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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCAGCTCTACAGGTTTCTTCGGCAGCAACTGTAGTAGAAAAGAAAGAGGGGAAGATTCGCAGTTCATATGGCAAAACCTGCTAATAGCATTGGCCGTAGgtaggtttgatactgcagctactgtttattcttaactgtttcttttccgtttctagcgctgattgataatttatctgttgcccacttgtctagtaacaccaaccaagtgttctttttctttctacggtgctcatggttgcacattgtaatttaattgtgaacattcatcatcaacag

Basic information

species Oryza sativa
transcript LOC_Os02g19510.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g19510.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G006507_T04 (Zea mays), 5'ss of exon 2
-TGCAGCTCTACAGGTTTCTTCGGCAGCAACTGTAGTAGAAAAGAAAGAGGGGAAGATTCGCAGTTCATATGGCAAAACCTGCTAATAGCATTGGCCGTAGgtaggtttgatactgcagctactgtttattcttaactgtttcttttccgtttctagcgctgattgataatttatctgttgcccacttgtctagtaacaccaaccaagtgttctttttctttctacggtgctcatggttgcacattgtaatttaattgtgaacattcatcatcaacag
 | | |||      ||| |  |      |  |   |  |    | || ||| ||   | ||||| || ||||||||| ||| | |||||||||||||||||||| |||   |||  || | ||                |||| |||   | | ||    |  |   |  ||  |||||     | ||  ||| ||      ||| | |||    |   ||| |   || ||| | |   | |||  |||||| | ||  || |||  ||| ||    
ATACTGCTTGTGGTGTTGCGCCAATTTAAGTTCCTGCTGTCC-GCAAAAGGAGAGCTTCCGCAGCTCCTATGGCAAAGCCTCCCAATAGCATTGGCCGTAGgtatgttcactaccacatccacaa-------------atttcattttaatatataaa--tagtccttgtttagtctgta---tatttaactactagtgt--acctaatgtcggataattttgt---gtcctcgttgccactcatcctaattttactgccaatatttgtcagcag---

upper sequence: LOC_Os02g19510.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G006507_T03 (Zea mays), 5'ss of exon 2
-TGCAGCTCTACAGGTTTCTTCGGCAGCAACTGTAGTAGAAAAGAAAGAGGGGAAGATTCGCAGTTCATATGGCAAAACCTGCTAATAGCATTGGCCGTAGgtaggtttgatactgcagctactgtttattcttaactgtttcttttccgtttctagcgctgattgataatttatctgttgcccacttgtctagtaacaccaaccaagtgttctttttctttctacggtgctcatggttgcacattgtaatttaattgtgaacattcatcatcaacag
 | | |||      ||| |  |      |  |   |  |    | || ||| ||   | ||||| || ||||||||| ||| | |||||||||||||||||||| |||   |||  || | ||                |||| |||   | | ||    |  |   |  ||  |||||     | ||  ||| ||      ||| | |||    |   ||| |   || ||| | |   | |||  |||||| | ||  || |||  ||| || |||
ATACTGCTTGTGGTGTTGCGCCAATTTAAGTTCCTGCTGTCC-GCAAAAGGAGAGCTTCCGCAGCTCCTATGGCAAAGCCTCCCAATAGCATTGGCCGTAGgtatgttcactaccacatccacaa-------------atttcattttaatatataaa--tagtccttgtttagtctgta---tatttaactactagtgt--acctaatgtcggataattttgt---gtcctcgttgccactcatcctaattttactgccaatatttgtcagcagcag
















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|88396973|gb|CI578122.1|CI578122
EST:     GGAAGATTCGCAGTTCATATGGCAAAACCTGCTAATAGCATTGGCCGTAG                         CACGCCAAGATCAAATGAGGGGATGAGGCTCATATTCTCGGCAGTTGTTGG
genomic: GGAAGATTCGCAGTTCATATGGCAAAACCTGCTAATAGCATTGGCCGTAGgtaggtttga ... tcatcaacagCACGCCAAGATCAAATGAGGGGATGAGGCTCATATTCTCGGCAGTTGTTGG
EST: gi|29646523|gb|CB651530.1|CB651530
EST:     GGAAGATTCGCAGTTCATATGGCAAAACCTGCTAATAGCATTGGCCGTAG                         CACGCCAAGATCAAATGAGGGGATGAGGCTCATATTCTCGGCAGTTGTTGG
genomic: GGAAGATTCGCAGTTCATATGGCAAAACCTGCTAATAGCATTGGCCGTAGgtaggtttga ... tcatcaacagCACGCCAAGATCAAATGAGGGGATGAGGCTCATATTCTCGGCAGTTGTTGG
EST: gi|58608259|gb|CK036292.1|CK036292
EST:     GGAAGATTCGCAGTTCATATGGCAAAACCTGCTAATAGCATTGGCCGTAG                         CACGCCAAGATCAAATGAGGGGATGAGGCTCATATTCTCGGCAGTTGTTGG
genomic: GGAAGATTCGCAGTTCATATGGCAAAACCTGCTAATAGCATTGGCCGTAGgtaggtttga ... tcatcaacagCACGCCAAGATCAAATGAGGGGATGAGGCTCATATTCTCGGCAGTTGTTGG
EST: gi|58669315|gb|CK058001.1|CK058001
EST:     GGAAGATTCGCAGTTCATATGGCAAAACCTGCTAATAGCATTGGCCGTAG                         CACGCCAAGATCAAATGAGGGGATGAGGCTCATATTCTCGGCAGTTGTTGG
genomic: GGAAGATTCGCAGTTCATATGGCAAAACCTGCTAATAGCATTGGCCGTAGgtaggtttga ... tcatcaacagCACGCCAAGATCAAATGAGGGGATGAGGCTCATATTCTCGGCAGTTGTTGG
EST: gi|88717707|gb|CI741217.1|CI741217
EST:     GGAAGATTCGCAGTTCATATGGCAAAACCTGCTAATAGCATTGGCCGTAG                         CACGCCAAGATCAAATGAGGGGATGAGGCTCATATNCTCGGCAGTTGTGGG
genomic: GGAAGATTCGCAGTTCATATGGCAAAACCTGCTAATAGCATTGGCCGTAGgtaggtttga ... tcatcaacagCACGCCAAGATCAAATGAGGGGATGAGGCTCATATTCTCGGCAGTTGTTGG
EST: gi|29673248|gb|CB669523.1|CB669523
EST:     GGAAGATTCGCAGTTCATATGGCAAAACCTGCTAATAGCATTGGCCGTAG                         CACGCCAAGATCAAATGAGGGGATGAGGCTCATATTCTCGGCAGTTGTTGG
genomic: GGAAGATTCGCAGTTCATATGGCAAAACCTGCTAATAGCATTGGCCGTAGgtaggtttga ... tcatcaacagCACGCCAAGATCAAATGAGGGGATGAGGCTCATATTCTCGGCAGTTGTTGG
EST: gi|58659150|gb|CK047830.1|CK047830
EST:     GGAAGATTCGCAGTTCATATGGCAAAACCTGCTAATAGCATTGGCCGTAG                         CACGCCAAGATCAAATGAGGGGATGAGGCTCATATTCTCGGCAGTTGTTGG
genomic: GGAAGATTCGCAGTTCATATGGCAAAACCTGCTAATAGCATTGGCCGTAGgtaggtttga ... tcatcaacagCACGCCAAGATCAAATGAGGGGATGAGGCTCATATTCTCGGCAGTTGTTGG
EST: gi|29641723|gb|CB646730.1|CB646730
EST:     GGAAGATTCGCAGTTCATATGGCAAAACCTGCTAATAGCATTGGCCGTAG                         CACGCCAAGATCAAATGAGGGGATGAGGCTCATATTCTCGGCAGTTGTTGG
genomic: GGAAGATTCGCAGTTCATATGGCAAAACCTGCTAATAGCATTGGCCGTAGgtaggtttga ... tcatcaacagCACGCCAAGATCAAATGAGGGGATGAGGCTCATATTCTCGGCAGTTGTTGG
EST: gi|29624841|gb|CB629852.1|CB629852
EST:     GGAAGATTCGCAGTTCATATGGCAAAACCTGCTAATAGCATTGGCCGTAG                         CACGCCAAGATCAAATGAGGGGATGAGGCTCATATTCTCGGCAGTTGTTGG
genomic: GGAAGATTCGCAGTTCATATGGCAAAACCTGCTAATAGCATTGGCCGTAGgtaggtttga ... tcatcaacagCACGCCAAGATCAAATGAGGGGATGAGGCTCATATTCTCGGCAGTTGTTGG
EST: gi|88360099|gb|CI610213.1|CI610213
EST:     GGAAGATTCGCAGTTCATATGGCAAAACCTGCTAATAGCATTGGCCGTAG                         CACGCCAAGATCAAATGAGGGGATGAGGCTCATATTC
genomic: GGAAGATTCGCAGTTCATATGGCAAAACCTGCTAATAGCATTGGCCGTAGgtaggtttga ... tcatcaacagCACGCCAAGATCAAATGAGGGGATGAGGCTCATATTC
EST: gi|11610396|gb|AU166072.1|AU166072
EST:     GGAAGATTCGCAGTTCATATGGCAAAACCTGCTAATAGCATTGGCCGTAG                         CACGCCAAGATCAAATGAGGGGATGAGGCTCATA
genomic: GGAAGATTCGCAGTTCATATGGCAAAACCTGCTAATAGCATTGGCCGTAGgtaggtttga ... tcatcaacagCACGCCAAGATCAAATGAGGGGATGAGGCTCATA
EST: gi|29676038|gb|CB672313.1|CB672313
EST:     GGAAGATTCGCAGTTCATATGGCAAAACCTGCTAATAGCATTGGCCGTAG                         CACGCCAAGATCAAATGAGGGGATGAGGCTCATATTCTCGGCAGTTGTTGG
genomic: GGAAGATTCGCAGTTCATATGGCAAAACCTGCTAATAGCATTGGCCGTAGgtaggtttga ... tcatcaacagCACGCCAAGATCAAATGAGGGGATGAGGCTCATATTCTCGGCAGTTGTTGG
EST: gi|88315187|gb|CI611851.1|CI611851
EST:     GGAAGATTCGCAGTTCATATGGCAAAACCTGCTAATAGCATTGGCCGTAG                         CACGCCAAGATCAAATGAGGGGATGAGGCTCAT
genomic: GGAAGATTCGCAGTTCATATGGCAAAACCTGCTAATAGCATTGGCCGTAGgtaggtttga ... tcatcaacagCACGCCAAGATCAAATGAGGGGATGAGGCTCAT
EST: gi|88728131|gb|CI751641.1|CI751641
EST:     GGAAGATTCGCAGTTCATATGGCAAAACCTGCTAATAGCATTGGCCGTAG                         CACGCCAAGATCAAATGAGGGGATGAGGCTCATATNCTCGGCAGTTGTTGG
genomic: GGAAGATTCGCAGTTCATATGGCAAAACCTGCTAATAGCATTGGCCGTAGgtaggtttga ... tcatcaacagCACGCCAAGATCAAATGAGGGGATGAGGCTCATATTCTCGGCAGTTGTTGG
EST: gi|29673598|gb|CB669873.1|CB669873
EST:     GGAAGATTCTCAGTTCATATGGCAAAACCTGCTAATAGCATTGGCCGTAG                         CACGCCAAGATCAAATGAGGGGATGAGGCTCATATTCTCGGCAGTTGTTGG
genomic: GGAAGATTCGCAGTTCATATGGCAAAACCTGCTAATAGCATTGGCCGTAGgtaggtttga ... tcatcaacagCACGCCAAGATCAAATGAGGGGATGAGGCTCATATTCTCGGCAGTTGTTGG
EST: gi|29640936|gb|CB645943.1|CB645943
EST:     GGAAGATTCGCAGTTCATATGGCAAAACCTGCTAATAGCATTGGCCGTAG                         CACGCCAAGATCAAATGAGGGGATGAGGCTCATATTCTCGGCAGTTGTTGG
genomic: GGAAGATTCGCAGTTCATATGGCAAAACCTGCTAATAGCATTGGCCGTAGgtaggtttga ... tcatcaacagCACGCCAAGATCAAATGAGGGGATGAGGCTCATATTCTCGGCAGTTGTTGG
EST: gi|58670226|gb|CK058912.1|CK058912
EST:     GGAAGATTCGCAGTTCATATGGCAAAACCTGCTAATAGCATTGGCCGTAG                         CACGCCAAGATCAAATGAGGGGATGAGGCTCATATTCTCGGCAGTTGTTGG
genomic: GGAAGATTCGCAGTTCATATGGCAAAACCTGCTAATAGCATTGGCCGTAGgtaggtttga ... tcatcaacagCACGCCAAGATCAAATGAGGGGATGAGGCTCATATTCTCGGCAGTTGTTGG
EST: gi|58672680|gb|CK061366.1|CK061366
EST:     GGAAGATTCGCAGTTCATATGGCAAAACCTGCTAATAGCATTGGCCGTAG                         CACGCCAAGATCAAATGAGGGGATGAGGCTCATATTCTCGGCAGTTGTTGG
genomic: GGAAGATTCGCAGTTCATATGGCAAAACCTGCTAATAGCATTGGCCGTAGgtaggtttga ... tcatcaacagCACGCCAAGATCAAATGAGGGGATGAGGCTCATATTCTCGGCAGTTGTTGG
EST: gi|29616238|gb|CB621250.1|CB621250
EST:     GGAAGATTCGCAGTTCATATGGCAAAACCTGCTAATAGCATTGGCCGTAG                         CACGCCAAGATCAAATGAGGGGATGAGGCTCATATTCTCGGCAGTTGTTGG
genomic: GGAAGATTCGCAGTTCATATGGCAAAACCTGCTAATAGCATTGGCCGTAGgtaggtttga ... tcatcaacagCACGCCAAGATCAAATGAGGGGATGAGGCTCATATTCTCGGCAGTTGTTGG
EST: gi|88356602|gb|CI626217.1|CI626217
EST:     GGAAGATTCGCAGTTCATATGGCAAAACCTGCTAATAGCATTGGCCGTAG                         CACGCCAAGATCAAATGAGGGGATGAGGCTCATATTCTCGGCAGTTGTTGG
genomic: GGAAGATTCGCAGTTCATATGGCAAAACCTGCTAATAGCATTGGCCGTAGgtaggtttga ... tcatcaacagCACGCCAAGATCAAATGAGGGGATGAGGCTCATATTCTCGGCAGTTGTTGG
EST: gi|88696183|gb|CI739758.1|CI739758
EST:     GGAAGATTCGCAGTTCATATGGCAAAACCTGCTAATAGCATTGGCCGTAG                         CACGCCAAGATCAAATGAGGGGATGAGGCTCATATTCTCGGCAGTTGTTGG
genomic: GGAAGATTCGCAGTTCATATGGCAAAACCTGCTAATAGCATTGGCCGTAGgtaggtttga ... tcatcaacagCACGCCAAGATCAAATGAGGGGATGAGGCTCATATTCTCGGCAGTTGTTGG
EST: gi|58691339|gb|CK080026.1|CK080026
EST:     GGAAGATTCGCAGTTCATATGGCAAAACCTGCTAATAGCATTGGCCGTAG                         CACGCCAAGATCAAATGAGGGGATGAGGCTCATATTCTCGGCAGTTGTTGG
genomic: GGAAGATTCGCAGTTCATATGGCAAAACCTGCTAATAGCATTGGCCGTAGgtaggtttga ... tcatcaacagCACGCCAAGATCAAATGAGGGGATGAGGCTCATATTCTCGGCAGTTGTTGG
EST: gi|58666569|gb|CK055255.1|CK055255
EST:     GGAAGATTCGCAGTTCATATGGCAAAACCTGCTAATAGCATTGGCCGTAG                         CACGCCAAGATCAAATGAGGGGATGAGGCTCATATTCTCGGCAGTTGTTGG
genomic: GGAAGATTCGCAGTTCATATGGCAAAACCTGCTAATAGCATTGGCCGTAGgtaggtttga ... tcatcaacagCACGCCAAGATCAAATGAGGGGATGAGGCTCATATTCTCGGCAGTTGTTGG
EST: gi|58690262|gb|CK078949.1|CK078949
EST:     GGAAGATTCGCAGTTCATATGGCAAAACCTGCTAATAGCATTGGCCGTAG                         CACGCCAAGATCAAATGAGGGGATGAGGCTCATATTCTCGGCAGTTGTTGG
genomic: GGAAGATTCGCAGTTCATATGGCAAAACCTGCTAATAGCATTGGCCGTAGgtaggtttga ... tcatcaacagCACGCCAAGATCAAATGAGGGGATGAGGCTCATATTCTCGGCAGTTGTTGG
EST: gi|88405374|gb|CI586195.1|CI586195
EST:     GGAAGATTCGCAGTTCATATGGCAAAACCTGCTAATAGCATTGGCCGTAG                         CACGCCAAGATCAAATGAGGGGATGAGGCTCATATTCTCGGCAGTTGTTGG
genomic: GGAAGATTCGCAGTTCATATGGCAAAACCTGCTAATAGCATTGGCCGTAGgtaggtttga ... tcatcaacagCACGCCAAGATCAAATGAGGGGATGAGGCTCATATTCTCGGCAGTTGTTGG
EST: gi|66913022|gb|CX099870.1|CX099870
EST:     GGAAGATTCGCAGTTCATATGGCAAAACCTGCTAATAGCATTGGCCGTAG                         CACGCCAAGATCAAATGAGGGGATGAGGCTCATATTCTCGGCAGTTGTTGG
genomic: GGAAGATTCGCAGTTCATATGGCAAAACCTGCTAATAGCATTGGCCGTAGgtaggtttga ... tcatcaacagCACGCCAAGATCAAATGAGGGGATGAGGCTCATATTCTCGGCAGTTGTTGG
EST: gi|58687148|gb|CK075835.1|CK075835
EST:     GGAAGATTCGCAGTTCATATGGCAAAACCTGCTAATAGCATTGGCCGTAG                         CACGCCAAGATCAAATGAGGGGATGAGGCTCATATTCTCGGCAGTTGTTGG
genomic: GGAAGATTCGCAGTTCATATGGCAAAACCTGCTAATAGCATTGGCCGTAGgtaggtttga ... tcatcaacagCACGCCAAGATCAAATGAGGGGATGAGGCTCATATTCTCGGCAGTTGTTGG
EST: gi|58680355|gb|CK069042.1|CK069042
EST:     GGAAGATTCGCAGTTCATATGGCAAAACCTGCTAATAGCATTGGCCGTAG                         CACGCCAAGATCAAATGAGGGGATGAGGCTCATATTCTCGGCAGTTGTTGG
genomic: GGAAGATTCGCAGTTCATATGGCAAAACCTGCTAATAGCATTGGCCGTAGgtaggtttga ... tcatcaacagCACGCCAAGATCAAATGAGGGGATGAGGCTCATATTCTCGGCAGTTGTTGG
EST: gi|58601351|gb|CK011879.1|CK011879
EST:     GGAAGATTCGCAGTTCATATGGCAAAACCTGCTAATAGCATTGGCCGTAG                         CACGCCAAGATCAAATGAGGGGATGAGGCTCATATTCTCGGCAGTTGTTGG
genomic: GGAAGATTCGCAGTTCATATGGCAAAACCTGCTAATAGCATTGGCCGTAGgtaggtttga ... tcatcaacagCACGCCAAGATCAAATGAGGGGATGAGGCTCATATTCTCGGCAGTTGTTGG
EST: gi|88445013|gb|CI589491.1|CI589491
EST:     GGAAGATTCGCAGTTCATATGGCAAAACCTGCTAATAGCATTGGCCGTAG                         CACGCCAAGATCAAAT
genomic: GGAAGATTCGCAGTTCATATGGCAAAACCTGCTAATAGCATTGGCCGTAGgtaggtttga ... tcatcaacagCACGCCAAGATCAAAT
EST: gi|58605686|gb|CK033719.1|CK033719
EST:     GGAAGATTCGGGGTTCATATGGCAAAACCTGCTAATAGCATTGGCCGTAG                         CACGCCAAGATCAAATGAGGGGATGAGGCTCATATTCTCGGCAGTTGTTGG
genomic: GGAAGATTCGCAGTTCATATGGCAAAACCTGCTAATAGCATTGGCCGTAGgtaggtttga ... tcatcaacagCACGCCAAGATCAAATGAGGGGATGAGGCTCATATTCTCGGCAGTTGTTGG

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: 69 (upstream exon), 62 (downstream exon)
Score: 27

TGCAGCTCTACAGGTTTCTTCGGCAGCAACTGTAGTAGAAAAGAAAGAGGGGAAGATTCGCAGTTCATATGGCAAAACCTGCTAATAGCATTGGCCGTAGgtaggtttga ... tcatcaacagCACGCCAAGATCAAATGAGGGGATGAGGCTCATATTCTCGGCAGTTGTTGGTGTTATGTTGGGATACTTGTTTGGGGTTTCCTTCCCTACAGTAAATATA




<











<


<









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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGCAGCTCTACAGGTTTCTTCGGCAGCAACTGTAGTAGAAAAGAAAGAGGGGAAGATTCGCAGTTCATATGGCAAAACCTGCTAATAGCATTGGCCGTAGgtaggtttgatactgcagctactgtttattcttaactgtttcttttccgtttctagcgctgattgataatttatctgttgcccacttgtctagtaacaccaaccaagtgttctttttctttctacggtgctcatggttgcacattgtaatttaattgtgaacattcatcatcaacag

- - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA