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

GAAATGCCAAACACTGGGACGGGCCCACAACGAAGTATGTGGAGAACGCCAAGTTTCCCAAGGATGGGTCATCACCCAAATCATTGCGATACATTGGAAGgtactaattcattcaacacccaatctttaaatgaaaatgctcatagcgaacgattggacaggtgaagataaactattatgtagtaaacgtctgatgtttcagaaggcactctacaacactcaagcttttgtggttgaataccgtgttgtggatttttgcttcttcag

Basic information

species Physcomitrella patens
transcript PP1S1_300V6.2
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S1_300V6.2 (Physcomitrella patens), 5'ss of exon 8
lower sequence: LOC_Os01g64660.4 (Oryza sativa), 5'ss of exon 7
GAAATGCCAAACACTGGGACGGGCCCACAACGAAGTATGTGGAGAACGCCAAGTTTCCCAAGGATGGGTCATCACCCAAATCATTGCGATACATTGGAAGgt-actaattcattcaacacccaatctttaaatgaaaatgctcatagcgaacgattggacaggtgaagataaactattatg--tagtaaacgtctgatgtttcagaaggcactctacaacactcaa-gcttttgtggttgaataccgtgttgtggatttttgcttcttcag
                                  || |||||||||   |||||| || |||||||| |||||||| ||||| ||| ||||||||||||||| |  | ||  ||       |||| | || |   |  |     |||  |   || |||    |   ||    || || ||  |  |||| || |    |   || | | | ||  || || | ||   | | |||   | ||  | |  ||  |||||            
----------------------------------GTTTGTGGAGAAGTGCAAGTTCCCTAAGGATGGTTCATCACCTAAATCCTTGAGATACATTGGAAGgtgatcattttttttgggtgacaatgtatata---acctagctgtagttattaataggagcttttttgaccctctgttgtgattcataaaagtttctaat---aggatgtaatcaccaccaattaacattgtagtgacagtattgcttcctgatgatttgcag--------

upper sequence: PP1S1_300V6.2 (Physcomitrella patens), 5'ss of exon 8
lower sequence: Vv18s0072g00770.t01 (Vitis vinifera), 5'ss of exon 9
GAAATGCCAAACACTGGGACGGGCCCACAACGAAGTATGTGGAGAACGCCAAGTTTCCCAAGGATGGGTCATCACCCAAATCATTGCGATACATTGGAAGgtactaattcattcaacacccaatctttaaatgaaaatgctcatagcgaacgattggacaggtgaagataaactattatgtagtaaacgtctgatgtttcagaaggcactctacaacactcaagcttttgtggttgaataccgtgttgtggatttttgcttcttcag
                                  ||||||||| ||   |||||| ||||| ||||| |||||||| |||||  | |||||||||||||||||  |  | | |   || || | | |  |||    |||   ||   ||| ||||       | |  |   || |   |   |  |||     || | |   |                                                                
----------------------------------GTATGTGGAAAAATGCAAGTTCCCCAAAGATGGTTCATCACCAAAATCTCTACGATACATTGGAAGgtatca--tgaattctcaacctaccctacaatatctatgggtatt-tgaatgatttatttcctcactagctaccacagttatgacaacaaaaaatatctacca----------------------------------------------------------------
















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|67694034|gb|BJ954267.1|BJ954267
EST:     AAGTTTCCCAAGGATGGGTCATCACCCAAATCATTGCGATACATTGGAAG                         TATGGTAGCAGACGTCCACAGAACTNTACTTTACGGAGGTATCTTTATGTA
genomic: AAGTTTCCCAAGGATGGGTCATCACCCAAATCATTGCGATACATTGGAAGgtactaattc ... gcttcttcagTATGGTAGCAGACGTCCACAGAACTCTACTTTACGGAGGTATCTTTATGTA
EST: gi|162278601|gb|FC454999.1|FC454999
EST:     AAGTTTCCCAAGGATGGGTCATCACCCAAATCATTGCGATACATTGGAAG                         TATGGTAGCAGACGTCCACAGAACTCTACTTTACGGAGGTATCTTTATGTA
genomic: AAGTTTCCCAAGGATGGGTCATCACCCAAATCATTGCGATACATTGGAAGgtactaattc ... gcttcttcagTATGGTAGCAGACGTCCACAGAACTCTACTTTACGGAGGTATCTTTATGTA
EST: gi|208365212|gb|DC950739.1|DC950739
EST:     AAGTTTCCCAAGGATGGGTCATCACCCAAATCATTGCGATACATTGGAAG                         TATGGTAGCAGACGTCCACAGAACTCTACTTTACGGAGGTATCTTTATGTA
genomic: AAGTTTCCCAAGGATGGGTCATCACCCAAATCATTGCGATACATTGGAAGgtactaattc ... gcttcttcagTATGGTAGCAGACGTCCACAGAACTCTACTTTACGGAGGTATCTTTATGTA
EST: gi|162193915|gb|FC371728.1|FC371728
EST:     AAGTTTCCCAAGGATGGGTCATCACCCAAATCATTGCGATACATTGGAAG                         TATGGTAGCAGACGTCCACAGAACTCTACTTTACGGAGGTATCTTTATGTA
genomic: AAGTTTCCCAAGGATGGGTCATCACCCAAATCATTGCGATACATTGGAAGgtactaattc ... gcttcttcagTATGGTAGCAGACGTCCACAGAACTCTACTTTACGGAGGTATCTTTATGTA
EST: gi|162171403|gb|FC346678.1|FC346678
EST:     AAGTTTCCCAAGGATGGGTCATCACCCAAATCATTGCGATACATTGGAAG                         TATGGTAGCAGACGTCCACAGAACTCTACTTTACGGAGGTATCTTTATGTA
genomic: AAGTTTCCCAAGGATGGGTCATCACCCAAATCATTGCGATACATTGGAAGgtactaattc ... gcttcttcagTATGGTAGCAGACGTCCACAGAACTCTACTTTACGGAGGTATCTTTATGTA
EST: gi|208378504|gb|DC927201.1|DC927201
EST:     AAGTTTCCCAAGGATGGGTCATCACCCAAATCATTGCGATACATTGGAAG                         TATGGTAGCAGACGTCCACAGAACTCTACTTTATGGAGGTATCTTTATGTA
genomic: AAGTTTCCCAAGGATGGGTCATCACCCAAATCATTGCGATACATTGGAAGgtactaattc ... gcttcttcagTATGGTAGCAGACGTCCACAGAACTCTACTTTACGGAGGTATCTTTATGTA
EST: gi|208396143|gb|DC924609.1|DC924609
EST:     AAGTTTCCCAAGGATGGGTCATCACCCAAATCATTGCGATACATTGGAAG                         TATGGTAGCAGACGTCCACAGAACTCTACTTTACGGAGGTATCTTTATGTA
genomic: AAGTTTCCCAAGGATGGGTCATCACCCAAATCATTGCGATACATTGGAAGgtactaattc ... gcttcttcagTATGGTAGCAGACGTCCACAGAACTCTACTTTACGGAGGTATCTTTATGTA
EST: gi|208348185|gb|DC920976.1|DC920976
EST:     AAGTTTCCCAAGGATGGGTCATCACCCAAATCATTGCGATACATTGGAAG                         TATGGTAGCAGACGTCCACAGAACTCTACTTTACGGAGGTATCTTTATGTA
genomic: AAGTTTCCCAAGGATGGGTCATCACCCAAATCATTGCGATACATTGGAAGgtactaattc ... gcttcttcagTATGGTAGCAGACGTCCACAGAACTCTACTTTACGGAGGTATCTTTATGTA
EST: gi|162152140|gb|FC328730.1|FC328730
EST:     AAGTTTCCCAAGGATGGGTCATCACCCAAATCATTGCGATACATTGGAAG                         TATGGTAGCAGACGTCCACAGAACTCTACTTTACGGAGGTATCTTTATGTA
genomic: AAGTTTCCCAAGGATGGGTCATCACCCAAATCATTGCGATACATTGGAAGgtactaattc ... gcttcttcagTATGGTAGCAGACGTCCACAGAACTCTACTTTACGGAGGTATCTTTATGTA
EST: gi|18333622|gb|BJ165637.1|BJ165637
EST:     AAGTTTCCCAAGGATGGGTCATCACCCAAATCATTGCGATACATTGGAAG                         TATGGTAGCAGACGTCCACAGAACTCTACTTTACGGAGGTATCTTTATGTA
genomic: AAGTTTCCCAAGGATGGGTCATCACCCAAATCATTGCGATACATTGGAAGgtactaattc ... gcttcttcagTATGGTAGCAGACGTCCACAGAACTCTACTTTACGGAGGTATCTTTATGTA
EST: gi|208394809|gb|DC920152.1|DC920152
EST:     AAGTTTCCCAAGGATGGGTCATCACCCAAATCATTGCGATACATTGGAAG                         TATGGTAGCAGACGTCCACAGAACTCTACTTTACGGAGATATCTTTATGTA
genomic: AAGTTTCCCAAGGATGGGTCATCACCCAAATCATTGCGATACATTGGAAGgtactaattc ... gcttcttcagTATGGTAGCAGACGTCCACAGAACTCTACTTTACGGAGGTATCTTTATGTA
EST: gi|37834323|gb|BJ592335.1|BJ592335
EST:     AAGTTTCCCAAGGATGGGTCATCACCCAAATCATTGCGATACATTGGAAG                         TATGGTAGCAGACGTCCACAGAACTCTACTTTACGGAGGTATCTTTATGTA
genomic: AAGTTTCCCAAGGATGGGTCATCACCCAAATCATTGCGATACATTGGAAGgtactaattc ... gcttcttcagTATGGTAGCAGACGTCCACAGAACTCTACTTTACGGAGGTATCTTTATGTA
EST: gi|208352801|gb|DC917765.1|DC917765
EST:     AAGTTTCCCAAGGATGGGTCATCACCCAAATCATTGCGATACATTGGAAG                         TATGGTAGCAGACGTCCACAGAACTCTACTTTACGGAGGTATCTTTATGTA
genomic: AAGTTTCCCAAGGATGGGTCATCACCCAAATCATTGCGATACATTGGAAGgtactaattc ... gcttcttcagTATGGTAGCAGACGTCCACAGAACTCTACTTTACGGAGGTATCTTTATGTA
EST: gi|208385201|gb|DC923581.1|DC923581
EST:     AAGTTTCCCAAGGATGGGTCATCACCCAAATCATTGCGATACATTGGAAG                         TATGGTAGCAGACGTCCACAGAACTCTACTTTACGGAGGTATCTTTATGTA
genomic: AAGTTTCCCAAGGATGGGTCATCACCCAAATCATTGCGATACATTGGAAGgtactaattc ... gcttcttcagTATGGTAGCAGACGTCCACAGAACTCTACTTTACGGAGGTATCTTTATGTA
EST: gi|208352520|gb|DC918229.1|DC918229
EST:     AAGTTTCCCAAGGATGGGTCATCACCCAAATCATTGCGATACATTGGAAG                         TATGGTAGCAGACGTCCACAGAACTCTACTTTACGGAGGTATCTTTATGTA
genomic: AAGTTTCCCAAGGATGGGTCATCACCCAAATCATTGCGATACATTGGAAGgtactaattc ... gcttcttcagTATGGTAGCAGACGTCCACAGAACTCTACTTTACGGAGGTATCTTTATGTA
EST: gi|162171402|gb|FC346677.1|FC346677
EST:     AAGTTTCCCAAGGATGGGTCATCACCCAAATCATTGCGATACATTGGAAG                         TATGGTAGCAGACGTCCACAGAACTCTACTTTACGGAGGTATCTTTATGTA
genomic: AAGTTTCCCAAGGATGGGTCATCACCCAAATCATTGCGATACATTGGAAGgtactaattc ... gcttcttcagTATGGTAGCAGACGTCCACAGAACTCTACTTTACGGAGGTATCTTTATGTA
EST: gi|208398545|gb|DC916516.1|DC916516
EST:     AAGTTTCCCAAGGATGGGTCATCACCCAAATCATTGCGATACATTGGAAG                         TATGGTAGCAGACGTCCACAGAACTCTACTTTACGGAGGTATCTTTATGTA
genomic: AAGTTTCCCAAGGATGGGTCATCACCCAAATCATTGCGATACATTGGAAGgtactaattc ... gcttcttcagTATGGTAGCAGACGTCCACAGAACTCTACTTTACGGAGGTATCTTTATGTA
EST: gi|208358947|gb|DC946376.1|DC946376
EST:     AAGTTTCCCAAGGATGGGTCATCACCCAAATCATTGCGATACATTGGAAG                         TATGGTAGCAGACGTCCACAGAACTCTACTTTACGGAGGTATCTTTATGTA
genomic: AAGTTTCCCAAGGATGGGTCATCACCCAAATCATTGCGATACATTGGAAGgtactaattc ... gcttcttcagTATGGTAGCAGACGTCCACAGAACTCTACTTTACGGAGGTATCTTTATGTA
EST: gi|18338549|gb|BJ170573.1|BJ170573
EST:     AAGTTTCCCAAGGATGGGTCATCACCCAAATCATTGCGATACATTGGAAG                         TATGGTAGCAGACGTCCACAGAACTCTACTTTACGGAGGTATCTTTATGTA
genomic: AAGTTTCCCAAGGATGGGTCATCACCCAAATCATTGCGATACATTGGAAGgtactaattc ... gcttcttcagTATGGTAGCAGACGTCCACAGAACTCTACTTTACGGAGGTATCTTTATGTA
EST: gi|162278600|gb|FC454998.1|FC454998
EST:     AAGTTTCCCAAGGATGGGTCATCACCCAAATCATTGCGATACATTGGAAG                         TATGGTAGCAGACGTCCACAGAACTTTACTTTACGGAGGTATCTTTATGTA
genomic: AAGTTTCCCAAGGATGGGTCATCACCCAAATCATTGCGATACATTGGAAGgtactaattc ... gcttcttcagTATGGTAGCAGACGTCCACAGAACTCTACTTTACGGAGGTATCTTTATGTA
EST: gi|208349119|gb|DC925902.1|DC925902
EST:     AAGTTTCCCAAGGATGGGTCATCACCCAAATCATTGCGATACATTGGAAG                         TATGGTAGCAGACGTCCACAGAACTCTACTTTACGGAGGTATCTTTATGTA
genomic: AAGTTTCCCAAGGATGGGTCATCACCCAAATCATTGCGATACATTGGAAGgtactaattc ... gcttcttcagTATGGTAGCAGACGTCCACAGAACTCTACTTTACGGAGGTATCTTTATGTA
EST: gi|67694190|gb|BJ954423.1|BJ954423
EST:     TGCGATACA-TGGAAG                         TATGGTAGCAGACGTCCACAGAACTCTACTTTACGGAGGTATCTTTATGTA
genomic: TGCGATACATTGGAAGgtactaattc ... gcttcttcagTATGGTAGCAGACGTCCACAGAACTCTACTTTACGGAGGTATCTTTATGTA

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: 26

GAAATGCCAAACACTGGGACGGGCCCACAACGAAGTATGTGGAGAACGCCAAGTTTCCCAAGGATGGGTCATCACCCAAATCATTGCGATACATTGGAAGgtactaattc ... gcttcttcagTATGGTAGCAGACGTCCACAGAACTCTACTTTACGGAGGTATCTTTATGTACCCTGGTGACAAGAAAAGCCCCAAAGGAAAGCTCAG




<











<


<









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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAAATGCCAAACACTGGGACGGGCCCACAACGAAGTATGTGGAGAACGCCAAGTTTCCCAAGGATGGGTCATCACCCAAATCATTGCGATACATTGGAAGgtactaattcattcaacacccaatctttaaatgaaaatgctcatagcgaacgattggacaggtgaagataaactattatgtagtaaacgtctgatgtttcagaaggcactctacaacactcaagcttttgtggttgaataccgtgttgtggatttttgcttcttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG