Skip to another splice site:
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 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgttatgtttgctgatcccgtttcaattttgttttctccttgatgaactagtgtttaacattaaacttgttcgttaattacccgggactgagcactagatttgactgtttcgccgcaatgttacagTAAGAGCATCAACAAGGGCATTGGAGTGGACAACATGCATTATCTCAATGACGGACTATGGAAG

Basic information

species Physcomitrella patens
transcript PP1S215_25V6.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S215_25V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GLYMA04G41130.1 (Glycine max), 3'ss of exon 5
gtacgttatgtttgctgatcccgtttcaattttgttttctccttgatgaactagtgtttaacattaaacttgttcgttaattacccgggactgagcactagatttgactgtttcgccgcaatgttacagTAAGAGCATCAACAAGGGCATTGGAGTGGACAACATGCATTATCTCAATGACGGACTATGGAAG
            |||||||   |    ||       || |  ||     |     ||||||| ||       || ||| |||         ||  ||  |  ||| | | ||||       |||| ||| ||    ||||| ||||||||||| || |||||| |||||||||||||||| || || ||||||
----------aatgctgatgtggaaataaagagaacttatgatttgcata-----gtttaacttt-----ccttggttgattcttt-----tgctcaagaagtttaaatatttc----tgttgtttcagAAAAGCAATCAATAAGGGCATTGGGGTTGACAACTTGCATTATCTCAATGATGGTCTTTGGAAG

upper sequence: PP1S215_25V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: AT1G09150.1 (Arabidopsis thaliana), 3'ss of exon 7
gtacgttatgtttgctgatcccgtttcaattttgttttctccttgatgaactagtgtttaacattaaacttgttcgttaattacccgggactgagcactagatttgactgtttcgccgcaatgttacagTAAGAGCATCAACAAGGGCATTGGAGTGGACAACATGCATTATCTCAATGACGGACTATGGAAG
                      | | ||    |   | | ||  ||| || |   |       ||   | |||| | | || |        |   | |     |  ||| ||     | |   | |||| |||||||| ||||| || || ||||| |||||||||||||| ||||| ||||| || ||||||
----------------------gataca--catacctgcaccaggatcaattttggcc--gtgtttcccctgtttgctcataaaatttcttt---cgcatcgctaaacttttcttgtgtatgttcacagAAAGAGCATTAACAAAGGAATAGGAGTTGACAACATGCATTACCTCAACGACGGTCTCTGGAAG

upper sequence: PP1S215_25V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: Vv14s0060g01920.t01 (Vitis vinifera), 3'ss of exon 6
gtacgttatgtttgctgatcccgtttcaattttgttttctccttgatgaactagtgtttaacattaaacttgttcgttaattacccgggactgagcactagatttgactgtttcgccgcaatgttacagTAAGAGCATCAACAAGGGCATTGGAGTGGACAACATGCATTATCTCAATGACGGACTATGGAAG
                           ||                 || ||| |  ||   | |   ||||  |  |    ||    ||  |  | |  |  ||  ||   ||    || |   | |||||     |||||||| || ||||| ||||| ||||||||||| ||||||||||| || ||||||
------------------------aaaaaaaaaaaaaaaaaaaaactgtacttggattatgcct---acttcattttcctctatgttggcatatgtaagaagttaaacgagttgcttgcgac--tgcagTAGAGCAATCAACAAAGGAATTGGCGTGGATAACATGCATTACCTCAATGACGGGCTGTGGAAG

upper sequence: PP1S215_25V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: EFJ21050 (Selaginella moellendorffii), 3'ss of exon 7
gtacgttatgtttgctgatcccgtttcaattttgttttctccttgatgaactagtgtttaacattaaacttgttcgttaattacccgggactgagcactagatttgactgtttcgccgcaatgttacagTAAGAGCATCAACAAGGGCATTGGAGTGGACAACATGCATTATCTCAATGACGGACTATGGAAG
                                                                     |    |     ||  |  |||   | || |  |  | | |||||      | | |  ||| ||||  |||||||| || |||||||||||||| ||||| |||||||| || ||||| ||||||
--------------------------------------------------------------------gtgagccaccggtttgcttgga---aacaatcaagctaagtgtttaa----actctcgcagAAAGAATATCAACAAAGGGATTGGAGTGGACAATATGCACTATCTCAACGATGGACTCTGGAAG

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|208376363|gb|DC932273.1|DC932273
EST:     AAAGAGCATGCTCTGGCTATAGGATACACCAAGATGTCTGCAAAAGACAT                         TAAGAGCATCAACAAGGGCATTGGAGTGGACAACATGCATTATCTCAATGA
genomic: AAAGAGCATGCTCTGGCTATAGGATACACCAAGATGTCTGCAAAAGACATgtacgttatg ... aatgttacagTAAGAGCATCAACAAGGGCATTGGAGTGGACAACATGCATTATCTCAATGA
EST: gi|18356615|gb|BJ188674.1|BJ188674
EST:     AAAGAGCATGCTCTGGCTATAGGATACACCAAGATGTCTGCAAAAGACAT                         TAAGAGCATCAACAAGGGCATTGGAGTGGACAACATGCATTATCTCAATGA
genomic: AAAGAGCATGCTCTGGCTATAGGATACACCAAGATGTCTGCAAAAGACATgtacgttatg ... aatgttacagTAAGAGCATCAACAAGGGCATTGGAGTGGACAACATGCATTATCTCAATGA
EST: gi|208345629|gb|DC909299.1|DC909299
EST:     AAAGAGCATGCTCTGGCTATAGGATACACCAAGATGTCTGCAAAAGACAT                         TAAGAGCATCAACAAGGGCATTGGAGTGGACAACATGCATTATCTCAATGA
genomic: AAAGAGCATGCTCTGGCTATAGGATACACCAAGATGTCTGCAAAAGACATgtacgttatg ... aatgttacagTAAGAGCATCAACAAGGGCATTGGAGTGGACAACATGCATTATCTCAATGA
EST: gi|162259779|gb|FC436759.1|FC436759
EST:     AAAGAGCATGCTCTGGCTATAGGATACACCAAGATGTCTGCAAAAGACAT                         TAAGAGCATCAACAAGGGCATTGGAGTGGACAACATGCATTATCTCAATGA
genomic: AAAGAGCATGCTCTGGCTATAGGATACACCAAGATGTCTGCAAAAGACATgtacgttatg ... aatgttacagTAAGAGCATCAACAAGGGCATTGGAGTGGACAACATGCATTATCTCAATGA
EST: gi|208363408|gb|DC947006.1|DC947006
EST:     AAAGAGCATGCTCTGGCTATAGGATACACCAAGATGTCTGCAAAAGACAT                         TAAGAGCATCAACAAGGGCATTGGAGTGGACAACATGCATTATCTCAATGA
genomic: AAAGAGCATGCTCTGGCTATAGGATACACCAAGATGTCTGCAAAAGACATgtacgttatg ... aatgttacagTAAGAGCATCAACAAGGGCATTGGAGTGGACAACATGCATTATCTCAATGA
EST: gi|18343486|gb|BJ175524.1|BJ175524
EST:     AAAGAGCATGCTCTGGCTATAGGATACACCAAGATGTCTGCAAAAGACAT                         TAAGAGCATCAACA
genomic: AAAGAGCATGCTCTGGCTATAGGATACACCAAGATGTCTGCAAAAGACATgtacgttatg ... aatgttacagTAAGAGCATCAACA
EST: gi|67700873|gb|BJ961106.1|BJ961106
EST:     AAGAGCATGCTCTGGCTATAGGGATACACCAAGATGTCTGCAAAAGACAT                         TAAGAGCATCAACAAGGGCATTGGAGTGGACAACATGCATTATCTCAATGA
genomic: AAGAGCATGCTCTGGCTATA-GGATACACCAAGATGTCTGCAAAAGACATgtacgttatg ... aatgttacagTAAGAGCATCAACAAGGGCATTGGAGTGGACAACATGCATTATCTCAATGA
EST: gi|22132705|gb|BQ827296.1|BQ827296
EST:     AAAGAGCATGCTCTGGCTATAGGATACACCAAGATGTCTGCAAAAGACAT                         TAAGAGCATCAACAAGGGCATTGGAGTGGACAACATGCATTATCTCAATGA
genomic: AAAGAGCATGCTCTGGCTATAGGATACACCAAGATGTCTGCAAAAGACATgtacgttatg ... aatgttacagTAAGAGCATCAACAAGGGCATTGGAGTGGACAACATGCATTATCTCAATGA
EST: gi|18341766|gb|BJ173801.1|BJ173801
EST:     GGATACACCAAGATGTCTGCAAAAGACAT                         TAAGAGCATCAACAAGGGCATTGGAGTGGACAACATGCATTATCTCAATGA
genomic: GGATACACCAAGATGTCTGCAAAAGACATgtacgttatg ... aatgttacagTAAGAGCATCAACAAGGGCATTGGAGTGGACAACATGCATTATCTCAATGA
EST: gi|208371667|gb|DC932496.1|DC932496
EST:     AAAGAGCATGCTCTGGCTATAGGATACACCAAGATGTCTGCAAAAGACAT                         TAAGAGCATCAACAAGGGCATTGGAGTGGACAACATGCATTATCTCAATGA
genomic: AAAGAGCATGCTCTGGCTATAGGATACACCAAGATGTCTGCAAAAGACATgtacgttatg ... aatgttacagTAAGAGCATCAACAAGGGCATTGGAGTGGACAACATGCATTATCTCAATGA
EST: gi|162259765|gb|FC436758.1|FC436758
EST:     AAAGAGCATGCTCTGGCTATAGGATACACCAAGATGTCTGCAAAAGACAT                         TAAGAGCATCAACAAGGGCATTGGAGTGGACAACATGCATTATCTCAATGA
genomic: AAAGAGCATGCTCTGGCTATAGGATACACCAAGATGTCTGCAAAAGACATgtacgttatg ... aatgttacagTAAGAGCATCAACAAGGGCATTGGAGTGGACAACATGCATTATCTCAATGA
EST: gi|162221749|gb|FC397081.1|FC397081
EST:     AAAGAGCATGCTCTGGCTATAGGATACACCAAGATGTCTGCAAAAGACAT                         TAAGAGCATCAACAAGGGCATTGGAGTGGACAACATGCATTATCTCAATGA
genomic: AAAGAGCATGCTCTGGCTATAGGATACACCAAGATGTCTGCAAAAGACATgtacgttatg ... aatgttacagTAAGAGCATCAACAAGGGCATTGGAGTGGACAACATGCATTATCTCAATGA
EST: gi|67578005|gb|BJ950172.1|BJ950172
EST:     AAAGAGCATGCTCTGGCTATAGGATACACCAAGATGTCTGCAAAAGACAT                         TAAGAGCATCAACAAGGGCATTGGAGTGGACAACATGCATTATCTCAATGA
genomic: AAAGAGCATGCTCTGGCTATAGGATACACCAAGATGTCTGCAAAAGACATgtacgttatg ... aatgttacagTAAGAGCATCAACAAGGGCATTGGAGTGGACAACATGCATTATCTCAATGA
EST: gi|37822681|gb|BJ580747.1|BJ580747
EST:     AAAGAGCATGCTCTGGCTATAGGATACACCAAGATGTCTGCAAAAGACAT                         TAAGAGCATCAACAAGGGCATTGGAGTGGACAACATGCATTATCTCAATGA
genomic: AAAGAGCATGCTCTGGCTATAGGATACACCAAGATGTCTGCAAAAGACATgtacgttatg ... aatgttacagTAAGAGCATCAACAAGGGCATTGGAGTGGACAACATGCATTATCTCAATGA
EST: gi|208365150|gb|DC946779.1|DC946779
EST:     AAAGAGCATGCTCTGGCTATAGGATACACCAAGATGTCTGCAAAAGACAT                         TAAGAGCATCAACAAGGGCATTGGAGTGGACAACATGCATTATCTCAATGA
genomic: AAAGAGCATGCTCTGGCTATAGGATACACCAAGATGTCTGCAAAAGACATgtacgttatg ... aatgttacagTAAGAGCATCAACAAGGGCATTGGAGTGGACAACATGCATTATCTCAATGA
EST: gi|22492644|gb|BU052567.1|BU052567
EST:     AAAGAGCATGCTCTGGCTATAGGATACACCAAGATGTCTGCAAAAGACAT                         TAAGAGCATCAACAAGGGCATTGGAGTGGACAACATGCATTATCTCAATGA
genomic: AAAGAGCATGCTCTGGCTATAGGATACACCAAGATGTCTGCAAAAGACATgtacgttatg ... aatgttacagTAAGAGCATCAACAAGGGCATTGGAGTGGACAACATGCATTATCTCAATGA
EST: gi|37829219|gb|BJ587231.1|BJ587231
EST:     TCTGCAAAAGACAT                         TAAGAGCATCACCAAGGGCATTGGAGTGGACAACATGCATTATCTCAATGA
genomic: TCTGCAAAAGACATgtacgttatg ... aatgttacagTAAGAGCATCAACAAGGGCATTGGAGTGGACAACATGCATTATCTCAATGA
EST: gi|208354986|gb|DC914250.1|DC914250
EST:     AAAGAGCATGCTCTGGCTATAGGATACACCAAGATGTCTGCAAAAGACAT                         TAAGAGCATCAACAAGGGCATTGGAGTGGACAACATGCATTATCTCAATGA
genomic: AAAGAGCATGCTCTGGCTATAGGATACACCAAGATGTCTGCAAAAGACATgtacgttatg ... aatgttacagTAAGAGCATCAACAAGGGCATTGGAGTGGACAACATGCATTATCTCAATGA
EST: gi|162228094|gb|FC404649.1|FC404649
EST:     AAAGAGCATGCTCTGGCTATAGGATACACCAAGATGTCTGCAAAAGACAT                         TAAGAGCATCAACAAGGGCATTGGAGTGGACAACATGCATTATCTCAATGA
genomic: AAAGAGCATGCTCTGGCTATAGGATACACCAAGATGTCTGCAAAAGACATgtacgttatg ... aatgttacagTAAGAGCATCAACAAGGGCATTGGAGTGGACAACATGCATTATCTCAATGA
EST: gi|208382460|gb|DC927994.1|DC927994
EST:     AAAGAGCATGCTCTGGCTATAGGATACACCAAGATGTCTGCAAAAGACAT                         TAAGAGCATCAACAAGGGCATTGGAGTGGACAACATGCATTATCTCAATGA
genomic: AAAGAGCATGCTCTGGCTATAGGATACACCAAGATGTCTGCAAAAGACATgtacgttatg ... aatgttacagTAAGAGCATCAACAAGGGCATTGGAGTGGACAACATGCATTATCTCAATGA
EST: gi|7584206|gb|AW700103.1|AW700103
EST:     AAAGAGCATGCTCTGGCTATAGGATACACCAAGATGTCTGCAAAAGACAT                         TAAGAGCATCAACAAGGGCATTGGAGTGGACAACATGCATTATCTCAATGA
genomic: AAAGAGCATGCTCTGGCTATAGGATACACCAAGATGTCTGCAAAAGACATgtacgttatg ... aatgttacagTAAGAGCATCAACAAGGGCATTGGAGTGGACAACATGCATTATCTCAATGA
EST: gi|208395953|gb|DC915713.1|DC915713
EST:     AAAGAGCATGCTCTGGCTATAGGATACACCAAGATGTCTGCAAAAGACAT                         TAAGAGCATCAACAAGGGCATTGGAGTGGACAACATGCATTATCTCAATGA
genomic: AAAGAGCATGCTCTGGCTATAGGATACACCAAGATGTCTGCAAAAGACATgtacgttatg ... aatgttacagTAAGAGCATCAACAAGGGCATTGGAGTGGACAACATGCATTATCTCAATGA
EST: gi|18350245|gb|BJ182296.1|BJ182296
EST:     AAAGAGCATGCTCTGGCTATAGGATACACCAAGATGTCTGCAAAAGACAT                         TAAGAGCATCAACAAGGGCATTGGAGTGGACAACATGCATTATCTCAATGA
genomic: AAAGAGCATGCTCTGGCTATAGGATACACCAAGATGTCTGCAAAAGACATgtacgttatg ... aatgttacagTAAGAGCATCAACAAGGGCATTGGAGTGGACAACATGCATTATCTCAATGA
EST: gi|67693833|gb|BJ954066.1|BJ954066
EST:     AAAGAGCATGCTCTGGCTATAGGATACACCAAGATGTCTGCAAAAGACAT                         TAAGAGCATCAACAAGGGCATTGGAGTGGACAACATGCATTATCTCAATGA
genomic: AAAGAGCATGCTCTGGCTATAGGATACACCAAGATGTCTGCAAAAGACATgtacgttatg ... aatgttacagTAAGAGCATCAACAAGGGCATTGGAGTGGACAACATGCATTATCTCAATGA
EST: gi|208382492|gb|DC923162.1|DC923162
EST:     AAAGAGCATGCTCTGGCTATAGGATACACCAAGATGTCTGCAAAAGACAT                         TAAGAGCATCAACAAGGGCATTGGAGTGGACAACATGCATTATCTCAATGA
genomic: AAAGAGCATGCTCTGGCTATAGGATACACCAAGATGTCTGCAAAAGACATgtacgttatg ... aatgttacagTAAGAGCATCAACAAGGGCATTGGAGTGGACAACATGCATTATCTCAATGA
EST: gi|162221748|gb|FC397080.1|FC397080
EST:     AAAGAGCATGCTCTGGCTATAGGATACACCAAGATGTCTGCAAAAGACAT                         TAAGAGCATCAACAAGGGCATTGGAGTGGACAACATGCATTATCTCAATGA
genomic: AAAGAGCATGCTCTGGCTATAGGATACACCAAGATGTCTGCAAAAGACATgtacgttatg ... aatgttacagTAAGAGCATCAACAAGGGCATTGGAGTGGACAACATGCATTATCTCAATGA

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), 30 (downstream exon)
Score: 8

GCAATCATGGCAGAAGGCAAAGAGCATGCTCTGGCTATAGGATACACCAAGATGTCTGCAAAAGACATgtacgttatg ... aatgttacagTAAGAGCATCAACAAGGGCATTGGAGTGGACAACATGCATTATCTCAATGACGGACTATGGAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgttaattacccgggactgagcactagatttgactgtttcgccgcaatgttacagTAAGAGCATCAACAAGGGCATTGGAGTGGACAACATGCATTATCTCAATGACGGACTATGGAAG
                           atttgac  putative branch site (score: 8)
                        tagattt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgttatgtttgctgatcccgtttcaattttgttttctccttgatgaactagtgtttaacattaaacttgttcgttaattacccgggactgagcactagatttgactgtttcgccgcaatgttacagTAAGAGCATCAACAAGGGCATTGGAGTGGACAACATGCATTATCTCAATGACGGACTATGGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG