Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttaggtcactttcgttaacaacaactagcaaattatatcacactacaaatattaagttccttgcggtaataattttaactgaggtgtgttctgtagGATGGGAAGATAAGCTACGAGGAGTTTGAGTTAATGATGTCAGCCGGAATGGACTGGAGGAATGCATCCCGGCAATACTCGAGAGCAGTTTACAACACTC

Basic information

species Oryza sativa
transcript LOC_Os12g12860.1
intron # 7
splice site 3'
intron type U2

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|89164851|gb|CI101939.1|CI101939
EST:     GTGACCAGAAGTCGATCGACGACATATTTCTGGATGTTGACATAGACAAG                         GATGGGAAGATAAGCTACGAGGAGTTTGAGTTAATGATGTCAGCCGGAATG
genomic: GTGACCAGAAGTCGATCGACGACATATTTCTGGATGTTGACATAGACAAGgttaggtcac ... tgttctgtagGATGGGAAGATAAGCTACGAGGAGTTTGAGTTAATGATGTCAGCCGGAATG
EST: gi|89163412|gb|CI100302.1|CI100302
EST:     GTGACCAGAAGTCGATCGACGACATATTTCTGGATGTTGACATAGACAAG                         GATGGGAAGATAAGCTACGAGGAGTTTGAGTTAATGATGTCAGCCGGAATG
genomic: GTGACCAGAAGTCGATCGACGACATATTTCTGGATGTTGACATAGACAAGgttaggtcac ... tgttctgtagGATGGGAAGATAAGCTACGAGGAGTTTGAGTTAATGATGTCAGCCGGAATG
EST: gi|89165462|gb|CI102552.1|CI102552
EST:     GTGACCAGAAGTCGATCGACGACATATTTCTGGATGTTGACATAGACAAG                         GATGGGAAGATAAGCTACGAGGAGTTTGAGTTAATGATGTCAGCCGGAATG
genomic: GTGACCAGAAGTCGATCGACGACATATTTCTGGATGTTGACATAGACAAGgttaggtcac ... tgttctgtagGATGGGAAGATAAGCTACGAGGAGTTTGAGTTAATGATGTCAGCCGGAATG
EST: gi|89162277|gb|CI104605.1|CI104605
EST:     GTGACCAGAAGTCGATCGACGACATATTTCTGGATGTTGACATAGACAAG                         GATGGGAAGATAAGCTACGAGGAGTTTGAGTNAATGATGTCAGCCGGAATG
genomic: GTGACCAGAAGTCGATCGACGACATATTTCTGGATGTTGACATAGACAAGgttaggtcac ... tgttctgtagGATGGGAAGATAAGCTACGAGGAGTTTGAGTTAATGATGTCAGCCGGAATG
EST: gi|89166339|gb|CI103429.1|CI103429
EST:     GTGACCAGAAGTCGATCGACGACATATTTCTGGATGTTGACATAGACAAG                         GATGGGAAGATAAGCTACGAGGAGTTTGAGTTAATGATGTCAGCCGGAATG
genomic: GTGACCAGAAGTCGATCGACGACATATTTCTGGATGTTGACATAGACAAGgttaggtcac ... tgttctgtagGATGGGAAGATAAGCTACGAGGAGTTTGAGTTAATGATGTCAGCCGGAATG
EST: gi|89163359|gb|CI100249.1|CI100249
EST:     GACCAGAAGTCGATCGACGACATATTTCTGGATGTTGACATAGACAAG                         GATGGGAAGATAAGCTACGAGGAGTTTGAGTTAATGATGTCAGCCGGAATG
genomic: GACCAGAAGTCGATCGACGACATATTTCTGGATGTTGACATAGACAAGgttaggtcac ... tgttctgtagGATGGGAAGATAAGCTACGAGGAGTTTGAGTTAATGATGTCAGCCGGAATG
EST: gi|89163563|gb|CI100453.1|CI100453
EST:     GTGACCAGAAGTCGATCGACGACATATTTCTGGATGTTGACATAGACAAG                         GATGGGAAGATAAGCTACGAGGAGTTTGAGTTAATGATGTCAGCCGGAATG
genomic: GTGACCAGAAGTCGATCGACGACATATTTCTGGATGTTGACATAGACAAGgttaggtcac ... tgttctgtagGATGGGAAGATAAGCTACGAGGAGTTTGAGTTAATGATGTCAGCCGGAATG
EST: gi|25803739|gb|CA759700.1|CA759700
EST:     GTGACCAGAAGTCGATCGACGACATATTTCTGGATGTTGACATAGACAAG                         GATGGGAAGATAAGCTACGAGGAGTTTGAGTTAATGATGTCAGCCGGAATG
genomic: GTGACCAGAAGTCGATCGACGACATATTTCTGGATGTTGACATAGACAAGgttaggtcac ... tgttctgtagGATGGGAAGATAAGCTACGAGGAGTTTGAGTTAATGATGTCAGCCGGAATG
EST: gi|89164496|gb|CI101584.1|CI101584
EST:     GTGACCAGAAGTCGATCGACGACATATTTCTGGATGTTGACATAGACAAG                         GATGGGAAGATAAGCTACGAGGAGTTTGAGTTAATGATGTCAGCCGGAATG
genomic: GTGACCAGAAGTCGATCGACGACATATTTCTGGATGTTGACATAGACAAGgttaggtcac ... tgttctgtagGATGGGAAGATAAGCTACGAGGAGTTTGAGTTAATGATGTCAGCCGGAATG
EST: gi|2317460|gb|C22514.1|C22514
EST:     GTGACCAGAAGTCGATCGACGACATATTTCTGGATGTTGACATAGACAAG                         GATGGGAAGATAAGCTACGAGGAGTTTGAGTTAATGATGTCAGCCGGAATG
genomic: GTGACCAGAAGTCGATCGACGACATATTTCTGGATGTTGACATAGACAAGgttaggtcac ... tgttctgtagGATGGGAAGATAAGCTACGAGGAGTTTGAGTTAATGATGTCAGCCGGAATG
EST: gi|86855791|gb|CI271010.1|CI271010
EST:     GTGACCAGAAGTCGATCGACGACATATTTCTGGATGTTGACATAGACAAG                         GATGGGAAGATAAGCTACGAGGAGTTTGAGTTAATGATGTCAGCCGGAATG
genomic: GTGACCAGAAGTCGATCGACGACATATTTCTGGATGTTGACATAGACAAGgttaggtcac ... tgttctgtagGATGGGAAGATAAGCTACGAGGAGTTTGAGTTAATGATGTCAGCCGGAATG
EST: gi|87029795|gb|CI274476.1|CI274476
EST:     GTGACCAGAAGTCGATCGACGACATATTTCTGGATGTTGACATAGACAAG                         GATGGGAAGATAAGCTACGAGGAGTTTGAGTTAATGATGTCAGCCGGAATG
genomic: GTGACCAGAAGTCGATCGACGACATATTTCTGGATGTTGACATAGACAAGgttaggtcac ... tgttctgtagGATGGGAAGATAAGCTACGAGGAGTTTGAGTTAATGATGTCAGCCGGAATG
EST: gi|89166572|gb|CI103858.1|CI103858
EST:     GTGACCAGAAGTCGATCGACGACATATTTCTGGATGTTGACATAGACAAG                         GATGGGAAGATAAGCTACGAGGAGTTTGAGTTAATGATGTCAGCCGGAATG
genomic: GTGACCAGAAGTCGATCGACGACATATTTCTGGATGTTGACATAGACAAGgttaggtcac ... tgttctgtagGATGGGAAGATAAGCTACGAGGAGTTTGAGTTAATGATGTCAGCCGGAATG
EST: gi|89167214|gb|CI104500.1|CI104500
EST:     GAAGTCGATCGACGACATATTTCTGGATGTTGACATAGACAAG                         GATGGGAAGATAAGCTACGAGGAGTTTGAGTTAATGATGTCAGCCGGAATG
genomic: GAAGTCGATCGACGACATATTTCTGGATGTTGACATAGACAAGgttaggtcac ... tgttctgtagGATGGGAAGATAAGCTACGAGGAGTTTGAGTTAATGATGTCAGCCGGAATG
EST: gi|86485531|gb|CI128164.1|CI128164
EST:     CAGAAGTCGATCGACGACATATTTCTGGATGTTGACATAGACAAG                         GATGGGAAGATAAGCTACGAGGAGTTTGAGTTAATGATGTCAGCCGGAATG
genomic: CAGAAGTCGATCGACGACATATTTCTGGATGTTGACATAGACAAGgttaggtcac ... tgttctgtagGATGGGAAGATAAGCTACGAGGAGTTTGAGTTAATGATGTCAGCCGGAATG
EST: gi|88223308|gb|CI223157.1|CI223157
EST:     GTGACCAGAAGTCGATCGACGACATATTTCTGGATGTTGACATAGACAAG                         GATGGGAAGATAAGCTACGAGGAGTTTGAGTTAATGATGTCAGCCGGAATG
genomic: GTGACCAGAAGTCGATCGACGACATATTTCTGGATGTTGACATAGACAAGgttaggtcac ... tgttctgtagGATGGGAAGATAAGCTACGAGGAGTTTGAGTTAATGATGTCAGCCGGAATG
EST: gi|89162922|gb|CI099812.1|CI099812
EST:     GTGACCAGAAGTCGATCGACGACATATTTCTGGATGTTGACATAGACAAG                         GATGGGAAGATAAGCTACGAGGAGTTTGAGTTAATGATGTCAGCCGGAATG
genomic: GTGACCAGAAGTCGATCGACGACATATTTCTGGATGTTGACATAGACAAGgttaggtcac ... tgttctgtagGATGGGAAGATAAGCTACGAGGAGTTTGAGTTAATGATGTCAGCCGGAATG

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), 72 (downstream exon)
Score: 101

CAGCGGGTACATAGAGATCGAAGAGTTGAAAGAAGCCCTCTCCCCAAGAGGTGACCAGAAGTCGATCGACGACATATTTCTGGATGTTGACATAGACAAGgttaggtcac ... tgttctgtagGATGGGAAGATAAGCTACGAGGAGTTTGAGTTAATGATGTCAGCCGGAATGGACTGGAGGAATGCATCCCGGCAATACTCGAGAGCAGTTTACAACACTC




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actacaaatattaagttccttgcggtaataattttaactgaggtgtgttctgtagGATGGGAAGATAAGCTACGAGGAGTTTGAGTTAATGATGTCAGCCGGAATGGACTGGAGGAATGCATCCCGGCAATACTCGAGAGCAGTTTACAACACTC
                               ttttaac  putative branch site (score: 101)
                         taataattttaactga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttaggtcactttcgttaacaacaactagcaaattatatcacactacaaatattaagttccttgcggtaataattttaactgaggtgtgttctgtagGATGGGAAGATAAGCTACGAGGAGTTTGAGTTAATGATGTCAGCCGGAATGGACTGGAGGAATGCATCCCGGCAATACTCGAGAGCAGTTTACAACACTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG