAAGATTTCTACAAGAGAACGGATATGTACTGGCAGATGGCTGCATATGAGCACACTCAACACACTGGAAAG

Basic information

species Oryza sativa
transcript LOC_Os04g40740.3
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g40740.3 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G100815_T01 (Zea mays), 3'ss of exon 14
gtgatgttgtaatcaacatt-----ttttttgt----tctaaatttgtttgaagttgttccgacaaa--------gtacatatactt---tgtttactca-gaggaactcttggctgataatttgttacacacagttaacaa--ttaaaaccatatatcactaat--tcccatattcacacttttaaagCCAGGAGAGTCACTAAAAGATTTCTACAAGAGAACGGATATGTACTGGCAGATGGCTGCATATGAGCACACTCAACACACTGGAAAG
|| |||||||| | |   ||     |||| |||    |||| |||| ||        || |   |          || |||||  |    ||| |  ||  ||  || || ||||  |  ||| |||||   ||||||||||    || |   | | |  || ||  |  | | |    | | | |||||| ||||| ||||| | ||||||||||||||| ||  ||||||||||||| |||||||| |||||||||||||||||||||||||||
gtaatgttgtacttagttttgtttattttctgtcacttctagatttattgctttccttttcattagctggctcctgtccatatcatcatatgtctgttctcgaacaaatcatggccaaccattcgttacctgcagttaacaaaaccaagatattgttttgcttatattttcttttgtttattctgaaagCCTGGAGAATCACTGAGAGATTTCTACAAGAGGACAAATATGTACTGGCAAATGGCTGCCTATGAGCACACTCAACACACTGGAAAG

upper sequence: LOC_Os04g40740.3 (Oryza sativa), 3'ss of exon 9
lower sequence: Vv17s0000g10130.t01 (Vitis vinifera), 3'ss of exon 17
gtgatgttgtaatcaacattttttttgttctaaatttgtttgaagttgttccgacaaagtacatatactttgtttactcagaggaactcttggctgataatttgttacacacagttaacaattaaaaccatatatcactaattcccatattcacacttttaaagCCAGGAGAGTCACTAAAAGATTTCTACAAGAGAACGGATATGTACTGGCAGATGGCTGCATATGAGCACACTCAACACACTGGAAAG
                                                               | |   ||||  |   | ||| ||  ||        |||  || ||     |  |  ||||       |  | | |  ||  ||| |  |   || | ||||| |||||  |  | || || ||||| ||| | ||  || |||||||||| ||||| ||| ||||||||||||||||||||||||||
--------------------------------------------------------------ttttgtgttgtgcatctaaaggcacatttaaact-ccattcttttcatctcatccatcattactttgtcaactgattgcttatcatttgtat-tttgtgaagCCTGGAGAAACCTTGAAGGACTTCTATAAGCGTACCAATTTGTACTGGCAAATGGCAGCACATGAGCACACTCAACACACTGGAAAG
















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|86534966|gb|CI175172.1|CI175172
EST:     AAGGACTCCAATG                         CCAGGAGAGTCACTAAAAGATTTCTACAAGAGAACGGATATGTACTGGCAG
genomic: AAGGACTCCAATGgtgatgttgt ... acttttaaagCCAGGAGAGTCACTAAAAGATTTCTACAAGAGAACGGATATGTACTGGCAG
EST: gi|89175699|gb|CI042720.1|CI042720
EST:     GGTTATGCTCGGTCTTTCTGATTCTCAAAGGACTCCAATG                         CCAGGAGAGTCACTAAAAGATTTCTACAAGAGAACGGATATGTACTGGCAG
genomic: GGTTATGCTCGGTCTTTCTGATTCTCAAAGGACTCCAATGgtgatgttgt ... acttttaaagCCAGGAGAGTCACTAAAAGATTTCTACAAGAGAACGGATATGTACTGGCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cacagttaacaattaaaaccatatatcactaattcccatattcacacttttaaagCCAGGAGAGTCACTAAAAGATTTCTACAAGAGAACGGATATGTACTGGCAGATGGCTGCATATGAGCACACTCAACACACTGGAAAG
                          cactaat  putative branch site (score: 2)
                                            cactttt  putative PPT
     ttaacaattaaaacca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgatgttgtaatcaacattttttttgttctaaatttgtttgaagttgttccgacaaagtacatatactttgtttactcagaggaactcttggctgataatttgttacacacagttaacaattaaaaccatatatcactaattcccatattcacacttttaaagCCAGGAGAGTCACTAAAAGATTTCTACAAGAGAACGGATATGTACTGGCAGATGGCTGCATATGAGCACACTCAACACACTGGAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG