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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtgtccaggcttttacgacgcttgttggttgtagcatccgtaattagttcatgaatgtgtctatgaatccatgtactatatgtatttatcgctgaggatctttgctctggtgtattggtttgtgcagGTTATTCGGTCATATCATGGTCATTTGAGTGGAGTTTATTGCTTAGCTCTTCATCCTACACTTGATATTCTCATGACTGGGGGTCGAGATTCAGTGTGCC

Basic information

species Physcomitrella patens
transcript PP1S402_49V6.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S402_49V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: LOC_Os03g21990.1 (Oryza sativa), 3'ss of exon 10
gtgtgtccaggcttttacgacgcttgttggttgtagcatccgtaattagttcatgaatgtgtctatgaatccatgtactatatgtatt--tatcgctgaggatctttgctctggtgtattggtttgtgcagGTTATTCGGTCATATCATGGTCATTTGAGTGGAGTTTATTGCTTAGCTCTTCATCCTACACTTGATATTCTCATGACTGGGGGTCGAGATTCAGTGTGCC
                                             |||| | ||   |   | ||     |  | |||      ||||   ||    |      |||| |    |  |||  |||    |||||||| |||| |||||||| ||||||||||| || || ||| | ||||| ||||| ||| | |||||  |  ||||||| ||||| |||||||| ||  
--------------------------------------------gttagcttatagttcgatgtagattgcagtatacagggcatattggcattatcgtaacattttgtttcttttcatt--ttta---agGTTATTAGGTCTTATCATGGCCATTTGAGTGGGGTGTACTGCCTTGCTCTACATCCAACAATCGATATCTTGCTGACTGGTGGTCGCGATTCAGTTTGTA

upper sequence: PP1S402_49V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: GLYMA09G04910.1 (Glycine max), 3'ss of exon 9
gtgtgtccaggcttttacgacgcttgttggttgtagcatccgtaattagttcatgaatgtgtctatgaatccatgtactatatgtatttatcgctgaggatctttgctctggtgtattggtttgtgcagGTTATTCGGTCATATCATGGTCATTTGAGTGGAGTTTATTGCTTAGCTCTTCATCCTACACTTGATATTCTCATGACTGGGGGTCGAGATTCAGTGTGCC
                     |   | |     |  |||   |  ||      ||||| | ||      | |  | |||  ||  | ||   |   |    ||    |      |||||   | |  |||||||| |||| |||||||||||| ||||||| ||||||||||| ||||||||||| ||| ||||  || |  | || || || || ||||| || ||||
---------------------gtcagatctccatttcatttattgttttggactgaatatttcagcagttactggaactccatcaaattgcaggcta----ctaaaatacatgatattg---tatttagGTTATTAGGTCTTATCATGGTCATCTGAGTGGTGTTTATTGCTTGGCTCTTCATCCCACAATTGACGTTTTACTAACCGGAGGACGTGATTCTGTCTGCC

upper sequence: PP1S402_49V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: GLYMA15G15960.2 (Glycine max), 3'ss of exon 8
gtgtgtccaggcttttacgacgcttgttggttgtagcatccgtaattagttcatgaatgtgtctatgaatccatgtactatatgtatttatcgctgaggatctttgctctggtgtat--tggtttgtgcagGTTATTCGGTCATATCATGGTCATTTGAGTGGAGTTTATTGCTTAGCTCTTCATCCTACACTTGATATTCTCATGACTGGGGGTCGAGATTCAGTGTGCC
                     |     |    ||  |||  ||||||  ||  || |  ||  |||   | ||     ||  ||  |  |||    |  |   |  ||    |  ||  |  | | |  |||||||| | || |||||||||||| ||||||| ||||||||||| ||||||||||| ||| ||||  || |  | || || || || ||||| || ||||
---------------------gtcaaatctccgtttcattagtaatt--tttctggac-tgaatat---ttcagcagttacttgactccatcaaataacaggct-actaaaatacatgatattgtatttagGTTATTAGATCTTATCATGGTCATCTGAGTGGTGTTTATTGCTTGGCTCTTCATCCCACAATTGACGTTTTACTAACCGGAGGACGTGATTCTGTCTGCC

upper sequence: PP1S402_49V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: AT3G16650.1 (Arabidopsis thaliana), 3'ss of exon 9
gtgtgtccaggcttttacgacgcttgttggttgtagcatccgtaatt-agttcatga-atgtgtctatgaatccatgtactatatgtatttatcgctgaggatctttgctctggtgtattggtttgtgcagGTTATTCGGTCATATCATGGTCATTTGAGTGGAGTTTATTGCTTAGCTCTTCATCCTACACTTGATATTCTCATGACTGGGGGTCGAGATTCAGTGTGCC
                             |||  | | ||  | ||  | |||||   || ||| ||| |||   | | ||     | |  |    | | |  |  ||   | |    |||  ||    |||||||||| || |||||||||||||||  ||| ||||| || ||||||||||||||||| |||||| || |  | || || || ||||| || || ||| 
-----------------------------gtttaaac-tcgatgatggatttcatctcatctgtatattaattactcttctcctgatctgaacttttcatgtccaatgtctttggaatttgtctttgatagGTTATTCGATCTTATCATGGTCATTTGCATGGCGTTTACTGTTTAGCTCTTCATCCTACTCTTGATGTTGTACTAACCGGAGGGCGAGACTCTGTCTGCA

upper sequence: PP1S402_49V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: AT4G15900.1 (Arabidopsis thaliana), 3'ss of exon 9
gtgtgtccaggcttttacgacgcttgttggttgtagcatccgtaattagttcatgaatgtgtctatgaatccatgtactatatgtatttatcgctgaggatctttgctctggtgtattggtttgtgcagGTTATTCGGTCATATCATGGTCATTTGAGTGGAGTTTATTGCTTAGCTCTTCATCCTACACTTGATATTCTCATGACTGGGGGTCGAGATTCAGTGTGCC
                                                         |    || | | ||  |  | ||| || |||| ||       ||  |  ||  |   | ||| ||||   ||||||| || || ||||||||||| |||||||| || |||||||||||||| || || ||  | ||| || |  | |||||||| ||||| || || ||| 
-------------------------------------------------------gttacaactct-attctcttcattatctggatttctcatatctaatgct--cttggaatttttgatttg-atagGTTATCCGATCTTATCATGGTCACTTGAGTGGTGTCTATTGCTTAGCTCTGCACCCAACTTTGGATGTTTTATTAACTGGGGGGCGAGACTCTGTCTGCA

upper sequence: PP1S402_49V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: Vv05s0077g02310.t01 (Vitis vinifera), 3'ss of exon 9
gtgtgtccaggcttttacgacgcttgttggttgtagcatccgtaattagttcatgaatgtgtctatgaatccatgtactatatgtatttatcgctgaggatctttgctctggtgtattggtttgtgcagGTTATTCGGTCATATCATGGTCATTTGAGTGGAGTTTATTGCTTAGCTCTTCATCCTACACTTGATATTCTCATGACTGGGGGTCGAGATTCAGTGTGCC
                                      |  | |  |  ||  | ||     |  ||||||| ||||||| | ||        || |     | |||| |  | | ||  ||||| |||||||||||||| |||||||||||| ||||||| |||||||| || || |||||||| ||| |||| ||| |  | |||||||| || ||||| || ||||
-------------------------------------gttagaacct--tttttaaactcaccgctgaatcc-tgtactacaagtg------actaaattcatatgctata-tatttttctttgttcagGTTATTCGGTCTTATCATGGTCATCTGAGTGGGGTTTATTGTTTGGCACTTCATCCCACAATTGACATTTTGCTTACTGGGGGACGTGATTCTGTCTGCC

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|162277474|gb|FC453001.1|FC453001
EST:     CAGCTGGTGATGACAAACAGGTCAAATGTTGGGATCTTGAATACAATAAG                         GTTATTCGGTCATATCATGGTCATTTGAGTGGAGTTTATTGCTTAGCTCTT
genomic: CAGCTGGTGATGACAAACAGGTCAAATGTTGGGATCTTGAATACAATAAGgtgtgtccag ... gtttgtgcagGTTATTCGGTCATATCATGGTCATTTGAGTGGAGTTTATTGCTTAGCTCTT




















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: 33 (upstream exon), 25 (downstream exon)
Score: 2

GCCTTGCAGTGAGCGCCCGGCATCCTTATTTATTCTCAGCTGGTGATGACAAACAGGTCAAATGTTGGGATCTTGAATACAATAAGgtgtgtccag ... gtttgtgcagGTTATTCGGTCATATCATGGTCATTTGAGTGGAGTTTATTGCTTAGCTCTTCATCCTACACTTGATATTCTCATGACTGGGGGTCGAGATTCAGTGTGCC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtactatatgtatttatcgctgaggatctttgctctggtgtattggtttgtgcagGTTATTCGGTCATATCATGGTCATTTGAGTGGAGTTTATTGCTTAGCTCTTCATCCTACACTTGATATTCTCATGACTGGGGGTCGAGATTCAGTGTGCC
     atatgtatttat  TA-rich tract