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'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   		14  
 5'  3'   		15  
 5'  3'   		16  
 5'  3'   		17  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTGAATGAGGATAAGAGTCCTTTTCAGCGTATATTTGTCAATCAGgtattccaaccttttatcttcgatctatctttttttgtgaatcacatcattttgcatgaaccttgttttattccactatgctgatttctacctggatact...

Basic information

species Oryza sativa
transcript LOC_Os01g61780.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g61780.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM5G879240_T01 (Zea mays), 5'ss of exon 2
TTGAATGAGGATAAGAGTCCTTTTCAGCGTATATTTGTCAATCAGgtattccaaccttttatct--tcgatctatctttttttgtg--aatcacatcattttgcatgaaccttgttttattccactatgctgatttctacctggatact
||||||||||||||||||||||| ||||||||||||||||| ||||||||||  ||  ||| |   |   || ||   ||||||||   ||||  | | |||||||  ||||| ||||||  ||| |   ||  || | | | || |  
TTGAATGAGGATAAGAGTCCTTTCCAGCGTATATTTGTCAACCAGgtattccc-ccacttacccgattcttcaatgcatttttgtgctgatcatcttactttgcatccacctttttttatcacacaaa--tgccttat-cttagacatg
















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|88368677|gb|CI658309.1|CI658309
EST:     TTGAATGAGGATAAGAGTCCTTTTCAGCGTATATTTGTCAATCAG                         GTAAAGCGATGCTCTGAAATGTCACGCAAACTAAGATTTTTCAATGATCAG
genomic: TTGAATGAGGATAAGAGTCCTTTTCAGCGTATATTTGTCAATCAGgtattccaac ... tctcctacagGTAAAGCGATGCTCTGAAATGTCACGCAAACTAAGATTTTTCAATGATCAG
EST: gi|88396314|gb|CI598426.1|CI598426
EST:     TTGAATGAGGATAAGAGTCCTTTTCAGCGTATATTTGTCAATCAG                         GTAAAGCGATGCTCTGAAATGTCACGCAAAC
genomic: TTGAATGAGGATAAGAGTCCTTTTCAGCGTATATTTGTCAATCAGgtattccaac ... tctcctacagGTAAAGCGATGCTCTGAAATGTCACGCAAAC
EST: gi|88368744|gb|CI646226.1|CI646226
EST:     TTGAATGAGGATAAGAGTCCTTTTCAGCGTATATTTGTCAATCAG                         GTAAAGCGATGCTCTGAAATGTCACGCAAACTAAGATTTTTC
genomic: TTGAATGAGGATAAGAGTCCTTTTCAGCGTATATTTGTCAATCAGgtattccaac ... tctcctacagGTAAAGCGATGCTCTGAAATGTCACGCAAACTAAGATTTTTC
EST: gi|88339186|gb|CI633757.1|CI633757
EST:     TTGAATGAGGATAAGAGTCCTTTTCAGCGTATATTTGTCAATCAG                         GTAAAGCGATGCTCTGAAATGTCACGCAAACTAAGATTTTTCAATGATCAG
genomic: TTGAATGAGGATAAGAGTCCTTTTCAGCGTATATTTGTCAATCAGgtattccaac ... tctcctacagGTAAAGCGATGCTCTGAAATGTCACGCAAACTAAGATTTTTCAATGATCAG
EST: gi|88582562|gb|CI699980.1|CI699980
EST:     TTGAATGAGGATAAGAGTCCTTTTCAGCGTATATTTGTCAATCAG                         GTAAAGCGATGCTCTGAAATGTCACGCAAACTAAGATTTTTCAATGATCAG
genomic: TTGAATGAGGATAAGAGTCCTTTTCAGCGTATATTTGTCAATCAGgtattccaac ... tctcctacagGTAAAGCGATGCTCTGAAATGTCACGCAAACTAAGATTTTTCAATGATCAG
EST: gi|88719573|gb|CI743083.1|CI743083
EST:     TTGAATGAGGATAAGAGTCCTTTTCAGCGTATATTTGTCAATCAG                         GTAAAGCGATGCTCTGAAATGTCACGCAAACTAAGATTTT
genomic: TTGAATGAGGATAAGAGTCCTTTTCAGCGTATATTTGTCAATCAGgtattccaac ... tctcctacagGTAAAGCGATGCTCTGAAATGTCACGCAAACTAAGATTTT
EST: gi|163921035|gb|EG710411.1|EG710411
EST:     TTGAATGAGGATAAGAGTCCTTTTCAGCGTATATTTGTCAATCAG                         GTAAAGCGATGCTCTGAAATGTCACGCAAACTAAGATTTTTCAATGATCAG
genomic: TTGAATGAGGATAAGAGTCCTTTTCAGCGTATATTTGTCAATCAGgtattccaac ... tctcctacagGTAAAGCGATGCTCTGAAATGTCACGCAAACTAAGATTTTTCAATGATCAG
EST: gi|88720621|gb|CI743920.1|CI743920
EST:     TTGAATGAGGATAAGAGTCCTTTTCAGCGTATATTTGTCAATCAG                         GTAAAGCGATGCTCTGAAATGTCACGCAAACTAAGATTTCTCAATGATCAG
genomic: TTGAATGAGGATAAGAGTCCTTTTCAGCGTATATTTGTCAATCAGgtattccaac ... tctcctacagGTAAAGCGATGCTCTGAAATGTCACGCAAACTAAGATTTTTCAATGATCAG
EST: gi|88334309|gb|CI642554.1|CI642554
EST:     TTGAATGAGGATAAGAGTCCTTTTCAGCGTATATTTGTCAATCAG                         GTAAAGCGATGCTCTGAAATGTCACGCAAACTAAGATTTTTCAATGATCAG
genomic: TTGAATGAGGATAAGAGTCCTTTTCAGCGTATATTTGTCAATCAGgtattccaac ... tctcctacagGTAAAGCGATGCTCTGAAATGTCACGCAAACTAAGATTTTTCAATGATCAG
EST: gi|88327614|gb|CI646807.1|CI646807
EST:     TTGAATGAGGATAAGAGTCCTTTTCAGCGTATATTTGTCAATCAG                         GTAAAGCGATGCTCTGAAATGTCACGCAAACTAAGATTTTTCAATGATCAG
genomic: TTGAATGAGGATAAGAGTCCTTTTCAGCGTATATTTGTCAATCAGgtattccaac ... tctcctacagGTAAAGCGATGCTCTGAAATGTCACGCAAACTAAGATTTTTCAATGATCAG
EST: gi|88333502|gb|CI656574.1|CI656574
EST:     TTGAATGAGGATAAGAGTCCTTTTCAGCGTATATTTGTCAATCAG                         GTAAAGCGATGCTCTGAAATGTCACGCAAACTAAGATTTTTCAATGATCAG
genomic: TTGAATGAGGATAAGAGTCCTTTTCAGCGTATATTTGTCAATCAGgtattccaac ... tctcctacagGTAAAGCGATGCTCTGAAATGTCACGCAAACTAAGATTTTTCAATGATCAG
EST: gi|88351023|gb|CI620683.1|CI620683
EST:     TTGAATGAGGATAAGAGTCCTTTTCAGCGTATATTTGTCAATCAG                         GTAAAGCGATGCTCTGAAATGTCACGCAAACTAAGATTTTTCAATGATCAG
genomic: TTGAATGAGGATAAGAGTCCTTTTCAGCGTATATTTGTCAATCAGgtattccaac ... tctcctacagGTAAAGCGATGCTCTGAAATGTCACGCAAACTAAGATTTTTCAATGATCAG
EST: gi|88368745|gb|CI646227.1|CI646227
EST:     TTGAATGAGGATAAGAGTCCTTTTCAGCGTATATTTGTCAATCAG                         GTAAAGCGATGCTCTGAAATGTCACGCAAACTAAGATTT
genomic: TTGAATGAGGATAAGAGTCCTTTTCAGCGTATATTTGTCAATCAGgtattccaac ... tctcctacagGTAAAGCGATGCTCTGAAATGTCACGCAAACTAAGATTT
EST: gi|88395114|gb|CI609430.1|CI609430
EST:     TTGAATGAGGATAAGAGTCCTTTTCAGCGTATATTTGTCAATCAG                         GTAAAGCGATGCTCTGAAATGTCACGCAAACTAAGATTTTTCAATGATCAG
genomic: TTGAATGAGGATAAGAGTCCTTTTCAGCGTATATTTGTCAATCAGgtattccaac ... tctcctacagGTAAAGCGATGCTCTGAAATGTCACGCAAACTAAGATTTTTCAATGATCAG
EST: gi|88329706|gb|CI650174.1|CI650174
EST:     TTGAATGAGGATAAGAGTCCTTTTCAGCGTATATTTGTCAATCAG                         GTAAAGCGATGCTCTGAAATGTCACGCAAACTAAGATT
genomic: TTGAATGAGGATAAGAGTCCTTTTCAGCGTATATTTGTCAATCAGgtattccaac ... tctcctacagGTAAAGCGATGCTCTGAAATGTCACGCAAACTAAGATT
EST: gi|88729638|gb|CI751441.1|CI751441
EST:     TTGAATGAGGATAAGAGTCCTTTTCAGCGTATATTTGTCAATCAG                         GTAAAGCGATGCTCTGAAATGTC
genomic: TTGAATGAGGATAAGAGTCCTTTTCAGCGTATATTTGTCAATCAGgtattccaac ... tctcctacagGTAAAGCGATGCTCTGAAATGTC

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: 45 (upstream exon), 65 (downstream exon)
Score: 18

TTGAATGAGGATAAGAGTCCTTTTCAGCGTATATTTGTCAATCAGgtattccaac ... tctcctacagGTAAAGCGATGCTCTGAAATGTCACGCAAACTAAGATTTTTCAATGATCAGATCAACAAGGCAGGTGTAAAGTCCTCTGTTCGACCTGCAATGCAACCAG




<











<


<









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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTGAATGAGGATAAGAGTCCTTTTCAGCGTATATTTGTCAATCAGgtattccaaccttttatcttcgatctatctttttttgtgaatcacatcattttgcatgaaccttgttttattccactatgctgatttctacctggatact

- - - GAGGAT