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'   		17  
 5'  3'   		18  
 5'  3'   		19  
 5'  3'   		20  
 5'  3'   
21  
 5'  3'   		22  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacttcaatccactacattttctgtatggaagctaaatgctctaccaagcttttattagggtctcctttttagtgtttttccaaacgcaatgaaaaatattactctggtatcgagtctcacctgcttctgatttttacagaactggtttctctaacctattgaattgtctccagATTGACGTGGATATTGGGTCGTCATCAGTGGCACGGAGTGTGGTAGGATTAGCTCTGGGTTATGTGACAAGCCTCGTTGTGGACCTTGCAATCCTCATTG

Basic information

species Physcomitrella patens
transcript PP1S91_96V6.1
intron # 21
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|37835079|gb|BJ593091.1|BJ593091
EST:     TGGGTAAAGCTGTTACTTGCAATTACTTGCGTAAAGACAATTTCCTTGAG                         ATTGACGTGGATATTGGGTCGTCATCAGTGGCACGGAGTGTGGTAGGATTA
genomic: TGGGTAAAGCTGTTACTTGCAATTACTTGCGTAAAGACAATTTCCTTGAGgtacttcaat ... ttgtctccagATTGACGTGGATATTGGGTCGTCATCAGTGGCACGGAGTGTGGTAGGATTA
EST: gi|162210675|gb|FC386571.1|FC386571
EST:     TGGGTAAAGCTGTTACTTGCAATTACTTGCGTAAAGACAATTTCCTTGAG                         ATTGACGTGGATATTGGGTCGTCATCAGTGGCACGGAGTGTGGTAGGATTA
genomic: TGGGTAAAGCTGTTACTTGCAATTACTTGCGTAAAGACAATTTCCTTGAGgtacttcaat ... ttgtctccagATTGACGTGGATATTGGGTCGTCATCAGTGGCACGGAGTGTGGTAGGATTA
EST: gi|18334680|gb|BJ166697.1|BJ166697
EST:     TGGGTAAAGCTGTTACTTGCAATTACTTGCGTAAAGACAATTTCCTTGAG                         ATTGACGTGGATATTGGGTCGTCATCAGTGGCACGGAGTGTGGTAGGATTA
genomic: TGGGTAAAGCTGTTACTTGCAATTACTTGCGTAAAGACAATTTCCTTGAGgtacttcaat ... ttgtctccagATTGACGTGGATATTGGGTCGTCATCAGTGGCACGGAGTGTGGTAGGATTA
EST: gi|18353608|gb|BJ185663.1|BJ185663
EST:     TGGGTAAAGCTGTTACTTGCAATTACTTGCGTAAAGACAATTTCCTTGAG                         ATTGACGTGGATATTGGGTCGTCATCA
genomic: TGGGTAAAGCTGTTACTTGCAATTACTTGCGTAAAGACAATTTCCTTGAGgtacttcaat ... ttgtctccagATTGACGTGGATATTGGGTCGTCATCA

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: 11 (upstream exon), 35 (downstream exon)
Score: 4

GGTTACTGGATGGTGAAACGTGCTGTTGGTACAAAAGCTTGTCTGCTGGGTAAAGCTGTTACTTGCAATTACTTGCGTAAAGACAATTTCCTTGAGgtacttcaat ... ttgtctccagATTGACGTGGATATTGGGTCGTCATCAGTGGCACGGAGTGTGGTAGGATTAGCTCTGGGTTATGTGACAAGCCTCGTTGTGGACCTTGCAATCCTCATTG




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acctgcttctgatttttacagaactggtttctctaacctattgaattgtctccagATTGACGTGGATATTGGGTCGTCATCAGTGGCACGGAGTGTGGTAGGATTAGCTCTGGGTTATGTGACAAGCCTCGTTGTGGACCTTGCAATCCTCATTG
                              ctctaac  putative branch site (score: 4)
                                             ttgtctcc  putative PPT
         tgattttta  TA-rich tract