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

TCGGGGAGTCACATGGCGGAGGAGTCGGGTGCATTATTGATGGATGCCCTCCCCGGTTGCCTCTTTCGGAAGAAGATATGCAAATCGACCTTGACAGAAGgtgaccttgcttccagacctgtatttggcgttctgttgagttcaggatctcatgtaggggctcacgctactgccctgggtaacagcgtaaaaagaatgtc...

Basic information

species Physcomitrella patens
transcript PP1S28_168V6.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S28_168V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: GLYMA20G31980.1 (Glycine max), 5'ss of exon 2
TCGGGGAGTCACATGGCGGAGGAGTCGGGTGCATTATTGATGGATGCCCTCCCCGGTTGCCTCTTTCGGAAGAAGATATGCAAATCGACCTTGACAGAAGgtgaccttgcttccagacctgtatttggcgttctgttgagttcaggatctcatgt-aggggctcacgctac-tgccctgggtaacagcgtaaaaagaatgtc
  ||||| |||||||| ||||| || || ||  ||||||||||||| ||||| ||  | ||||| || ||||  ||||||||| | || ||||||||||||||   |||| ||   |    | | |     |   ||||  |     | |  ||  ||     |||  |    |     |  ||   | | | | ||  || 
ATGGGGAATCACATGGAGGAGGTGTTGGTTGTGTTATTGATGGATGTCCTCCTCGCCTTCCTCTCTCTGAAGCTGATATGCAAGTGGATCTTGACAGAAGgtg--tttgcctctgaaatcatctctttatcttcattgaactacttgtattgtgggagaaaaacactttggacgttgaagagaaatactttataggatagtt
















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|100446747|gb|CJ971046.1|CJ971046
EST:     CCCCGGTTGCCTCTTTCGGAANAAGATATGCAAATCGACCTTGACAGAAG                         GAGGCCAGGGCAGAGCAGAATTACAACCCCTCGGANTGAAACAGACACTTG
genomic: CCCCGGTTGCCTCTTTCGGAAGAAGATATGCAAATCGACCTTGACAGAAGgtgaccttgc ... gctttcacagGAGGCCAGGGCAGAGCAGAATTACAACCCCTCGGAGTGAAACAGACACTTG
EST: gi|208358357|gb|DC934550.1|DC934550
EST:     CCCCGGTTGCCTCTTTCGGAAGAAGATATGCAAATCGACCTTGACAGAAG                         GAGGCCAGGGCAGAGCAGAATTACAACCCCTCGGAGTGAAACAGACACTTG
genomic: CCCCGGTTGCCTCTTTCGGAAGAAGATATGCAAATCGACCTTGACAGAAGgtgaccttgc ... gctttcacagGAGGCCAGGGCAGAGCAGAATTACAACCCCTCGGAGTGAAACAGACACTTG
EST: gi|208390477|gb|DC933734.1|DC933734
EST:     TTGCCTCTTTCGGAAGAAGATATGCAAATCGACCTTGACAGAAG                         GAGGCCAGGGCAGAGCAGAATTACAACCCCTCGGAGTGAAACAGACACTTG
genomic: TTGCCTCTTTCGGAAGAAGATATGCAAATCGACCTTGACAGAAGgtgaccttgc ... gctttcacagGAGGCCAGGGCAGAGCAGAATTACAACCCCTCGGAGTGAAACAGACACTTG
EST: gi|18347517|gb|BJ179564.1|BJ179564
EST:     CCCCGGTTGCCTCTTTCGGAAGAAGATATGCAAATCGACCTTGACAGAAG                         GAGGCCAGGGCAGAGCA
genomic: CCCCGGTTGCCTCTTTCGGAAGAAGATATGCAAATCGACCTTGACAGAAGgtgaccttgc ... gctttcacagGAGGCCAGGGCAGAGCA
EST: gi|67508161|gb|BJ941032.1|BJ941032
EST:     CCCCGGTTGCCTCTTTCGGAAGAAGATATGCAAATCGACCTTGACAGAAG                         GAGGCCAGGGCAGAGCAGAATTACAACCCCTCGGAGTGAAACAGACACTTG
genomic: CCCCGGTTGCCTCTTTCGGAAGAAGATATGCAAATCGACCTTGACAGAAGgtgaccttgc ... gctttcacagGAGGCCAGGGCAGAGCAGAATTACAACCCCTCGGAGTGAAACAGACACTTG
EST: gi|18343114|gb|BJ175152.1|BJ175152
EST:     CCCCGGTTGCCTCTTTCGGAAGAAGATATGCAAATCGACCTTGACAGAAG                         GAGGCCAGGGCANAGCANAATTACAACCCCTCGGAGTGAAACAGACACTTG
genomic: CCCCGGTTGCCTCTTTCGGAAGAAGATATGCAAATCGACCTTGACAGAAGgtgaccttgc ... gctttcacagGAGGCCAGGGCAGAGCAGAATTACAACCCCTCGGAGTGAAACAGACACTTG
EST: gi|162159689|gb|FC336075.1|FC336075
EST:     CCCCGGTTGCCTCTTTCGGAAGAAGATATGCAAATCGACCTTGACAGAAG                         GAGGCCAGGGCAGAGCAGAATTACAACCCCTCGGAGTGAAACAGACACTTG
genomic: CCCCGGTTGCCTCTTTCGGAAGAAGATATGCAAATCGACCTTGACAGAAGgtgaccttgc ... gctttcacagGAGGCCAGGGCAGAGCAGAATTACAACCCCTCGGAGTGAAACAGACACTTG
EST: gi|162189601|gb|FC365823.1|FC365823
EST:     CCCCGGTTGCCTCTTTCGGAAGAAGATATGCAAATCGACCTTGACAGAAG                         GAGGCCAGGGCAGAGCAGAATTACAACCCCTCGGAGTGAAACAGACACTTG
genomic: CCCCGGTTGCCTCTTTCGGAAGAAGATATGCAAATCGACCTTGACAGAAGgtgaccttgc ... gctttcacagGAGGCCAGGGCAGAGCAGAATTACAACCCCTCGGAGTGAAACAGACACTTG
EST: gi|67572551|gb|BJ945375.1|BJ945375
EST:     CCCCGGTTGCCTCTTTCGGAAGAAGATATGCAAATCGACCTTGACAGAAG                         GAGGCCAGGGCAGAGCAGAATTACAACCCCTCGGAGTGAAACAGACACTTG
genomic: CCCCGGTTGCCTCTTTCGGAAGAAGATATGCAAATCGACCTTGACAGAAGgtgaccttgc ... gctttcacagGAGGCCAGGGCAGAGCAGAATTACAACCCCTCGGAGTGAAACAGACACTTG
EST: gi|100439543|gb|BY961986.1|BY961986
EST:     CCCCGGTTGCCTCTTTCGGAAGAAGATATGCAAATCGACCTTGACAGAAG                         GAGGCCAGGGCAGAGCAGAATTACAACCCCTCGGAGTGAAACAGACACTTG
genomic: CCCCGGTTGCCTCTTTCGGAAGAAGATATGCAAATCGACCTTGACAGAAGgtgaccttgc ... gctttcacagGAGGCCAGGGCAGAGCAGAATTACAACCCCTCGGAGTGAAACAGACACTTG
EST: gi|67508549|gb|BJ941412.1|BJ941412
EST:     CCCCGGTTGCCTCTTTCGGAAGAAGATATGCAAATCGACCTTGACAGAAG                         GAGGCCAGGGCAGAGCAGAATTACAACCCCTCGGAGTGAAACAGACACTTG
genomic: CCCCGGTTGCCTCTTTCGGAAGAAGATATGCAAATCGACCTTGACAGAAGgtgaccttgc ... gctttcacagGAGGCCAGGGCAGAGCAGAATTACAACCCCTCGGAGTGAAACAGACACTTG
EST: gi|162152501|gb|FC328779.1|FC328779
EST:     CCCCGGTTGCCTCTTTCGGAAGAAGATATGCAAATCGACCTTGACAGAAG                         GAGGCCAGGGCAGAGCAGAATTACAACCCCTCGGAGTGAAACAGACACTTG
genomic: CCCCGGTTGCCTCTTTCGGAAGAAGATATGCAAATCGACCTTGACAGAAGgtgaccttgc ... gctttcacagGAGGCCAGGGCAGAGCAGAATTACAACCCCTCGGAGTGAAACAGACACTTG
EST: gi|162188362|gb|FC364232.1|FC364232
EST:     CCCCGGTTGCCTCTTTCGGAAGAAGATATGCAAATCGACCTTGACAGAAG                         GAGGCCAGGGCAGAGCAGAATTACAACCCCTCGGAGTGAAACAGACACTTG
genomic: CCCCGGTTGCCTCTTTCGGAAGAAGATATGCAAATCGACCTTGACAGAAGgtgaccttgc ... gctttcacagGAGGCCAGGGCAGAGCAGAATTACAACCCCTCGGAGTGAAACAGACACTTG

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), 35 (downstream exon)
Score: 11

TCGGGGAGTCACATGGCGGAGGAGTCGGGTGCATTATTGATGGATGCCCTCCCCGGTTGCCTCTTTCGGAAGAAGATATGCAAATCGACCTTGACAGAAGgtgaccttgc ... gctttcacagGAGGCCAGGGCAGAGCAGAATTACAACCCCTCGGAGTGAAACAGACACTTGCAAAATTCTTTCAGGCGTTGGAAACG




<











<


<









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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCGGGGAGTCACATGGCGGAGGAGTCGGGTGCATTATTGATGGATGCCCTCCCCGGTTGCCTCTTTCGGAAGAAGATATGCAAATCGACCTTGACAGAAGgtgaccttgcttccagacctgtatttggcgttctgttgagttcaggatctcatgtaggggctcacgctactgccctgggtaacagcgtaaaaagaatgtc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaaagaa