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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gttacacggttcaaagcttacgttatcaaagggcaatatatagccttagtttctttcttttatgtagtcgttgctgaccgggaattgaacacacttgcagGTGATGTGTCCAACATGTCTCTGCACAGGCATGGCACTGGCTAGTGAACACGATCCTCGCATTGACCCTTTCCA

Basic information

species Physcomitrella patens
transcript PP1S237_60V6.2
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S237_60V6.2 (Physcomitrella patens), 3'ss of exon 8
lower sequence: LOC_Os02g43500.1 (Oryza sativa), 3'ss of exon 7
------------gttacacggt-----tcaaagcttacgttat-caaagggca-atatatagccttagtttctttcttttat--gtagtcgttgctgaccgggaattgaacacacttgcagGTGATGTGTCCAACATGTCTCTGCACAGGCATGGCACTGGCTAGTGAACACGATCCTCGCATTGACCCTTTCCA--------------------------
             || |||  |      |||     | || || ||||    | |   |||     | || || | ||  ||    |  |    ||||     ||   || |   |||||||||||||||||||||||||||||||| || |||||| |||| ||||| ||||| ||||| ||||| || ||  |                          
gtaaatcagccttttgcacaatgattcccaacaacaatgtcattcaaataatatacgcatatttccacttgctattttggattgaaaaacagccctgatttcaaac--aaaatgtttgcagGTGATGTGTCCAACATGTCTCTGCACGGGGATGGCAATGGCAAGTGAGCACGACCCTCGAATTGATCCGTTTGATTAAAATGCACGTCATAGTTCAGAAA

upper sequence: PP1S237_60V6.2 (Physcomitrella patens), 3'ss of exon 8
lower sequence: GLYMA09G36770.2 (Glycine max), 3'ss of exon 7
gttacacggttcaaagcttacgttatcaaag-----ggcaatatatagccttagtttctttcttttatgtagtcgttgctgaccgggaattgaacacacttgcagGTGATGTGTCCAACATGTCTCTGCACAGGCATGGCACTGGCTAGTGAACACGATCCTCGCATTGACCCTTTCCA------
 | |   ||| |||    |    |  | | |      |||| |  | |   | |  | ||| |||     | || |     ||   ||||        ||||||||| ||||||||||||||||||||||| || |||||  |||| || ||||| ||||| || ||||| |||||  |      
-taaattggtacaagttatttacttgctaggttcacagcaaca-gtggttgttgagtttttttttatcccaatcatgttcaactctgaatc---tcttcttgcagGTTATGTGTCCAACATGTCTCTGCACTGGAATGGCCATGGCAAGCGAACATGATCCACGAATTGATCCTTTTGATTAGAG

upper sequence: PP1S237_60V6.2 (Physcomitrella patens), 3'ss of exon 8
lower sequence: GLYMA09G36770.3 (Glycine max), 3'ss of exon 7
gttacacggttcaaagcttacgttatcaaag-----ggcaatatatagccttagtttctttcttttatgtagtcgttgctgaccgggaattgaacacacttgcagGTGATGTGTCCAACATGTCTCTGCACAGGCATGGCACTGGCTAGTGAACACGATCCTCGCATTGACCCTTTCCA--------------------------
 | |   ||| |||    |    |  | | |      |||| |  | |   | |  | ||| |||     | || |     ||   ||||        ||||||||| ||||||||||||||||||||||| || |||||  |||| || ||||| ||||| || ||||| |||||  |                          
-taaattggtacaagttatttacttgctaggttcacagcaaca-gtggttgttgagtttttttttatcccaatcatgttcaactctgaatc---tcttcttgcagGTTATGTGTCCAACATGTCTCTGCACTGGAATGGCCATGGCAAGCGAACATGATCCACGAATTGATCCTTTTGATTAGAGGTTCAATAATTATAGTTATC

upper sequence: PP1S237_60V6.2 (Physcomitrella patens), 3'ss of exon 8
lower sequence: GLYMA12G00600.1 (Glycine max), 3'ss of exon 7
gttacacggttcaaagc-ttacgttatcaaagggcaatat-atagccttagtttc-tttcttttatgtagtcgttgctgaccgggaattgaacacacttgcagGTGATGTGTCCAACATGTCTCTGCACAGGCATGGCACTGGCTAGTGAACACGATCCTCGCATTGACCCTTTCCA--------------------------
 | |   ||| |||    |||| |  |       ||  |  | ||   | |||   | | |||| |    || |     ||   ||||         |||||||| ||||||||||||||||| ||||| || |||||  |||| || ||||| ||||| || ||||| || ||  |                          
ataaattggtacaagttgttacttgctaggtccacagcaccacagtggttgttgagtgttttttcttctatcatgctcaactctgaatc---tctgattgcagGTTATGTGTCCAACATGTCTTTGCACTGGAATGGCCATGGCAAGCGAACATGATCCACGAATTGATCCATTTGATTAGAGGTTCAGTAATTATAGTTATC

upper sequence: PP1S237_60V6.2 (Physcomitrella patens), 3'ss of exon 8
lower sequence: GLYMA12G00600.3 (Glycine max), 3'ss of exon 7
gttacacggttcaaagc-ttacgttatcaaagggcaatat-atagccttagtttc-tttcttttatgtagtcgttgctgaccgggaattgaacacacttgcagGTGATGTGTCCAACATGTCTCTGCACAGGCATGGCACTGGCTAGTGAACACGATCCTCGCATTGACCCTTTCCA------
 | |   ||| |||    |||| |  |       ||  |  | ||   | |||   | | |||| |    || |     ||   ||||         |||||||| ||||||||||||||||| ||||| || |||||  |||| || ||||| ||||| || ||||| || ||  |      
ataaattggtacaagttgttacttgctaggtccacagcaccacagtggttgttgagtgttttttcttctatcatgctcaactctgaatc---tctgattgcagGTTATGTGTCCAACATGTCTTTGCACTGGAATGGCCATGGCAAGCGAACATGATCCACGAATTGATCCATTTGATTAGAG

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|162153743|gb|FC329146.1|FC329146
EST:     CTTCATCAAGTTCCACCGAACGTTGCCCGAATTGCGCTGGTGCTACCAAG                         GTGATGTGTCCAACATGTCTCTGCACAGGCATGGCACTGGCTAGTGAACAC
genomic: CTTCATCAAGTTCCACCGAACGTTGCCCGAATTGCGCTGGTGCTACCAAGgttcttaatc ... acacttgcagGTGATGTGTCCAACATGTCTCTGCACAGGCATGGCACTGGCTAGTGAACAC
EST: gi|162153223|gb|FC329005.1|FC329005
EST:     CTTCATCAAGTTCCACCGAACGTTGCCCGAATTGCGCTGGTGCTACCGAG                         GTGATGTGTCCAACATGTCTCTGCACAGGCATGACACTGGCTAGTGAACAC
genomic: CTTCATCAAGTTCCACCGAACGTTGCCCGAATTGCGCTGGTGCTACCAAGgttcttaatc ... acacttgcagGTGATGTGTCCAACATGTCTCTGCACAGGCATGGCACTGGCTAGTGAACAC
EST: gi|162154879|gb|FC331921.1|FC331921
EST:     CTTCATCAAGTTCCACCGAACGTTGCCCGAATTGCGCTGGTGCTACCAAG                         GTGATGTGTCCAACATGTCTCTGCACAGGCATGGCACTGGCTAGTGAACAC
genomic: CTTCATCAAGTTCCACCGAACGTTGCCCGAATTGCGCTGGTGCTACCAAGgttcttaatc ... acacttgcagGTGATGTGTCCAACATGTCTCTGCACAGGCATGGCACTGGCTAGTGAACAC
EST: gi|162154880|gb|FC331922.1|FC331922
EST:     CTTCATCAAGTTCCACCGAACGTTGCCCGAATTGCGCTGGTGCTACCAAG                         GTGATGTGTCCAACATGTCTCTGCACAGGCATGGCACTGGCTAGTGAACAC
genomic: CTTCATCAAGTTCCACCGAACGTTGCCCGAATTGCGCTGGTGCTACCAAGgttcttaatc ... acacttgcagGTGATGTGTCCAACATGTCTCTGCACAGGCATGGCACTGGCTAGTGAACAC
EST: gi|162150938|gb|FC327418.1|FC327418
EST:     CTTCATCAAGTTCCACCGAACGTTGCCCGAATTGCGCTGGTGCTACCAAG                         GTGATGTGTCCAACATGTCTCTGCACAGGCATGGCACTGGCTAGTGAACAC
genomic: CTTCATCAAGTTCCACCGAACGTTGCCCGAATTGCGCTGGTGCTACCAAGgttcttaatc ... acacttgcagGTGATGTGTCCAACATGTCTCTGCACAGGCATGGCACTGGCTAGTGAACAC
EST: gi|19785698|gb|BQ040360.1|BQ040360
EST:     CTTCATCAAGTTCCACCGAACGTTGCCCGAATTGCGCTGGTGCTACCAAG                         GTGATGTGTCCAACATGTCTCTGCACAGGCATGGCACTGGCTAGTGAACAC
genomic: CTTCATCAAGTTCCACCGAACGTTGCCCGAATTGCGCTGGTGCTACCAAGgttcttaatc ... acacttgcagGTGATGTGTCCAACATGTCTCTGCACAGGCATGGCACTGGCTAGTGAACAC
EST: gi|208382991|gb|DC927741.1|DC927741
EST:     CTTCATCAAGTTCCACCGAACGTTGCCCGAATTGCGCTGGTGCTACCAAG                         GTGATGTGTCCAACATGTCTCTGCACAGGCATGGCNCTGGNTAGTGAACAC
genomic: CTTCATCAAGTTCCACCGAACGTTGCCCGAATTGCGCTGGTGCTACCAAGgttcttaatc ... acacttgcagGTGATGTGTCCAACATGTCTCTGCACAGGCATGGCACTGGCTAGTGAACAC
EST: gi|162215023|gb|FC391311.1|FC391311
EST:     CTTCATCAAGTTCCACCGAACGTTGCCCGAATTGCGCTGGTGCTACCAAG                         GTGATGTGTCCAACATGTCTCTGCACAGGCATGGCACTGGCTAGTGAACAC
genomic: CTTCATCAAGTTCCACCGAACGTTGCCCGAATTGCGCTGGTGCTACCAAGgttcttaatc ... acacttgcagGTGATGTGTCCAACATGTCTCTGCACAGGCATGGCACTGGCTAGTGAACAC
EST: gi|67694476|gb|BJ954709.1|BJ954709
EST:     CTTCATCAAGTTCCACCGAACGTTGCCCGAATTGCGCTGGTGCTACCAAG                         GTGATGTGTCCAACATGTCTCTGCACAGGCATGGCACTGGCTAGTGAACAC
genomic: CTTCATCAAGTTCCACCGAACGTTGCCCGAATTGCGCTGGTGCTACCAAGgttcttaatc ... acacttgcagGTGATGTGTCCAACATGTCTCTGCACAGGCATGGCACTGGCTAGTGAACAC

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: 14 (upstream exon), 34 (downstream exon)
Score: 5

TTCTGGGTCCATTGTTGGTATGGAGAACGGTGGAACCACAGCTGCTTTAGCTTCATCAAGTTCCACCGAACGTTGCCCGAATTGCGCTGGTGCTACCAAGgttcttaatc ... acacttgcagGTGATGTGTCCAACATGTCTCTGCACAGGCATGGCACTGGCTAGTGAACACGATCCTCGCATTGACCCTTTCCA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttagtttctttcttttatgtagtcgttgctgaccgggaattgaacacacttgcagGTGATGTGTCCAACATGTCTCTGCACAGGCATGGCACTGGCTAGTGAACACGATCCTCGCATTGACCCTTTCCA
                          tgctgac  putative branch site (score: 5)
        tttcttttat  TA-rich tract