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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGTCCAATTTTGCCATTGAGGGTGCTTGTCCCCGCTAGCTACCCTAAGTGCTCCCCGGTTCTCCTAGACAAGTTCCCAGATGAACAAAGgtcagtatccaatgttttatcagattctacgccaggtactacatattaggctgtcctgattctctgtacataaataaactaaggatgttgcattgtgcttgtgaatctgctatag

Basic information

species Oryza sativa
transcript LOC_Os08g45080.1
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g45080.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM2G020920_T02 (Zea mays), 5'ss of exon 3
AGTCCAATTTTGCCATTGAGGGTGCTTGTCCCCGCTAGCTACCCTAAGTGCTCCCCGGTTCTCCTAGACAAGTTCCCAGATGAACAAAGgtcagtatccaatgttttatcagattctacgccaggtactacatattaggctgtcctgattctctgtacataaataaactaaggatgttgcattgtgcttgtgaatctgctatag
|||||||||||||| |||||| ||||||| || ||||||||||| || ||||||||||| || ||||||||||| || ||||||||| |||  |  |  | ||   |||||           | ||| || || ||| |      || |||   | ||| |    | || | | || ||| |||||  ||              
AGTCCAATTTTGCCGTTGAGGTTGCTTGTTCCTGCTAGCTACCCGAAATGCTCCCCGGTGCTTCTAGACAAGTTTCCTGATGAACAATGgt--gcgtgtactggcatatca-----------atgta-tatatgttaag------tgcttccgcgaacaaa----acctcacggtggtgctttgtggctgcag-----------

upper sequence: LOC_Os08g45080.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM2G020920_T03 (Zea mays), 5'ss of exon 9
AGTCCAATTTTGCCATTGAGGGTGCTTGTCCCCGCTAGCTACCCTAAGTGCTCCCCGGTTCTCCTAGACAAGTTCCCAGATGAACAAAGgtcagtatccaatgttttatcagattctacgccaggtactacatattaggctgtcctgattctctgtacataaataaactaaggatgttgcattgtgcttgtgaatctgctatag
|||||||||||||| |||||| ||||||| || ||||||||||| || ||||||||||| || ||||||||||| || ||||||||| |||  |  |  | ||   |||||           | ||| || || ||| |      || |||   | ||| |    | || | | || ||| |||||  ||              
AGTCCAATTTTGCCGTTGAGGTTGCTTGTTCCTGCTAGCTACCCGAAATGCTCCCCGGTGCTTCTAGACAAGTTTCCTGATGAACAATGgt--gcgtgtactggcatatca-----------atgta-tatatgttaag------tgcttccgcgaacaaa----acctcacggtggtgctttgtggctgcagcag--------

upper sequence: LOC_Os08g45080.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM5G833477_T01 (Zea mays), 5'ss of exon 4
AGTCCAATTTTGCCATTGAGGGTGCTTGTCCCCGCTAGCTACCCTAAGTGCTCCCCGGTTCTCCTAGACAAGTTCCCAGATGAACAAAGgtcagtatc-caatgttttatcagattctacgccaggtactacatattaggctgtcctgattctctgtacataaataaactaaggatgttgcattgtgcttgtgaatctgctatag
|||||||||||||| |||||| ||||||| || | ||||||||| || ||||||||||| || ||||||||||| || ||||||||| |||  || |       | |||    ||  || |  |||| || |     ||         |  |||   ||     |   ||  || ||  |||                       
AGTCCAATTTTGCCGTTGAGGTTGCTTGTTCCTGGTAGCTACCCAAAATGCTCCCCGGTGCTTCTAGACAAGTTTCCTGATGAACAATGgtgcgtgtagtggcatattactgtata-tatgttaggtgcttcggcaaaga--------aacctc---acgggggtgctctgtggttgcagcag----------------------

upper sequence: LOC_Os08g45080.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM5G833477_T02 (Zea mays), 5'ss of exon 4
AGTCCAATTTTGCCATTGAGGGTGCTTGTCCCCGCTAGCTACCCTAAGTGCTCCCCGGTTCTCCTAGACAAGTTCCCAGATGAACAAAGgtcagtatccaatgttttatcagattctacgccaggtactacatattaggctgtcctgattctctgtacataaataaactaaggatgttgcattgtgcttgtgaatctgctatag
|||||||||||||| |||||| ||||||| || | ||||||||| || ||||||||||| || ||||||||||| || ||||||||| |||  |  |  | ||   ||| |   | ||          || || |||||   |        || | |   ||  || || | |  | |||  |||| |||              
AGTCCAATTTTGCCGTTGAGGTTGCTTGTTCCTGGTAGCTACCCAAAATGCTCCCCGGTGCTTCTAGACAAGTTTCCTGATGAACAATGgt--gcgtgtagtggcatatta--ctgta----------tatatgttaggtgct--------tcggca---aagaaacctcacgggggtgctctgtggttgcag-----------

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|29622616|gb|CB627627.1|CB627627
EST:     TACCCTAAGTGCTCCCCGGTTCTCCTAGACAAGTTCCCAGATGAACAAAG                         AAACTCGGATGACCTGTCGACCAAAGCGAGGTCGAAGTTCAGCATATTGCT
genomic: TACCCTAAGTGCTCCCCGGTTCTCCTAGACAAGTTCCCAGATGAACAAAGgtcagtatcc ... tctgctatagAAACTCGGATGACCTGTCGACCAAAGCGAGGTCGAAGTTCAGCATATTGCT
EST: gi|4714888|gb|AU056005.1|AU056005
EST:     ACCCCTAAGTNCTCCCCGGTTCTCCTAGACAAGTTCCCCGATGAACAAAG                         AAACNCGGATGACCTGTCGACCAAAGCGAGGTCGAAGTTCAGCATATTGCT
genomic: A-CCCTAAGTGCTCCCCGGTTCTCCTAGACAAGTTCCCAGATGAACAAAGgtcagtatcc ... tctgctatagAAACTCGGATGACCTGTCGACCAAAGCGAGGTCGAAGTTCAGCATATTGCT
EST: gi|87022799|gb|CI269735.1|CI269735
EST:     TACCCTAAGTGCTCCCCGGTTCTCCTAGACAAGTTCCCAGATGAACAAAG                         AAACTCGGATGACCTGTCGACCAAAGCGAGGTCGAAGTTCAGCATATTGCT
genomic: TACCCTAAGTGCTCCCCGGTTCTCCTAGACAAGTTCCCAGATGAACAAAGgtcagtatcc ... tctgctatagAAACTCGGATGACCTGTCGACCAAAGCGAGGTCGAAGTTCAGCATATTGCT
EST: gi|58656289|gb|CK044969.1|CK044969
EST:     TACCCTAAGTGCTCCCCGGTTCTCCTAGACAAGTTCCCAGATGAACAAAG                         AAACTCGGATGACCTGTCGACCAAAGCGAGGTCGAAGTTCAGCATATTGCT
genomic: TACCCTAAGTGCTCCCCGGTTCTCCTAGACAAGTTCCCAGATGAACAAAGgtcagtatcc ... tctgctatagAAACTCGGATGACCTGTCGACCAAAGCGAGGTCGAAGTTCAGCATATTGCT
EST: gi|88837309|gb|CI078669.1|CI078669
EST:     GATGAACAAAG                         AAACTCGGATGACCTGTCGACCAAAGCGAGGTCGAAGTTCAGCATATTGCT
genomic: GATGAACAAAGgtcagtatcc ... tctgctatagAAACTCGGATGACCTGTCGACCAAAGCGAGGTCGAAGTTCAGCATATTGCT
EST: gi|29678977|gb|CB675252.1|CB675252
EST:     TACCGTAAGTGCTCCCCGGTTTTCCTAGACAAGTTCCCAGATGAACAAAG                         AAACTCGGATGACCTGTCGACCAAAGCGAGGTCGAAGTTCAGCATATTGCT
genomic: TACCCTAAGTGCTCCCCGGTTCTCCTAGACAAGTTCCCAGATGAACAAAGgtcagtatcc ... tctgctatagAAACTCGGATGACCTGTCGACCAAAGCGAGGTCGAAGTTCAGCATATTGCT
EST: gi|29628192|gb|CB633203.1|CB633203
EST:     TACCCTAAGTGCTCCCCGGTTCTCCTAGACAAGTTCCCAGATGAACAAAG                         AAACTCGGATGACCTGTCGACCAAAGCGAGGTCGAAGTTCAGCATATTGCT
genomic: TACCCTAAGTGCTCCCCGGTTCTCCTAGACAAGTTCCCAGATGAACAAAGgtcagtatcc ... tctgctatagAAACTCGGATGACCTGTCGACCAAAGCGAGGTCGAAGTTCAGCATATTGCT
EST: gi|86481789|gb|CI124422.1|CI124422
EST:     TACCCTAAGTGCTCCCCGGTTCTCCTAGACAAGTTCCCAGATGAACAAAG                         AAACTCGGATGACCTGTCGACCAAAGCGAGGTCGAAGTTCAGCATATTGCT
genomic: TACCCTAAGTGCTCCCCGGTTCTCCTAGACAAGTTCCCAGATGAACAAAGgtcagtatcc ... tctgctatagAAACTCGGATGACCTGTCGACCAAAGCGAGGTCGAAGTTCAGCATATTGCT
EST: gi|87021007|gb|CI271814.1|CI271814
EST:     TACCATAAGTGCTCCCCGGTTCTCCTAGACAAGTTCCCAGATGAACAAAG                         AAACTCGGATGACCTGTCGACCAAAGCGAGGTCGAAGTTCAGCATATTGCT
genomic: TACCCTAAGTGCTCCCCGGTTCTCCTAGACAAGTTCCCAGATGAACAAAGgtcagtatcc ... tctgctatagAAACTCGGATGACCTGTCGACCAAAGCGAGGTCGAAGTTCAGCATATTGCT
EST: gi|89183682|gb|CI046247.1|CI046247
EST:     TTCCCAGATGAACAAAG                         AAACTCGGATGACCTGTCGACCAAAGCGAGGTCGAAGTTCAGCATATTGCT
genomic: TTCCCAGATGAACAAAGgtcagtatcc ... tctgctatagAAACTCGGATGACCTGTCGACCAAAGCGAGGTCGAAGTTCAGCATATTGCT
EST: gi|66917654|gb|CX104502.1|CX104502
EST:     TACCCTAAGTGCTCCCCGGTTCTCCTAGACAAGTTCCCAGATGAACAAAG                         AAACTCGGATGACCTGTCGACCAAAGCGAGGTCGAAGTTCAGCATATTGCT
genomic: TACCCTAAGTGCTCCCCGGTTCTCCTAGACAAGTTCCCAGATGAACAAAGgtcagtatcc ... tctgctatagAAACTCGGATGACCTGTCGACCAAAGCGAGGTCGAAGTTCAGCATATTGCT
EST: gi|58588407|gb|CF986715.1|CF986715
EST:     TACCCTAAGTGCTCCCCGGTTCTCCTAGACAAGTTCCCAGATGAACAAAG                         AAGGTCGGATGACCTGTCGACCAAAGCGAGGTCGAAGTTCAGCATATTGCT
genomic: TACCCTAAGTGCTCCCCGGTTCTCCTAGACAAGTTCCCAGATGAACAAAGgtcagtatcc ... tctgctatagAAACTCGGATGACCTGTCGACCAAAGCGAGGTCGAAGTTCAGCATATTGCT
EST: gi|33677747|gb|CF305986.1|CF305986
EST:     TACCCTAAGTGCTCCCCGGTTCTCCTAGACAAGTTCCCAGATGAACAAAG                         AAACTCGGATGACCTGTCGACCAAAGCGAGGTCGAAGTTCAGCATATTGCT
genomic: TACCCTAAGTGCTCCCCGGTTCTCCTAGACAAGTTCCCAGATGAACAAAGgtcagtatcc ... tctgctatagAAACTCGGATGACCTGTCGACCAAAGCGAGGTCGAAGTTCAGCATATTGCT

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: 56 (upstream exon), 64 (downstream exon)
Score: 10

AGTCCAATTTTGCCATTGAGGGTGCTTGTCCCCGCTAGCTACCCTAAGTGCTCCCCGGTTCTCCTAGACAAGTTCCCAGATGAACAAAGgtcagtatcc ... tctgctatagAAACTCGGATGACCTGTCGACCAAAGCGAGGTCGAAGTTCAGCATATTGCTTCGGGGTTTAGCTGAGCCCATGTCACTAAGAGAAATTGCGAGGACGTGG




<











<


<









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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGTCCAATTTTGCCATTGAGGGTGCTTGTCCCCGCTAGCTACCCTAAGTGCTCCCCGGTTCTCCTAGACAAGTTCCCAGATGAACAAAGgtcagtatccaatgttttatcagattctacgccaggtactacatattaggctgtcctgattctctgtacataaataaactaaggatgttgcattgtgcttgtgaatctgctatag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG