Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...accataaaatattgccacgagcgttgcataaatttctgcatcgaatggcgttttcagtggagcatttcataatttgtagtttggttttgtactcatgcagCTAGCGGCAGAATACTCAGAATGTCCATCAGGCAAGAAAGGAGGAGACCTCGGGTGGTTTCCTCGTGGCAAGATGGCTGGACCTTTCCAGGAGGTGGCCT

Basic information

species Physcomitrella patens
transcript PP1S217_91V6.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S217_91V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: LOC_Os09g24540.1 (Oryza sativa), 3'ss of exon 2
acca-taaaatattgccacgagcgttgcataaatttctgcatcgaatggcgttttcagtggagcatttcataatttg--tagt-ttggttttgtactcatgcagCTAGCGGCAGAATACTCAGAATGTCCATCAGGCAAGAAAGGAGGAGACCTCGGGTGGTTTCCTCGTGGCAAGATGGCTGGACCTTTCCAGGAGGTGGCCT
 ||| | | || ||||     ||  |   ||   |   ||  |            |     |  || |    ||  |  |  | ||  | || |  |  ||||| ||||   ||||||||| ||||||||||| || |||||||| ||||| || || ||||| || ||||| || |||||||| ||||| ||||| || || |
-ccacttacatgttgctt---gctgtctgtaggctcaggctgctttcataacccactagacactatgtatatatccgactgatattactattttgatactgcagATAGCCCAAGAATACTCTGAATGTCCATCTGGAAAGAAAGGTGGAGATCTTGGATGGTTCCCGCGTGGAAAAATGGCTGGCCCTTTTCAGGATGTTGCAT

upper sequence: PP1S217_91V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GRMZM2G048277_T03 (Zea mays), 3'ss of exon 2
---accataaaatattgccacga-gcgttgcataaatttctgcatcgaatggcgttttcagtggagcatttcataatttgtagtttggttttgtactcatgcagCTAGCGGCAGAATACTCAGAATGTCCATCAGGCAAGAAAGGAGGAGACCTCGGGTGGTTTCCTCGTGGCAAGATGGCTGGACCTTTCCAGGAGGTGGCCT
      |  || || | |  ||| |  || |  | |||| |    | | |      | |  ||  |    | |||  |  |   ||  |||| |   | | ||| ||||   ||| || || ||||| |||||||| |||||||| ||||| || || ||||| || ||||||||||||||||| |||||||||||||| || |
aatctgactaactacttcgtcgaagtttttctcatattttttgtgccattattagataccatgatga---taatagatcctgactttattttttgtac-tacagGTAGCACAAGAGTATTCTGAATGCCCATCAGGGAAGAAAGGTGGAGATCTTGGTTGGTTCCCGCGTGGCAAGATGGCTGGTCCTTTCCAGGAGGTTGCTT

upper sequence: PP1S217_91V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GLYMA06G21080.1 (Glycine max), 3'ss of exon 3
accataaaatattgccacgagcg---ttgcataaatttctgcatcgaatggcgttttcagtggagcatttcataatttgtagtttggttttgtactcatgcagCTAGCGGCAGAATACTCAGAATGTCCATCAGGCAAGAAAGGAGGAGACCTCGGGTGGTTTCCTCGTGGCAAGATGGCTGGACCTTTCCAGGAGGTGGCCT
     |||  ||    | ||      |  | | || ||   |     |     | ||  ||  |     | || ||   |||| |     ||   |||  ||| ||||   ||| || ||||||||||||||||| ||||| || |||||||| || |||||||| || || ||||||||||| || || ||||| || ||||
-ttgaaaaggataaataagaatctgttcacttgaaattaacctagagacaaaatattttgtccaattggttattatcaatagtatttcactgacttca--cagGTAGCACAAGAGTATTCAGAATGTCCATCAGGAAAGAAGGGTGGAGACCTTGGATGGTTTCCCCGAGGAAAGATGGCTGGGCCATTTCAGGAAGTTGCCT

upper sequence: PP1S217_91V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GLYMA04G33180.2 (Glycine max), 3'ss of exon 3
-----accataaaatattgccacgagcgttgcataaatttctgcatcgaatggcgttttcagtggagcatttcataatttgtagtttggttttgtactcatgcagCTAGCGGCAGAATACTCAGAATGTCCATCAGGCAAGAAAGGAGGAGACCTCGGGTGGTTTCCTCGTGGCAAGATGGCTGGACCTTTCCAGGAGGTGGCCT
     |  |||||  |    |  |  | ||  |  |||   |  |  ||    | ||||   |  |   | |  | ||   ||  ||     ||   |||  ||| ||||   ||| || ||||||||||| ||||| ||||| || |||||||| || |||||||| || || ||||||||||| || || ||||| || ||||
ttgaaaggataaataagaatctggttcatttga--aatcaatctagagacaaacatttttt-tccaatttgttgttatcaataacttttcactgacttca--cagATAGCTCAAGAGTATTCAGAATGTCCTTCAGGAAAGAAGGGTGGAGACCTTGGATGGTTTCCCCGAGGAAAGATGGCTGGGCCATTTCAGGATGTTGCCT

upper sequence: PP1S217_91V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: AT1G26550.1 (Arabidopsis thaliana), 3'ss of exon 3
---accataaaatattgccacgagcgttgcataaatttctgcat-cgaatggcgttttcagtggagcatttcataatttgtagtttggttttgtactcatgcagCTAGCGGCAGAATACTCAGAATGTCCATCAGGCAAGAAAGGAGGAGACCTCGGGTGGTTTCCTCGTGGCAAGATGGCTGGACCTTTCCAGGAGGTGGCCT
   | |   || | |        | |||  ||| |||||   |   |  ||   |     |||||| || |  |||   | | ||  || | | ||     ||| | || ||||| ||||| || ||||||||||| || ||||||||||| || || ||||| ||||| || |||||||| || || ||||| || || ||||
gacatctacaagtttcagttttcg-gttagatatatttcgatagatgtgtgttatgaattgtggagaatct--taacacg-atttgtgtgtggaacgatctcagATTGCAGCAGAGTACTCTGAGTGTCCATCAGGGAAAAAAGGAGGAGATCTTGGATGGTTCCCTCGAGGAAAGATGGCAGGTCCATTCCAAGATGTCGCCT

upper sequence: PP1S217_91V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: Vv17s0000g06430.t01 (Vitis vinifera), 3'ss of exon 3
accataaaatattgccacgagcgttgcataaatttctgcatcga---atggcgttttcagtggagcatttcataatttgtagtttggttt-tgtactcatgcagCTAGCGGCAGAATACTCAGAATGTCCATCAGGCAAGAAAGGAGGAGACCTCGGGTGGTTTCCTCGTGGCAAGATGGCTGGACCTTTCCAGGAGGTGGCCT
  |   | | ||  |||    | |  ||  || |        ||   |      | |   |||||  |    | ||   || |||  ||  | || |    |||||||| |||||||| ||||||||||||||||| ||||| || || ||||| || |||||||| ||||||||||||||||| || || ||||| || ||||
--ctgcatacatctccatct-catcacactaactgaaaagaagatagaaaattctcttcttggagt-tcctgtgataattatttttcttcctttattttctcagCTAGCAGCAGAATATTCAGAATGTCCATCAGGGAAGAAGGGTGGTGACCTTGGATGGTTTCCGCGTGGCAAGATGGCTGGTCCATTTCAGGATGTTGCCT

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|162222778|gb|FC399032.1|FC399032
EST:     GTGGAGATAAAGTTCCACCAGCTGAGTTCGCGAAG                         CTAGCGGCAGAATACTCAGAATGTCCATCAGGCAAGAAAGGAGGAGACCTC
genomic: GTGGAGATAAAGTTCCACCAGCTGAGTTCGCGAAGgttaatgcta ... actcatgcagCTAGCGGCAGAATACTCAGAATGTCCATCAGGCAAGAAAGGAGGAGACCTC
EST: gi|162239202|gb|FC416484.1|FC416484
EST:     AGGGATGGCTCGATAGTGGAGATAAAGTTCCACCAGCTGAGTTCGCGAAG                         CTAGCGGCAGAATACTCAGAATGTCCATCAGGCAAGAAAGGAGGAGACCTC
genomic: AGGGATGGCTCGATAGTGGAGATAAAGTTCCACCAGCTGAGTTCGCGAAGgttaatgcta ... actcatgcagCTAGCGGCAGAATACTCAGAATGTCCATCAGGCAAGAAAGGAGGAGACCTC
EST: gi|18372342|gb|BJ203944.1|BJ203944
EST:     AGGGATGGCTCGATAGTGGAGATAAAGTTCCACCAGCTGAGTTCGCGAAG                         CTAGCGGCAGAATACTCAGAATGTCCATCAGGCAAGAAAGGAGGAGACCTC
genomic: AGGGATGGCTCGATAGTGGAGATAAAGTTCCACCAGCTGAGTTCGCGAAGgttaatgcta ... actcatgcagCTAGCGGCAGAATACTCAGAATGTCCATCAGGCAAGAAAGGAGGAGACCTC
EST: gi|37821957|gb|BJ580023.1|BJ580023
EST:     AGGGATGGCTCGATAGTGGAGATAAAGTTCCACCAGCTGAGTTCGCGAAG                         CTAGCGGCAGAATACTCAGAATGTCCATCAGGCAAGAAAGGAGGAGACCTC
genomic: AGGGATGGCTCGATAGTGGAGATAAAGTTCCACCAGCTGAGTTCGCGAAGgttaatgcta ... actcatgcagCTAGCGGCAGAATACTCAGAATGTCCATCAGGCAAGAAAGGAGGAGACCTC
EST: gi|18325545|gb|BJ157542.1|BJ157542
EST:     AGGGATGGCTCGATAGTGGAGATAAAGTTCCACCAGCTGAGTTCGCGAAG                         CTAGCGGCAGAATACTCAGAATGTCCATCAGGCAAGAAAGGAGGAGACCTC
genomic: AGGGATGGCTCGATAGTGGAGATAAAGTTCCACCAGCTGAGTTCGCGAAGgttaatgcta ... actcatgcagCTAGCGGCAGAATACTCAGAATGTCCATCAGGCAAGAAAGGAGGAGACCTC
EST: gi|162223114|gb|FC399693.1|FC399693
EST:     AGGGATGGCTCGATAGTGGAGATAAAGTTCCACCAGCTGAGTTCGCGAAG                         CTAGCGGCAGAATACTCAGAATGTCCATCAGGCAAGAAAGGAGGAGACCTC
genomic: AGGGATGGCTCGATAGTGGAGATAAAGTTCCACCAGCTGAGTTCGCGAAGgttaatgcta ... actcatgcagCTAGCGGCAGAATACTCAGAATGTCCATCAGGCAAGAAAGGAGGAGACCTC
EST: gi|37850127|gb|BJ608135.1|BJ608135
EST:     AGGGATGGCTCGATAGTGGAGATAAAGTTCCACCAGCTGAGTTCGCGAAG                         CTAGCGGCAGAATACTCAGAATGTCCATCAGGCAAGAAAGGAGGAGACCTC
genomic: AGGGATGGCTCGATAGTGGAGATAAAGTTCCACCAGCTGAGTTCGCGAAGgttaatgcta ... actcatgcagCTAGCGGCAGAATACTCAGAATGTCCATCAGGCAAGAAAGGAGGAGACCTC
EST: gi|162227771|gb|FC402387.1|FC402387
EST:     AGGGATGGCTCGATAGTGGAGATAAAGTTCCACCAGCTGAGTTCGCGAAG                         CTAGCGGCAGAATACTCAGAATGTCCATCAGGCAAGAAAGGAGGAGACCTC
genomic: AGGGATGGCTCGATAGTGGAGATAAAGTTCCACCAGCTGAGTTCGCGAAGgttaatgcta ... actcatgcagCTAGCGGCAGAATACTCAGAATGTCCATCAGGCAAGAAAGGAGGAGACCTC
EST: gi|18368840|gb|BJ200925.1|BJ200925
EST:     AGGGATGGCTCGATAGTGGAGATAAAGTTCCACCAGCTGAGTTCGCGAAG                         CTAGCGGCAGAATACTCAGAATGTCCATCAGGCAAGAAAGGAGGAGACCTC
genomic: AGGGATGGCTCGATAGTGGAGATAAAGTTCCACCAGCTGAGTTCGCGAAGgttaatgcta ... actcatgcagCTAGCGGCAGAATACTCAGAATGTCCATCAGGCAAGAAAGGAGGAGACCTC
EST: gi|37852029|gb|BJ610037.1|BJ610037
EST:     AGGGATGGCTCGATAGTGGAGATAAAGTTCCACCAGCTGAGTTCGCGAAG                         CTAGCGGCAGAATACTCAGAATGTCCATCAGGCAAGAAAGGAGGAGACCTC
genomic: AGGGATGGCTCGATAGTGGAGATAAAGTTCCACCAGCTGAGTTCGCGAAGgttaatgcta ... actcatgcagCTAGCGGCAGAATACTCAGAATGTCCATCAGGCAAGAAAGGAGGAGACCTC
EST: gi|162233101|gb|FC408508.1|FC408508
EST:     AGGGATGGCTCGATAGTGGAGATAAAGTTCCACCAGCTGAGTTCGCGAAG                         CTAGCGGCAGAATACTCAGAATGTCCATCAGGCAAGAAAGGAGGAGACCTC
genomic: AGGGATGGCTCGATAGTGGAGATAAAGTTCCACCAGCTGAGTTCGCGAAGgttaatgcta ... actcatgcagCTAGCGGCAGAATACTCAGAATGTCCATCAGGCAAGAAAGGAGGAGACCTC
EST: gi|18333507|gb|BJ165522.1|BJ165522
EST:     GAGATAAAGTTCCACCAGCTGAGTTCGCGAAG                         CTAGCGGCAGAATACTCAGAATGTCCATCAGGCAAGAAAGGAGGAGACCTC
genomic: GAGATAAAGTTCCACCAGCTGAGTTCGCGAAGgttaatgcta ... actcatgcagCTAGCGGCAGAATACTCAGAATGTCCATCAGGCAAGAAAGGAGGAGACCTC
EST: gi|18372510|gb|BJ204112.1|BJ204112
EST:     AGGGATGGCTCGATAGTGGAGATAAAGTTCCACCAGCTGAGTTCGCGAAG                         CTAGCGGCAGAATACTCAGAATGTCCATCAGGCAAGAAAGGAGGAGACCTC
genomic: AGGGATGGCTCGATAGTGGAGATAAAGTTCCACCAGCTGAGTTCGCGAAGgttaatgcta ... actcatgcagCTAGCGGCAGAATACTCAGAATGTCCATCAGGCAAGAAAGGAGGAGACCTC
EST: gi|162233100|gb|FC408507.1|FC408507
EST:     AGGGATGGCTCGATAGTGGAGATAAAGTTCCACCAGCTGAGTTCGCGAAG                         CTAGCGGCAGAATACTCAGAATGTCCATCAGGCAAGAAAGGAGGAGACCTC
genomic: AGGGATGGCTCGATAGTGGAGATAAAGTTCCACCAGCTGAGTTCGCGAAGgttaatgcta ... actcatgcagCTAGCGGCAGAATACTCAGAATGTCCATCAGGCAAGAAAGGAGGAGACCTC
EST: gi|162227772|gb|FC402388.1|FC402388
EST:     AGGGATGGCTCGATAGTGGAGATAAAGTTCCACCAGCTGAGTTCGCGAAG                         CTAGCGGCAGAATACTCAGAATGTCCATCAGGCAAGAAAGGAGGAGACCTC
genomic: AGGGATGGCTCGATAGTGGAGATAAAGTTCCACCAGCTGAGTTCGCGAAGgttaatgcta ... actcatgcagCTAGCGGCAGAATACTCAGAATGTCCATCAGGCAAGAAAGGAGGAGACCTC
EST: gi|37834706|gb|BJ592718.1|BJ592718
EST:     AGGGATGGCTCGATAGTGGAGATAAAGTTCCACCAGCTGAGTTCGCGAAG                         CTAGCGGCAGAATACTCAGAATGTCCATCAGGCAAGAAAGGAGGAGACCTC
genomic: AGGGATGGCTCGATAGTGGAGATAAAGTTCCACCAGCTGAGTTCGCGAAGgttaatgcta ... actcatgcagCTAGCGGCAGAATACTCAGAATGTCCATCAGGCAAGAAAGGAGGAGACCTC
EST: gi|18342813|gb|BJ174849.1|BJ174849
EST:     AGGGATGGCTCGATAGTGGAGATAAAGTTCCACCAGCTGAGTTCGCGAAG                         CTAGCGGCAGAATACTCAGAATGTCCATCAGGCAAGAAAGGAGGAGACCTC
genomic: AGGGATGGCTCGATAGTGGAGATAAAGTTCCACCAGCTGAGTTCGCGAAGgttaatgcta ... actcatgcagCTAGCGGCAGAATACTCAGAATGTCCATCAGGCAAGAAAGGAGGAGACCTC

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), 32 (downstream exon)
Score: 27

TTTATGTGAAAAGCAGGGCAAGATTAATGAAGCGTACAAGAAGCTCAAGGAGGGATGGCTCGATAGTGGAGATAAAGTTCCACCAGCTGAGTTCGCGAAGgttaatgcta ... actcatgcagCTAGCGGCAGAATACTCAGAATGTCCATCAGGCAAGAAAGGAGGAGACCTCGGGTGGTTTCCTCGTGGCAAGATGGCTGGACCTTTCCAGGAGGTGGCCT




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggcgttttcagtggagcatttcataatttgtagtttggttttgtactcatgcagCTAGCGGCAGAATACTCAGAATGTCCATCAGGCAAGAAAGGAGGAGACCTCGGGTGGTTTCCTCGTGGCAAGATGGCTGGACCTTTCCAGGAGGTGGCCT
                  atttcataatttgta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
accataaaatattgccacgagcgttgcataaatttctgcatcgaatggcgttttcagtggagcatttcataatttgtagtttggttttgtactcatgcagCTAGCGGCAGAATACTCAGAATGTCCATCAGGCAAGAAAGGAGGAGACCTCGGGTGGTTTCCTCGTGGCAAGATGGCTGGACCTTTCCAGGAGGTGGCCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - -ttctgca