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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAATCCGTGTAGCACGAATTTTTAACACCTATGGGCCTCGCATGAATATCGACGATGGGCGAGTAGTCAGCAATTTTATTGCTCAAGCATTAAGgtactggtcctcaaggtctcaaaattcaatatttccttaacttaatgaactcaacacatttgacatgatgtacgggtgtgtag

Basic information

species Physcomitrella patens
transcript PP1S189_118V6.1
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S189_118V6.1 (Physcomitrella patens), 5'ss of exon 9
lower sequence: GLYMA12G06990.1 (Glycine max), 5'ss of exon 9
AAATCCGTGTAGCACGAATTTTTAACACCTATGGGCCTCGCATGAATATCGACGATGGGCGAGTAGTCAGCAATTTTATTGCTCAAGCATTAAGgtact----ggtcctcaaggtctcaaaattcaatatttccttaacttaatgaactcaacacatttgacatgatgtacgggtgtgtag---------------
|||| ||||| ||| |||| |||||||| |||||||| ||||||||||| || ||||| || || |||||||| || |||||||||||| |  |||| |    |    |    || |  |  ||  ||  |    |    |  | |  || ||     |    |||| |     ||  | |               
AAATACGTGTTGCAAGAATCTTTAACACATATGGGCCGCGCATGAATATTGATGATGGACGTGTTGTCAGCAACTTCATTGCTCAAGCAATTCGgtaattaaagcatttttcagtttgtagtttatatgctgtactgtagtgtt-atttctacgtgccttgtttgatctgttaatg-atggtttttgattgccaca

upper sequence: PP1S189_118V6.1 (Physcomitrella patens), 5'ss of exon 9
lower sequence: GLYMA11G15020.1 (Glycine max), 5'ss of exon 9
AAATCCGTGTAGCACGAATTTTTAACACCTATGGGCCTCGCATGAATATCGACGATGGGCGAGTAGTCAGCAATTTTATTGCTCAAGCATTAAGgtact----ggtcctcaaggtctcaaaattcaatatttccttaacttaatgaactcaacacatttgacatgatgtacgggtgtgtag---------------
|||| ||||| ||| |||| |||||||| |||||||| ||||||||||| || ||||| || || |||||||| || |||||||||||  |  |||| |         |    || |  |  ||  || ||    |    |  | |  || |      |    |||| |     ||  | |               
AAATACGTGTTGCAAGAATCTTTAACACATATGGGCCACGCATGAATATTGATGATGGACGTGTTGTCAGCAACTTCATTGCTCAAGCGATTCGgtaattaaaacatttttcagtttgtagtttatatgttgtactgtagtgtt-atttctatgtgccttgtttgatctgttaatg-atggtttttgattgctgca

upper sequence: PP1S189_118V6.1 (Physcomitrella patens), 5'ss of exon 9
lower sequence: GLYMA15G04500.1 (Glycine max), 5'ss of exon 10
AAATCCGTGTAGCACGAATTTTTAACACCTATGGGCCTCGCATGAATATCGACGATGGGCGAGTAGTCAGCAATTTTATTGCTCAAGCATTAAGgtactggtcctcaaggtctcaaaattcaatatttcct-taacttaatgaactcaacacatttgacatg---atgtacgggtg--tgtag-----------
|||| ||  | ||| |||| |||||||| ||||| || ||||||||||| || |||||||| || |||||||| || |||||||||||| |  |||| |     |   | | ||    || |||   | || |||  |  | |  ||  ||  | |    |    || | | | ||  | | |           
AAATACGCATTGCAAGAATCTTTAACACATATGGACCACGCATGAATATTGATGATGGGCGTGTTGTCAGCAACTTCATTGCTCAAGCACTGCGgtaattactttactgttatctggtttaaatgcatgctataatgttgttacttctgcatgtcttttttatatatattctgatggttttggttgtcagaagg

upper sequence: PP1S189_118V6.1 (Physcomitrella patens), 5'ss of exon 9
lower sequence: GLYMA13G40960.1 (Glycine max), 5'ss of exon 10
AAATCCGTGTAGCACGAATTTTTAACACCTATGGGCCTCGCATGAATATCGACGATGGGCGAGTAGTCAGCAATTTTATTGCTCAAGCATTAAGgtactggtcctcaaggtctcaaaattcaatatttcct-taacttaatgaactcaacacatttgacatgatgtacgggtg-tgtag---------------
|||| ||  | ||| |||| |||||||| ||||| || ||||||||||| || |||||||| || || ||||| || |||||||||||| |  |||| |         | | ||    || |||   | || |||  |  | |  ||   | || |    |||| | | | || | | |               
AAATACGCATTGCAAGAATCTTTAACACATATGGACCACGCATGAATATTGATGATGGGCGTGTTGTTAGCAACTTCATTGCTCAAGCACTTCGgtaattacttgactgttatctggttttaatgcatgctataatgttgttacttctgtatatctattttgatattctgatggttttgattgccagaaggatc

upper sequence: PP1S189_118V6.1 (Physcomitrella patens), 5'ss of exon 9
lower sequence: GLYMA12G06980.2 (Glycine max), 5'ss of exon 8
AAATCCGTGTAGCACGAATTTTTAACACCTATGGGCCTCGCATGAATATCGACGATGGGCGAGTAGTCAGCAATTTTATTGCTCAAGCATTAAGgta-----ctggtcctcaaggtctca-----aaattcaatatttccttaacttaat-----gaactcaacacatttga-----catgatgtacgggtgtgtag
|||| ||  | ||  |||| |||||||| ||||| || ||||||||||| || |||||||| || ||||| || || || ||||||||| |  ||||      |   | | |   | | |     ||  |  ||||     ||| | | |       |||  | | || | |     || ||   |  | |||    
AAATACGCATTGCGAGAATCTTTAACACATATGGACCACGCATGAATATTGATGATGGGCGTGTTGTCAGTAACTTCATCGCTCAAGCAATTCGgtaattcctttaactttataatgttataggcaagatggatatgctgataaataattttttaagactttatatatctcaactctcaagaaacattgatgta---

upper sequence: PP1S189_118V6.1 (Physcomitrella patens), 5'ss of exon 9
lower sequence: GLYMA11G15010.1 (Glycine max), 5'ss of exon 9
AAATCCGTGTAGCACGAATTTTTAACACCTATGGGCCTCGCATGAATATCGACGATGGGCGAGTAGTCAGCAATTTTATTGCTCAAGCATTAAGgta-----ctggtcctcaaggtctca-aaattcaatatttccttaacttaatgaactcaacacatttgacatgatgtacgggtgtgtag------------
|||| ||  | ||  |||| || ||||| ||||| || ||||||||||| || |||||||| || ||||| || || |||||||||||| |  ||||      |   | | |   | | | |      ||   |       | |||    |    | | || | || || | |   | |  ||            
AAATACGCATTGCGAGAATCTTCAACACATATGGACCACGCATGAATATTGATGATGGGCGTGTTGTCAGTAACTTCATTGCTCAAGCAATTCGgtaaatcctttaacttaataatgttataggcaagatggatatgctgataaatagttttttaagactttatattatct-caactctcaagaaacattgatgc

upper sequence: PP1S189_118V6.1 (Physcomitrella patens), 5'ss of exon 9
lower sequence: AT5G59290.2 (Arabidopsis thaliana), 5'ss of exon 8
AAATCCGTGTAGCACGAATTTTTAACACCTATGGGCCTCGCATGAATATCGACGATGGGCGAGTAGTCAGCAATTTTATTGCTCAAGCATTAAGgtactggtcctcaaggtctcaaaattcaatatttccttaacttaatgaa-ctcaacacatttgacatgatgtacgggtgtgtag---
|||||||  | ||  |||| || ||||| ||||| ||||| ||||| ||||| |||||||| || || ||||| || |||||||||||| |  ||||   ||| | |        || |||| |    ||     ||  |  | |||  |  |  ||   |    |     ||||| |   
AAATCCGCATTGCTAGAATCTTCAACACATATGGTCCTCGAATGAACATCGATGATGGGCGTGTTGTGAGCAACTTCATTGCTCAAGCACTCCGgtaa-agtcattagctctctcaacttcattgaaaccaagttttgtttcatctctgcttagctgtgtttccat-taaatgtgttgtag

upper sequence: PP1S189_118V6.1 (Physcomitrella patens), 5'ss of exon 9
lower sequence: Vv06s0004g04390.t01 (Vitis vinifera), 5'ss of exon 9
AAATCCGTGTAGCACGAATTTTTAACACCTATGGGCCTCGCATGAATATCGACGATGGGCGAGTAGTCAGCAATTTTATTGCTCAAGCATTAAGgtactggtcctcaaggtctcaaa--attcaatatttccttaacttaatgaactcaa-----cacatttgacatgatgtacgggtgtgtag----------
|||| ||  | ||  ||||||| ||||| |||||||| ||||||||||| || ||||| || || ||||||||||| || ||||||||| |  ||||            |||   |    || |  || |   |||  || |    |||      ||   ||    | || | |  |     |           
AAATACGCATTGCTAGAATTTTCAACACATATGGGCCCCGCATGAATATTGATGATGGACGTGTTGTCAGCAATTTCATAGCTCAAGCACTTCGgtatgtccttatgtagtccttagctgttgatcatatttgtaagctactattttcatttaatcatgctttgtttaatttccaagatgacatccactgaact

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|208390897|gb|DC945914.1|DC945914
EST:     AATATCGACGATGGGCGAGTAGTCAGCAATTTTATTGCTCAAGCATTAAG                         AGGGGAGACGATGACGGTGCAGGCTCCAGGCACTCAAACTCGTAGTTTTTG
genomic: AATATCGACGATGGGCGAGTAGTCAGCAATTTTATTGCTCAAGCATTAAGgtactggtcc ... gggtgtgtagAGGGGAGACGATGACGGTGCAGGCTCCAGGCACTCAAACTCGTAGTTTTTG
EST: gi|37850860|gb|BJ608868.1|BJ608868
EST:     AATATCGACGATGGGTGAGTAGTCAGCAATTTTATTGCTCAAGCATTAAG                         AGGGGAGACGATGACGGTGCAGGCTCCAGGCACTCAAACTCGTAGTTTTTG
genomic: AATATCGACGATGGGCGAGTAGTCAGCAATTTTATTGCTCAAGCATTAAGgtactggtcc ... gggtgtgtagAGGGGAGACGATGACGGTGCAGGCTCCAGGCACTCAAACTCGTAGTTTTTG
EST: gi|67692844|gb|BJ953077.1|BJ953077
EST:     AATATCGACGATGGGCGAGTAGTCAGCAATTTTATTGCTCAAGCATTAAG                         AGGGGAGACGATGACGGTGCAGGCTCCAGGCACTCAAACTCGTAGTTTTTG
genomic: AATATCGACGATGGGCGAGTAGTCAGCAATTTTATTGCTCAAGCATTAAGgtactggtcc ... gggtgtgtagAGGGGAGACGATGACGGTGCAGGCTCCAGGCACTCAAACTCGTAGTTTTTG
EST: gi|67697660|gb|BJ957893.1|BJ957893
EST:     AATATCGACGATGGGCGAGTAGTCAGCAATTTTATTGCTCAAGCATTAAG                         AGGGGAGACGATGACGGTGCAGGCTCCAGGCACTCAAACTCGTAGTTTTTG
genomic: AATATCGACGATGGGCGAGTAGTCAGCAATTTTATTGCTCAAGCATTAAGgtactggtcc ... gggtgtgtagAGGGGAGACGATGACGGTGCAGGCTCCAGGCACTCAAACTCGTAGTTTTTG
EST: gi|208385608|gb|DC948967.1|DC948967
EST:     AATATCGACGATGGGCGAGTAGTCAGCAATTTTATTGCTCAAGCATTAAG                         AGGGGAGACGATGACGGTGCAGGCTCCAGGCACTCAAACTCGTAGTTTTTG
genomic: AATATCGACGATGGGCGAGTAGTCAGCAATTTTATTGCTCAAGCATTAAGgtactggtcc ... gggtgtgtagAGGGGAGACGATGACGGTGCAGGCTCCAGGCACTCAAACTCGTAGTTTTTG
EST: gi|37843082|gb|BJ601090.1|BJ601090
EST:     AATATCGACGATGGGTGAGTAGTCAGCAATTTTATTGCTCAAGCATTAAG                         AGGGGAGACGATGACGGTGCAGGCTCCAGGCACTCAAACTCGTAGTTTTTG
genomic: AATATCGACGATGGGCGAGTAGTCAGCAATTTTATTGCTCAAGCATTAAGgtactggtcc ... gggtgtgtagAGGGGAGACGATGACGGTGCAGGCTCCAGGCACTCAAACTCGTAGTTTTTG
EST: gi|208385977|gb|DC956493.1|DC956493
EST:     AATATCGACGATGGGCGAGTAGTCAGCAATTTTATTGCTCAAGCATTAAG                         AGGGGAGACGATGACGGTGCAGGCTCCAGGCACTCAAACTCGTAGTTTTTG
genomic: AATATCGACGATGGGCGAGTAGTCAGCAATTTTATTGCTCAAGCATTAAGgtactggtcc ... gggtgtgtagAGGGGAGACGATGACGGTGCAGGCTCCAGGCACTCAAACTCGTAGTTTTTG
EST: gi|37830721|gb|BJ588733.1|BJ588733
EST:     AATATCGACGATGGGCGAGTAGTCAGCAATTTTATTGCTCAAGCATTAAG                         AGGGGAGACGATGACGGTGCAGGCTCCAGGCACTCAAACTCGTAGTTTTTG
genomic: AATATCGACGATGGGCGAGTAGTCAGCAATTTTATTGCTCAAGCATTAAGgtactggtcc ... gggtgtgtagAGGGGAGACGATGACGGTGCAGGCTCCAGGCACTCAAACTCGTAGTTTTTG
EST: gi|208371231|gb|DC956009.1|DC956009
EST:     AATATCGACGATGGGCGAGTAGTCAGCAATTTTATTGCTCAAGCATTAAG                         AGGGGAGACGATGACGGTGCAGGCTCCAGGCACTCAAACTCGTAGTTTTTG
genomic: AATATCGACGATGGGCGAGTAGTCAGCAATTTTATTGCTCAAGCATTAAGgtactggtcc ... gggtgtgtagAGGGGAGACGATGACGGTGCAGGCTCCAGGCACTCAAACTCGTAGTTTTTG

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), 30 (downstream exon)
Score: 2

AAATCCGTGTAGCACGAATTTTTAACACCTATGGGCCTCGCATGAATATCGACGATGGGCGAGTAGTCAGCAATTTTATTGCTCAAGCATTAAGgtactggtcc ... gggtgtgtagAGGGGAGACGATGACGGTGCAGGCTCCAGGCACTCAAACTCGTAGTTTTTGCTACGTCTCTGATATG




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