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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTGAGTTGAAGAAGAAGAGTTCCAAGTCAAAGCGGCCAACTATCAAGACATTATTTGgtattgagcactattattacctattggttccttatacaccatgtaccgtttttcatgatatgtttaacttgcttttatccttaaaacag

Basic information

species Oryza sativa
transcript LOC_Os05g43570.1
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g43570.3 (Oryza sativa), 5'ss of exon 13
lower sequence: GRMZM2G375904_T01 (Zea mays), 5'ss of exon 12
CTGAGTTGAAGAAGAAGAGTTCCAAGTCAAAGCGGCCAACTATCAAGACATTATTTGgtattgagcactattattacctattggttccttatac-accatgtaccgttt-----ttcatgatatgtttaacttgcttttatccttaaaacag
| ||||||||||| |||||||||||  ||||||| ||||| ||||||||| | ||||||| |||||  | ||   |   |||    |  | ||| | |     |||||      |  | |||    ||| ||||| || |||  | || |||
CAGAGTTGAAGAAAAAGAGTTCCAAACCAAAGCGACCAACCATCAAGACAATGTTTGgtaatgagccatcttgc-atgaatttcacctctctactatctctctccgttaaggcatgaacgatccacttaccttgcattcatctctgaa-cag
















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|86413248|gb|CI067653.1|CI067653
EST:     GAAGAAGAAGAGTTCCAAGTCAAAGCGGCCAACTATCAAGACATTATTTG                         AGAGCATGGATGAAGATGAGCCTGTTCAAGGAAGTTTCTTAAATATGTTGC
genomic: GAAGAAGAAGAGTTCCAAGTCAAAGCGGCCAACTATCAAGACATTATTTGgtattgagca ... cttaaaacagAGAGCATGGATGAAGATGAGCCTGTTCAAGGAAGTTTCTTAAATATGTTGC
EST: gi|88260620|gb|CI362913.1|CI362913
EST:     TCAAGACATTATTTG                         AGAGCATGGATGAAGATGAGCCTGTTCAAGGAAGTTTCTTAAATATGTTGC
genomic: TCAAGACATTATTTGgtattgagca ... cttaaaacagAGAGCATGGATGAAGATGAGCCTGTTCAAGGAAGTTTCTTAAATATGTTGC
EST: gi|88273784|gb|CI394190.1|CI394190
EST:     TCAAGACATTATTTG                         AGAGCATGGATGAAGATGAGCCTGTTCAAGGAAGTTTCTTAAATATGTTGC
genomic: TCAAGACATTATTTGgtattgagca ... cttaaaacagAGAGCATGGATGAAGATGAGCCTGTTCAAGGAAGTTTCTTAAATATGTTGC
EST: gi|88264036|gb|CI367810.1|CI367810
EST:     AGACATTATTTG                         AGAGCATGGATGAAGATGAGCCTGTTCAAGGAAGTTTCTTAAATATGTTGC
genomic: AGACATTATTTGgtattgagca ... cttaaaacagAGAGCATGGATGAAGATGAGCCTGTTCAAGGAAGTTTCTTAAATATGTTGC
EST: gi|325494464|gb|JG458988.1|JG458988
EST:     GAAGAAGAAGAGTTCCAAGTCAAAGCGGCCAACTATCAAGACATTATTTG                         AGAGCATGGATGAAGATGAGCCTGTTCAAGGAAGTTTCTTAAATATGTTGC
genomic: GAAGAAGAAGAGTTCCAAGTCAAAGCGGCCAACTATCAAGACATTATTTGgtattgagca ... cttaaaacagAGAGCATGGATGAAGATGAGCCTGTTCAAGGAAGTTTCTTAAATATGTTGC
EST: gi|86827108|gb|CI270824.1|CI270824
EST:     GAAGAAGAAGAGTTCCAAGTCAAAGCGGCCAACTATCAAGACATTATTTG                         AGAGCATGGATGAAGATGAGCCTGTTCAAGGAAGTTTCTTAAATATGTTGC
genomic: GAAGAAGAAGAGTTCCAAGTCAAAGCGGCCAACTATCAAGACATTATTTGgtattgagca ... cttaaaacagAGAGCATGGATGAAGATGAGCCTGTTCAAGGAAGTTTCTTAAATATGTTGC
EST: gi|86477542|gb|CI120175.1|CI120175
EST:     GAAGAAGAAGAGTTCCAAGTCAAAGCGGCCAACTATCAAGACATTATTTG                         AGGGCATGGATGAAGATGAGCCTGTTCAAGGAAGTTTCTTAAATATGTTGC
genomic: GAAGAAGAAGAGTTCCAAGTCAAAGCGGCCAACTATCAAGACATTATTTGgtattgagca ... cttaaaacagAGAGCATGGATGAAGATGAGCCTGTTCAAGGAAGTTTCTTAAATATGTTGC
EST: gi|88975445|gb|CI023696.1|CI023696
EST:     GAGTTCCAAGTCAAAGCGGCCGACTATCAAGACATTATTTG                         AGAGCATGGATGAAGATGAGCCTGTTCAAGGAAGTTTCTTAAATATGTTGC
genomic: GAGTTCCAAGTCAAAGCGGCCAACTATCAAGACATTATTTGgtattgagca ... cttaaaacagAGAGCATGGATGAAGATGAGCCTGTTCAAGGAAGTTTCTTAAATATGTTGC
EST: gi|55408515|gb|CV720891.1|CV720891
EST:     GAAGAAGAAGAGTTCCAAGTCAAAGCGGCCAACTATCAAGACATTATTTG                         AGAGCATGGATGAAGATGAGCCTGTTCAAGGAAGTTTCTTAAATATGTTGC
genomic: GAAGAAGAAGAGTTCCAAGTCAAAGCGGCCAACTATCAAGACATTATTTGgtattgagca ... cttaaaacagAGAGCATGGATGAAGATGAGCCTGTTCAAGGAAGTTTCTTAAATATGTTGC
EST: gi|88850051|gb|CI091346.1|CI091346
EST:     GAAGAAGAAGAGTTCCAAGTCAAAGCGGCCAACTATCAAGACATTATTTG                         AGAGCATGGATGAAGATGAGCCTGTTCAAGGAAGTTTCTTAAATATGTTGC
genomic: GAAGAAGAAGAGTTCCAAGTCAAAGCGGCCAACTATCAAGACATTATTTGgtattgagca ... cttaaaacagAGAGCATGGATGAAGATGAGCCTGTTCAAGGAAGTTTCTTAAATATGTTGC
EST: gi|86841681|gb|CI337375.1|CI337375
EST:     GAAGAAGAAGAGTTCCAAGTCAAAGCGGCCAACTATCAAGACATTATTTG                         AGAGCATGGATGAAGATGAGCCTGTTCAAGGAAGTTTCTTAAATATGTTGC
genomic: GAAGAAGAAGAGTTCCAAGTCAAAGCGGCCAACTATCAAGACATTATTTGgtattgagca ... cttaaaacagAGAGCATGGATGAAGATGAGCCTGTTCAAGGAAGTTTCTTAAATATGTTGC
EST: gi|29623780|gb|CB628791.1|CB628791
EST:     GAAGAAGAAGAGTTCCAAGTCAAAGCGGCCAACTATCAAGACATTATTTG                         AGAGCATGGATGAAGATGAGCCTGTTCAAGGAAGTTTCTTAAATATGTTGC
genomic: GAAGAAGAAGAGTTCCAAGTCAAAGCGGCCAACTATCAAGACATTATTTGgtattgagca ... cttaaaacagAGAGCATGGATGAAGATGAGCCTGTTCAAGGAAGTTTCTTAAATATGTTGC

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: 71 (upstream exon), 50 (downstream exon)
Score: 5

CTGAGTTGAAGAAGAAGAGTTCCAAGTCAAAGCGGCCAACTATCAAGACATTATTTGgtattgagca ... cttaaaacagAGAGCATGGATGAAGATGAGCCTGTTCAAGGAAGTTTCTTAAATATGTTGCCCCATAAGGAGGGGCAACCTTCATCTCACTCCACCATTCCACCAGAACA




<











<


<









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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTGAGTTGAAGAAGAAGAGTTCCAAGTCAAAGCGGCCAACTATCAAGACATTATTTGgtattgagcactattattacctattggttccttatacaccatgtaccgtttttcatgatatgtttaacttgcttttatccttaaaacag

- - - - AAGAAG
- - - - -  AAGAAG