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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagaaactagaaaaacttcatgattcctcgctcatattttccttgcgtcaaaattctgaaggttcatttaaccttagttgttctgtccttcagCTGATGGGAGCAGTAAATTCTGAAAGTTTACTCGGAGG

Basic information

species Oryza sativa
transcript LOC_Os07g04990.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g04990.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G111954_T03 (Zea mays), 3'ss of exon 2
gtaagaaactagaa-----aaacttcatgattcctcgctcatattttcct--tgcgtcaaa----attctgaaggttcatttaaccttagtt-------gttctgtccttcagCTGATGGGAGCAGTAAATTCTGAAAGTTTACTCGGAGG
||||||||||| |      || || ||| ||  ||| |||||  || |||  | |  || |     |||||||||  ||  |     ||  |       |||||||||| ||||||||||||||||| |||||||||| |||||| |||||
gtaagaaactaaactaaacaagctacat-atagctcactcattcttccctgctcctccagattcagttctgaaggcacacctgtatctaactaagaatggttctgtcctacagCTGATGGGAGCAGTCAATTCTGAAACTTTACTAGGAGG
















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|38478740|gb|CF962873.1|CF962873
EST:     TAGATAATGGGATGACCTTATTTGATACAGCAGAAGTTTATGGTACAGCG                         CTGATGGGAGCAGTAAATTCTGAAAGTTTACTCGGAGG
genomic: TAGATAATGGGATGACCTTATTTGATACAGCAGAAGTTTATGGTACAGCGgtaagaaact ... tgtccttcagCTGATGGGAGCAGTAAATTCTGAAAGTTTACTCGGAGG
EST: gi|38477681|gb|CF961814.1|CF961814
EST:     TAGAT-ATGGGATGACCTTATTTGATACAGCAGAAGTTTATGGTACAGCG                         CTGATGGGAGCAGTAAATTCTGAAAGTTTACTCGGAGG
genomic: TAGATAATGGGATGACCTTATTTGATACAGCAGAAGTTTATGGTACAGCGgtaagaaact ... tgtccttcagCTGATGGGAGCAGTAAATTCTGAAAGTTTACTCGGAGG
EST: gi|58586534|gb|CF984842.1|CF984842
EST:     TAGATAATGGGATGACCTTATTTGATACAGCAGAAGTTTATGGTACAGCG                         CTGATGGGAGCAGTAAATTCTGAAAGTTTACTCGGAGG
genomic: TAGATAATGGGATGACCTTATTTGATACAGCAGAAGTTTATGGTACAGCGgtaagaaact ... tgtccttcagCTGATGGGAGCAGTAAATTCTGAAAGTTTACTCGGAGG
EST: gi|58605103|gb|CK033136.1|CK033136
EST:     TAGATAATGGGATGACCTTATTTGATGCGGCAGAAGTTTATGGTACAGCG                         CTGATGGGAGCAGTAAATTCTGAAAGTTTACTCGGAGG
genomic: TAGATAATGGGATGACCTTATTTGATACAGCAGAAGTTTATGGTACAGCGgtaagaaact ... tgtccttcagCTGATGGGAGCAGTAAATTCTGAAAGTTTACTCGGAGG
EST: gi|58590950|gb|CF989258.1|CF989258
EST:     TAGATAATGGGATGACCTTATTTGATACAGCAGAAGTTTATGGTACAGCG                         CTGATGGGAGCAGTAAATTCTGGGAAGTTTACTCGGAGG
genomic: TAGATAATGGGATGACCTTATTTGATACAGCAGAAGTTTATGGTACAGCGgtaagaaact ... tgtccttcagCTGATGGGAGCAGTAAATTCT-GAAAGTTTACTCGGAGG
EST: gi|58592358|gb|CF990666.1|CF990666
EST:     TAGAT-ATGGGATGAGCTTATTTGATACAGCAGAAGTTTATGGTACAGCG                         CTGATGGGAGCAGTAAATTCTGAAAGTTTACTCGGAGG
genomic: TAGATAATGGGATGACCTTATTTGATACAGCAGAAGTTTATGGTACAGCGgtaagaaact ... tgtccttcagCTGATGGGAGCAGTAAATTCTGAAAGTTTACTCGGAGG
EST: gi|29685611|gb|CB681886.1|CB681886
EST:     TAGATAATGGGATGACCTTATTTGATACAGCAGAAGTTTATGGTACAGCG                         CTGATGGGAGCAGTAAATTCTGAAAGTTTACTCGGAGG
genomic: TAGATAATGGGATGACCTTATTTGATACAGCAGAAGTTTATGGTACAGCGgtaagaaact ... tgtccttcagCTGATGGGAGCAGTAAATTCTGAAAGTTTACTCGGAGG
EST: gi|38469835|gb|CF953966.1|CF953966
EST:     TAGATAATGGGATGACCTTATTTGATACAGCAGAAGTTTATGGTACAGCG                         CTGATGGGAGCAGTAAATTCTGAAAGTTTACTCGGAGG
genomic: TAGATAATGGGATGACCTTATTTGATACAGCAGAAGTTTATGGTACAGCGgtaagaaact ... tgtccttcagCTGATGGGAGCAGTAAATTCTGAAAGTTTACTCGGAGG
EST: gi|38483088|gb|CF966890.1|CF966890
EST:     TAGAT-ATGGGATGACCTTATTTGATACAGCAGAAGTTTATGGTACAGCG                         CTGAT-GGAGCAGTAAATTCTGAAAGTTTACTCGGAGG
genomic: TAGATAATGGGATGACCTTATTTGATACAGCAGAAGTTTATGGTACAGCGgtaagaaact ... tgtccttcagCTGATGGGAGCAGTAAATTCTGAAAGTTTACTCGGAGG
EST: gi|58589665|gb|CF987973.1|CF987973
EST:     TAGATAATGGGATGACCTTATTTGATACAGCAGAAGTTTATGGTACAGCG                         CTGATGGGAGCAGTAAATTCTGAAAGTGGACTCGGAGG
genomic: TAGATAATGGGATGACCTTATTTGATACAGCAGAAGTTTATGGTACAGCGgtaagaaact ... tgtccttcagCTGATGGGAGCAGTAAATTCTGAAAGTTTACTCGGAGG
EST: gi|38480259|gb|CF964348.1|CF964348
EST:     TAGATAATGGGATGACCTTATTTGATACAGCAGAAGTTTATGGTACAGCG                         CTGATGGGAGCAGTAAATTCTGAAAGTTTACTCGGGGG
genomic: TAGATAATGGGATGACCTTATTTGATACAGCAGAAGTTTATGGTACAGCGgtaagaaact ... tgtccttcagCTGATGGGAGCAGTAAATTCTGAAAGTTTACTCGGAGG

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 75 (upstream exon), 38 (downstream exon)
Score: 94

ACAGGAGACTGCAGGAGGCTAAAGCAGCATTTGACACAAGCATAGATAATGGGATGACCTTATTTGATACAGCAGAAGTTTATGGTACAGCGgtaagaaact ... tgtccttcagCTGATGGGAGCAGTAAATTCTGAAAGTTTACTCGGAGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttccttgcgtcaaaattctgaaggttcatttaaccttagttgttctgtccttcagCTGATGGGAGCAGTAAATTCTGAAAGTTTACTCGGAGG
                           atttaac  putative branch site (score: 94)
                                       ttgttctgtccttc  putative PPT
                        ttcatttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagaaactagaaaaacttcatgattcctcgctcatattttccttgcgtcaaaattctgaaggttcatttaaccttagttgttctgtccttcagCTGATGGGAGCAGTAAATTCTGAAAGTTTACTCGGAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG