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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCCTGCTCAGAATGTTGAGAGCTCACAATGCATCACCATGATGGAGGCTGTCAATGGAGGTCAAGACTTGCATGTCTCTGTTACGATGCCTTCCATTGAGgtatgtacttgatttttcaattaacagtgcttttagatgctgcaataagtgaagtttgcccgactgattttaaaatctatattacagtgctattatgaatgcttatggatatttccattatttatttgttttacag

Basic information

species Physcomitrella patens
transcript PP1S1_155V6.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S1_155V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: LOC_Os02g48330.1 (Oryza sativa), 5'ss of exon 4
TCCTGCTCAGAATGTTGAGAGCTCACAATGCATCACCATGATGGAGGCTGTCAATGGAGGTCAAGACTTGCATGTCTCTGTTACGATGCCTTCCATTGAGgtatgtacttgatttttcaattaacagtgcttttagatgctgcaataagtgaagtttgcccgactgattttaaaatctatattacagtgc-tattatgaatgcttatggatatttccattatttatttgttttacag
|||||| || |||||||| ||||||||||||||||||||| |||| |  || ||||  ||  | ||  | ||| ||||||| || ||||| |||||||||||   || ||  |  ||  | |  | || | |        |      | |  ||  |  ||  ||    |||||         | | |   ||  ||  |                                     
TCCTGCACAAAATGTTGAAAGCTCACAATGCATCACCATGTTGGAAGAAGTAAATGATGGAGATGATCTTCATATCTCTGTCACCATGCCGTCCATTGAGgtgattatttattcgttttactttccgttcctacctgcattatgtagattatagcataacctgctagccttaaatggagctgcaaaatctatagcataga-------------------------------------

upper sequence: PP1S1_155V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: GRMZM2G135085_T01 (Zea mays), 5'ss of exon 3
TCCTGCTCAGAATGTTGAGAGCTCACAATGCATCACCATGATGGAGGCTGTCAATGGAGGTCAAGACTTGCATGTCTCTGTTACGATGCCTTCCATTGAGgtatg--tacttgatttttcaattaa--cagtgcttttagatgctgcaataagtgaagtttgcccgactgattttaaaatctatattacagtgctattatgaatgcttatggatatttccattattt--atttgttttacag-------------------------------
|||||| ||||| ||||| |||||||| |||||||||||||||||||| || ||||  ||    ||  | ||  ||||||| || |||||||||||||||||| |  |  | |   |    ||  |   |||  | | |  |  ||    || |  |          |  ||| |    || | ||||       |||     ||||| |   | |  |  ||  |   ||  || || |                                 
TCCTGCCCAGAACGTTGAAAGCTCACAGTGCATCACCATGATGGAGGCAGTGAATGACGGAGGCGATCTTCACATCTCTGTGACCATGCCTTCCATTGAGgtaaggcttataggcatactgatacagttagtattataaagttttgttggaattataaaaccaatagcccattatcct-tccagattatttgctcattcctcgtgcttttatttctcccatttgatcgaatgcgtatttcgtgtcaataataatttgtccactccattctcag

upper sequence: PP1S1_155V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: GLYMA11G09330.1 (Glycine max), 5'ss of exon 3
TCCTGCTCAGAATGTTGAGAGCTCACAATGCATCACCATGATGGAGGCTGTCAATGGAGGTCAAGACTTGCATGTCTCTGTTACGATGCCTTCCATTGAGgtatgt--acttgatttttcaattaacagtgcttttagatgctgcaataagtgaagtttgcccgactgattttaaaatctatattacagtgctattatgaatgcttatggatatttccattatttatttgttttacag
 |||||||||||||| ||||| || || ||||| || |||||||| ||||| ||||  ||  | ||| | ||  |||||||||| ||||||||||||||||||||   | || | |  | | |||     |  || |  |  ||  ||   | ||   |     |   || |||      |  ||  |||    | |  |                                      
CCCTGCTCAGAATGTGGAGAGTTCTCACTGCATAACTATGATGGAAGCTGTGAATGATGGCAAGGACCTTCACATCTCTGTTACTATGCCTTCCATTGAGgtatgcccaattaactaattacttattttggtcttaaattcttgttatgttttaatgctctttaat--atgttaggggtgactttttagtatagtaaataga------------------------------------

upper sequence: PP1S1_155V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: GLYMA01G36080.1 (Glycine max), 5'ss of exon 3
TCCTGCTCAGAATGTTGAGAGCTCACAATGCATCACCATGATGGAGGCTGTCAATGGAGGTCAAGACTTGCATGTCTCTGTTACGATGCCTTCCATTGAGgtatgtacttgatttttcaattaacagtgcttttagatgctgcaataagtgaagtttgcccgactgattttaaaatctatattacagtgctattatgaatgcttatggatatttccattatttatttgttttacag
 |||||||||||||| ||||| || || ||||| ||||||||||| ||||| ||||  ||  | ||| | ||  |||||||||| ||||||||| ||||||||||  ||| |||  | | |||     |  || |  |  ||  ||   | ||   |     | |  ||            | |   |  ||    ||||                                    
CCCTGCTCAGAATGTGGAGAGTTCTCACTGCATAACCATGATGGAAGCTGTGAATGATGGCAAGGACCTTCACATCTCTGTTACTATGCCTTCCCTTGAGgtatg--cttaattaattacttattttggtcttaaattcttgttatgctttaatgctctttcattacttaggggtgactcttcattatagtaaacagaatag----------------------------------

upper sequence: PP1S1_155V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: GLYMA09G32850.1 (Glycine max), 5'ss of exon 7
TCCTGCTCAGAATGTTGAGAGCTCACAATGCATCACCATGATGGAGGCTGTCAATGGAGGTCAAGACTTGCATGTCTCTGTTACGATGCCTTCCATTGAGgtatgtacttgatttttcaattaacagtgcttttagatgctgcaataagtgaagtttgcccgactgattttaaaatctatattacagtgctattatgaatgcttatggatatttccattatttatttgttttacag
|||||| |||||||| ||||| || || ||||||||||||||||| ||| ||||||  ||  | ||| | ||||| || || || ||||| ||||||||||||   ||| | || |   ||    | || | ||      |    || ||  ||| |     |    || |  | |  |||||    ||   |  |  ||||                                  
TCCTGCCCAGAATGTGGAGAGTTCTCACTGCATCACCATGATGGAAGCTATCAATGATGGCAAGGACCTTCATGTTTCCGTGACCATGCCCTCCATTGAGgtac-cact-gtttctctgatcttaaatggtgttgtcctttt---taggtagagtattgttcatattttatgtagtggatatttgtctgaattagtatatgcaag-------------------------------

upper sequence: PP1S1_155V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: GLYMA16G21620.1 (Glycine max), 5'ss of exon 4
TCCTGCTCAGAATGTTGAGAGCTCACAATGCATCACCATGATGGAGGCTGTCAATGGAGGTCAAGACTTGCATGTCTCTGTTACGATGCCTTCCATTGAGgtatgtacttgatttttcaattaacagtgcttttagatgctgcaataagtgaagtttgcccgactgattttaaaatctatattacagtgctattatgaatgcttatggatatttccattatttatttgttttacag
|||||| |||||||| ||||| || || ||||||||||||||||| ||| ||||||  ||  | ||| | || || || || || ||||| ||||||||||||   ||| | || |   ||    | || | ||      |    || ||  ||| |     |    || | || |  |||||    ||   |  |  ||||                                  
TCCTGCCCAGAATGTGGAGAGTTCTCACTGCATCACCATGATGGAAGCTATCAATGATGGCAAGGACCTTCACGTTTCGGTGACCATGCCCTCCATTGAGgtac-cact-gtttctctgatcttaaatggtgttgtcctttt---taggtagagtatagttcatattttatgaagtggatattcgtctgaattagtagatgcaag-------------------------------

upper sequence: PP1S1_155V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: Vv04s0044g01740.t01 (Vitis vinifera), 5'ss of exon 4
TCCTGCTCAGAATGTTGAGAGCTCACAATGCATCACCATGATGGAGGCTGTCAATGGAGGTCAAGACTTGCATGTCTCTGTTACGATGCCTTCCATTGAGgtatgtacttgatttttcaattaacagtgcttttagatgctgcaataagtgaagtttgcccgactgattttaaaat-ctatattacagtgctattatgaatgcttatggatatttccattatttatttgttttacag
||||||||||||||| |||||||| || |||||||| |||||||| ||||| ||||  ||  | ||| | ||| |||| || || ||||||||||||||||||  |  ||       | ||  |   || || |   ||||        || |||    | |||| |     ||||  || | || |    |  ||||  ||| |   |                            
TCCTGCTCAGAATGTAGAGAGCTCCCACTGCATCACGATGATGGAAGCTGTGAATGATGGGAAGGACCTTCATATCTCAGTCACCATGCCTTCCATTGAGgtaaatcattagcaacaccatccattctg-ttatgtttgct--------tgtagt--agcagactaagaaagaaatattagactaaacatatggtatgggtgcatgcag----------------------------

upper sequence: PP1S1_155V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: Vv03s0038g04100.t01 (Vitis vinifera), 5'ss of exon 3
TCCTGCTCAGAATGTTGAGAGCTCACAATGCATCACCATGATGGAGGCTGTCAATGGAGGTCAAGACTTGCATGTCTCTGTTACGATGCCTTCCATTGAGgtatgtactt-gatttttcaattaacagtgcttttagatgctgcaataagtgaagtttgcccgactgattttaaaatctatattacagtgctattatgaatgcttatggatatttccattatttatttgttttacag
 || || |||||||| |||||||| || || ||||||||||||||||||||||| |  ||  ||||| | || ||||| || || ||||| || || ||||||  || |   |    || |     |     || |  | ||| || ||     |||      |   | | | | |     | || | |   |||   ||   || ||  |   | ||                   
CCCCGCCCAGAATGTGGAGAGCTCTCACTGTATCACCATGATGGAGGCTGTCAACGATGGAAAAGACCTCCACGTCTCAGTCACCATGCCCTCTATCGAGgtaattaatccaaaccctctaaccctaccatattgaatttctgaaaaaaa-atggttcaaatcaagaactgtgatactgggacta-atta--atttctaactattgtgtttgaattcag------------------

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|162245365|gb|FC421267.1|FC421267
EST:     TCAATGGAGGTCAAGACTTGCATGTCTCTGTTACGATGCCTTCCATTGAG                         GTGGGAACTGTCGGCGGTGGTACACAATTGGCATCACAATCAGCTTGCTTA
genomic: TCAATGGAGGTCAAGACTTGCATGTCTCTGTTACGATGCCTTCCATTGAGgtatgtactt ... tgttttacagGTGGGAACTGTCGGCGGTGGTACACAATTGGCATCACAATCAGCTTGCTTA
EST: gi|162219577|gb|FC395573.1|FC395573
EST:     TCAATGGAGGTCAAGACTTGCATGTCTCTGTTACGATGCCTTCCATTGAG                         GTGGGAACTGTCGGCGGTGGTACACAATTGGCATCACAATCAGCTTGCTTA
genomic: TCAATGGAGGTCAAGACTTGCATGTCTCTGTTACGATGCCTTCCATTGAGgtatgtactt ... tgttttacagGTGGGAACTGTCGGCGGTGGTACACAATTGGCATCACAATCAGCTTGCTTA
EST: gi|37835168|gb|BJ593180.1|BJ593180
EST:     TCAATGGAGGTCAAGACTTGCATGTCTCTGTTACGATGCCTTCCATTGAG                         GTGGGAACTGTCGGCGGTGGTACACAATTGGCATCACAATCAGCTTGCTTA
genomic: TCAATGGAGGTCAAGACTTGCATGTCTCTGTTACGATGCCTTCCATTGAGgtatgtactt ... tgttttacagGTGGGAACTGTCGGCGGTGGTACACAATTGGCATCACAATCAGCTTGCTTA
EST: gi|37848555|gb|BJ606563.1|BJ606563
EST:     TCAATGGAGGTCAAGACTTGCATGTCTCTGTTACGATGCCTTCCATTGAG                         GTGGGAACTGTCGGCGGTGGTACACAATTGGCATCACAATCAGCTTGCTTA
genomic: TCAATGGAGGTCAAGACTTGCATGTCTCTGTTACGATGCCTTCCATTGAGgtatgtactt ... tgttttacagGTGGGAACTGTCGGCGGTGGTACACAATTGGCATCACAATCAGCTTGCTTA
EST: gi|37827414|gb|BJ585426.1|BJ585426
EST:     TCAATGGAGGTCAAGACTTGCATGTCTCTGTTACGATGCCTTCCATTGAG                         GTGGGAACTGTCGGCGGTGGTACACAATTGGCATCACAATCAGCTTGCTTA
genomic: TCAATGGAGGTCAAGACTTGCATGTCTCTGTTACGATGCCTTCCATTGAGgtatgtactt ... tgttttacagGTGGGAACTGTCGGCGGTGGTACACAATTGGCATCACAATCAGCTTGCTTA
EST: gi|162154783|gb|FC331097.1|FC331097
EST:     TCAATGGAGGTCAAGACTTGCATGTCTCTGTTACGATGCCTTCCATTGAG                         GTGGGAACTGTCGGCGGTGGTACACAATTGGCATCACAATCAGCTTGCTTA
genomic: TCAATGGAGGTCAAGACTTGCATGTCTCTGTTACGATGCCTTCCATTGAGgtatgtactt ... tgttttacagGTGGGAACTGTCGGCGGTGGTACACAATTGGCATCACAATCAGCTTGCTTA
EST: gi|162257972|gb|FC433858.1|FC433858
EST:     TCAATGGAGGTCAAGACTTGCATGTCTCTGTTACGATGCCTTCCATTGAG                         GTGGGAACTGTCGGCGGTGGTACACAATTGGCATCACAATCAGCTTGCTTA
genomic: TCAATGGAGGTCAAGACTTGCATGTCTCTGTTACGATGCCTTCCATTGAGgtatgtactt ... tgttttacagGTGGGAACTGTCGGCGGTGGTACACAATTGGCATCACAATCAGCTTGCTTA
EST: gi|162152969|gb|FC329271.1|FC329271
EST:     TCAATGGAGGTCAAGACTTGCATGTCTCTGTTACGATGCCTTCCATTGAG                         GTGGGAACTGTCGGCGGTGGTACACAATTGGCATCACAATCAGCTTGCTTA
genomic: TCAATGGAGGTCAAGACTTGCATGTCTCTGTTACGATGCCTTCCATTGAGgtatgtactt ... tgttttacagGTGGGAACTGTCGGCGGTGGTACACAATTGGCATCACAATCAGCTTGCTTA
EST: gi|162157133|gb|FC333703.1|FC333703
EST:     TCAATGGAGGTCAAGACTTGCATGTCTCTGTTACGATGCCTTCCATTGAG                         GTGGGAACTGTCGGCGGTGGTACACAATTGGCATCACAATCAGCTTGCTTA
genomic: TCAATGGAGGTCAAGACTTGCATGTCTCTGTTACGATGCCTTCCATTGAGgtatgtactt ... tgttttacagGTGGGAACTGTCGGCGGTGGTACACAATTGGCATCACAATCAGCTTGCTTA
EST: gi|208397972|gb|DC916727.1|DC916727
EST:     TCAATGGAGGTCAAGACTTGCATGTCTCTGTTACGATGCCTTCCATTGAG                         GTGGGAACTGTCGGCGGTGGTACACAATTGGCATCACAATCAGCTTGCTTA
genomic: TCAATGGAGGTCAAGACTTGCATGTCTCTGTTACGATGCCTTCCATTGAGgtatgtactt ... tgttttacagGTGGGAACTGTCGGCGGTGGTACACAATTGGCATCACAATCAGCTTGCTTA
EST: gi|37846529|gb|BJ604537.1|BJ604537
EST:     TCAATGGAGGTCAAGACTTGCATGTCTCTGTTACGATGCCTTCCATTGAG                         GTGGGAACTGTCGGCGGTGGTACACAATTGGCATCACAATCAGCTTGCTTA
genomic: TCAATGGAGGTCAAGACTTGCATGTCTCTGTTACGATGCCTTCCATTGAGgtatgtactt ... tgttttacagGTGGGAACTGTCGGCGGTGGTACACAATTGGCATCACAATCAGCTTGCTTA
EST: gi|162245366|gb|FC421268.1|FC421268
EST:     TCAATGGAGGTCAAGACTTGCATGTCTCTGTTACGATGCCTTCCATTGAG                         GTGGGAACTGTCGGCGGTGGTACACAATTGGCATCACAATCAGCTTGCTTA
genomic: TCAATGGAGGTCAAGACTTGCATGTCTCTGTTACGATGCCTTCCATTGAGgtatgtactt ... tgttttacagGTGGGAACTGTCGGCGGTGGTACACAATTGGCATCACAATCAGCTTGCTTA
EST: gi|162234161|gb|FC410765.1|FC410765
EST:     TCAATGGAGGTCAAGACTTGCATGTCTCTGTTACGATGCCTTCCATTGAG                         GTGGGAACTGTCGGCGGTGGTACACAATTGGCATCACAATCAGCTTGCTTA
genomic: TCAATGGAGGTCAAGACTTGCATGTCTCTGTTACGATGCCTTCCATTGAGgtatgtactt ... tgttttacagGTGGGAACTGTCGGCGGTGGTACACAATTGGCATCACAATCAGCTTGCTTA
EST: gi|37828391|gb|BJ586403.1|BJ586403
EST:     TCAATGGAGGTCAAGACTTGCATGTCTCTGTTACGATGCCTTCCATTGAG                         GTGGGAACTGTCGGCGGTGGTACACAATTGGCATCACAATCAGCTTGCTTA
genomic: TCAATGGAGGTCAAGACTTGCATGTCTCTGTTACGATGCCTTCCATTGAGgtatgtactt ... tgttttacagGTGGGAACTGTCGGCGGTGGTACACAATTGGCATCACAATCAGCTTGCTTA
EST: gi|162154782|gb|FC331096.1|FC331096
EST:     GTTACGATGCCTTCCATTGAG                         GTGGGAACTGTCGGCGGTGGTACACAATTGGCATCACAATCAGCTTGCTTA
genomic: GTTACGATGCCTTCCATTGAGgtatgtactt ... tgttttacagGTGGGAACTGTCGGCGGTGGTACACAATTGGCATCACAATCAGCTTGCTTA
EST: gi|37850616|gb|BJ608624.1|BJ608624
EST:     TCAATGGAGGTCAAGACTTGCATGTCTCTGTTACGATGCCTTCCATTGAG                         GTGGGAACTGTCGGCGGTGGTACACAATTGGCATCACAATCAGCTTGCTTA
genomic: TCAATGGAGGTCAAGACTTGCATGTCTCTGTTACGATGCCTTCCATTGAGgtatgtactt ... tgttttacagGTGGGAACTGTCGGCGGTGGTACACAATTGGCATCACAATCAGCTTGCTTA
EST: gi|162234162|gb|FC410766.1|FC410766
EST:     TCAATGGAGGTCAAGACTTGCATGTCTCTGTTACGATGCCTTCCATTGAG                         GTGGGAACTGTCGGCGGTGGTACACAATTGGCATCACAATCAGCTTGCTTA
genomic: TCAATGGAGGTCAAGACTTGCATGTCTCTGTTACGATGCCTTCCATTGAGgtatgtactt ... tgttttacagGTGGGAACTGTCGGCGGTGGTACACAATTGGCATCACAATCAGCTTGCTTA
EST: gi|162157134|gb|FC333704.1|FC333704
EST:     TCAATGGAGGTCAAGACTTGCATGTCTCTGTTACGATGCCTTCCATTGAG                         GTGGGAACTGTCGGCGGTGGTACACAATTGGCATCACAATCAGCTTGCTTA
genomic: TCAATGGAGGTCAAGACTTGCATGTCTCTGTTACGATGCCTTCCATTGAGgtatgtactt ... tgttttacagGTGGGAACTGTCGGCGGTGGTACACAATTGGCATCACAATCAGCTTGCTTA

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: 52

TCCTGCTCAGAATGTTGAGAGCTCACAATGCATCACCATGATGGAGGCTGTCAATGGAGGTCAAGACTTGCATGTCTCTGTTACGATGCCTTCCATTGAGgtatgtactt ... tgttttacagGTGGGAACTGTCGGCGGTGGTACACAATTGGCATCACAATCAGCTTGCTTAAACCTACTTGGAGTGAAGGGAGCTAATGTAGAGTCCCCAGGGGCTAATG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCCTGCTCAGAATGTTGAGAGCTCACAATGCATCACCATGATGGAGGCTGTCAATGGAGGTCAAGACTTGCATGTCTCTGTTACGATGCCTTCCATTGAGgtatgtacttgatttttcaattaacagtgcttttagatgctgcaataagtgaagtttgcccgactgattttaaaatctatattacagtgctattatgaatgcttatggatatttccattatttatttgttttacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG