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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agtttccatgtattttgcgacggttttgatcttctgactcttttgacggctagtttcttatgtaaatgtatatttgtatctgctatatcaatttgttcagGATTCTGCCGTGAAGCTGGCTATTGTAATGAAGGTGATTGGTCGCACTGGGTCCCGAGGTCAGGTGACCCAAGTTCGTGTTAAGTTTCTGGATGATCAAA

Basic information

species Physcomitrella patens
transcript PP1S41_71V6.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S41_71V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GLYMA03G36580.1 (Glycine max), 3'ss of exon 1
-agtttccatgtattttgcgacggttttgatcttc--tgactcttttgacg-gctagtttcttatgtaaatgt-atatttgtatctgctatatcaatttgttcagGATTCTGCCGTGAAGCTGGCTATTGTAATGAAGGTGATTGGTCGCACTGGGTCCCGAGGTCAGGTGACCCAAGTTCGTGTTAAGTTTCTGGATGATCAAA
    ||      || ||    | | |||     ||  ||| || ||  ||    | ||||   |  |  || | |||   || |    | | |           ||| |||   |||||||  ||  ||||  | || || || ||||| ||||| ||| |||| ||||||||||| ||| | || |||||||||||||||    
tgcatttggaagatgttattcctgatttatctgtcattgattcattaaacacatttgttttccactttcatctcataacggt-ttgattgtgtttgagcagGATGGAGTCTCAGGTGAAGCACGCACTTGTTGTCAAAGTAATGGGTCGTACTGGATCCAGAGGACAGGTGACCCAGGTTAGAGTGAAGTTTCTGGATGAT----
















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|162236258|gb|FC412014.1|FC412014
EST:     GCCCCGTCTGCACCCGCTGTACACGTGCTTCCCTCCGCCTTACCATCATG                         GATTCTGCCGTGAAGCTGGCTATTGTAATGAAGGTGATTGGTCGCACTGGG
genomic: GCCCCGTCTGCACCCGCTGTACACGTGCTTCCCTCCGCCTTACCATCATGgttcgcgccc ... atttgttcagGATTCTGCCGTGAAGCTGGCTATTGTAATGAAGGTGATTGGTCGCACTGGG
EST: gi|15727821|gb|BI740480.1|BI740480
EST:     GCCCCGTCTGCACCCGCTGTACACGTGCTTCCCTCCGCCTTACCATCATG                         GATTCTGCCGTGAAGCTGGCTATTGTAATGAAGGTGATTGGTCGCACTGGG
genomic: GCCCCGTCTGCACCCGCTGTACACGTGCTTCCCTCCGCCTTACCATCATGgttcgcgccc ... atttgttcagGATTCTGCCGTGAAGCTGGCTATTGTAATGAAGGTGATTGGTCGCACTGGG
EST: gi|67695413|gb|BJ955646.1|BJ955646
EST:     GCCCCGTCTGCACCCGCTGTACACGTGCTTCCCTCCGCCTTACCATCATG                         GATTCTGCCGTGAAGCTGGCTATTGTAATGAAGGTGATTGGTCGCACTGGG
genomic: GCCCCGTCTGCACCCGCTGTACACGTGCTTCCCTCCGCCTTACCATCATGgttcgcgccc ... atttgttcagGATTCTGCCGTGAAGCTGGCTATTGTAATGAAGGTGATTGGTCGCACTGGG
EST: gi|15727930|gb|BI740534.1|BI740534
EST:     GCCCCGTCTGCACCCGCTGTACACGTGCTTCCCTCCGCCTTACCATCATG                         GATTCTGCCGTGAAGCTGGCTATTGTAATGAAGGTGATTGGTCGCACTGGG
genomic: GCCCCGTCTGCACCCGCTGTACACGTGCTTCCCTCCGCCTTACCATCATGgttcgcgccc ... atttgttcagGATTCTGCCGTGAAGCTGGCTATTGTAATGAAGGTGATTGGTCGCACTGGG
EST: gi|67572047|gb|BJ944871.1|BJ944871
EST:     GCCCCGTCTGCACCCGCTGTACACGTGCTTCCCTCCGCCTTACCATCATG                         GATTCTGCCGTGAAGCTGGCTATTGTAATGAAGGTGATTGGTCGCACTGGG
genomic: GCCCCGTCTGCACCCGCTGTACACGTGCTTCCCTCCGCCTTACCATCATGgttcgcgccc ... atttgttcagGATTCTGCCGTGAAGCTGGCTATTGTAATGAAGGTGATTGGTCGCACTGGG

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: 29 (upstream exon), 34 (downstream exon)
Score: 4

CGTCAAGCCCTCCTCGCTCGAGCTCCCAGCGTCGAAACCATCTCTGCATCGCCCCGTCTGCACCCGCTGTACACGTGCTTCCCTCCGCCTTACCATCATGgttcgcgccc ... atttgttcagGATTCTGCCGTGAAGCTGGCTATTGTAATGAAGGTGATTGGTCGCACTGGGTCCCGAGGTCAGGTGACCCAAGTTCGTGTTAAGTTTCTGGATGATCAAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acggctagtttcttatgtaaatgtatatttgtatctgctatatcaatttgttcagGATTCTGCCGTGAAGCTGGCTATTGTAATGAAGGTGATTGGTCGCACTGGGTCCCGAGGTCAGGTGACCCAAGTTCGTGTTAAGTTTCTGGATGATCAAA
 ttttgac  putative branch site (score: 4)
                                              tttgttc  putative PPT
        tttcttatgtaaatgt  TA-rich tract