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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGTTCACCATGTTCATCGCGATCACCTTCCCGTTCTTCGGTGGATTGCTTGGGTTCTTCGGTGGATTCGCCTTCGCGCCAACTACTTACTTCgtaagttttccattgatcatttcgttttgatgggtgagagtctgagagatgatcagagttcagaactgacggttatttttttctgtgttctttggcag

Basic information

species Oryza sativa
transcript LOC_Os08g03350.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g03350.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G180659_T02 (Zea mays), 5'ss of exon 6
CGTTCACCATGTTCATCGCGATCACCTTCCCGTTCTTCGGTGGATTGCTTGGGTTCTTCGGTGGATTCGCCTTCGCGCCAACTACTTACTTCgtaagtttt--------ccattgatcatttcgttttgatgggtgagagtctgagagatgatcagagttcagaac----tgac--ggttatttttttctgtgttctttggcag
||||||| |||||||| || ||||||||||| |||||||||||  |||| || |||||||| || |||||||||||||| || || || |||||| | |||        ||||||||   | | | |     | |       ||  |    |||   |||   |||    |||     |  | || ||||   |  | || |||
CGTTCACGATGTTCATAGCCATCACCTTCCCCTTCTTCGGTGGGCTGCTCGGTTTCTTCGGCGGGTTCGCCTTCGCGCCGACCACCTATTTCgtatgcttttcttcctcccattgattgatccatctatcctgtttttttcttgcaatcacatctctgtttctaacaacctgatcaaatcttcttcttcttcttcttctgccag

upper sequence: LOC_Os08g03350.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G046743_T01 (Zea mays), 5'ss of exon 5
CGTTCACCATGTTCATCGCGATCACCTTCCCGTTCTTCGGTGGATTGCTTGGGTTCTTCGGTGGATTCGCCTTCGCGCCAACTACTTACTTCgtaagttttccattga--tcatttcgttttga--tgggtgagagtctgaga-------------------gatgatcagagttcagaactgacggttatttttttc-tgtgttctttggcag
||||||| ||||||||||| ||||||||||| |||||||| ||| |||| || |||||||| ||||||||||| || || || || || |||||||| | ||  | |    |  | || |  ||  ||  |  |  |||| |                    | || |   | || |||||   |    || || | |   || | | || |||
CGTTCACAATGTTCATCGCCATCACCTTCCCCTTCTTCGGCGGACTGCTCGGCTTCTTCGGCGGATTCGCCTTTGCACCGACGACCTATTTCgtaagctctcagtgggatccgatccgatccgacttgcatctgtatctgtggttctgatgtccaagcacttggtgctagaacttgagaacaagctaacatgttctccgcttggtttctgccag
















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|29616822|gb|CB621834.1|CB621834
EST:     GATTGCTTGGGTTCTTCGGTGGATTCGCCTTCGCGCCGACTACTTACTTC                         CTTCCCTGCATCATGTGGCTAGCAATCTACAAGCCAAGAAGGTTCAGTCTC
genomic: GATTGCTTGGGTTCTTCGGTGGATTCGCCTTCGCGCCAACTACTTACTTCgtaagttttc ... tctttggcagCTTCCCTGCATCATGTGGCTAGCAATCTACAAGCCAAGAAGGTTCAGTCTC
EST: gi|4716501|gb|AU057617.1|AU057617
EST:     GATTGCTTGGGTTCTTCGGTGGATTCGCCTTCGCGCCAACTACTTACTTC                         CTTCCCTGCATCATGTGGCTAGCAATCTACAAGCCAAGAAGGTTCAGTCTC
genomic: GATTGCTTGGGTTCTTCGGTGGATTCGCCTTCGCGCCAACTACTTACTTCgtaagttttc ... tctttggcagCTTCCCTGCATCATGTGGCTAGCAATCTACAAGCCAAGAAGGTTCAGTCTC
EST: gi|89162523|gb|CI099215.1|CI099215
EST:     GATTGCTTGGGTTCTTCGGTGGATTCGCCTTCGCGCCAACTACTTACTTC                         CTTCCCTGCATCATGTGGCTAGCAATCTACAAGCCAAGAAGGTTCAGTCTC
genomic: GATTGCTTGGGTTCTTCGGTGGATTCGCCTTCGCGCCAACTACTTACTTCgtaagttttc ... tctttggcagCTTCCCTGCATCATGTGGCTAGCAATCTACAAGCCAAGAAGGTTCAGTCTC
EST: gi|86598121|gb|CI278511.1|CI278511
EST:     GATTGCTTGGGTTCTTCGGTGGATTCGCCTTCGCGCCAACTACTTACTTC                         CTTCCCTGCATCATGTGGCTAGCAATCTACAAGCCAAGAAGGTTCAGTCTC
genomic: GATTGCTTGGGTTCTTCGGTGGATTCGCCTTCGCGCCAACTACTTACTTCgtaagttttc ... tctttggcagCTTCCCTGCATCATGTGGCTAGCAATCTACAAGCCAAGAAGGTTCAGTCTC
EST: gi|89164964|gb|CI102052.1|CI102052
EST:     TCGCGCCAACTACTTACTTC                         CTTCCCTGCATCATGTGGCTAGCAATCTACAAGCCAAGAAGGTTCAGTCTC
genomic: TCGCGCCAACTACTTACTTCgtaagttttc ... tctttggcagCTTCCCTGCATCATGTGGCTAGCAATCTACAAGCCAAGAAGGTTCAGTCTC
EST: gi|86853761|gb|CI250012.1|CI250012
EST:     GATTGCTTGGGTTCTTCGGTGGATTCGCCTTCGCGCCAACTACTTACTTC                         CTTCCCTGCATCATGTGGCTAGCAATCTACAAGCCAAGAAGGTTCAGTCTC
genomic: GATTGCTTGGGTTCTTCGGTGGATTCGCCTTCGCGCCAACTACTTACTTCgtaagttttc ... tctttggcagCTTCCCTGCATCATGTGGCTAGCAATCTACAAGCCAAGAAGGTTCAGTCTC
EST: gi|88245570|gb|CI245419.1|CI245419
EST:     GGTGGATTCGCCTTCGCGCCAACTACTTACTTC                         CTTCCCTGCATCATGTGGCTAGCAATCTACAAGCCAAGAAGGTTCAGTCTC
genomic: GGTGGATTCGCCTTCGCGCCAACTACTTACTTCgtaagttttc ... tctttggcagCTTCCCTGCATCATGTGGCTAGCAATCTACAAGCCAAGAAGGTTCAGTCTC
EST: gi|86497707|gb|CI140340.1|CI140340
EST:     GATTGCTTGGGTTCTTCGGTGGATTCGCCTTCGCGCCAACTACTTACTTC                         CTTCCCTGCATCATGTGGCTAGCAATCTACAAGCCAAGAAGGTTCAGTCTC
genomic: GATTGCTTGGGTTCTTCGGTGGATTCGCCTTCGCGCCAACTACTTACTTCgtaagttttc ... tctttggcagCTTCCCTGCATCATGTGGCTAGCAATCTACAAGCCAAGAAGGTTCAGTCTC
EST: gi|29630538|gb|CB635547.1|CB635547
EST:     GATTGCTTGGGTTCTTCGGTGGATTCGCCTTCGCGCCGACTACTTACTTC                         CTTCCCTGCATCATGTGGCTAGCAATCTACAAGCCAAGAAGGTTCAGTCTC
genomic: GATTGCTTGGGTTCTTCGGTGGATTCGCCTTCGCGCCAACTACTTACTTCgtaagttttc ... tctttggcagCTTCCCTGCATCATGTGGCTAGCAATCTACAAGCCAAGAAGGTTCAGTCTC
EST: gi|88247938|gb|CI247787.1|CI247787
EST:     GATTGCTTGGGTTCTTCGGTGGATTCGCCTTCGCGCCAACTACTTACTTC                         CTTCCCTGCATCATGTGGCTAGCAATCTACAAGCCAAGAAGGTTCAGTCTC
genomic: GATTGCTTGGGTTCTTCGGTGGATTCGCCTTCGCGCCAACTACTTACTTCgtaagttttc ... tctttggcagCTTCCCTGCATCATGTGGCTAGCAATCTACAAGCCAAGAAGGTTCAGTCTC
EST: gi|4716084|gb|AU057200.1|AU057200
EST:     GATTGCTTGGGTTCTTCGGTGGATTCGCCTTCGCGCCAACTACTTACTTC                         CTTCCCTGCATCATGTGGCTAGCAATCTACAAGCCAAGAAGGTTCAGTCTC
genomic: GATTGCTTGGGTTCTTCGGTGGATTCGCCTTCGCGCCAACTACTTACTTCgtaagttttc ... tctttggcagCTTCCCTGCATCATGTGGCTAGCAATCTACAAGCCAAGAAGGTTCAGTCTC
EST: gi|89177928|gb|CI391107.1|CI391107
EST:     GATTGCTTGGGTTCTTCGGTGGATTCGCCTTCGCGCCAACTACTTACTTC                         CTTCCCTGCATCATGTGGCTAGCAATCTACAAGCCAAGAAGGTTCAGTCTC
genomic: GATTGCTTGGGTTCTTCGGTGGATTCGCCTTCGCGCCAACTACTTACTTCgtaagttttc ... tctttggcagCTTCCCTGCATCATGTGGCTAGCAATCTACAAGCCAAGAAGGTTCAGTCTC
EST: gi|88901693|gb|CI001801.1|CI001801
EST:     GATTGCTTGGGTTCTTCGGTGGATTCGCCTTCGCGCCAACTACTTACTTC                         CTTCCCTGCATCATGTGGCTAGCAATCTACAAGCCAAGAAGGTTCAGTCTC
genomic: GATTGCTTGGGTTCTTCGGTGGATTCGCCTTCGCGCCAACTACTTACTTCgtaagttttc ... tctttggcagCTTCCCTGCATCATGTGGCTAGCAATCTACAAGCCAAGAAGGTTCAGTCTC

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), 69 (downstream exon)
Score: 61

CGTTCACCATGTTCATCGCGATCACCTTCCCGTTCTTCGGTGGATTGCTTGGGTTCTTCGGTGGATTCGCCTTCGCGCCAACTACTTACTTCgtaagttttc ... tctttggcagCTTCCCTGCATCATGTGGCTAGCAATCTACAAGCCAAGAAGGTTCAGTCTCTCATGGTTCACCAACTGG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGTTCACCATGTTCATCGCGATCACCTTCCCGTTCTTCGGTGGATTGCTTGGGTTCTTCGGTGGATTCGCCTTCGCGCCAACTACTTACTTCgtaagttttccattgatcatttcgttttgatgggtgagagtctgagagatgatcagagttcagaactgacggttatttttttctgtgttctttggcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA