Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcgtacaagtggcatttgcgctaggaaatacagttatggtgattcttcttcttgtcacgtgctgactctaactgcttgcctctttccattggtgttacagCTTACAAATGAACCGCACTTTTCACAAGGAATGTTCCATTTCGACTACAGG

Basic information

species Physcomitrella patens
transcript PP1S367_8V6.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S367_8V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: EFJ38844 (Selaginella moellendorffii), 3'ss of exon 4
gcgtacaagtggcatttgcgctaggaaatacagttatggtgattcttcttcttgtcacgtgctgactctaactgcttgcctctttccattggtgttacagCTTACAAATGAACCGCACTTTTCACAAGGAATGTTCCATTTCGACTACAGG
                           |     | | | |      || |   | ||  ||  |||  |        |  ||||  |  |||     ||| | || || || || ||||||||||| ||||||||||| |||||||||| |
-------------------------gtacgatataacgattgcatctccttcgggcatttgtagacgtttctaatgcgtttcttgtccatgg-----cagTTAACCAACGAGCCACACTTTTCACAGGGAATGTTCCAGTTCGACTACAAG

upper sequence: PP1S367_8V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: EFJ15593 (Selaginella moellendorffii), 3'ss of exon 4
gcgtacaagtggcatttgcgctaggaaatacagttatggtgattct---tcttcttgtcacgtgctgactctaactgcttgcctctttccattggtgttacagCTTACAAATGAACCGCACTTTTCACAAGGAATGTTCCATTTCGACTACAGG
                            ||| | |||   |||||    || |   | ||  ||  |||  |        |  ||||  |  |||     ||| | || || || || ||||||||||| ||||||||||| |||||||||| |
---------------------------gtac-gatataacgattccatctccttccggcatttgtagacgtttctaatgcgtttcttgtccatgg-----cagTTAACCAACGAGCCACACTTTTCACAGGGAATGTTCCAGTTCGACTACAAG
















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|162208677|gb|FC385074.1|FC385074
EST:     GAATCAAGTATGACTTCACCGATAGATTTTCAGTAAAAGTGAACGCGCAG                         CTTACAAATGAACCGCACTTTTCACAAGGAATGTTCCATTTCGACTACAGG
genomic: GAATCAAGTATGACTTCACCGATAGATTTTCAGTAAAAGTGAACGCGCAGgtaaatgatg ... ggtgttacagCTTACAAATGAACCGCACTTTTCACAAGGAATGTTCCATTTCGACTACAGG
EST: gi|208398286|gb|DC912299.1|DC912299
EST:     GAATCAAGTATGACTTCACCGATAGATTTTCAGTAAAAGTGAACGCGCAG                         CTTACAAATGAACCGCACTTTTCACAAGGAATGTTCCATTTCGACTACAGG
genomic: GAATCAAGTATGACTTCACCGATAGATTTTCAGTAAAAGTGAACGCGCAGgtaaatgatg ... ggtgttacagCTTACAAATGAACCGCACTTTTCACAAGGAATGTTCCATTTCGACTACAGG
EST: gi|37846861|gb|BJ604869.1|BJ604869
EST:     AATCAAGTATGACTTCCCCCGATAGATTTTCAGTAAAAGTGAACGCGCAG                         CTTACAAATGAACCGCACTTTTCACAAGGAATGTTCCATTTCGACTACAGG
genomic: AATCAAGTATGACTT-CACCGATAGATTTTCAGTAAAAGTGAACGCGCAGgtaaatgatg ... ggtgttacagCTTACAAATGAACCGCACTTTTCACAAGGAATGTTCCATTTCGACTACAGG
EST: gi|208370718|gb|DC948255.1|DC948255
EST:     GAATCNAGTATGACTTCACCGATAGATTTTCAGTAAAAGTGAACGCGCAG                         CTTACAAATGAACCGCACTTTTCACAAGGAATGTTCCATTTCGACTACAGG
genomic: GAATCAAGTATGACTTCACCGATAGATTTTCAGTAAAAGTGAACGCGCAGgtaaatgatg ... ggtgttacagCTTACAAATGAACCGCACTTTTCACAAGGAATGTTCCATTTCGACTACAGG
EST: gi|208360525|gb|DC950071.1|DC950071
EST:     GAATCAAGTATGACTTCACCGATAGATTTTCAGTAAAAGTGAACGCGCAG                         CTTACAAATGAACCGCACTTTTCACAAGGAATGTTCCATTTCGACTACAGG
genomic: GAATCAAGTATGACTTCACCGATAGATTTTCAGTAAAAGTGAACGCGCAGgtaaatgatg ... ggtgttacagCTTACAAATGAACCGCACTTTTCACAAGGAATGTTCCATTTCGACTACAGG
EST: gi|18366481|gb|BJ198560.1|BJ198560
EST:     GAATCAAGTATGACTTCACCGATAGATTTTCAGTAAAAGTGAACGCGCAG                         CTTACAAATGAACCGCACTTTTCACAAGGAATGTTCCATTTCGACTACAGG
genomic: GAATCAAGTATGACTTCACCGATAGATTTTCAGTAAAAGTGAACGCGCAGgtaaatgatg ... ggtgttacagCTTACAAATGAACCGCACTTTTCACAAGGAATGTTCCATTTCGACTACAGG
EST: gi|100390127|gb|BY989207.1|BY989207
EST:     GAATCAAGTATGACTTCACCGATAGATTTTCAGTAAAAGTGAACGCGCAG                         CTTACAAATGAACCGCACTTTTCACAAGGAATGTTCCATTTCGACTACGGG
genomic: GAATCAAGTATGACTTCACCGATAGATTTTCAGTAAAAGTGAACGCGCAGgtaaatgatg ... ggtgttacagCTTACAAATGAACCGCACTTTTCACAAGGAATGTTCCATTTCGACTACAGG
EST: gi|162242295|gb|FC418872.1|FC418872
EST:     GAATCAAGTATGACTTCACCGATAGATTTTCAGTAAAAGTGAACGCGCAG                         CTTACAAATGAACCGCACTTTTCACAAGGAATGTTCCATTTCGACTACAGG
genomic: GAATCAAGTATGACTTCACCGATAGATTTTCAGTAAAAGTGAACGCGCAGgtaaatgatg ... ggtgttacagCTTACAAATGAACCGCACTTTTCACAAGGAATGTTCCATTTCGACTACAGG
EST: gi|67575990|gb|BJ948814.1|BJ948814
EST:     GAATCAAGTATGACTTCACCGATAGATTTTCAGTAAAAGTGAACGCGCAG                         CTTACAAATGAACCGCACTTTTCACAAGGAATGTTCCATTTCGACTACAG
genomic: GAATCAAGTATGACTTCACCGATAGATTTTCAGTAAAAGTGAACGCGCAGgtaaatgatg ... ggtgttacagCTTACAAATGAACCGCACTTTTCACAAGGAATGTTCCATTTCGACTACAG
EST: gi|67717560|gb|BJ967819.1|BJ967819
EST:     GAATCAAGTATGACTTCACCGATAGATTTTCAGTAAAAGTGAACGCGCAG                         CTTACAAATGAACCGCACTTTTCACAAGGAATGTTCCATTTCGACTAC
genomic: GAATCAAGTATGACTTCACCGATAGATTTTCAGTAAAAGTGAACGCGCAGgtaaatgatg ... ggtgttacagCTTACAAATGAACCGCACTTTTCACAAGGAATGTTCCATTTCGACTAC
EST: gi|67716961|gb|BJ967220.1|BJ967220
EST:     GAATCAAGTATGACTTCACCGATAGATTTTCAGTAAAAGTGAACGCGCAG                         CTTACAAATGAACCGCACTTTTCACAAGGAATGTTCCATTTCGACTACNGG
genomic: GAATCAAGTATGACTTCACCGATAGATTTTCAGTAAAAGTGAACGCGCAGgtaaatgatg ... ggtgttacagCTTACAAATGAACCGCACTTTTCACAAGGAATGTTCCATTTCGACTACAGG
EST: gi|162242296|gb|FC418873.1|FC418873
EST:     GAATCAAGTATGACTTCACCGATAGATTTTCAGTAAAAGTGAACGCGCAG                         CTTACAAATGAACCGCACTTTTCACAAGGAATGTTCCATTTCGACTACAGG
genomic: GAATCAAGTATGACTTCACCGATAGATTTTCAGTAAAAGTGAACGCGCAGgtaaatgatg ... ggtgttacagCTTACAAATGAACCGCACTTTTCACAAGGAATGTTCCATTTCGACTACAGG
EST: gi|208357650|gb|DC934116.1|DC934116
EST:     GAATCAAGTATGACTTCACCGATAGATTTTCAGTAAAAGTGAACGCGCAG                         CTTACAAATGAACCGCACTTTTCACAAGGAATGTTCCATTTCGACTACAGG
genomic: GAATCAAGTATGACTTCACCGATAGATTTTCAGTAAAAGTGAACGCGCAGgtaaatgatg ... ggtgttacagCTTACAAATGAACCGCACTTTTCACAAGGAATGTTCCATTTCGACTACAGG
EST: gi|162208676|gb|FC385073.1|FC385073
EST:     AATCAAGTATGACTTCACCGATAGATTTTCAGTAAAAGTGAACGCGCAG                         CTTACAAATGAACCGCACTTTTCACAAGGAATGTTCCATTTCGACTACAGG
genomic: AATCAAGTATGACTTCACCGATAGATTTTCAGTAAAAGTGAACGCGCAGgtaaatgatg ... ggtgttacagCTTACAAATGAACCGCACTTTTCACAAGGAATGTTCCATTTCGACTACAGG
EST: gi|67726076|gb|BJ976335.1|BJ976335
EST:     GAATCAAGTATGACTTCACCGATAGATTTTCAGTAAAAGTGAACGCGCAG                         CTTACAAATGAACCGCACTTTTCACAAGGAATGTTCCATTTCGACTACAGG
genomic: GAATCAAGTATGACTTCACCGATAGATTTTCAGTAAAAGTGAACGCGCAGgtaaatgatg ... ggtgttacagCTTACAAATGAACCGCACTTTTCACAAGGAATGTTCCATTTCGACTACAGG
EST: gi|208344796|gb|DC912630.1|DC912630
EST:     GAATCAAGTATGACTTCACCGATAGATTTTCAGTAAAAGTGAACGCGCAG                         CTTACAAATGAACCGCACTTTTCACAAGGAATGTTCCATTTCGACTACAGG
genomic: GAATCAAGTATGACTTCACCGATAGATTTTCAGTAAAAGTGAACGCGCAGgtaaatgatg ... ggtgttacagCTTACAAATGAACCGCACTTTTCACAAGGAATGTTCCATTTCGACTACAGG
EST: gi|208348734|gb|DC926409.1|DC926409
EST:     GAATCAAGTATGACTTCACCGATAGATTTTCAGTAAAAGTGAACGCGCAG                         CTTACAAATGAACCGCACTTTTCACAAGGAATGTTCCATTTCGACTACAGG
genomic: GAATCAAGTATGACTTCACCGATAGATTTTCAGTAAAAGTGAACGCGCAGgtaaatgatg ... ggtgttacagCTTACAAATGAACCGCACTTTTCACAAGGAATGTTCCATTTCGACTACAGG
EST: gi|208374571|gb|DC940760.1|DC940760
EST:     GAATCAAGTATGACTTCACCGATAGATTTTCAGTAAAAGTGAACGCGCAG                         CTTACAAATGAACCGCACTTTTCACAAGGAATGTTCCATTTCGACTACAGG
genomic: GAATCAAGTATGACTTCACCGATAGATTTTCAGTAAAAGTGAACGCGCAGgtaaatgatg ... ggtgttacagCTTACAAATGAACCGCACTTTTCACAAGGAATGTTCCATTTCGACTACAGG
EST: gi|100413081|gb|BY992578.1|BY992578
EST:     GAATCAAGTATGACTTCACCGATAGATTTTCAGTANAAGTGAACGCGCAG                         CTTACAAATGAACCGCACTTTTCACAAGGAATGTTCCATTTCGACTACNGG
genomic: GAATCAAGTATGACTTCACCGATAGATTTTCAGTAAAAGTGAACGCGCAGgtaaatgatg ... ggtgttacagCTTACAAATGAACCGCACTTTTCACAAGGAATGTTCCATTTCGACTACAGG

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: 23 (upstream exon), 13 (downstream exon)
Score: 2

ATGATGATGCTTATTGGGCGTATTTTGACGGACGGTCGTATGAGCGCTCGAATCAAGTATGACTTCACCGATAGATTTTCAGTAAAAGTGAACGCGCAGgtaaatgatg ... ggtgttacagCTTACAAATGAACCGCACTTTTCACAAGGAATGTTCCATTTCGACTACAGG




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcttcttgtcacgtgctgactctaactgcttgcctctttccattggtgttacagCTTACAAATGAACCGCACTTTTCACAAGGAATGTTCCATTTCGACTACAGG
                    ctctaac  putative branch site (score: 2)
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcgtacaagtggcatttgcgctaggaaatacagttatggtgattcttcttcttgtcacgtgctgactctaactgcttgcctctttccattggtgttacagCTTACAAATGAACCGCACTTTTCACAAGGAATGTTCCATTTCGACTACAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA