Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtgttcatgctcttgttgtaatcctgtgtgttcagtttttttatgaggaatttggttgcttttcgtgcaattttgtcgtattgggagttcagtattagatctgagcattcaaactgtgtttttgctggttgatgtggtgtctgaggattgaatcgtggaggtggtttgtgtgtgcagGACCTGGAGGTACCTGGATAAGTAGTGAGAAATTAGGGGATTTTTAAGTGATTAGTAGCGATGGCACAGGTGATGGGATTGACAGCATTGCCGTCATGCG

Basic information

species Physcomitrella patens
transcript PP1S44_78V6.1
intron # 1
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|18373748|gb|BJ205326.1|BJ205326
EST:     TACAAGTGGTCGTCTGTTCTGCCAGAAACAAACCAATCTGCAGCACGCAG                         GACCTGGAGGTACCTGGATAAGTAGTGAGAAATTAGGGGATTTTTAAGTGA
genomic: TACAAGTGGTCGTCTGTTCTGCCAGAAACAAACCAATCTGCAGCACGCAGgtttgtgttc ... gtgtgtgcagGACCTGGAGGTACCTGGATAAGTAGTGAGAAATTAGGGGATTTTTAAGTGA
EST: gi|18344781|gb|BJ176822.1|BJ176822
EST:     TACAAGTGGTCGTCTGTTCTGCCAGAAACAAACCAATCTGCAGCACGCAG                         GACCTGGAGGTACCTGGATAAGTAGTGAGAAATTAAGGGATTTTTAAGTGA
genomic: TACAAGTGGTCGTCTGTTCTGCCAGAAACAAACCAATCTGCAGCACGCAGgtttgtgttc ... gtgtgtgcagGACCTGGAGGTACCTGGATAAGTAGTGAGAAATTAGGGGATTTTTAAGTGA
EST: gi|18368031|gb|BJ200115.1|BJ200115
EST:     TACAAGTGGTCGTCTGTTCTGCCAGAAACAAACCAATCTGCAGCACGCAG                         GACCTGGAGGTACCTGGATAAGTAGTGAGAAATTAGGGGATTTTTAAGTGA
genomic: TACAAGTGGTCGTCTGTTCTGCCAGAAACAAACCAATCTGCAGCACGCAGgtttgtgttc ... gtgtgtgcagGACCTGGAGGTACCTGGATAAGTAGTGAGAAATTAGGGGATTTTTAAGTGA
EST: gi|18360221|gb|BJ192283.1|BJ192283
EST:     TACAAGTGGTCGTCTGTTCTGCCAGAAACAAACCAATCTGCAGCACGCAG                         GACCTGGAGGTACCTGGATAAGTAGTGAGAAATTAGGGGATTTTTAAGTGA
genomic: TACAAGTGGTCGTCTGTTCTGCCAGAAACAAACCAATCTGCAGCACGCAGgtttgtgttc ... gtgtgtgcagGACCTGGAGGTACCTGGATAAGTAGTGAGAAATTAGGGGATTTTTAAGTGA
EST: gi|18353798|gb|BJ185853.1|BJ185853
EST:     TACAAGTGGTCGTCTGTTCTGCCAGAAACAAACCAATCTGCAGCACGCAG                         GACCTGGAGGTACCTGGATAAGTAGTGAGAAATTAAGGGATTTTTAAGTGA
genomic: TACAAGTGGTCGTCTGTTCTGCCAGAAACAAACCAATCTGCAGCACGCAGgtttgtgttc ... gtgtgtgcagGACCTGGAGGTACCTGGATAAGTAGTGAGAAATTAGGGGATTTTTAAGTGA
EST: gi|18324946|gb|BJ156941.1|BJ156941
EST:     TACAAGTGGTCGTCTGTTCTGCCAGAAACAAACCAATCTGCAGCACGCAG                         GACCTGGAGGTACCTGGATAAGTAGTGAGAAATTAGGGGATTTTTAAGTGA
genomic: TACAAGTGGTCGTCTGTTCTGCCAGAAACAAACCAATCTGCAGCACGCAGgtttgtgttc ... gtgtgtgcagGACCTGGAGGTACCTGGATAAGTAGTGAGAAATTAGGGGATTTTTAAGTGA
EST: gi|67570206|gb|BJ943030.1|BJ943030
EST:     ACAAGTGGNTCGTCTGTTCTGCCAGAAACAAACCAATCTGCAGCACGCAG                         GACCTGGAGGTACCTGGATAAGTAGTGAGAAATTAGGGGATTTTTAAGTGA
genomic: ACAAGTGG-TCGTCTGTTCTGCCAGAAACAAACCAATCTGCAGCACGCAGgtttgtgttc ... gtgtgtgcagGACCTGGAGGTACCTGGATAAGTAGTGAGAAATTAGGGGATTTTTAAGTGA

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: 33 (upstream exon), 35 (downstream exon)
Score: 23

CGAGATTCAATTCCAATCACACTCCCTACCCCCCCTCAGCCTCCACTTACTACAAGTGGTCGTCTGTTCTGCCAGAAACAAACCAATCTGCAGCACGCAGgtttgtgttc ... gtgtgtgcagGACCTGGAGGTACCTGGATAAGTAGTGAGAAATTAGGGGATTTTTAAGTGATTAGTAGCGATGGCACAGGTGATGGGATTGACAGCATTGCCGTCATGCG




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgctggttgatgtggtgtctgaggattgaatcgtggaggtggtttgtgtgtgcagGACCTGGAGGTACCTGGATAAGTAGTGAGAAATTAGGGGATTTTTAAGTGATTAGTAGCGATGGCACAGGTGATGGGATTGACAGCATTGCCGTCATGCG
    ggttgat  putative branch site (score: 23)
                        attgaat  TA-rich tract