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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGCAAGAGAAAAGGCAACAAAGCGCTTGCTGCAGGAGATTCAGATCTTTCAGCCTCAACATCAGAGGATGAAGAGTCGGATGATGAGACTACTGAAGAGgtactcaatctttttttaccattcatttgtcctgctggagcactgtgtagtagacagttcaagctagtcatcttagaaaatcactattccccttaaaatagtccgtgtgaatcataacaaatttcaattactgatgtaaaacggacagcag

Basic information

species Oryza sativa
transcript LOC_Os01g05800.2
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g05800.2 (Oryza sativa), 5'ss of exon 10
lower sequence: GRMZM2G110063_T01 (Zea mays), 5'ss of exon 11
GAGCAAGAGAAAAGGCAACAAAGCGCTTGCTGCAGGAGATTCAGATCTTTCAGCCTCAACAT------CAGAGGATGAAGAGTCGGATGATGAGACTACTGAAGAGgtactcaatctttttttaccattcatttgtcctgctggagcactgtgtagtagacagttcaagctagtcatcttagaaa-atcactattccccttaaaatagtccgtgtgaatcataacaaatttcaattactgatgtaaaacggacagcag
      |||||||| ||||||||| || ||||||||||| ||| ||   ||  | ||||| |        |||||||||||||||||||| ||||| || |||||||||| |  |     |||      || |  | | | ||| ||| ||||  |  ||    |||     |  |    | |    || |||   | | ||||  |   ||||  | ||||  |   || |   || ||   | | | | | |||||
------GAGAAAAGTCAACAAAGCACTCGCTGCAGGAGACTCAAATGCATCGTCATCAACGTATGACATGGAGGATGAAGAGTCGGATGACGAGACCACAGAAGAGgtacactcttcacctttttttcccactattacagttgg-gcattgtggggatgaagaatcatatcggaaaaaaaacacttgtccctacagctcctaaagaa---cgtgaaattcatcccctgttacttata-tgtaatcatatgca-agcag
















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|4714906|gb|AU056023.1|AU056023
EST:     CAGCCTCAACATCAGAGGATGAAGAGTCGGATGATGAGACTACTGAAGAG                         GGAGGACCTGAGGAAAGATACAATTCCAGTAGCAACAAGAAACTTCCAAAT
genomic: CAGCCTCAACATCAGAGGATGAAGAGTCGGATGATGAGACTACTGAAGAGgtactcaatc ... cggacagcagGGAGGACCTGAGGAAAGATACAATTCCAGTAGCAACAAGAAACTTCCAAAT
EST: gi|88994803|gb|CI036384.1|CI036384
EST:     CAGCCTCAACATCAGAGGATGAAGAGTCGGATGATGAGACTACTGAAGAG                         GGAGGACCTGAGGAAAGATACAATTCCAGTGGCAACAAGAAACTTCCAAAT
genomic: CAGCCTCAACATCAGAGGATGAAGAGTCGGATGATGAGACTACTGAAGAGgtactcaatc ... cggacagcagGGAGGACCTGAGGAAAGATACAATTCCAGTAGCAACAAGAAACTTCCAAAT
EST: gi|86905375|gb|CI285338.1|CI285338
EST:     CAGCCTCAACATCAGAGGATGAAGAGTCGGATGATGAGACTACTGAAGAG                         GGAGGACCTGAGGAAAGATACAATTCCAGTAGCAACAAGAAACTTCCAAAT
genomic: CAGCCTCAACATCAGAGGATGAAGAGTCGGATGATGAGACTACTGAAGAGgtactcaatc ... cggacagcagGGAGGACCTGAGGAAAGATACAATTCCAGTAGCAACAAGAAACTTCCAAAT
EST: gi|88983200|gb|CI020764.1|CI020764
EST:     CAGCCTCAACATCAGAGGATGAAGAGTCGGATGATGAGACTACTGAAGAG                         GGAGGACCTGAGGAAAGATACAATTCCAGTAGCAACAAGAAACTTCCAAAT
genomic: CAGCCTCAACATCAGAGGATGAAGAGTCGGATGATGAGACTACTGAAGAGgtactcaatc ... cggacagcagGGAGGACCTGAGGAAAGATACAATTCCAGTAGCAACAAGAAACTTCCAAAT
EST: gi|14713818|gb|AU197781.1|AU197781
EST:     CAGCCTCAACATCAGAGGATGAAGAGTCGGATGATGAGACTACTGAAGAG                         C
genomic: CAGCCTCAACATCAGAGGATGAAGAGTCGGATGATGAGACTACTGAAGAGgtactcaatc ... cggacagcag-
EST: gi|14713818|gb|AU197781.1|AU197781
EST:     CAGCCTCAACATCAGAGGATGAAGAGTCGGATGATGAGACTACTGAAGAG                         C
genomic: CAGCCTCAACATCAGAGGATGAAGAGTCGGATGATGAGACTACTGAAGAGgtactcaatc ... cggacagcag-
EST: gi|14713818|gb|AU197781.1|AU197781
EST:     CAGCCTCAACATCAGAGGATGAAGAGTCGGATGATGAGACTACTGAAGAG                         C
genomic: CAGCCTCAACATCAGAGGATGAAGAGTCGGATGATGAGACTACTGAAGAGgtactcaatc ... cggacagcag-
EST: gi|4714905|gb|AU056022.1|AU056022
EST:     CAGCCTCAACATCAGAGGATGAAGAGTCGGATGATGAGACTACTGAAGAG                         GGAGGACCTGAGGANAGATACAATTCCAGTAGCAACAAGAAACTTCCAAAT
genomic: CAGCCTCAACATCAGAGGATGAAGAGTCGGATGATGAGACTACTGAAGAGgtactcaatc ... cggacagcagGGAGGACCTGAGGAAAGATACAATTCCAGTAGCAACAAGAAACTTCCAAAT
EST: gi|84117524|gb|CD151291.1|CD151291
EST:     CAGCCTCAACATCAGAGGACGAAGAATCGGATGATGAGATTACTGAAGAG                         GGAGGACCTGAGGAAAGATACAATTCCAGTAGCAACAAGAAACTTCCAAAT
genomic: CAGCCTCAACATCAGAGGATGAAGAGTCGGATGATGAGACTACTGAAGAGgtactcaatc ... cggacagcagGGAGGACCTGAGGAAAGATACAATTCCAGTAGCAACAAGAAACTTCCAAAT
EST: gi|89173571|gb|CI041464.1|CI041464
EST:     AGAGGATGAAGAGTCGGATGATGAGACTACTGAAGAGCAG                       
genomic: AGAGGATGAAGAGTCGGATGATGAGACTACTG-A-AG-AGgtactcaatc ... cggacagc
EST: gi|29620328|gb|CB625340.1|CB625340
EST:     CAGCCTCAACATCAGAGGACGAAGAATCGGATGATGAGATTACTGAAGAG                         GGAGGACCTGAGGAAAGATACAATTCCAGTAGCAACAAGAAACTTCCAAAT
genomic: CAGCCTCAACATCAGAGGATGAAGAGTCGGATGATGAGACTACTGAAGAGgtactcaatc ... cggacagcagGGAGGACCTGAGGAAAGATACAATTCCAGTAGCAACAAGAAACTTCCAAAT

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), 73 (downstream exon)
Score: 64

GAGCAAGAGAAAAGGCAACAAAGCGCTTGCTGCAGGAGATTCAGATCTTTCAGCCTCAACATCAGAGGATGAAGAGTCGGATGATGAGACTACTGAAGAGgtactcaatc ... cggacagcagGGAGGACCTGAGGAAAGATACAATTCCAGTAGCAACAAGAAACTTCCAAATTACTCCGGAAAGAAGGGCAAAAGATCAAAGAGGAAGCGCATGGTTCAGT




<











<


<









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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAGCAAGAGAAAAGGCAACAAAGCGCTTGCTGCAGGAGATTCAGATCTTTCAGCCTCAACATCAGAGGATGAAGAGTCGGATGATGAGACTACTGAAGAGgtactcaatctttttttaccattcatttgtcctgctggagcactgtgtagtagacagttcaagctagtcatcttagaaaatcactattccccttaaaatagtccgtgtgaatcataacaaatttcaattactgatgtaaaacggacagcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA