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'   		15  
 5'  3'   		16  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttccaatagtcactttgtaaacctatctaattgaagacagcccaatggtttagttgaaggttactcatcttgtttactctggtttgatttcttgtttagCATGAAATTGTCCTGGAATGTGCTGTTCTCGGCTTACCTGACGAAGCTTATGGAGAGATTATCTGTGCAATAATTGTGCCTAAGGAGGACTCAAAGAAAA

Basic information

species Oryza sativa
transcript LOC_Os01g55590.1
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g55590.1 (Oryza sativa), 3'ss of exon 14
lower sequence: GRMZM2G460078_T01 (Zea mays), 3'ss of exon 14
tttccaatagtcactttgtaaacctatctaa----ttgaa-gacagcccaatggtttagttgaaggttactcatcttgtttactctggtttgatttcttgttt--agCATGAAATTGTCCTGGAATGTGCTGTTCTCGGCTTACCTGACGAAGCTTATGGAGAGATTATCTGTGCAATAATTGTGCCTAAGGAGGACTCAAAGAAAA
     |||| |    |   |    || | ||    ||| |  ||   | |||       ||     |||||||| ||  ||| |    | || | | |||| |  |||||||   ||| |||||||||||||| || ||||| ||||| ||||| ||||| ||| |||| ||||||||||||||||||||||||||  |||||||||
--cataatattaggctgaaatgtttaccgaaggctttgcacaactatcaaataaccccctt---tcttactcatgttacttatt--aatctggtctgttgtcttcagCATGATGCTGTACTGGAATGTGCTGTCCTTGGCTTGCCTGATGAAGCCTATGGGGAGGTTATATGTGCAATAATTGTGCCTAAGGAGGATGCAAAGAAAA
















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|86863465|gb|CI345208.1|CI345208
EST:     TGGTTATAAGCTGTCTGCATTAGAAATTGAGTCAGTGCTGTTACAG                         CATGAAATTGTCCTGGAATGTGCTGTTCTCGGCTTACCTGACGAAGCTTAT
genomic: TGGTTATAAGCTGTCTGCATTAGAAATTGAGTCAGTGCTGTTACAGgtaaatatcc ... tcttgtttagCATGAAATTGTCCTGGAATGTGCTGTTCTCGGCTTACCTGACGAAGCTTAT
EST: gi|10852848|gb|AT003358.1|AT003358
EST:     TTGGTGGTTATAAGCTGTCTGCATTAGAAATTGNGTCAGTGCTGTTNCAG                         CATGAAATTGTCCTGGAATGTGCTGTTCTCGGGCTTNCCTGACGAAGCTTA
genomic: TTGGTGGTTATAAGCTGTCTGCATTAGAAATTGAGTCAGTGCTGTTACAGgtaaatatcc ... tcttgtttagCATGAAATTGTCCTGGAATGTGCTGTTCTC-GGCTTACCTGACGAAGCTTA
EST: gi|89185889|gb|CI047758.1|CI047758
EST:     TTGGTGGTTATAAGCTGTCTGCATTAGAAATTGAGTCAGTGCTGTTACAG                         CATGAAATTGTCCTGGAATGTGCTGTTCTCGGCTTACCTGACGAAGCTTAT
genomic: TTGGTGGTTATAAGCTGTCTGCATTAGAAATTGAGTCAGTGCTGTTACAGgtaaatatcc ... tcttgtttagCATGAAATTGTCCTGGAATGTGCTGTTCTCGGCTTACCTGACGAAGCTTAT
EST: gi|29689640|gb|CB685915.1|CB685915
EST:     TTGGTGGTTATAAGCTGTCTGCATTAGAAATTGAGTCAGTGCTGTTACAG                         CATGAAATTGTCCTGGAATGTGCTGTTCTCGGCTTACCTGACGAAGCTTAT
genomic: TTGGTGGTTATAAGCTGTCTGCATTAGAAATTGAGTCAGTGCTGTTACAGgtaaatatcc ... tcttgtttagCATGAAATTGTCCTGGAATGTGCTGTTCTCGGCTTACCTGACGAAGCTTAT
EST: gi|58603395|gb|CK013923.1|CK013923
EST:     TTGGTGGTTATAAGCTGTCTGCATTAGAAATTGAGTCAGTGCTGTTACAG                         CATGAAATTGTCCTGGAATGTGCTGTTCTCGGCTTACCTGACGAAGCTTAT
genomic: TTGGTGGTTATAAGCTGTCTGCATTAGAAATTGAGTCAGTGCTGTTACAGgtaaatatcc ... tcttgtttagCATGAAATTGTCCTGGAATGTGCTGTTCTCGGCTTACCTGACGAAGCTTAT
EST: gi|88558329|gb|CI488809.1|CI488809
EST:     CATTAGAAATTGAGTCAGTGCTGTTACAG                         CATGAAATTGTCCTGGAATGTGCTGTTCTCGGCTTACCTGACGAAGCTTAT
genomic: CATTAGAAATTGAGTCAGTGCTGTTACAGgtaaatatcc ... tcttgtttagCATGAAATTGTCCTGGAATGTGCTGTTCTCGGCTTACCTGACGAAGCTTAT
EST: gi|88557745|gb|CI488179.1|CI488179
EST:     TTGGTGGTTATAAGCTGTCTGCATTAGAAATTGAGTCAGTGCTGTTACAG                         CATGAAATTGTCCTGGAATGTGCTGTTCTCGGCTTACCTGACGAAGCTTAT
genomic: TTGGTGGTTATAAGCTGTCTGCATTAGAAATTGAGTCAGTGCTGTTACAGgtaaatatcc ... tcttgtttagCATGAAATTGTCCTGGAATGTGCTGTTCTCGGCTTACCTGACGAAGCTTAT

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: 20

GCACAAATGCTGACATCATGAAAGTTGGTGGTTATAAGCTGTCTGCATTAGAAATTGAGTCAGTGCTGTTACAGgtaaatatcc ... tcttgtttagCATGAAATTGTCCTGGAATGTGCTGTTCTCGGCTTACCTGACGAAGCTTATGGAGAGATTATCTGTGCAATAATTGTGCCTAAGGAGGACTCAAAGAAAA




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atggtttagttgaaggttactcatcttgtttactctggtttgatttcttgtttagCATGAAATTGTCCTGGAATGTGCTGTTCTCGGCTTACCTGACGAAGCTTATGGAGAGATTATCTGTGCAATAATTGTGCCTAAGGAGGACTCAAAGAAAA
                                     gtttgat  putative branch site (score: 20)
                                           tttcttgttt  CT-rich tract
                                      tttgattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttccaatagtcactttgtaaacctatctaattgaagacagcccaatggtttagttgaaggttactcatcttgtttactctggtttgatttcttgtttagCATGAAATTGTCCTGGAATGTGCTGTTCTCGGCTTACCTGACGAAGCTTATGGAGAGATTATCTGTGCAATAATTGTGCCTAAGGAGGACTCAAAGAAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - -aaaccta