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

gtatgctatctttatccgtcttaagtgatctatgaatgtgtttattgtacgagacttgctgattgttgatatttttttgtacaacttctacagAAACCCAACAGTGCGGTTGATGGTGCCAACGATGCTATGCTATATACACTTCCTAAGGAAGAGTTGTTAGAATTGTTTCTAACTGTGAGCAGCCAACTTT

Basic information

species Oryza sativa
transcript LOC_Os12g06800.1
intron # 6
splice site 3'
intron type U2

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|58668425|gb|CK057111.1|CK057111
EST:     CTACCAAGGGTGTTGGGCACTTGGCTGGCATTTTACATGACTTTCTGGAG                         AAACCCAACAGTGCGGTTGATGGTGCCAACGATGCTATGCTATATACACTT
genomic: CTACCAAGGGTGTTGGGCACTTGGCTGGCATTTTACATGACTTTCTGGAGgtatgctatc ... acttctacagAAACCCAACAGTGCGGTTGATGGTGCCAACGATGCTATGCTATATACACTT
EST: gi|58655081|gb|CK043761.1|CK043761
EST:     CTACCAAGGGTGTTGGGCACTTGGCTGGCATTTTACATGACTTTCTGGAG                         AAACCCAACAGTGCGGTTGATGGTGCCAACGATGCTATGCTATATACACTT
genomic: CTACCAAGGGTGTTGGGCACTTGGCTGGCATTTTACATGACTTTCTGGAGgtatgctatc ... acttctacagAAACCCAACAGTGCGGTTGATGGTGCCAACGATGCTATGCTATATACACTT
EST: gi|58662681|gb|CK051367.1|CK051367
EST:     CTACCAAGGGTGTTGGGCACTTGGCTGGCATTTTACATGACTTTCTGGAG                         AAACCCAACAGTGCGGTTGATGGTGCCAACGATGCTATGCTATATACACTT
genomic: CTACCAAGGGTGTTGGGCACTTGGCTGGCATTTTACATGACTTTCTGGAGgtatgctatc ... acttctacagAAACCCAACAGTGCGGTTGATGGTGCCAACGATGCTATGCTATATACACTT
EST: gi|58668458|gb|CK057144.1|CK057144
EST:     CTACCAAGGGTGTTGGGCACTTGGCTGGCATTTTACATGACTTTCTGGAG                         AAACCTAACAGTGCGGTTGATGGTGCCAACGATGCTATGCTATATACACTT
genomic: CTACCAAGGGTGTTGGGCACTTGGCTGGCATTTTACATGACTTTCTGGAGgtatgctatc ... acttctacagAAACCCAACAGTGCGGTTGATGGTGCCAACGATGCTATGCTATATACACTT

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: 44 (upstream exon), 75 (downstream exon)
Score: 7

TCAGCCTGCAAAATCAGGTCTACCTAATTCAAATAAAGTTTTCCCGGCAACTACCAAGGGTGTTGGGCACTTGGCTGGCATTTTACATGACTTTCTGGAGgtatgctatc ... acttctacagAAACCCAACAGTGCGGTTGATGGTGCCAACGATGCTATGCTATATACACTTCCTAAGGAAGAGTTGTTAGAATTGTTTCTAACTGTGAGCAGCCAACTTT




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtttattgtacgagacttgctgattgttgatatttttttgtacaacttctacagAAACCCAACAGTGCGGTTGATGGTGCCAACGATGCTATGCTATATACACTTCCTAAGGAAGAGTTGTTAGAATTGTTTCTAACTGTGAGCAGCCAACTTT
                                              cttctac  CT-rich tract
                       attgttgatatttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgctatctttatccgtcttaagtgatctatgaatgtgtttattgtacgagacttgctgattgttgatatttttttgtacaacttctacagAAACCCAACAGTGCGGTTGATGGTGCCAACGATGCTATGCTATATACACTTCCTAAGGAAGAGTTGTTAGAATTGTTTCTAACTGTGAGCAGCCAACTTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG