Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CATAGAGCCTGAAGAGCTTCGAGAGGCTCTAGTGGACGATGGAGCAGGTGACAGCATGGAAGTGGTGAACGACATATTGCAAGAAGTTGACACTGATAAGgtgatgatatttctgaatacaaccattcttttggtaatatcgttcaaaacttttttttatctaaataacatatgttttcttttcactgcag

Basic information

species Oryza sativa
transcript LOC_Os01g61590.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g61590.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G311220_T01 (Zea mays), 5'ss of exon 6
CATAGAGCCTGAAGAGCTTCGAGAGGCTCTAGTGGACGATGGAGCAGGTGACAGCATGGA---AGTGGTGAACGACATATTGCAAGAAGTTGACACTGATAAGgtga-tgatatttctg-------aatacaacca-ttcttttggtaat---atcgttcaa-aacttttttttatctaaataacatatgttttcttttcactgcag
    ||||| || ||||||||||||||||| |||||||| || || |  |||||||||||   |||||||||||||||| |||||||||| ||||| || ||||| | ||| | |           | ||  ||   || |||||||  |    ||||   |  |     | |  ||    |    |  |||| | |     |||||
---CGAGCCCGAGGAGCTTCGAGAGGCTCTGGTGGACGACGGGGCGGCCGACAGCATGGAGGAAGTGGTGAACGACATACTGCAAGAAGTCGACACCGACAAGgtcactgacactctcatgtctctagtaggacgggttattttggtcctctggtcgtctgatgaacgagtgtcgtccgtctcttgtccgtttacatcgatgtgcag
















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|88978852|gb|CI385175.1|CI385175
EST:     GTTGACACTGATAAG                         GATGGCAAGATTAGCTATGACGAATTTGTAGCAATGATGAAGACGGGCACA
genomic: GTTGACACTGATAAGgtgatgatat ... ttcactgcagGATGGCAAGATTAGCTATGACGAATTTGTAGCAATGATGAAGACGGGCACA
EST: gi|88997408|gb|CI390074.1|CI390074
EST:     TTGACACTGATAAG                         GATGGCAAGATTAGCTATGACGAATTTGTAGCAAATGATGAAGACGGGCAC
genomic: TTGACACTGATAAGgtgatgatat ... ttcactgcagGATGGCAAGATTAGCTATGACGAATTTGTAGC-AATGATGAAGACGGGCAC
EST: gi|86593036|gb|CI270593.1|CI270593
EST:     ACAGCATGGAAGTGGTGAACGACATATTGCAAGAAGTTGACACTGATAAG                         GATGGCAAGATTAGCTATGACGAATTTGTAGCAATGATGAAGACGGGCACA
genomic: ACAGCATGGAAGTGGTGAACGACATATTGCAAGAAGTTGACACTGATAAGgtgatgatat ... ttcactgcagGATGGCAAGATTAGCTATGACGAATTTGTAGCAATGATGAAGACGGGCACA
EST: gi|3767694|gb|AU031721.1|AU031721
EST:     TTGACACTGATAAG                         GATGGCAAGATTAGCTATGACGAATTTGTAGCAATGATGAAGACGGGCACA
genomic: TTGACACTGATAAGgtgatgatat ... ttcactgcagGATGGCAAGATTAGCTATGACGAATTTGTAGCAATGATGAAGACGGGCACA
EST: gi|2317402|gb|C22456.1|C22456
EST:     ACAGCATGGAAGTGGTGAACGACATATTGCAAGAAGTTGACACTGATAAG                         GATGGCAAGATTAGCTA
genomic: ACAGCATGGAAGTGGTGAACGACATATTGCAAGAAGTTGACACTGATAAGgtgatgatat ... ttcactgcagGATGGCAAGATTAGCTA
EST: gi|25806968|gb|CA762929.1|CA762929
EST:     ACAGCATGGAAGTGGTGAACGACATATTGCAAGAAGTTGACACTGATAAG                         GATGGCAAGATTAGCTATGACGAATTTGTAGCAATGATGAAGACGGGCACA
genomic: ACAGCATGGAAGTGGTGAACGACATATTGCAAGAAGTTGACACTGATAAGgtgatgatat ... ttcactgcagGATGGCAAGATTAGCTATGACGAATTTGTAGCAATGATGAAGACGGGCACA
EST: gi|88997802|gb|CI390346.1|CI390346
EST:     ACACTGATAAG                         GATGGCAAGATTAGCTATGACGAATTTGTAGCAATGATGAAGACGGGCACA
genomic: ACACTGATAAGgtgatgatat ... ttcactgcagGATGGCAAGATTAGCTATGACGAATTTGTAGCAATGATGAAGACGGGCACA
EST: gi|88971512|gb|CI017826.1|CI017826
EST:     ACAGCATGGAAGTGGTGAACGACATATTGCAAGAAGTTGACACTGATAAG                         GATGGCAAGATTAGCTATGACGAATTTGTAGCAATGATGAAGACGGGCACA
genomic: ACAGCATGGAAGTGGTGAACGACATATTGCAAGAAGTTGACACTGATAAGgtgatgatat ... ttcactgcagGATGGCAAGATTAGCTATGACGAATTTGTAGCAATGATGAAGACGGGCACA
EST: gi|88268336|gb|CI378271.1|CI378271
EST:     CAGCATGGAAGTGGTGAACGACATATTGCAAGAAGTTGACACTGATAAG                         GATGGCAAGATTAGCTATGACGAATTTGTAGCAAATGATGAAGACGGGCAC
genomic: CAGCATGGAAGTGGTGAACGACATATTGCAAGAAGTTGACACTGATAAGgtgatgatat ... ttcactgcagGATGGCAAGATTAGCTATGACGAATTTGTAGC-AATGATGAAGACGGGCAC
EST: gi|27547979|gb|CA766009.2|CA766009
EST:     ACAGCATGGAAGTGGTGAACGACATATTGCAAGAAGTTGACACTGATAAG                         GATGGCAAGATTAGCTATGACGAATTTGTAGCAATGATGAAGACGGGCACA
genomic: ACAGCATGGAAGTGGTGAACGACATATTGCAAGAAGTTGACACTGATAAGgtgatgatat ... ttcactgcagGATGGCAAGATTAGCTATGACGAATTTGTAGCAATGATGAAGACGGGCACA
EST: gi|88956634|gb|CI092826.1|CI092826
EST:     ACAGCATGGAAGTGGTGAACGACATATTGCAAGAAGTTGACACTGATAAG                         GATGGCAAGATTAGCTATGACGAATTTGTAGCAATGATGAAGACGGGCACA
genomic: ACAGCATGGAAGTGGTGAACGACATATTGCAAGAAGTTGACACTGATAAGgtgatgatat ... ttcactgcagGATGGCAAGATTAGCTATGACGAATTTGTAGCAATGATGAAGACGGGCACA
EST: gi|88994239|gb|CI116203.1|CI116203
EST:     ACAGCATGGAAGTGGTGAACGACATATTGCAAGAAGATGACACTGATAAG                         GATGGCAAGATTAGCTATGACGAATTTGTAGCAATGATGAAGACGGGCACA
genomic: ACAGCATGGAAGTGGTGAACGACATATTGCAAGAAGTTGACACTGATAAGgtgatgatat ... ttcactgcagGATGGCAAGATTAGCTATGACGAATTTGTAGCAATGATGAAGACGGGCACA

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: 74 (upstream exon), 75 (downstream exon)
Score: 36

CATAGAGCCTGAAGAGCTTCGAGAGGCTCTAGTGGACGATGGAGCAGGTGACAGCATGGAAGTGGTGAACGACATATTGCAAGAAGTTGACACTGATAAGgtgatgatat ... ttcactgcagGATGGCAAGATTAGCTATGACGAATTTGTAGCAATGATGAAGACGGGCACAGATTGGAGAAAGGCGTCCCGGCATTACTCTAGAGGAAGATTCAACAGCC




<











<


<









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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CATAGAGCCTGAAGAGCTTCGAGAGGCTCTAGTGGACGATGGAGCAGGTGACAGCATGGAAGTGGTGAACGACATATTGCAAGAAGTTGACACTGATAAGgtgatgatatttctgaatacaaccattcttttggtaatatcgttcaaaacttttttttatctaaataacatatgttttcttttcactgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT