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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgtgttgtaaattggtgaatgcttgtgcagagtgtttcgttttctttcgtatatcttatattttattcgtatatcttacattatattgtaactttacagGAAGAACCGAAGGAGGAGAGTGATGACGACATGGGCTTCAGCTTGTTTGATTAGAGTTGCCCAATGGGTTGTGTTGGATCTCGTTCATGCCAAGTTCTGA

Basic information

species Physcomitrella patens
transcript PP1S49_284V6.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S49_284V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GLYMA04G40720.1 (Glycine max), 3'ss of exon 2
ttgtgttgtaaattggtgaatgcttgtgcagagtgtttcgttttctttcgtatatcttata----ttttattcgtatatctta--cattatattgtaactttacagGAAGAACCGAAGGAGGAGAGTGATGACGACATGGGCTTCAGCTTGTTTGATTAGAGTTGCCCAATGGGTTGT-GTTGGATCTCGTTCATGCCAAGTTCTGA
   |    |   |||||     || |||  | ||   || |||   || ||   |  |  |    || | ||  | ||| ||   | ||  | |||   |||||||||||||  |||||| || ||||| || |||||||| ||| |||||||||||||||  |    |    ||||| |   ||| | |    |    | ||   |
--atacctttttttggtt----ctagtgttgtgttcctcttttctatttgttatttatgcaaggcttctgtttatgtattttgttcctttcaatgtgtgtttacagGAAGAAGTGAAGGAAGAAAGTGACGATGACATGGGTTTCGGCTTGTTTGATTAGATCTTTTTATATAGTTGTAGCCAGATTTTGAGTCT-TTGAATTGAAA

upper sequence: PP1S49_284V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GLYMA03G42180.1 (Glycine max), 3'ss of exon 3
----ttgtgttgtaaattggtgaatgcttgtgcagagtgtttcgttttctttcgtatatcttatattttattcgtatatcttacattatattgtaactttacagGAAGAACCGAAGGAGGAGAGTGATGACGACATGGGCTTCAGCTTGTTTGATTAGAG--TTGCCCAATGGGTTGTGTTGGATCTCGTTCATGCCAAGTTCTGA---
       | | || || | ||   | ||  |   |  | |      | | ||    || ||||||| |   |  |||      |    | ||| || | || ||||||||||| | || ||||||||||| || ||||| ||| |||||||||||||| |   | | |||||  ||| |||  || | ||   |    |  | | |   
gtaaccctctggtgaaattgttgttcctgctattgtttttgaatcctgccttgtggtagcttatatgtatctaatatggaaatctgcttgttgcaattctataggaagAACCGGAAGAAGAGAGTGATGATGATATGGGATTCGGCTTGTTTGATTAGGGACATTCTCAATGATTTG-GTTAAATTTTGTGGTTCTTTACCTTTTAAGG

upper sequence: PP1S49_284V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GLYMA03G42180.3 (Glycine max), 3'ss of exon 3
----ttgtgttgtaaattggtgaatgcttgtgcagagtgtttcgttttctttcgtatatcttatattttattcgtatatcttacattatattgtaactttacagGAAGAACCGAAGGAGGAGAGTGATGACGACATGGGCTTCAGCTTGTTTGATTAGAG--TTGCCCAATGGGTTGTGTTGGATCTCGTTCATGCCAAGTTCTGA
       | | || || | ||   | ||  |   |  | |      | | ||    || ||||||| |   |  |||      |    | ||| || | || ||||||||||| | || ||||||||||| || ||||| ||| |||||||||||||| |   | | |||||  ||| |||  || | ||   |    |  | |  
gtaaccctctggtgaaattgttgttcctgctattgtttttgaatcctgccttgtggtagcttatatgtatctaatatggaaatctgcttgttgcaattctatagGAAGAACCGGAAGAAGAGAGTGATGATGATATGGGATTCGGCTTGTTTGATTAGGGACATTCTCAATGATTTG-GTTAAATTTTGTGGTTCTTTACCTTTT-

upper sequence: PP1S49_284V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: Vv15s0048g02610.t01 (Vitis vinifera), 3'ss of exon 3
---ttgtgttgtaaattggtgaatgct-tgtgcagagtgtttcgttttctt--tcgtatatcttatattttattcgtatatcttacat-tatattgtaactttacagGAAGAACCGAAGGAGGAGAGTGATGACGACATGGGCTTCAGCTTGTTTGATTAGAGTTGCCCAAT--GGGTTGTGTTGGATCTCGTTC-ATGCCAAGTTCTGA
    |   |||    ||| |   ||   | || || |  ||    ||| ||  |  |     |  | | |||||  | |   | |  | | |||| |     | ||||||||||| ||||| ||||||||||| ||||||||||| |||||||||||||||         ||  || ||||      | | || |  ||  || |     
gtaattcattgggttttgttatttgaaatttgaagggcattggacttttttggtttttaggttggtttcttatttctctgattgatttatgtattttcttaatgcagGAAGAACCCAAGGAAGAGAGTGATGATGACATGGGCTTTAGCTTGTTTGATTAGGAGCTTTTGATTTGGTTTGTCGCTAGTTTAGTCCTGTGTTAAATCT---

upper sequence: PP1S49_284V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: Vv16s0098g01010.t01 (Vitis vinifera), 3'ss of exon 2
ttgtgttgta-aattggtg-aatgcttgtgcagagtgtttcgttttctttcgtatatcttatattttattcgtatat--cttacattatattgtaactttacagGAAGAACCGAAGGAGGAGAGTGATGACGACATGGGCTTCAGCTTGTTTGATTAGAGTTGCCCAATGGGTTGT-GTTGGATCTCGTTCATGCCAAGTTCTGA
 | | ||  | | ||  ||  |||  | |      | ||||   |    | |  | | |  | ||| ||| |  |||  |||   ||  | ||| |   ||||||||||||| ||||| || ||||| ||||||||||| |||||||||||||| |||     ||    || ||   ||  ||| | |||| |         |  
-tatttttcatagttactgtgatgagtttttttcatatttctaatgacattgagtttttcttgtttgatttgcttattacttgtttttgaatgtga---tacagGAAGAACCAAAGGAAGAAAGTGACGACGACATGGGATTCAGCTTGTTTGACTAGGAGCTCCTTTCGGCTTTCAGTATGATATTGTTCTTTTTGCAAATTA-

upper sequence: PP1S49_284V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: Vv02s0025g02780.t01 (Vitis vinifera), 3'ss of exon 3
----------------ttgtgttgta-aattggtgaatgcttgtgcagagtgtttcgttttctttcgtatatcttatattttattcgtatatcttacattatattgt---aactttacagGAAGAACCGAAGGAGGAGAGTGATGACGACATGGGCTTCAGCTTGTTTGATTAGAGTTGCCCAATGGGTTGTGTTGGATCTCGTTCATGCCAAGTTCTGA-
                |  | || |   | |  |  || | |||   || | |    |  | |||  | | | || |   | ||  || |   ||    |   |||    ||   ||||||| ||||| ||||| ||||||||||| |||||||| ||||| ||||||||||||     ||     |  ||  | | || | |   ||   | |   | | 
gtaggagctattcctttaattttatttgagtaatacatacatgttttgattatggtttcatttttttttttttttttgcctaatgtgtttggtttgttctgggttgccaaaatactacagGAGGAACCAAAGGAAGAGAGTGATGAGGACATGGGATTCAGTTTGTTTGATTAGGAGCTCCTTTCAGTATGAATAGTATTTTGCA-ATTTTATGACTTCAT

upper sequence: PP1S49_284V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: EFJ07677 (Selaginella moellendorffii), 3'ss of exon 3
ttgtgttgtaaattggtgaatgcttgtgcagagtgtttcgttttctttcgtatatcttatattttattcgtatatcttacatta--tattgtaacttta--cagGAAGAACCGAAGGAGGAGAGTGATGACGACATGGGCTTCAGCTTGTTTGATTAGAGTTGCCCAATGGGTTGTGTTGGATCTCGTTCATGCCAAGTTCTGA
                                       || |   || |    | |||   | |  ||   |  || | ||||  | || |  ||| |  ||||| ||| |||| || ||||| ||||| ||||||||||| |||||||| ||||||                                              
---------------------------------------gtatgaatttgggggtgttac--tctggtctcttggctgaaattaggttttttggcttgaaacagGAGGAAGCGAAAGAAGAGAGCGATGATGACATGGGCTTTAGCTTGTTCGATTAG----------------------------------------------

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|67696799|gb|BJ957032.1|BJ957032
EST:     CACCTGCTGCTTCCGCTGCTGTTGAGGCACCCAAGGAAGAGGAGAAGAAG                         GAAGAACCGAAGGAGGAGAGTGATGACGACATGGGCTTCAGCTTGTTTGAT
genomic: CACCTGCTGCTTCCGCTGCTGTTGAGGCACCCAAGGAAGAGGAGAAGAAGgtaagttcta ... aactttacagGAAGAACCGAAGGAGGAGAGTGATGACGACATGGGCTTCAGCTTGTTTGAT
EST: gi|67709489|gb|BJ965305.1|BJ965305
EST:     CACCTGCTGCTTCCGCTGCTGTTGAGGCACCCAAGGAAGAGGAGAAGAAG                         GAAGAACCGAAGGAGGAGAGTGATGACGACATGGGCTTCAGCTTGTTTGAT
genomic: CACCTGCTGCTTCCGCTGCTGTTGAGGCACCCAAGGAAGAGGAGAAGAAGgtaagttcta ... aactttacagGAAGAACCGAAGGAGGAGAGTGATGACGACATGGGCTTCAGCTTGTTTGAT
EST: gi|162265808|gb|FC442395.1|FC442395
EST:     CACCTGCTGCTTCCGCTGCTGTTGAGGCACCCAAGGAAGAGGAGAAGAAG                         GAAGAACCGAAGGAGGAGAGTGATGACGACATGGGCTTCAGCTTGTTTGAT
genomic: CACCTGCTGCTTCCGCTGCTGTTGAGGCACCCAAGGAAGAGGAGAAGAAGgtaagttcta ... aactttacagGAAGAACCGAAGGAGGAGAGTGATGACGACATGGGCTTCAGCTTGTTTGAT
EST: gi|18368145|gb|BJ200230.1|BJ200230
EST:     CACCTGCTGCTTCCGCTGCTGTTGAGGCACCCAAGGAAGAGGAGAAGAAG                         GAAGAACCGAAGGAGGAGAGTGATGACGACATGGGCTTCAGCTTGTTTGAT
genomic: CACCTGCTGCTTCCGCTGCTGTTGAGGCACCCAAGGAAGAGGAGAAGAAGgtaagttcta ... aactttacagGAAGAACCGAAGGAGGAGAGTGATGACGACATGGGCTTCAGCTTGTTTGAT
EST: gi|18343044|gb|BJ175081.1|BJ175081
EST:     CACCTGCTGCTTCCGCTGCTGTTGAGGCACCCAAGGAAGAGGAGAAGAAG                         GAAGAACCGAAGGAGGAGAGTGATGACGACATGGGCTTCAGCTTGTTTGAT
genomic: CACCTGCTGCTTCCGCTGCTGTTGAGGCACCCAAGGAAGAGGAGAAGAAGgtaagttcta ... aactttacagGAAGAACCGAAGGAGGAGAGTGATGACGACATGGGCTTCAGCTTGTTTGAT
EST: gi|67720340|gb|BJ970599.1|BJ970599
EST:     CACCTGCTGCTTCCGCTGCTGTTGAGGCACCCAAGGAAGAGGAGAAGAAG                         GAAGAACCGAAGGAGGAGAGTGATGACGACATGGGCTTCAGCTTGTTTGAT
genomic: CACCTGCTGCTTCCGCTGCTGTTGAGGCACCCAAGGAAGAGGAGAAGAAGgtaagttcta ... aactttacagGAAGAACCGAAGGAGGAGAGTGATGACGACATGGGCTTCAGCTTGTTTGAT
EST: gi|37822193|gb|BJ580259.1|BJ580259
EST:     CACCTGCTGCTTCCGCTGCTGTTGAGGCACCCAAGGAAGAGGAGAAGAAG                         GAAGAACCGAAGGAGGAGAGTGATGACGACATGGGCTTCAGCTTGTTTGAT
genomic: CACCTGCTGCTTCCGCTGCTGTTGAGGCACCCAAGGAAGAGGAGAAGAAGgtaagttcta ... aactttacagGAAGAACCGAAGGAGGAGAGTGATGACGACATGGGCTTCAGCTTGTTTGAT
EST: gi|67573418|gb|BJ946242.1|BJ946242
EST:     CACCTGCTGCTTCCGCTGCTGTTGAGGCACCCAAGGAAGAGGAGAAGAAG                         GAAGAACCGAAGGAGGAGAGTGATGACGACATGGGCTTCAGCTTGTTTGAT
genomic: CACCTGCTGCTTCCGCTGCTGTTGAGGCACCCAAGGAAGAGGAGAAGAAGgtaagttcta ... aactttacagGAAGAACCGAAGGAGGAGAGTGATGACGACATGGGCTTCAGCTTGTTTGAT
EST: gi|18327667|gb|BJ159670.1|BJ159670
EST:     CACCTGCTGCTTCCGCTGCTGCTGAGGCACCCAAGGAAGAGGAGAAGAAG                         GAAGAACCGAAGGAGGAGAGTGATGACGACATGGGCTTCAGCTTGTTTGAT
genomic: CACCTGCTGCTTCCGCTGCTGTTGAGGCACCCAAGGAAGAGGAGAAGAAGgtaagttcta ... aactttacagGAAGAACCGAAGGAGGAGAGTGATGACGACATGGGCTTCAGCTTGTTTGAT
EST: gi|18335904|gb|BJ167925.1|BJ167925
EST:     CACCTGCTGCTTCCGCTGCTGTTGAGGCACCCAAGGAAGAGGAGAAGAAG                         GAAGAACCGAAGGAGGAGAGTGATGACGACATGGGCTTCAGCTTGTTTGAT
genomic: CACCTGCTGCTTCCGCTGCTGTTGAGGCACCCAAGGAAGAGGAGAAGAAGgtaagttcta ... aactttacagGAAGAACCGAAGGAGGAGAGTGATGACGACATGGGCTTCAGCTTGTTTGAT
EST: gi|162265807|gb|FC442394.1|FC442394
EST:     CACCTGCTGCTTCCGCTGCTGTTGAGGCACCCAAGGAAGAGGAGAAGAAG                         GAAGAACCGAAGGAGGAGAGTGATGACGACATGGGCTTCAGCTTGTTTGAT
genomic: CACCTGCTGCTTCCGCTGCTGTTGAGGCACCCAAGGAAGAGGAGAAGAAGgtaagttcta ... aactttacagGAAGAACCGAAGGAGGAGAGTGATGACGACATGGGCTTCAGCTTGTTTGAT

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), 35 (downstream exon)
Score: 33

GTGGTGGTGGTGCAGTCGCTGTGAGTGCAGCACCTGCTGCTTCCGCTGCTGTTGAGGCACCCAAGGAAGAGGAGAAGAAGgtaagttcta ... aactttacagGAAGAACCGAAGGAGGAGAGTGATGACGACATGGGCTTCAGCTTGTTTGATTAGAGTTGCCCAATGGGTTGTGTTGGATCTCGTTCATGCCAAGTTCTGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttcgtatatcttatattttattcgtatatcttacattatattgtaactttacagGAAGAACCGAAGGAGGAGAGTGATGACGACATGGGCTTCAGCTTGTTTGATTAGAGTTGCCCAATGGGTTGTGTTGGATCTCGTTCATGCCAAGTTCTGA
                                         ttgtaac  putative branch site (score: 33)
     tatatcttatatttta  TA-rich tract