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

TTGTGTTGTTGTTGAAGACAGTACTATAGGGCTTGCAGCAGCCAAAGCTGCTGGTATGAAGTGTATCGTAACAAAAAGCGGgtaagattttttttttccatgaaatatttcagttgcatcaaatcgctttcactaattttgcatgtattccataataaaggcatctgttgatctcttctgg...

Basic information

species Oryza sativa
transcript LOC_Os03g36750.1
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g36750.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G094978_T02 (Zea mays), 5'ss of exon 7
TTGTGTTGTTGTTGAAGACAGTACTATAGGGCTTGCAGCAGCCAAAGCTGCTGGTATGAAGTGTATCGTAACAAAAAGCGGgta-agattttttttttccatgaaatatttcagttgcatcaaatcgctttcactaattttgcatgtattccataa--taaaggcatctgttgatctcttctgg---
 ||||||||| |||||||||||||||||||||| ||||| || |||||||| || ||||||||||||||||||||||||||||| ||||||| ||||||   | || | ||  |     |  | | |     ||     | |   | |||     |  || |  || ||| |  ||     ||    
CTGTGTTGTTATTGAAGACAGTACTATAGGGCTCGCAGCGGCAAAAGCTGCCGGCATGAAGTGTATCGTAACAAAAAGCGGgtacagattttctttttc---ggaacacttagggc---ttgattgggagcaaccggaatggagggaattaagggagctataatcacctgctattcaaaattgaata

upper sequence: LOC_Os03g36750.1 (Oryza sativa), 5'ss of exon 7
lower sequence: Vv17s0000g09910.t01 (Vitis vinifera), 5'ss of exon 7
TTGTGTTGTTGTTGAAGACAGTACTATAGGGCTTGCAGCAGCCAAAGCTGCTGGTATGAAGTGTATCGTAACAAAAAGCGGgtaagattttttttttccatgaaatatttcagttgcatca----aatcgctttcactaattttgcatgtattccataataaaggcatctgttgatctcttctgg--------------
 ||||| || || || |||||| | || || |||||||| ||||| |||||||| ||||||||||| |||||||| |||||||||| | ||| |||       |||  |  | || |  ||    |||        |||| |||  ||   |   |      |||  | |    |  |||||                 
ATGTGTGGTGGTAGAGGACAGTGCCATTGGTCTTGCAGCTGCCAAGGCTGCTGGAATGAAGTGTATTGTAACAAAGAGCGGgtaagttgtttctttctttatgaatgctctatttactacacttgaatgatgaatcctaaatttttatagctgtgagttgtgaggtctttcaacaaatcttcaaaatctatggttgcag
















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|12405331|gb|AU166932.1|AU166932
EST:     CTTGCAGCAGCCAAAGCTGCTGGTATGAAGTGTATCGTAACAAAAAGCGG                         ATACACTGCAGAAGAGGACTTTGCAACAGCTGATGCTGTGTTCGATTGCAT
genomic: CTTGCAGCAGCCAAAGCTGCTGGTATGAAGTGTATCGTAACAAAAAGCGGgtaagatttt ... cgctgtgcagATACACTGCAGAAGAGGACTTTGCAACAGCTGATGCTGTGTTCGATTGCAT
EST: gi|33684374|gb|CF312613.1|CF312613
EST:     CTTGCAGCAGCCAAAGCTGCTGGTATGAAGTGTATCGTAACAAAAAGCGG                         ATACACTGCAGA
genomic: CTTGCAGCAGCCAAAGCTGCTGGTATGAAGTGTATCGTAACAAAAAGCGGgtaagatttt ... cgctgtgcagATACACTGCAGA
EST: gi|88479052|gb|CI416323.1|CI416323
EST:     TTGCAGCAGCCAAAGCTGGCTGGTATGAANTGTATCGTAACAANAAGCGG                         ATACAGTGCAGAAGAGGACTTTGCAACAGCTGATGCTGTGTTCGATTGCAT
genomic: TTGCAGCAGCCAAAGCT-GCTGGTATGAAGTGTATCGTAACAAAAAGCGGgtaagatttt ... cgctgtgcagATACACTGCAGAAGAGGACTTTGCAACAGCTGATGCTGTGTTCGATTGCAT
EST: gi|86862357|gb|CI345350.1|CI345350
EST:     CTTGCAGCAGCCAAAGCTGCTGGTATGAAGTGTATCGTAACAAAAAGC-G                         ATACACTGCAGAAGAGGACTTTGCAACAGCTGATGCTGTGTTCGATTGCAT
genomic: CTTGCAGCAGCCAAAGCTGCTGGTATGAAGTGTATCGTAACAAAAAGCGGgtaagatttt ... cgctgtgcagATACACTGCAGAAGAGGACTTTGCAACAGCTGATGCTGTGTTCGATTGCAT
EST: gi|88503981|gb|CI431487.1|CI431487
EST:     TTCCAGCAGCCAAANCCTGCTGGTATGAANTGTATCGTAACAAAAAGCGG                         ATACACTGCAGAAGAGGACTTTGCAACAGCTGATGCTGTGTTCGATTGCAT
genomic: TTGCAGCAGCCAAA-GCTGCTGGTATGAAGTGTATCGTAACAAAAAGCGGgtaagatttt ... cgctgtgcagATACACTGCAGAAGAGGACTTTGCAACAGCTGATGCTGTGTTCGATTGCAT
EST: gi|88258818|gb|CI359208.1|CI359208
EST:     CTTGCAGCAGCCAAAGCTGCTGGTATGAAGTGTATCGTAACAAAAAGCGG                         ATACACTGCAGAAGAGGACTTTGCAACAGCTGATGCTGTGTTCGATTGCAT
genomic: CTTGCAGCAGCCAAAGCTGCTGGTATGAAGTGTATCGTAACAAAAAGCGGgtaagatttt ... cgctgtgcagATACACTGCAGAAGAGGACTTTGCAACAGCTGATGCTGTGTTCGATTGCAT
EST: gi|38472504|gb|CF956636.1|CF956636
EST:     TAGCAGCAGCCAAAGCTGCTGGTATGAAGTAGTATCGTAACAAAAAGCGG                         ATACACTGCAGAAGAGGACTTTGCAACAGCTGATGCTGTGTTCGATTGCAT
genomic: TTGCAGCAGCCAAAGCTGCTGGTATGAAGT-GTATCGTAACAAAAAGCGGgtaagatttt ... cgctgtgcagATACACTGCAGAAGAGGACTTTGCAACAGCTGATGCTGTGTTCGATTGCAT
EST: gi|29625469|gb|CB630480.1|CB630480
EST:     CTTGCAGCAGCCAAAGCTGCTGGTATGAAGTGTATCGTAACAAAAAGCGG                         ATACACTGCAGAAGAGGACTTTGCAACAGCTGATGCTGTGTTCGATTGCAT
genomic: CTTGCAGCAGCCAAAGCTGCTGGTATGAAGTGTATCGTAACAAAAAGCGGgtaagatttt ... cgctgtgcagATACACTGCAGAAGAGGACTTTGCAACAGCTGATGCTGTGTTCGATTGCAT
EST: gi|38473540|gb|CF957672.1|CF957672
EST:     CTTGCAGCAGCCAAAGCTGCTGGTATGAAGTGTATCGTAACAAAAAGCGG                         ATACACTGCAGAAGAGGACTTTGCAACAGCTGATGCTGTGTTCGATTGCAT
genomic: CTTGCAGCAGCCAAAGCTGCTGGTATGAAGTGTATCGTAACAAAAAGCGGgtaagatttt ... cgctgtgcagATACACTGCAGAAGAGGACTTTGCAACAGCTGATGCTGTGTTCGATTGCAT
EST: gi|33797557|gb|CF324638.1|CF324638
EST:     CTTGCAGCAGCCAAAGCTGCTGGTATGAAGTGTATCGTAACAAAAAGCGG                         ATACACTGCAGAAGAGGACTTTGCAACAGCTGATGCTGTGTTCGATTGCAT
genomic: CTTGCAGCAGCCAAAGCTGCTGGTATGAAGTGTATCGTAACAAAAAGCGGgtaagatttt ... cgctgtgcagATACACTGCAGAAGAGGACTTTGCAACAGCTGATGCTGTGTTCGATTGCAT
EST: gi|117242305|gb|CT842941.1|CT842941
EST:     CTTGCAGCAGCCAAAGCTGCTGGTATGAAGTGTATCGTAACAAAAAGCGG                         ATACACTGCAGAAGAGGACTTTGCAACAGCTGATGCTGTGTTCGATTGCAT
genomic: CTTGCAGCAGCCAAAGCTGCTGGTATGAAGTGTATCGTAACAAAAAGCGGgtaagatttt ... cgctgtgcagATACACTGCAGAAGAGGACTTTGCAACAGCTGATGCTGTGTTCGATTGCAT
EST: gi|29657435|gb|CB653710.1|CB653710
EST:     CTTGCAGCAGCCAAAGCTGCTGGTATGAAGTGTATCGTAACAAAAAGCGG                         ATACACTGCAGAAGAGGACTTTGCAACAGCTGATGCTGTGTTCGATTGCAT
genomic: CTTGCAGCAGCCAAAGCTGCTGGTATGAAGTGTATCGTAACAAAAAGCGGgtaagatttt ... cgctgtgcagATACACTGCAGAAGAGGACTTTGCAACAGCTGATGCTGTGTTCGATTGCAT
EST: gi|38475316|gb|CF959449.1|CF959449
EST:     GTTGCAGCAGCCAAAGCTGCTGGTATGAAGTGTATCGTAACAAAAAGCGG                         ATACACTGCAGAAGAGGACTTTGCAACAGCTGATGCTGTGTTCGATTGCAT
genomic: CTTGCAGCAGCCAAAGCTGCTGGTATGAAGTGTATCGTAACAAAAAGCGGgtaagatttt ... cgctgtgcagATACACTGCAGAAGAGGACTTTGCAACAGCTGATGCTGTGTTCGATTGCAT
EST: gi|58586453|gb|CF984761.1|CF984761
EST:     CTTGCAGCAGCCAAAGCTGCTGGTATGAAGTGTATCGTAACAAACAGCGG                         ATACACTGCAGAAGAGGACTTTGCAACAGCTGATGCTGTGTTCGATTGCCT
genomic: CTTGCAGCAGCCAAAGCTGCTGGTATGAAGTGTATCGTAACAAAAAGCGGgtaagatttt ... cgctgtgcagATACACTGCAGAAGAGGACTTTGCAACAGCTGATGCTGTGTTCGATTGCAT
EST: gi|88257860|gb|CI360446.1|CI360446
EST:     CTTGCAGCAGCCAAAGCTGCTGGTATGAAGTGTATCGTAACAAAAAGCGG                         ATACACTGCAGGAGAGGACTTTGCAACAGCTGATGCTGTGTTCGATTGCAT
genomic: CTTGCAGCAGCCAAAGCTGCTGGTATGAAGTGTATCGTAACAAAAAGCGGgtaagatttt ... cgctgtgcagATACACTGCAGAAGAGGACTTTGCAACAGCTGATGCTGTGTTCGATTGCAT
EST: gi|38478320|gb|CF962453.1|CF962453
EST:     CTTGCAGCAGCCAAAGCTGCTGGTATGAAGTGTATCGTAACAAAAAGCGG                         ATACACTGCAGAAGAGGACTTTGCAAGGGCTGATGCTGTGTTCGATTGCAT
genomic: CTTGCAGCAGCCAAAGCTGCTGGTATGAAGTGTATCGTAACAAAAAGCGGgtaagatttt ... cgctgtgcagATACACTGCAGAAGAGGACTTTGCAACAGCTGATGCTGTGTTCGATTGCAT
EST: gi|38471972|gb|CF956103.1|CF956103
EST:     CTTGCAGCAGCCAAAGCTGCTGGTATGAAGTGTATCGTAACAAAAAGCGG                         ATACACTGCAGAAGAGGACTTTGCAACAGCTGATGCTGTGTTCGATTGCAT
genomic: CTTGCAGCAGCCAAAGCTGCTGGTATGAAGTGTATCGTAACAAAAAGCGGgtaagatttt ... cgctgtgcagATACACTGCAGAAGAGGACTTTGCAACAGCTGATGCTGTGTTCGATTGCAT
EST: gi|29687538|gb|CB683813.1|CB683813
EST:     CTTGCAGCAGCCAAAGCTGCTGGTATGAAGTGTATCGTAACAAAAAGCGG                         ATACACTGCAGAAGAGGACTTTGCAACAGCTGATGCTGTGTTCGATTGCAT
genomic: CTTGCAGCAGCCAAAGCTGCTGGTATGAAGTGTATCGTAACAAAAAGCGGgtaagatttt ... cgctgtgcagATACACTGCAGAAGAGGACTTTGCAACAGCTGATGCTGTGTTCGATTGCAT

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: 65 (upstream exon), 70 (downstream exon)
Score: 40

TTGTGTTGTTGTTGAAGACAGTACTATAGGGCTTGCAGCAGCCAAAGCTGCTGGTATGAAGTGTATCGTAACAAAAAGCGGgtaagatttt ... cgctgtgcagATACACTGCAGAAGAGGACTTTGCAACAGCTGATGCTGTGTTCGATTGCATTGGTGACCCTCCAGAAGTACGCTTTGATTTGGAGTTCTGCGCCAACCTC




<











<


<









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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTGTGTTGTTGTTGAAGACAGTACTATAGGGCTTGCAGCAGCCAAAGCTGCTGGTATGAAGTGTATCGTAACAAAAAGCGGgtaagattttttttttccatgaaatatttcagttgcatcaaatcgctttcactaattttgcatgtattccataataaaggcatctgttgatctcttctgg

- - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - GCTGCT