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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tacattagggttcggtctattgtctaaagaatttaaatgacttgctcttcgttgggagggcttggattcaaattggtgacaaatttggacgatcgtgcagGTAGAGCTGGAGTGCCTATGGAGGTGATGGGGCTGATGCTTGGGGAGTTCGTGGACGAGTACACTGTTCGTGTTGTGGATGTATTTGCTATGCCACAGAG

Basic information

species Physcomitrella patens
transcript PP1S46_324V6.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S46_324V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: LOC_Os01g16190.1 (Oryza sativa), 3'ss of exon 1
tacattagggttcggtctattgtctaaagaatttaaatgacttgctcttcgttgggaggg----cttggattcaaattggtgacaaatttggacgatcgtgcagGTAGAGCTGGAGTGCCTATGGAGGTGATGGGGCTGATGCTTGGGGAGTTCGTGGACGAGTACACTGTTCGTGTTGTGGATGTATTTGCTATGCCACAGAG
                             | |     |  | | ||| ||  ||   |||     |  | ||    ||| |      ||||   |  || |||||  | || || ||||| ||||||||||||||||||||||| ||||||||||| ||||| ||||| ||  | || || || || || || ||||| |||||
--------------------------gtcagtccccctctcctcctcctcaatgatgggggatattaaggtttccgttgattttggttttgcg-gcgcgcgcagGGCGGGCCGGCGTGCCGATGGAGGTGATGGGGCTGATGCTCGGGGAGTTCGTCGACGACTACACCGTCAGGGTGGTCGACGTCTTCGCCATGCCGCAGAG

upper sequence: PP1S46_324V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: LOC_Os05g30800.1 (Oryza sativa), 3'ss of exon 1
tacattagggttcggtctattgtctaaagaatttaaatgacttgctcttcgttgggagggcttggattcaaattggtgacaaatttggacgatcgtgcagGTAGAGCTGGAGTGCCTATGGAGGTGATGGGGCTGATGCTTGGGGAGTTCGTGGACGAGTACACTGTTCGTGTTGTGGATGTATTTGCTATGCCACAGAG
                            |  |        ||    ||| | | ||    ||  |  ||   ||| | ||     ||  ||     ||||| || || || ||||| ||||||||||||||||||||||| ||||||||||| ||||| ||||| ||  | || || || || || || ||||| |||||
--------------------------gtgcgtccccccctctcctgcttggctagggtttctgcggctctt-ttgctcacccgcctgcgcgcc---gcagGGAGGGCCGGCGTGCCGATGGAGGTGATGGGGCTGATGCTGGGGGAGTTCGTCGACGACTACACGGTCAGGGTGGTCGACGTCTTCGCCATGCCGCAGAG

upper sequence: PP1S46_324V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GLYMA17G36230.1 (Glycine max), 3'ss of exon 1
----tac-attagggttc--ggtctattgtctaaagaatttaaatgacttgctcttcgttgggagggcttggattcaaattggtgac-----aaatttggacgatcgtgcagGTAGAGCTGGAGTGCCTATGGAGGTGATGGGGCTGATGCTTGGGGAGTTCGTGGACGAGTACACTGTTCGTGTTGTGGATGTATTTGCTATGCCACAGAG
    | | |||||  |||    | | |  |||  |     |   |   ||    |||    |      ||    |  |  |  | |      |||     |     ||| ||| ||||||||||| || ||||| |||||||| |||||| | |||||||||||||| |||||||| ||||| ||||||||||| ||||| ||||| |||| 
ggtatgctattagaattcttattttctcttctcgatccccttcttcgtttcactttcccatgttttttttattgttcatcttataattttgaaaaccctaatttgtgtgtaGGAAGAGCTGGAGTACCGATGGAAGTGATGGGTCTGATGTTGGGGGAGTTCGTGGATGAGTACACCGTTCGCGTTGTGGATGTGTTTGCGATGCCTCAGA-

upper sequence: PP1S46_324V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GLYMA14G08940.1 (Glycine max), 3'ss of exon 1
----tacattagggttcgg--tctattgtctaaagaatttaaatgacttgctcttcgttgggagggcttggattcaaattggtgacaaa-tttggacgatcgtgcagGTAGAGCTGGAGTGCCTATGGAGGTGATGGGGCTGATGCTTGGGGAGTTCGTGGACGAGTACACTGTTCGTGTTGTGGATGTATTTGCTATGCCACAGAG
       |||||  |||    | | |  |||  |    || | ||     || ||| || |      ||    ||  ||   |  ||||      |     ||| ||| |||||||| || || ||||| |||||||| |||||| | |||||||||||||| |||||||| ||||| ||||||||||| ||||| ||||| |||||
gtacgctattagaattcttcttttctcttctcgatcccttcactggtccacttttcctttgtttttgtttttgtctgataattttcaaaaccctaatttctgtgtagGAAGAGCTGGGGTACCCATGGAAGTGATGGGTCTGATGTTGGGGGAGTTCGTGGATGAGTACACCGTTCGCGTTGTGGATGTGTTTGCGATGCCTCAGAG

upper sequence: PP1S46_324V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GLYMA13G29660.1 (Glycine max), 3'ss of exon 1
tacattagggttcggtctattgtctaaagaatttaaatgacttgctcttcgttgggagggcttggattc-aaattggtga---caaatttggacgatcgtgcagGTAGAGCTGGAGTGCCTATGGAGGTGATGGGGCTGATGCTTGGGGAGTTCGTGGACGAGTACACTGTTCGTGTTGTGGATGTATTTGCTATGCCACAGAG
           |  ||| |     |   |  |||||   | | |    || |  ||||  |  |  ||| ||||| | |    |   |||     ||  |||||| || ||||| || || ||||||||||||||  |||||||||| || ||||||||||||||||| |||||||| || ||||| || || ||||| |||||
----------gtaagtccaaaagttcccgtttttaacctaatcgag--tcat--ggagtacccgatttctaaattagggttttcgtgtttctgtaat--tgcagGAAGGGCTGGGGTTCCCATGGAGGTGATGGGTTTGATGCTTGGAGAATTCGTGGACGAGTACACCGTTCGTGTGGTTGATGTCTTCGCAATGCCGCAGAG

upper sequence: PP1S46_324V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GLYMA15G09410.1 (Glycine max), 3'ss of exon 1
-tacattagggttcggtctattgtctaaagaatttaaatgacttgctcttcgttgggagggcttggattcaaattggtgacaaatttggacgatcgtgcagGTAGAGCTGGAGTGCCTATGGAGGTGATGGGGCTGATGCTTGGGGAGTTCGTGGACGAGTACACTGTTCGTGTTGTGGATGTATTTGCTATGCCACAGAG
 || | |         ||  || | ||    | |  | | |   | |   || |   |    | || ||    || |||     |||     ||  |||||| || ||||| || || ||||| ||||||||  |||||||||| || ||||||||||||||||| |||||||| || ||||| || || ||||| |||||
gtaaagtccaaaagtttccgttttttagcctaatcgagtcatggggtacccgattacaaaattagggtt----ttcgtg-----tttttgtaat--tgcagGAAGGGCTGGGGTTCCCATGGAAGTGATGGGTTTGATGCTTGGAGAATTCGTGGACGAGTACACCGTTCGTGTGGTTGATGTCTTCGCAATGCCGCAGAG

upper sequence: PP1S46_324V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: Vv18s0001g10820.t01 (Vitis vinifera), 3'ss of exon 1
---------------------------tacattagggttcggtctattgtctaa----agaatttaaatgacttgctcttcgttgggagggcttggattcaaattggtgaca---aatttggacgatcgtg-----cagGTAGAGCTGGAGTGCCTATGGAGGTGATGGGGCTGATGCTTGGGGAGTTCGTGGACGAGTACACTGTTCGTGTTGTGGATGTATTTGCTATGCCACAGAG
                           ||  | |   || || ||  | | | |       |||   || |||| |    | |    |||| ||   ||||| ||| |  |     ||||||  ||| | |      ||| ||||||||||| || ||||| || ||||| |||||||| || |||||||| || |||||||| |||||||| || ||||| || || ||||| |||||
gtaacatcttgacgccaagacaagttttatttcaattttagggctgctttgtgatttttttattcgcatcacttccaaaccctaattagggttt---ttcaatttgttttcttttgatttggg-gattgggaataatagGGAGAGCTGGAGTTCCCATGGAAGTCATGGGTCTGATGCTGGGAGAGTTCGTTGATGAGTACACAGTTCGTGTAGTAGATGTGTTCGCGATGCCGCAGAG

upper sequence: PP1S46_324V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: EFJ37436 (Selaginella moellendorffii), 3'ss of exon 1
tacattagggttcggtctattgtctaaagaatttaaatgacttgctcttcgttgggagggcttggattc---aaattggtgacaaatttggacgatcgt---gcagGTAGAGCTGGAGTGCCTATGGAGGTGATGGGGCTGATGCTTGGGGAGTTCGTGGACGAGTACACTGTTCGTGTTGTGGATGTATTTGCTATGCCACAGAG
                                                  ||  ||||||   |   ||   |  || |||  | |  |   || |  |   ||||| ||||||||||| || ||||| || ||||| |||||||||||||| || |||||||||||||||||||| || ||||| || ||||| ||||| |||||
--------------------------------------------------gtaaggagggagagagctccgcattttcgtgctagagctttgcgcttctttcgcagGGAGAGCTGGAGTCCCCATGGAAGTCATGGGACTGATGCTTGGGGACTTTGTGGACGAGTACACTGTTCGCGTGGTGGACGTCTTTGCGATGCCTCAGAG

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|67573473|gb|BJ946297.1|BJ946297
EST:     GGAGCAAGTGTACATTTCCTCTCTGGCGCTGCTCAAAATGCTCAAACATG                         GTAGAGCTGGAGTGCCTATGGAGGTGATGGGGCTGATGCTTGGGGAGTTCG
genomic: GGAGCAAGTGTACATTTCCTCTCTGGCGCTGCTCAAAATGCTCAAACATGgtacgctgct ... gatcgtgcagGTAGAGCTGGAGTGCCTATGGAGGTGATGGGGCTGATGCTTGGGGAGTTCG
EST: gi|208388020|gb|DC933140.1|DC933140
EST:     GGAGCAAGTGTACATTTCCTCTCTGGCGCTGCTCAAAATGCTCAAACATG                         GTAGAGCTGGAGTGCCTATGGAGGTGATGGGGCTGATGCTTGGGGAGTTCG
genomic: GGAGCAAGTGTACATTTCCTCTCTGGCGCTGCTCAAAATGCTCAAACATGgtacgctgct ... gatcgtgcagGTAGAGCTGGAGTGCCTATGGAGGTGATGGGGCTGATGCTTGGGGAGTTCG
EST: gi|208384664|gb|DC915239.1|DC915239
EST:     GGAGCAAGTGTACATTTCCTCTCTGGCGCTGCTCAAAATGCTCAAACATG                         GTAGAGCTGGAGTGCCTATGGAGGTGATGGGGCTGATGCTTGGGGAGTTCG
genomic: GGAGCAAGTGTACATTTCCTCTCTGGCGCTGCTCAAAATGCTCAAACATGgtacgctgct ... gatcgtgcagGTAGAGCTGGAGTGCCTATGGAGGTGATGGGGCTGATGCTTGGGGAGTTCG
EST: gi|162173753|gb|FC349929.1|FC349929
EST:     GGAGCAAGTGTACATTTCCTCTCTGGCGCTGCTCAAAATGCTCAAACATG                         GTAGAGCTGGAGTGCCTATGGAGGTGATGGGGCTGATGCTTGGGGAGTTCG
genomic: GGAGCAAGTGTACATTTCCTCTCTGGCGCTGCTCAAAATGCTCAAACATGgtacgctgct ... gatcgtgcagGTAGAGCTGGAGTGCCTATGGAGGTGATGGGGCTGATGCTTGGGGAGTTCG
EST: gi|208390625|gb|DC937557.1|DC937557
EST:     GGAGCAAGTGTACATTTCCTCTCTGGCGCTGCTCAAAATGCTCAAACATG                         GTAGAGCTGGAGTGCCTATGGAGGTGATGGGGCTGATGCTTGGGGAGTTCG
genomic: GGAGCAAGTGTACATTTCCTCTCTGGCGCTGCTCAAAATGCTCAAACATGgtacgctgct ... gatcgtgcagGTAGAGCTGGAGTGCCTATGGAGGTGATGGGGCTGATGCTTGGGGAGTTCG
EST: gi|208400245|gb|DC908906.1|DC908906
EST:     GGAGCAAGTGTACATTTCCTCTCTGGCGCTGCTCAAAATGCTCAAACATG                         GTAGAGCTGGAGTGCCTATGGAGGTGATGGGGCTGATGCTTGGGGAGTTCG
genomic: GGAGCAAGTGTACATTTCCTCTCTGGCGCTGCTCAAAATGCTCAAACATGgtacgctgct ... gatcgtgcagGTAGAGCTGGAGTGCCTATGGAGGTGATGGGGCTGATGCTTGGGGAGTTCG
EST: gi|208378125|gb|DC902598.1|DC902598
EST:     GGAGCAAGTGTACATTTCCTCTCTGGCGCTGCTCAAAATGCTCAAACATG                         GTAGAGCTGGAGTGCCTATGGAGGTGATGGGGCTGATGCTTGGGGAGTTCG
genomic: GGAGCAAGTGTACATTTCCTCTCTGGCGCTGCTCAAAATGCTCAAACATGgtacgctgct ... gatcgtgcagGTAGAGCTGGAGTGCCTATGGAGGTGATGGGGCTGATGCTTGGGGAGTTCG
EST: gi|22131888|gb|BQ826859.1|BQ826859
EST:     GGAGCAAGTGTACATTTCCTCTCTGGCGCTGCTCAAAATGCTCAAACATG                         GTAGAGCTGGAGTGCCTATGGAGGTGATGGGGCTGATGCTTGGGGAGTTCG
genomic: GGAGCAAGTGTACATTTCCTCTCTGGCGCTGCTCAAAATGCTCAAACATGgtacgctgct ... gatcgtgcagGTAGAGCTGGAGTGCCTATGGAGGTGATGGGGCTGATGCTTGGGGAGTTCG
EST: gi|67570106|gb|BJ942930.1|BJ942930
EST:     GGAGCAAGTGTACATTTCCTCTCTGGCGCTGCTCAAAATGCTCAAACATG                         GTAGAGCTGGAGTGCCTATGGAGGTGATGGGGCTGATGCTTGGGGAGTTCG
genomic: GGAGCAAGTGTACATTTCCTCTCTGGCGCTGCTCAAAATGCTCAAACATGgtacgctgct ... gatcgtgcagGTAGAGCTGGAGTGCCTATGGAGGTGATGGGGCTGATGCTTGGGGAGTTCG
EST: gi|18329512|gb|BJ161518.1|BJ161518
EST:     GGAGCAAGTGTACATTTCCTCTCTGGCGCTGCTCAAAATGCTCAAACATG                         GTAGAGCTGGAGTGCCTATGGAGGTGATGGGGCTGATGCTTGGGGAGTTCG
genomic: GGAGCAAGTGTACATTTCCTCTCTGGCGCTGCTCAAAATGCTCAAACATGgtacgctgct ... gatcgtgcagGTAGAGCTGGAGTGCCTATGGAGGTGATGGGGCTGATGCTTGGGGAGTTCG
EST: gi|208362822|gb|DC950622.1|DC950622
EST:     CTCAAAATGCTCAAACATG                         GTAGAGCTGGAGTGCCTATGGAGGTGATGGGGCTGATGCTTGGGGAGTTCG
genomic: CTCAAAATGCTCAAACATGgtacgctgct ... gatcgtgcagGTAGAGCTGGAGTGCCTATGGAGGTGATGGGGCTGATGCTTGGGGAGTTCG
EST: gi|162150910|gb|FC327390.1|FC327390
EST:     GGAGCAAGTGTACATTTCCTCTCTGGCGCTGCTCAAAATGCTCAAACATG                         GTAGAGCTGGAGTGCCTATGGAGGTGATGGGGCTGATGCTTGGGGAGTTCG
genomic: GGAGCAAGTGTACATTTCCTCTCTGGCGCTGCTCAAAATGCTCAAACATGgtacgctgct ... gatcgtgcagGTAGAGCTGGAGTGCCTATGGAGGTGATGGGGCTGATGCTTGGGGAGTTCG
EST: gi|67569711|gb|BJ942535.1|BJ942535
EST:     GGAGCAAGTGTACATTTCCTCTCTGGCGCTGCTCAAAATGCTCAAACATG                         GTAGAGCTGGAGTGCCTATGGAGGTGATGGGGCTGATGCTTGGGGAGTTCG
genomic: GGAGCAAGTGTACATTTCCTCTCTGGCGCTGCTCAAAATGCTCAAACATGgtacgctgct ... gatcgtgcagGTAGAGCTGGAGTGCCTATGGAGGTGATGGGGCTGATGCTTGGGGAGTTCG
EST: gi|208387484|gb|DC933347.1|DC933347
EST:     GGAGCAAGTGTACATTTCCTCTCTGGCGCTGCTCAAAATGCTCAAACATG                         GTAGAGCTGGAGTGCCTATGGAGGTGATGGGGCTGATGCTTGGGGAGTTCG
genomic: GGAGCAAGTGTACATTTCCTCTCTGGCGCTGCTCAAAATGCTCAAACATGgtacgctgct ... gatcgtgcagGTAGAGCTGGAGTGCCTATGGAGGTGATGGGGCTGATGCTTGGGGAGTTCG
EST: gi|18327697|gb|BJ159700.1|BJ159700
EST:     GGAGCAAGTGTACATTTCCTCTCTGGCGCTGCTCAAAATGCTCAAACATG                         GTAGAGCTGGAGTGCCTATGGAGGTGATGGGGCTGATGCTTGGGGAGTTCG
genomic: GGAGCAAGTGTACATTTCCTCTCTGGCGCTGCTCAAAATGCTCAAACATGgtacgctgct ... gatcgtgcagGTAGAGCTGGAGTGCCTATGGAGGTGATGGGGCTGATGCTTGGGGAGTTCG
EST: gi|100420708|gb|BY993475.1|BY993475
EST:     GGAGCAAGTGTACATTTCCTCTCTGGCGCTGCTCAAAATGCTCAAACATG                         GTAGAGCTGGAGTGCCTATGGAGGTGATGGGGCTGATGCTTGGGGAGTTCG
genomic: GGAGCAAGTGTACATTTCCTCTCTGGCGCTGCTCAAAATGCTCAAACATGgtacgctgct ... gatcgtgcagGTAGAGCTGGAGTGCCTATGGAGGTGATGGGGCTGATGCTTGGGGAGTTCG

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), 25 (downstream exon)
Score: 8

GGCGGTTCTGGAGGTGGACCGCATCCAGATTCACCCCTCGTTGATTCGTCGGAGCAAGTGTACATTTCCTCTCTGGCGCTGCTCAAAATGCTCAAACATGgtacgctgct ... gatcgtgcagGTAGAGCTGGAGTGCCTATGGAGGTGATGGGGCTGATGCTTGGGGAGTTCGTGGACGAGTACACTGTTCGTGTTGTGGATGTATTTGCTATGCCACAGAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttcgttgggagggcttggattcaaattggtgacaaatttggacgatcgtgcagGTAGAGCTGGAGTGCCTATGGAGGTGATGGGGCTGATGCTTGGGGAGTTCGTGGACGAGTACACTGTTCGTGTTGTGGATGTATTTGCTATGCCACAGAG
                    attcaaatt  TA-rich tract