Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgaaataattgtgggcatatcaagctgtcgtaattgtcaggaattttctactactatttatttagtttcgggaagtaacccgcgcgttggtgtgatccagGCAGCAGTGGTATCGCTGGCCAAAGATCCAGCTATTTGGGACGCATTCGTGAAAAACGAGAAGGTTCAGGAACTCATGCGAGCACGCCCAATGACTGTAT

Basic information

species Physcomitrella patens
transcript PP1S9_37V6.5
intron # 4
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|18333102|gb|BJ165116.1|BJ165116
EST:     TCCTGACGTTCAG                         GCAGCAGTGGTATCGCTGGCCAAAGATCCAGCTATTTGGGACGCATTCGTG
genomic: TCCTGACGTTCAGgtacgttctc ... tgtgatccagGCAGCAGTGGTATCGCTGGCCAAAGATCCAGCTATTTGGGACGCATTCGTG
EST: gi|208393082|gb|DC929577.1|DC929577
EST:     ATGTTGTAGCTCGATGCATCGATCTAATGCAAACCGATCCTGACGTTCAG                         GCAGCAGTGGTATCGCTGGCCAAAGATCCAGCTATTTGGGACGCATTCGTG
genomic: ATGTTGTAGCTCGATGCATCGATCTAATGCAAACCGATCCTGACGTTCAGgtacgttctc ... tgtgatccagGCAGCAGTGGTATCGCTGGCCAAAGATCCAGCTATTTGGGACGCATTCGTG
EST: gi|208383754|gb|DC928057.1|DC928057
EST:     ATGTTGTAGCTCGATGCATCGATCTAATGCAAACCGATCCTGACGTTCAG                         GCAGCAGTGGTATCGCTGGCCAAAGATCCAGCTATTTGGGACGCACTCGTG
genomic: ATGTTGTAGCTCGATGCATCGATCTAATGCAAACCGATCCTGACGTTCAGgtacgttctc ... tgtgatccagGCAGCAGTGGTATCGCTGGCCAAAGATCCAGCTATTTGGGACGCATTCGTG
EST: gi|162196408|gb|FC373554.1|FC373554
EST:     ATGTTGTAGCTCGATGCATCGATCTAATGCAAACCGATCCTGACGTTCAG                         GCAGCAGTGGTATCGCTGGCCAAAGATCCAGCTATTTGGGACGCATTCGTG
genomic: ATGTTGTAGCTCGATGCATCGATCTAATGCAAACCGATCCTGACGTTCAGgtacgttctc ... tgtgatccagGCAGCAGTGGTATCGCTGGCCAAAGATCCAGCTATTTGGGACGCATTCGTG
EST: gi|162185462|gb|FC361205.1|FC361205
EST:     ATGTTGTAGCTCGATGCATCGATCTAATGCAAACCGATCCTGACGTTCAG                         GCAGCAGTGGTATCGCTGGCCAAAGATCCAGCTATTTGGGACGCATTCGTG
genomic: ATGTTGTAGCTCGATGCATCGATCTAATGCAAACCGATCCTGACGTTCAGgtacgttctc ... tgtgatccagGCAGCAGTGGTATCGCTGGCCAAAGATCCAGCTATTTGGGACGCATTCGTG
EST: gi|208350152|gb|DC926107.1|DC926107
EST:     ATGNTGTAGCTCGATGCATCGATNTAATGCCAACCGATCCTGACGTTCAG                         GCAGCAGTGGTATCGCTGNCCAAAGATCCAGCTATTTGGGACGCATTCGTG
genomic: ATGTTGTAGCTCGATGCATCGATCTAATGCAAACCGATCCTGACGTTCAGgtacgttctc ... tgtgatccagGCAGCAGTGGTATCGCTGGCCAAAGATCCAGCTATTTGGGACGCATTCGTG
EST: gi|208378446|gb|DC923082.1|DC923082
EST:     ATGTTGTAGCTCGATGCATCGATTTAATGCCAACCGATCCTGACGTTCAG                         GCAGCAGTGGTATCGCTGGCCAAAGATCCAGCTATTTGGGACGCATTCGTG
genomic: ATGTTGTAGCTCGATGCATCGATCTAATGCAAACCGATCCTGACGTTCAGgtacgttctc ... tgtgatccagGCAGCAGTGGTATCGCTGGCCAAAGATCCAGCTATTTGGGACGCATTCGTG
EST: gi|208356450|gb|DC914312.1|DC914312
EST:     ATGTTGTAGCTCGATGCATCGATCTAATGCAAACCGATCCTGACGTTCAG                         GCAGCAGTGGTATCGCTGGCCAAAGATCCAGCTATTTGGGACGCACTCGTG
genomic: ATGTTGTAGCTCGATGCATCGATCTAATGCAAACCGATCCTGACGTTCAGgtacgttctc ... tgtgatccagGCAGCAGTGGTATCGCTGGCCAAAGATCCAGCTATTTGGGACGCATTCGTG
EST: gi|208398405|gb|DC912334.1|DC912334
EST:     ATGTTGTAGCTCGATGCATCGATCTAATGCAAACCGATCCTGACGTTCAG                         GCAGCAGTGGTATCGCTGGCCAAAGATCCAGCTATTTGGGACGCATTCGTG
genomic: ATGTTGTAGCTCGATGCATCGATCTAATGCAAACCGATCCTGACGTTCAGgtacgttctc ... tgtgatccagGCAGCAGTGGTATCGCTGGCCAAAGATCCAGCTATTTGGGACGCATTCGTG
EST: gi|100404598|gb|BY973658.1|BY973658
EST:     ATGTTGTAGCTCGATGCATCGATCTAATGCAAACCGATCCTGACGTTCAG                         GCAGCAGTGGTATCGCTGGCCAAAGATCCAGCTA
genomic: ATGTTGTAGCTCGATGCATCGATCTAATGCAAACCGATCCTGACGTTCAGgtacgttctc ... tgtgatccagGCAGCAGTGGTATCGCTGGCCAAAGATCCAGCTA

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

GTCAGCTGAGCATAGTCACGCTCTATCCCTTTTAGCACCGGGAGGAAGCCATGTTGTAGCTCGATGCATCGATCTAATGCAAACCGATCCTGACGTTCAGgtacgttctc ... tgtgatccagGCAGCAGTGGTATCGCTGGCCAAAGATCCAGCTATTTGGGACGCATTCGTGAAAAACGAGAAGGTTCAGGAACTCATGCGAGCACGCCCAATGACTGTAT




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctactactatttatttagtttcgggaagtaacccgcgcgttggtgtgatccagGCAGCAGTGGTATCGCTGGCCAAAGATCCAGCTATTTGGGACGCATTCGTGAAAAACGAGAAGGTTCAGGAACTCATGCGAGCACGCCCAATGACTGTAT
                           aagtaac  putative branch site (score: 11)
      tactatttatttagtt  TA-rich tract