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'   		14  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtatttcatagtaagctcaattagtatcttcgggccattcattttttttcttcatttatttgattgtgttaatttcctctgcagAATGACTTGGTTCATGGATGGGGCCTTGATTTTGCTCTCAGGAAATGCGTGGAG

Basic information

species Oryza sativa
transcript LOC_Os05g01760.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g01760.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM5G846339_T01 (Zea mays), 3'ss of exon 11
gtttgtatttcatagtaagctcaattagtatcttcgggccattcattttttttcttcatttatttgattgtgttaatttcctctgcagAATGACTTGGTTCATGGATGGGGCCTTGATTTTGCTCTCAGGAAATGCGTGGAG
||| || | ||      |  ||   | || |||   | | ||    ||   | ||| |  || ||| | |   |   ||     |||||| |||||||||||||| |||||| | |||||||| ||||||||||| ||||||
gttcgtctgtctgtcatacttctccttgtgtct---gtctatc---ttcggtcctttacataattgttcggcattgctttggacgcagAACGACTTGGTTCATGGTTGGGGCTTGGATTTTGCGCTCAGGAAATGTGTGGAG

upper sequence: LOC_Os05g01760.1 (Oryza sativa), 3'ss of exon 11
lower sequence: AT1G08040.2 (Arabidopsis thaliana), 3'ss of exon 11
-------------------------------------------------------------------------------gtttgtatttca--tagtaagctcaattagtatcttcgggccattcattttttttcttcatttatttgattgtgttaatttcctctgcagAATGACTTGGTTCATGGATGGGGCCTTGATTTTGCTCTCAGGAAATGCGTGGAG
                                                                               |||| |  || |  ||  ||    | || || |  ||   |    |||   ||     | |  |    ||  ||||  ||||   ||||||||||  | |||||||||||||| || ||||||||||||||   |||||| |||
gtttttgtttaactttattcacctttttacgatcggtattcacatgacccaaatttgtggcattgatgaatctacgttggtttctgattaagctatcaaaaggagtttgtctagtcttccagaccatcacttggtagcctaaaaacaatcttgtttgtttctggtgcagAATGATCTTGTTCATGGATGGGGTCTCGATTTTGCTCTCAGACGATGCGTTGAG
















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|86256753|gb|CI061516.1|CI061516
EST:     AGATGCATGGAGATGTGTATGGCATATGATTCAG                         AATGACTTGGTTCATGGATGGGGCCTTGATTTTGCTCTCAGGAAATGCGTG
genomic: AGATGCATGGAGATGTGTATGGCATATGATTCAGgtttgtattt ... tcctctgcagAATGACTTGGTTCATGGATGGGGCCTTGATTTTGCTCTCAGGAAATGCGTG
EST: gi|88247670|gb|CI247519.1|CI247519
EST:     ATGGCATATGATTCAG                         AATGACTTGGTTCATGGATGGGGCCTTGATTTTGCTCTCAGGAAATGCGTG
genomic: ATGGCATATGATTCAGgtttgtattt ... tcctctgcagAATGACTTGGTTCATGGATGGGGCCTTGATTTTGCTCTCAGGAAATGCGTG
EST: gi|86480070|gb|CI122703.1|CI122703
EST:     ATATGATTCAG                         AATGACTTGGTTCATGGATGGGGCCTTGATTTTGCTCTCAGGAAATGCGTG
genomic: ATATGATTCAGgtttgtattt ... tcctctgcagAATGACTTGGTTCATGGATGGGGCCTTGATTTTGCTCTCAGGAAATGCGTG
EST: gi|29674708|gb|CB670983.1|CB670983
EST:     CTCCAGTCTTCTCTAGAGATGCATGGAGATGTGTATGGCATATGATTCAG                         AATGACTTGGTTCATGGATGGGGCCTTGATTTTGCTCTCAGGAAATGCGTG
genomic: CTCCAGTCTTCTCTAGAGATGCATGGAGATGTGTATGGCATATGATTCAGgtttgtattt ... tcctctgcagAATGACTTGGTTCATGGATGGGGCCTTGATTTTGCTCTCAGGAAATGCGTG
EST: gi|86480080|gb|CI122713.1|CI122713
EST:     CTCCAGTCTTCTCTAGAGATGCATGGAGATGTGTATGGCATATGATTCAG                         AATGACTTGGTTCATGGATGGGGCCTTGATTTTGCTCTCAGGAAATGCGTG
genomic: CTCCAGTCTTCTCTAGAGATGCATGGAGATGTGTATGGCATATGATTCAGgtttgtattt ... tcctctgcagAATGACTTGGTTCATGGATGGGGCCTTGATTTTGCTCTCAGGAAATGCGTG
EST: gi|86479999|gb|CI122632.1|CI122632
EST:     CTCCAGTCTTCTCTAGAGATGCATGGAGATGTGTATGGCATATGATTCAG                         AATGACTTGGTTCATGGATGGGGCCTTGATTTTGCTCTCAGGAAATGCGTG
genomic: CTCCAGTCTTCTCTAGAGATGCATGGAGATGTGTATGGCATATGATTCAGgtttgtattt ... tcctctgcagAATGACTTGGTTCATGGATGGGGCCTTGATTTTGCTCTCAGGAAATGCGTG

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: 73 (upstream exon), 65 (downstream exon)
Score: 29

CTTTGTTGAAATAATGGCTCCAGTCTTCTCTAGAGATGCATGGAGATGTGTATGGCATATGATTCAGgtttgtattt ... tcctctgcagAATGACTTGGTTCATGGATGGGGCCTTGATTTTGCTCTCAGGAAATGCGTGGAG




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcgggccattcattttttttcttcatttatttgattgtgttaatttcctctgcagAATGACTTGGTTCATGGATGGGGCCTTGATTTTGCTCTCAGGAAATGCGTGGAG
                                     tgttaat  putative branch site (score: 29)
                                           tttcctctgc  CT-rich tract
           attttttttcttcatt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgtatttcatagtaagctcaattagtatcttcgggccattcattttttttcttcatttatttgattgtgttaatttcctctgcagAATGACTTGGTTCATGGATGGGGCCTTGATTTTGCTCTCAGGAAATGCGTGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG