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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCTCTCGTCTTTCAATTTCTGCGTCTCGCTGATCTCGCCGATTTCGCACCATGCAGAACGAGGAGGGCGACAATGTGGATCTCTACATCCCCAGGAAGTGgtgggttttttttgtttcatcgtcgtatcttccccccatttagagtttttcttacttctactttcctcctatttgataaaccctagattcattccggatt...

Basic information

species Physcomitrella patens
transcript PP1S372_10V6.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S372_10V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: LOC_Os03g46490.1 (Oryza sativa), 5'ss of exon 2
TCTCTCGTCTTTCAATTTCTGCGTCTCGCTGATCTCGCCGATTTCGCACCATGCAGAACGAGGAGGGCGACAATGTGGATCTCTACATCCCCAGGAAGTGgtgggttttttttgtttc--atcgtcgtatcttccccccatttagagtttttct-tacttctactttcctcctat-ttgataaaccctagattcattccggatt
         || |  ||   | || |   | ||||  |||      || ||||||||||||||||||  | |  ||||| |||||| |||||||||||||||  |||| | |  ||    ||  |    | |      ||  | | ||||   | ||||| ||| | | |  | | ||| |   |   ||              
---------TTGCTGTTGTGGTGTTTTCTTCATCT-ACCGT-----CATCATGCAGAACGAGGAGGGTCAGATGGTGGACCTCTACGTCCCCAGGAAGTGgtatgtttctgtcattcttgatgttttggtgtctaattcaactggtgtttagatgtacttttacatgcgtgttgtgttggtttcctgcag--------------

upper sequence: PP1S372_10V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: GRMZM2G125300_T02 (Zea mays), 5'ss of exon 2
TCTCTCGTCTTTCAATTTCTGCGTCT-CGCTGATCTCGCCGATTTCGCACCATGCAGAACGAGGAGGGCGACAATGTGGATCTCTACATCCCCAGGAAGTGgtgggttttttttgtttcatcgtcgta-tcttccccccatttagagtttttcttacttctactttcctcctatttgataaaccctagattcattccggatt
                   |||   | || |  |  | || | |   |||||||||||||||||||||  | | |||||| |||||  |||||||||||||||  ||||   |  |    | || | | | || |  |  |  |  |||  | ||        ||   | |||   | |  |   ||  ||| ||| |    
------------------TTGCTCTTGCGGTAGTTCCCCCAACTGT-CACCATGCAGAACGAGGAGGGTAAGACTGTGGACCTCTATGTCCCCAGGAAGTGgtacgtttgcctcatcctcttgtagaaatatttctgctctgcatggttggttttg-------ttgtgtgctaa--ggttgagtttatgttctttcag----

upper sequence: PP1S372_10V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: GRMZM2G125300_T03 (Zea mays), 5'ss of exon 1
---TCTCTCGTCTTTCAATTTCTGCGTCTCGCTGATCTCGCCGATTTCGCACCATGCAGAACGAGGAGGGCGACAATGTGGATCTCTACATCCCCAGGAAGTGgtgggttttttttgtttcatcgtcgta-tcttccccccatttagagtttttcttacttctactttcctcctatttgataaaccctagattcattccggatt
    |||| || ||||| || ||   |  || |  |  | || | |   |||||||||||||||||||||  | | |||||| |||||  |||||||||||||||  ||||   |  |    | || | | | || |  |  |  |  |||  | ||        ||   | |||   | |  |   ||  ||| ||| |    
GGTCCTCTTGTATTTCAGTTGCTC--TTGCGGTAGTTCCCCCAACTGT-CACCATGCAGAACGAGGAGGGTAAGACTGTGGACCTCTATGTCCCCAGGAAGTGgtacgtttgcctcatcctcttgtagaaatatttctgctctgcatggttggttttg-------ttgtgtgctaa--ggttgagtttatgttctttcag----

upper sequence: PP1S372_10V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: GRMZM2G093574_T01 (Zea mays), 5'ss of exon 2
TCTCTCGTCTTTCAATTTCTGCGTCT-CGCTGATCTCGCCGATTTCGCACCATGCAGAACGAGGAGGGCGACAATGTGGATCTCTACATCCCCAGGAAGTGgtgggttttttttgtttcatcgtcgta-tcttccccccatttagagtttttcttacttctactttcctcctatttgataaaccctagattcattccggatt
                   |||   | || |  |  | || | | | |||||||||||||||||||||  | | |||||| |||||  |||||||||||||||  ||||   |  |    | || | | | || |  |  |  |  |||  | ||        ||   | |||   | |  |   ||  ||| ||| |    
------------------TTGCTCTTGCGGTAGTTCCCCCAACTGC-CACCATGCAGAACGAGGAGGGTAAGACTGTGGACCTCTATGTCCCCAGGAAGTGgtacgtttgcctcatcctcttgtagaaatatttctgctctgcatggttggttttg-------ttgtgtgctaa--ggttgagtttatgttctttcag----

upper sequence: PP1S372_10V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: GRMZM2G134109_T01 (Zea mays), 5'ss of exon 2
TCTCTCGTCTTTCAATTTCTGCGTCTCGCTGATCTCGCCGATTTCGCACCATGCAGAACGAGGAGGGCGACAATGTGGATCTCTACATCCCCAGGAAGTGgtgggttttttttgtttcatcgtcgtatcttccccccatttagagtttttcttacttctactttcctcctatttgataaaccctagattcattccggatt
                   |||  || || |   || || |     || ||||||||||||||||||  | |  ||||| |||||| |||||||||||||||  ||||  | |  ||  | ||   | | |   ||| | |  |    |  ||| || |  | |  |  ||||   |      |   ||| | | |    
------------------TTGCTGCT-GCGGTAGTCCCCAACCAT-CATCATGCAGAACGAGGAGGGTAAGACGGTGGACCTCTACGTCCCCAGGAAGTGgtacgtttgctgtactttcttgtttaaacctttgccc-tctgca----tggttaattatgttgtgttaatattgagt-----ttctgttcttgcag----

upper sequence: PP1S372_10V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: EFJ15472 (Selaginella moellendorffii), 5'ss of exon 1
-TCTCTCGTCTTTCAATTT-CTGCGTCTCGCTGATCTCGCCGATTTCGCACCATGCAGAACGAGGAGGGCGACAATGTGGATCTCTACATCCCCAGGAAGTGgtgggttttttttgtttcatcgtcgtatcttccccccatttagagtttttcttacttctactttcctcctatttgataaaccctagattcattccggatt
 |      ||||||  | | ||||| || |  ||       ||   | || ||||||||||||||||||||| || || |||||||||||||||||||||||||  |      |       |     | |   | | |   | || |   ||  |  |  | |                                       
ATTAGGGTTCTTTCGTTGTGCTGCGGCT-GAGGAGGAGAAAGAGCGC-CATCATGCAGAACGAGGAGGGCGAGAACGTCGATCTCTACATCCCCAGGAAGTGgtaagcgcgaatctcccgcttcctttgtggccgctctcatcagcgcgattgattttcttgcgcag-----------------------------------

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|162232484|gb|FC408359.1|FC408359
EST:     ATGCAGAACGAGGAGGGCGACAATGTGGATCTCTACATCCCCAGGAAGTG                         TTCTTCAACCAACAGGTTGATCACTTCCAAGGATGTTGCCTCAGTTCAGCT
genomic: ATGCAGAACGAGGAGGGCGACAATGTGGATCTCTACATCCCCAGGAAGTGgtgggttttt ... ctttttgcagTTCTTCAACCAACAGGTTGATCACTTCCAAGGATGTTGCCTCAGTTCAGCT
EST: gi|162209539|gb|FC385635.1|FC385635
EST:     ATGCAGAACGAGGAGGGCGACAATGTGGATCTCTACATCCCCAGGAAGTG                         TTCTTCAACCAACAGGTTGATCACTTCCAAGGATGTTGCCTCAGTTCAGCT
genomic: ATGCAGAACGAGGAGGGCGACAATGTGGATCTCTACATCCCCAGGAAGTGgtgggttttt ... ctttttgcagTTCTTCAACCAACAGGTTGATCACTTCCAAGGATGTTGCCTCAGTTCAGCT
EST: gi|162251424|gb|FC425544.1|FC425544
EST:     ATGCAGAACGAGGAGGGCGACAATGTGGATCTCTACATCCCCAGGAAGTG                         TTCTTCAACCAACAGGTTGATCACTTCCAAGGATGTTGCCTCAGTTCAGCT
genomic: ATGCAGAACGAGGAGGGCGACAATGTGGATCTCTACATCCCCAGGAAGTGgtgggttttt ... ctttttgcagTTCTTCAACCAACAGGTTGATCACTTCCAAGGATGTTGCCTCAGTTCAGCT
EST: gi|67694588|gb|BJ954821.1|BJ954821
EST:     ATGCAGAACGAGGAGGGCGACAATGTGGATCTCTACATCCCCAGGAAGTG                         TTCTTCAACCAACAGGTTGATCACTTCCAAGGATGTTGCCTCAGTTCAGCT
genomic: ATGCAGAACGAGGAGGGCGACAATGTGGATCTCTACATCCCCAGGAAGTGgtgggttttt ... ctttttgcagTTCTTCAACCAACAGGTTGATCACTTCCAAGGATGTTGCCTCAGTTCAGCT
EST: gi|162227865|gb|FC403673.1|FC403673
EST:     ATGCAGAACGAGGAGGGCGACAATGTGGATCTCTACATCCCCAGGAAGTG                         TTCTTCAACCAACAGGTTGATCACTTCCAAGGATGTTGCCTCAGTTCAGCT
genomic: ATGCAGAACGAGGAGGGCGACAATGTGGATCTCTACATCCCCAGGAAGTGgtgggttttt ... ctttttgcagTTCTTCAACCAACAGGTTGATCACTTCCAAGGATGTTGCCTCAGTTCAGCT
EST: gi|162223439|gb|FC400629.1|FC400629
EST:     ATGCAGAACGAGGAGGGCGACAATGTGGATCTCTACATCCCCAGGAAGTG                         TTCTTCAACCAACAGGTTGATCACTTCCAAGGATGTTGCCTCAGTTCAGCT
genomic: ATGCAGAACGAGGAGGGCGACAATGTGGATCTCTACATCCCCAGGAAGTGgtgggttttt ... ctttttgcagTTCTTCAACCAACAGGTTGATCACTTCCAAGGATGTTGCCTCAGTTCAGCT
EST: gi|162217587|gb|FC393991.1|FC393991
EST:     ATGCAGAACGAGGAGGGCGACAATGTGGATCTCTACATCCCCAGGAAGTG                         TTCTTCAACCAACAGGTTGATCACTTCCAAGGATGTTGCCTCAGTTCAGCT
genomic: ATGCAGAACGAGGAGGGCGACAATGTGGATCTCTACATCCCCAGGAAGTGgtgggttttt ... ctttttgcagTTCTTCAACCAACAGGTTGATCACTTCCAAGGATGTTGCCTCAGTTCAGCT
EST: gi|162220057|gb|FC397028.1|FC397028
EST:     ATGCAGAACGAGGAGGGCGACAATGTGGATCTCTACATCCCCAGGAAGTG                         TTCTTCAACCAACAGGTTGATCACTTCCAAGGATGTTGCCTCAGTTCAGCT
genomic: ATGCAGAACGAGGAGGGCGACAATGTGGATCTCTACATCCCCAGGAAGTGgtgggttttt ... ctttttgcagTTCTTCAACCAACAGGTTGATCACTTCCAAGGATGTTGCCTCAGTTCAGCT
EST: gi|19782337|gb|BQ039841.1|BQ039841
EST:     ATGCAGAACGAGGAGGGCGACAATGTGGATCTCTACATCCCCAGGAAGTG                         TTCTTCAACCAACAGGTTGATCACTTCCAAGGATGTTGCCTCAGTTCAGCT
genomic: ATGCAGAACGAGGAGGGCGACAATGTGGATCTCTACATCCCCAGGAAGTGgtgggttttt ... ctttttgcagTTCTTCAACCAACAGGTTGATCACTTCCAAGGATGTTGCCTCAGTTCAGCT
EST: gi|18343942|gb|BJ175981.1|BJ175981
EST:     ATGCAGAACGAGGAGGGCGACAATGTGGATCTCTACATCCCCAGGAAGTG                         TTCTTCAACCAACAGGTTGATCACTTCCAAGGATGTTGCCTCAGTTCAGCT
genomic: ATGCAGAACGAGGAGGGCGACAATGTGGATCTCTACATCCCCAGGAAGTGgtgggttttt ... ctttttgcagTTCTTCAACCAACAGGTTGATCACTTCCAAGGATGTTGCCTCAGTTCAGCT
EST: gi|37837393|gb|BJ595401.1|BJ595401
EST:     ATGCAGAACGAGGAGGGCGACAATGTGGATCTCTACATCCCCAGGAAGTG                         TTCTTCAACCAACAGGTTGATCACTTCCAAGGATGTTGCCTCAGTTCAGCT
genomic: ATGCAGAACGAGGAGGGCGACAATGTGGATCTCTACATCCCCAGGAAGTGgtgggttttt ... ctttttgcagTTCTTCAACCAACAGGTTGATCACTTCCAAGGATGTTGCCTCAGTTCAGCT
EST: gi|18354317|gb|BJ186373.1|BJ186373
EST:     ATGCAGAACGAGGAGGGCGACAATGTGGATCTCTACATCCCCAGGAAGTG                         TTCTTCAACCAACAGGTTGATCACTTCCAAGGATGTTGCCTCAGTTCAGCT
genomic: ATGCAGAACGAGGAGGGCGACAATGTGGATCTCTACATCCCCAGGAAGTGgtgggttttt ... ctttttgcagTTCTTCAACCAACAGGTTGATCACTTCCAAGGATGTTGCCTCAGTTCAGCT
EST: gi|162230732|gb|FC406363.1|FC406363
EST:     ATGCAGAACGAGGAGGGCGACAATGTGGATCTCTACATCCCCAGGAAGTG                         TTCTTCAACCAACAGGTTGATCACTTCCAAGGATGTTGCCTCAGTTCAGCT
genomic: ATGCAGAACGAGGAGGGCGACAATGTGGATCTCTACATCCCCAGGAAGTGgtgggttttt ... ctttttgcagTTCTTCAACCAACAGGTTGATCACTTCCAAGGATGTTGCCTCAGTTCAGCT
EST: gi|162217586|gb|FC393990.1|FC393990
EST:     ATGCAGAACGAGGAGGGCGACAATGTGGATCTCTACATCCCCAGGAAGTG                         TTCTTCAACCAACAGGTTGATCACTTCCAAGGATGTTGCCTCAGTTCAGCT
genomic: ATGCAGAACGAGGAGGGCGACAATGTGGATCTCTACATCCCCAGGAAGTGgtgggttttt ... ctttttgcagTTCTTCAACCAACAGGTTGATCACTTCCAAGGATGTTGCCTCAGTTCAGCT
EST: gi|162209538|gb|FC385634.1|FC385634
EST:     ATGCAGAACGAGGAGGGCGACAATGTGGATCTCTACATCCCCAGGAAGTG                         TTCTTCAACCAACAGGTTGATCACTTCCAAGGATGTTGCCTCAGTTCAGCT
genomic: ATGCAGAACGAGGAGGGCGACAATGTGGATCTCTACATCCCCAGGAAGTGgtgggttttt ... ctttttgcagTTCTTCAACCAACAGGTTGATCACTTCCAAGGATGTTGCCTCAGTTCAGCT
EST: gi|162224880|gb|FC401088.1|FC401088
EST:     ATGCAGAACGAGGAGGGCGACAATGTGGATCTCTACATCCCCAGGAAGTG                         TTCTTCAACCAACAGGTTGATCACTTCCAAGGATGTTGCCTCAGTTCAGCT
genomic: ATGCAGAACGAGGAGGGCGACAATGTGGATCTCTACATCCCCAGGAAGTGgtgggttttt ... ctttttgcagTTCTTCAACCAACAGGTTGATCACTTCCAAGGATGTTGCCTCAGTTCAGCT
EST: gi|37835788|gb|BJ593800.1|BJ593800
EST:     ATGCAGAACGAGGAGGGCGACAATGTGGATCTCTACATCCCCAGGAAGTG                         TTCTTCAACCAACAGGTTGATCACTTCCAAGGATGTTGCCTCAGTTCAGCT
genomic: ATGCAGAACGAGGAGGGCGACAATGTGGATCTCTACATCCCCAGGAAGTGgtgggttttt ... ctttttgcagTTCTTCAACCAACAGGTTGATCACTTCCAAGGATGTTGCCTCAGTTCAGCT
EST: gi|162226817|gb|FC403837.1|FC403837
EST:     ATGCAGAACGAGGAGGGCGACAATGTGGATCTCTACATCCCCAGGAAGTG                         TTCTTCAACCAACAGGTTGATCACTTCCAAGGATGTTGCCTCAGTTCAGCT
genomic: ATGCAGAACGAGGAGGGCGACAATGTGGATCTCTACATCCCCAGGAAGTGgtgggttttt ... ctttttgcagTTCTTCAACCAACAGGTTGATCACTTCCAAGGATGTTGCCTCAGTTCAGCT
EST: gi|18358029|gb|BJ190088.1|BJ190088
EST:     ATGCAGAACGAGGAGGGCGACAATGTGGATCTCTACATCCCCAGGAAGTG                         TTCTTCAACCAACAGGTTGATCACTTCCAAGGATGTTGCCTCAGTTCAGCT
genomic: ATGCAGAACGAGGAGGGCGACAATGTGGATCTCTACATCCCCAGGAAGTGgtgggttttt ... ctttttgcagTTCTTCAACCAACAGGTTGATCACTTCCAAGGATGTTGCCTCAGTTCAGCT
EST: gi|67571269|gb|BJ944093.1|BJ944093
EST:     ATGCAGAACGAGGAGGGCGACAATGTGGATCTCTACATCCCCAGGAAGTG                         TTCTTCAACCAACAGGTTGATCACTTCCAAGGATGTTGCCTCAGTTCAGCT
genomic: ATGCAGAACGAGGAGGGCGACAATGTGGATCTCTACATCCCCAGGAAGTGgtgggttttt ... ctttttgcagTTCTTCAACCAACAGGTTGATCACTTCCAAGGATGTTGCCTCAGTTCAGCT
EST: gi|67698725|gb|BJ958958.1|BJ958958
EST:     ATGCAGAACGAGGAGGGCGACAATGTGGATCTCTACATCCCCAGGAAGTG                         TTCTTCAACCAACAGGTTGATCACTTCCAAGGATGTTGCCTCAGTTCAGCT
genomic: ATGCAGAACGAGGAGGGCGACAATGTGGATCTCTACATCCCCAGGAAGTGgtgggttttt ... ctttttgcagTTCTTCAACCAACAGGTTGATCACTTCCAAGGATGTTGCCTCAGTTCAGCT
EST: gi|67575264|gb|BJ948088.1|BJ948088
EST:     ATGCAGAACGAGGAGGGCGACAATGTGGATCTCTACATCCCCAGGAAGTG                         TTCTTCAACCAACAGGTTGATCACTTCCAAGGATGTTGCCTCAGTTCAGCT
genomic: ATGCAGAACGAGGAGGGCGACAATGTGGATCTCTACATCCCCAGGAAGTGgtgggttttt ... ctttttgcagTTCTTCAACCAACAGGTTGATCACTTCCAAGGATGTTGCCTCAGTTCAGCT
EST: gi|162241160|gb|FC414165.1|FC414165
EST:     ATGCAGAACGAGGAGGGCGACAATGTGGATCTCTACATCCCCAGGAAGTG                         TTCTTCAACCAACAGGTTGATCACTTCCAAGGATGTTGCCTCAGTTCAGCT
genomic: ATGCAGAACGAGGAGGGCGACAATGTGGATCTCTACATCCCCAGGAAGTGgtgggttttt ... ctttttgcagTTCTTCAACCAACAGGTTGATCACTTCCAAGGATGTTGCCTCAGTTCAGCT
EST: gi|162217613|gb|FC394017.1|FC394017
EST:     ATGCAGAACGAGGAGGGCGACAATGTGGATCTCTACATCCCCAGGAAGTG                         TTCTTCAACCAACAGGTTGATCACTTCCAAGGATGTTGCCTCAGTTCAGCT
genomic: ATGCAGAACGAGGAGGGCGACAATGTGGATCTCTACATCCCCAGGAAGTGgtgggttttt ... ctttttgcagTTCTTCAACCAACAGGTTGATCACTTCCAAGGATGTTGCCTCAGTTCAGCT
EST: gi|162218209|gb|FC394201.1|FC394201
EST:     ATGCAGAACGAGGAGGGCGACAATGTGGATCTCTACATCCCCAGGAAGTG                         TTCTTCAACCAACAGGTTGATCACTTCCAAGGATGTTGCCTCAGTTCAGCT
genomic: ATGCAGAACGAGGAGGGCGACAATGTGGATCTCTACATCCCCAGGAAGTGgtgggttttt ... ctttttgcagTTCTTCAACCAACAGGTTGATCACTTCCAAGGATGTTGCCTCAGTTCAGCT
EST: gi|37823133|gb|BJ581199.1|BJ581199
EST:     ATGCAGAACGAGGAGGGCGACAATGTGGATCTCTACATCCCCAGGAAGTG                         TTCTTCAACCAACAGGTTGATCACTTCCAAGGATGTTGCCTCAGTTCAGCT
genomic: ATGCAGAACGAGGAGGGCGACAATGTGGATCTCTACATCCCCAGGAAGTGgtgggttttt ... ctttttgcagTTCTTCAACCAACAGGTTGATCACTTCCAAGGATGTTGCCTCAGTTCAGCT

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: 35 (upstream exon), 35 (downstream exon)
Score: 103

TCTCTCGTCTTTCAATTTCTGCGTCTCGCTGATCTCGCCGATTTCGCACCATGCAGAACGAGGAGGGCGACAATGTGGATCTCTACATCCCCAGGAAGTGgtgggttttt ... ctttttgcagTTCTTCAACCAACAGGTTGATCACTTCCAAGGATGTTGCCTCAGTTCAGCTCAATGTGGGTCATGTTGACGAAAATGGTGTCTACACCGGGCAGTTCACC




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Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCTCTCGTCTTTCAATTTCTGCGTCTCGCTGATCTCGCCGATTTCGCACCATGCAGAACGAGGAGGGCGACAATGTGGATCTCTACATCCCCAGGAAGTGgtgggttttttttgtttcatcgtcgtatcttccccccatttagagtttttcttacttctactttcctcctatttgataaaccctagattcattccggatt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG