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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGTTTTGCAGCTGTTATTATGCGAATAAGGGAGCCAAAAACGACTGCCCTCATTTTTGCATCTGGTAAAATGgtattgtcccagtcgcttttatttggatcgtgaaattgaaattgtggctttatttggatcacctgaataggttcgaactgggtatcatgcacactaattt...

Basic information

species Physcomitrella patens
transcript PP1S246_34V6.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S246_34V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: LOC_Os03g45410.1 (Oryza sativa), 5'ss of exon 4
CGTTTTGCAGCTGTTATTATGCGAATAAGGGAGCCAAAAACGACTGCCCTCATTTTTGCATCTGGTAAAATGgtattgtcccagtcgcttttatttggatcgtgaaattgaaattgtggctttatttggatcacct---gaataggttcgaactgggtatcatgcacactaattt
|||||||| || ||||| ||| ||||||| || |||||||| || || || || |||||||| ||||||||||||| || | | |  ||| ||    ||  |  ||  |    || ||    | |    ||   ||   |||| | || |   |  ||   |||  ||    |  
CGTTTTGCTGCGGTTATCATGAGAATAAGAGAACCAAAAACTACAGCTCTGATATTTGCATCGGGTAAAATGgtatggttcaactt-cttgtaccgtgactgcaaatgttctgttttgttcatctgcttattgacttgtgaattgttttgttatctgtccaatggccagctgt--

upper sequence: PP1S246_34V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: GLYMA09G41330.1 (Glycine max), 5'ss of exon 4
CGTTTTGCAGCTGTTATTATGCGAATAAGGGAGCCAAAAACGACTGCCCTCATTTTTGCATCTGGTAAAATGgtattgtcccagtcgcttttatttggatcgtgaaattgaa---attgtggctttatttggatcacctg-aataggttcgaactgggtatcatgcacactaattt--
|||||||| |||||||||||| | || ||||| |||||||| ||||| ||||||||||||||||| || |||||||| |     |   ||||  ||| |||  | | ||      | |   | |  | ||| || || || |||| |||  |  || || | || || |  | ||   
CGTTTTGCTGCTGTTATTATGAGGATCAGGGAACCAAAAACTACTGCACTCATTTTTGCATCTGGCAAGATGgtattttt----ttttttttggttgaatctggtacttctgtccaattaagttggaattgcatgacatgcaataagtt-aatgtgagt-tgatacagatcagttgat

upper sequence: PP1S246_34V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: GLYMA18G44460.1 (Glycine max), 5'ss of exon 3
-CGTTTTGCAGCTGTTATTATGCGAATAAGGGAGCCAAAAACGACTGCCCTCATTTTTGCATCTGGTAAAATGgtattgtcccagtcgcttttatttggatcgtgaaattgaaattgt-ggctttatttggatcacctgaataggttcgaactgggtatca-tgcacactaattt
 |||||||| |||||||||||| | || ||||| |||||||| ||||| ||||||||||||||||| || ||||||| || | | ||| ||  || |||  | |      ||  | || ||  ||   || || |    |||   |  ||  |    |  |    | |  |||  
GCGTTTTGCTGCTGTTATTATGAGGATCAGGGAACCAAAAACTACTGCACTCATTTTTGCATCTGGCAAGATggtat-gttctattcg-ttgaatctggtacttctgtccgatttagttggagttgcatgaattattgaaattaatgtgagttcacaactaactgatagaaatc-

upper sequence: PP1S246_34V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: GLYMA19G28780.1 (Glycine max), 5'ss of exon 4
CGTTTTGCAGCTGTTATTATGCGAATAAGGGAGCCAAAAACGACTGCCCTCATTTTTGCATCTGGTAAAATGgtattgtcccagtcgcttttatttggatcgtgaaattgaaattgtggctttatttggatcacctgaataggttcgaactgggtatcatgcacactaattt-
|||||||| |||||||||||| | || ||||| |||||||| ||||| ||||||||||||||||| || |||||| | |    || |  | |  |      ||  |||| || |||    |  ||      ||      ||   ||       || |    ||||  || |  
CGTTTTGCTGCTGTTATTATGAGGATCAGGGAACCAAAAACTACTGCACTCATTTTTGCATCTGGCAAGATGgtacttttttggttgaatctggtacttctgtccaatt-aagttggaattgcatgacatgcaataagttaatgtcagttgatgttttgcacacaaaaagtat

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|18346530|gb|BJ178575.1|BJ178575
EST:     GAATAAGGGAGCCAAAAACGACTGCCCTCATTTTTGCATCTGGTAAAATG                         GTGTGCACGGGTGCCAAGAGTGAGCAACAGTCAAAGTTGGCTGCAAGAAAG
genomic: GAATAAGGGAGCCAAAAACGACTGCCCTCATTTTTGCATCTGGTAAAATGgtattgtccc ... atactctcagGTGTGCACGGGTGCCAAGAGTGAGCAACAGTCAAAGTTGGCTGCAAGAAAG
EST: gi|100438401|gb|BY979938.1|BY979938
EST:     GAATAAGGGAGCCAAAAACGACTGCCCTCATTTTTGCATCTGGTNAAATG                         GTGTGCACGGGTGCCAAGAGTGAGCAACAGTCAAAGTTGGCTGCAAGAAAG
genomic: GAATAAGGGAGCCAAAAACGACTGCCCTCATTTTTGCATCTGGTAAAATGgtattgtccc ... atactctcagGTGTGCACGGGTGCCAAGAGTGAGCAACAGTCAAAGTTGGCTGCAAGAAAG
EST: gi|100441350|gb|BY962639.1|BY962639
EST:     GAATAAGGGAGCCAAAAACGACTGCCCTCATTTTTGCATCTGGTAAAATG                         GTGTGCACGGGTGCCAAGAGTGAGCAACAGTCAAAGTTGGCTGCAAGAAAG
genomic: GAATAAGGGAGCCAAAAACGACTGCCCTCATTTTTGCATCTGGTAAAATGgtattgtccc ... atactctcagGTGTGCACGGGTGCCAAGAGTGAGCAACAGTCAAAGTTGGCTGCAAGAAAG
EST: gi|208354942|gb|DC914206.1|DC914206
EST:     GAATAAGGGAGCCAAAAACGACTGCCCTCATTTTTGCATCTGGTAAAATG                         GTGTGCACGGGTGCCAAGAGTGAGCAACAGTCAAAGTTGGCTGCAAGAAAG
genomic: GAATAAGGGAGCCAAAAACGACTGCCCTCATTTTTGCATCTGGTAAAATGgtattgtccc ... atactctcagGTGTGCACGGGTGCCAAGAGTGAGCAACAGTCAAAGTTGGCTGCAAGAAAG
EST: gi|208376207|gb|DC910783.1|DC910783
EST:     GAATAAGGGAGCCAAAAACGACTGCCCTCATTTTTGCATCTGGTAAAATG                         GTGTGCACGGGTGCCAAGAGTGAGCAACAGTCAAAGTTGGCTGCAAGAAAG
genomic: GAATAAGGGAGCCAAAAACGACTGCCCTCATTTTTGCATCTGGTAAAATGgtattgtccc ... atactctcagGTGTGCACGGGTGCCAAGAGTGAGCAACAGTCAAAGTTGGCTGCAAGAAAG
EST: gi|208373747|gb|DC936560.1|DC936560
EST:     GAATAAGGGAGCCAAAAACGACTGCCCTCATTTTTGCATCTGGTAAAATG                         GTGTGCACGGGTGCCAAGAGTGAGCAGCAGTCAAAGTTGGCTGCAAGAAAG
genomic: GAATAAGGGAGCCAAAAACGACTGCCCTCATTTTTGCATCTGGTAAAATGgtattgtccc ... atactctcagGTGTGCACGGGTGCCAAGAGTGAGCAACAGTCAAAGTTGGCTGCAAGAAAG
EST: gi|208360850|gb|DC934746.1|DC934746
EST:     GAATAAGGGAGCCAAAAACGACTGCCCTCATTTTTGCATCTGGT-----G                         -TG--CACGGGTGCCAAGAGTGAGCAACAGTCAAAGTTGGCTGCAAGAAAG
genomic: GAATAAGGGAGCCAAAAACGACTGCCCTCATTTTTGCATCTGGTAAAATGgtattgtccc ... atactctcagGTGTGCACGGGTGCCAAGAGTGAGCAACAGTCAAAGTTGGCTGCAAGAAAG
EST: gi|100430149|gb|BY978271.1|BY978271
EST:     GAATAAGGGAGCCAAAAACGACTGCCCTCATTTTTGCATCTGGTAAAATG                         GTGTGCACGGGTGCCAAGAGTGAGCAACAGTCAAAGTTGGCTGCAAGAAAG
genomic: GAATAAGGGAGCCAAAAACGACTGCCCTCATTTTTGCATCTGGTAAAATGgtattgtccc ... atactctcagGTGTGCACGGGTGCCAAGAGTGAGCAACAGTCAAAGTTGGCTGCAAGAAAG
EST: gi|208382418|gb|DC927952.1|DC927952
EST:     AAGGGAGCCAAAAACGACTGCCCTCATTTTTGCATCTGGTAAAATG                         GTGTGCACGGGTGCCAAGAGTGAGCAACAGTCAAAGTTGGCTGCAAGAAAG
genomic: AAGGGAGCCAAAAACGACTGCCCTCATTTTTGCATCTGGTAAAATGgtattgtccc ... atactctcagGTGTGCACGGGTGCCAAGAGTGAGCAACAGTCAAAGTTGGCTGCAAGAAAG
EST: gi|100410692|gb|BY992221.1|BY992221
EST:     GAATAAGGGAGCCAAAAACGACTGCCCTCATTTTTGCATCTGGTAAAATG                         GTGTGCACGGGTGCCAAGAGTGAGCAACAGTCAAAGTTGGCTGCAAGAAAG
genomic: GAATAAGGGAGCCAAAAACGACTGCCCTCATTTTTGCATCTGGTAAAATGgtattgtccc ... atactctcagGTGTGCACGGGTGCCAAGAGTGAGCAACAGTCAAAGTTGGCTGCAAGAAAG
EST: gi|18373885|gb|BJ205463.1|BJ205463
EST:     GAATAAGGGAGCCAAAAACGACTGCCCTCATTTTTGCATCTGGTAAAATG                         GTGTGCACGGGTGCCAAGAGTGAGCAACAGTCAAAGTTGGCTGCAAGAAAG
genomic: GAATAAGGGAGCCAAAAACGACTGCCCTCATTTTTGCATCTGGTAAAATGgtattgtccc ... atactctcagGTGTGCACGGGTGCCAAGAGTGAGCAACAGTCAAAGTTGGCTGCAAGAAAG

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: 8 (upstream exon), 32 (downstream exon)
Score: 4

CGTTTTGCAGCTGTTATTATGCGAATAAGGGAGCCAAAAACGACTGCCCTCATTTTTGCATCTGGTAAAATGgtattgtccc ... atactctcagGTGTGCACGGGTGCCAAGAGTGAGCAACAGTCAAAGTTGGCTGCAAGAAAG




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