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'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   		14  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgaacatccgctcctgtgtttttgtaacccctctttatttgagctaaaatttgtcttgtatttatgttggagtatcaagtgacagttgatgagtaatgattgatatttgaatgaacttatctagggctgggtgataattctaagttgcgttgcgctttccagGGACTTGAGCTGATCCCGTCAGAGAATTTTACGTCCGTATCAGTTATGCAGGCAGTGGGTTCAGTCATGACCAATAAGTACAGTGAAGGTTACCCCGGTG

Basic information

species Physcomitrella patens
transcript PP1S79_54V6.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S79_54V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: LOC_Os03g52840.2 (Oryza sativa), 3'ss of exon 3
gtatgaacatccgctcctgtgtttttgtaacccctctttatttgagctaaaatttgtcttgtatttatgttggagtatcaagtgacagttgatgagtaatgattgatatttgaatgaacttatctagggctgggtgataattctaagttgcgttgcgctttccagGGACTTGAGCTGATCCCGTCAGAGAATTTTACGTCCGTATCAGTTATGCAGGCAGTGGGTTCAGTCATGACCAATAAGTACAGTGAAGGTTACCCCGGTG
                                                                | |      |  | |||   | |  ||  | | | || |   | ||||  |  ||  |   |  ||||  |  |      ||  ||  | | ||     |||| || ||||| |||||||| ||||| || || || || ||||| |||||||| ||||| || ||||||||||| |||||||| || || |||||||| |
---------------------------------------------------------------gtaaccagcaaccaccaaaaaaaaagtg-cgtggattgttcagtgtttgg-tccaccgacgcattgctgaattgtggc---aatctgtttggtgc-----agGGTCTGGAGCTCATCCCGTCGGAGAACTTCACCTCGGTGTCAGTGATGCAGGCGGTGGGATCCGTCATGACCAACAAGTACAGCGAGGGGTACCCCGGCG

upper sequence: PP1S79_54V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GRMZM2G135283_T01 (Zea mays), 3'ss of exon 3
gtatgaacatccgctcctgtgttttt-gtaacccctctttatttgagctaaaatttgtcttgtatttatgttggagtatcaagtgacagt--tgatgagtaatgattgatatttgaatgaacttatctagggctgggtgataattctaagttgcgttgcgctt---tccagGGACTTGAGCTGATCCCGTCAGAGAATTTTACGTCCGTATCAGTTATGCAGGCAGTGGGTTCAGTCATGACCAATAAGTACAGTGAAGGTTACCCCGGTG
            |  ||||| | ||  || | |  |   |||  |  ||          ||  | | || |     | || ||| |  ||  || ||  | || |||  ||||||  |    ||  | ||  |    |||    | |  ||  |  ||||  |     ||||| || ||||| |||||||| |||||||| ||||| || ||||| ||||||||||||||||| ||||||||||| |||||||| || || ||||| || |
------------gtccctgtttcttcagtcatcttttcctatacgtact--------cttttcagtcatttccacttctccagtcattgttttgttggattat-attattatttgttt---ttttccaagaccctactgagttctgtccgtgtcaatgcgtctggtggcagGGTCTGGAGCTCATCCCGTCGGAGAATTTCACGTCGGTGTCAGTGATGCAGGCAGTGGGTTCCGTCATGACCAACAAGTACAGCGAGGGGTACCCTGGCG

upper sequence: PP1S79_54V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: AT5G26780.3 (Arabidopsis thaliana), 3'ss of exon 3
gtatgaacatccgctcctgtgtttttgtaacccctctttatttgagctaaaatttgtcttgtatttatgttggagtatcaagtgacagttgatgagtaatgattgatatttgaatgaacttatctagggctgggtgataattctaagttgcgttgcgctttccagGGACTTGAGCTGATCCCGTCAGAGAATTTTACGTCCGTATCAGTTATGCAGGCAGTGGGTTCAGTCATGACCAATAAGTACAGTGAAGGTTACCCCGGTG
                                                            ||||  |      |  ||  ||||| | |     | |    ||  |||   |  |  | ||||   |   |||| ||| ||  ||    | |||    ||| |||||| |||| || || |||||||||||||| || ||  |||| || ||||| || || ||||| || ||||| |||||||| |||||||| ||||| || |
------------------------------------------------------------gtatcaac-----aaaatttagtgagaatgatcaaattcacatatatagaagctttgatttatt--gatttgggggatgatgtta---cgagtt----ttttcagGGATTTGAACTTATACCGTCAGAGAATTTCACTTCTCTATCTGTGATGCAAGCCGTTGGTTCTGTTATGACTAATAAGTATAGTGAAGGATACCCTGGAG

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|162179835|gb|FC355906.1|FC355906
EST:     ATCCCGAGATCACTGACATCATTGAACACGAGAAGAATCGTCAATGGAAG                         GGACTTGAGCTGATCCCGTCAGAGAATTTTACGTCCGTATCAGTTATGCAG
genomic: ATCCCGAGATCACTGACATCATTGAACACGAGAAGAATCGTCAATGGAAGgtatgaacat ... cgctttccagGGACTTGAGCTGATCCCGTCAGAGAATTTTACGTCCGTATCAGTTATGCAG
EST: gi|162182305|gb|FC357176.1|FC357176
EST:     ATCCCGAGATCACTGACATCATTGAACACGAGAAGAATCGTCAATGGAAG                         GGACTTGAGCTGATCCCGTCAGAGAATTTTACGTCCGTATCAGTTATGCAG
genomic: ATCCCGAGATCACTGACATCATTGAACACGAGAAGAATCGTCAATGGAAGgtatgaacat ... cgctttccagGGACTTGAGCTGATCCCGTCAGAGAATTTTACGTCCGTATCAGTTATGCAG
EST: gi|18369273|gb|BJ201358.1|BJ201358
EST:     ATCCCGAGATCACTGACATCATTGAACACGAGAAGAATCGTCAATGGAAG                         GGACTTGAGCTGATCCCGTCAGAGAATTTTACGTCCGTATCAGTTATGCAG
genomic: ATCCCGAGATCACTGACATCATTGAACACGAGAAGAATCGTCAATGGAAGgtatgaacat ... cgctttccagGGACTTGAGCTGATCCCGTCAGAGAATTTTACGTCCGTATCAGTTATGCAG
EST: gi|100385980|gb|BY951174.1|BY951174
EST:     ATCCCGAGATCACTGACATCATTGAACACGAGAAGAATCGTCAATGGAAG                         GGACTTGAGCTGATCCCGTCAGAGAATTTTACGTCCGTATCAGTTATGCAG
genomic: ATCCCGAGATCACTGACATCATTGAACACGAGAAGAATCGTCAATGGAAGgtatgaacat ... cgctttccagGGACTTGAGCTGATCCCGTCAGAGAATTTTACGTCCGTATCAGTTATGCAG
EST: gi|18365567|gb|BJ197644.1|BJ197644
EST:     ATCCCGAGATCACTGACATCATTGAACACGAGAAGAATCGTCAATGGAAG                         GGACTTGAGCTGATCCCGTCAGAGAATTTTACGTCCGTATCAGTTATGCAG
genomic: ATCCCGAGATCACTGACATCATTGAACACGAGAAGAATCGTCAATGGAAGgtatgaacat ... cgctttccagGGACTTGAGCTGATCCCGTCAGAGAATTTTACGTCCGTATCAGTTATGCAG
EST: gi|18362808|gb|BJ194880.1|BJ194880
EST:     ATCCCGAGATCACTGACATCATTGAACACGAGAAGAATCGTCAATGGAAG                         GGACTTGAGCTGATCCCGTCAGAGAATTTTACGTCCGTATCAGTTATGCAG
genomic: ATCCCGAGATCACTGACATCATTGAACACGAGAAGAATCGTCAATGGAAGgtatgaacat ... cgctttccagGGACTTGAGCTGATCCCGTCAGAGAATTTTACGTCCGTATCAGTTATGCAG
EST: gi|208358811|gb|DC935197.1|DC935197
EST:     ATCCCGAGATCACTGACATCATTGAACACGAGAAGAATCGTCAATGGAAG                         GGACTTGAGCTGATCCCGTCAGAGAATTTTACGTCCGTATCAGTTATGCAG
genomic: ATCCCGAGATCACTGACATCATTGAACACGAGAAGAATCGTCAATGGAAGgtatgaacat ... cgctttccagGGACTTGAGCTGATCCCGTCAGAGAATTTTACGTCCGTATCAGTTATGCAG
EST: gi|100428360|gb|BY977766.1|BY977766
EST:     ATCCCGAGATCACTGACATCATTGAACACGGGAAGAATCGTCAATGGAAG                         GGACTTGAGCTGATCCCGTCAGAGAATTTTACGTCCGTATCAGTTATGCAG
genomic: ATCCCGAGATCACTGACATCATTGAACACGAGAAGAATCGTCAATGGAAGgtatgaacat ... cgctttccagGGACTTGAGCTGATCCCGTCAGAGAATTTTACGTCCGTATCAGTTATGCAG
EST: gi|18361307|gb|BJ193373.1|BJ193373
EST:     ATCCCGAGATCACTGACATCATTGAACACGAGAAGAATCGTCAATGGAAG                         GGACTTGAGCTGATCCCGTCAGAGAATTTTACGTCCGTATCAGTTATGCAG
genomic: ATCCCGAGATCACTGACATCATTGAACACGAGAAGAATCGTCAATGGAAGgtatgaacat ... cgctttccagGGACTTGAGCTGATCCCGTCAGAGAATTTTACGTCCGTATCAGTTATGCAG
EST: gi|18374142|gb|BJ205720.1|BJ205720
EST:     ATCCCGAGATCACTGACATCATTGAACACGAGAAGAATCGTCAATGGAAG                         GGACTTGAGCTGATCCCGTCAGAGAATTTTACGTCCGTATCAGTTATGCAG
genomic: ATCCCGAGATCACTGACATCATTGAACACGAGAAGAATCGTCAATGGAAGgtatgaacat ... cgctttccagGGACTTGAGCTGATCCCGTCAGAGAATTTTACGTCCGTATCAGTTATGCAG
EST: gi|18360348|gb|BJ192410.1|BJ192410
EST:     ATCCCGAGATCACTGACATCATTGAACACGAGAAGAATCGTCAATGGAAG                         GGACTTGAGCTGATCCCGTCAGAGAATTTTACGTCCGTATCAGTTATGCAG
genomic: ATCCCGAGATCACTGACATCATTGAACACGAGAAGAATCGTCAATGGAAGgtatgaacat ... cgctttccagGGACTTGAGCTGATCCCGTCAGAGAATTTTACGTCCGTATCAGTTATGCAG
EST: gi|18369196|gb|BJ201281.1|BJ201281
EST:     ATCCCGAGATCACTGACATCATTGAACACGATAAGAATCGTCAATGGAAG                         GGACTTGAGCTGATCCCGTCAGATAATTTTACGTCCGTATCATTTATGCAN
genomic: ATCCCGAGATCACTGACATCATTGAACACGAGAAGAATCGTCAATGGAAGgtatgaacat ... cgctttccagGGACTTGAGCTGATCCCGTCAGAGAATTTTACGTCCGTATCAGTTATGCAG
EST: gi|208379665|gb|DC903720.1|DC903720
EST:     ATCCCGAGATCACTGACATCATTGAACACGAGAAGAATCGTCAATGGAAG                         GGACTTGAGCTGATCCCGTCAGAGAATTTTACGTCCGTATCAGTTATGCAG
genomic: ATCCCGAGATCACTGACATCATTGAACACGAGAAGAATCGTCAATGGAAGgtatgaacat ... cgctttccagGGACTTGAGCTGATCCCGTCAGAGAATTTTACGTCCGTATCAGTTATGCAG
EST: gi|162155361|gb|FC331767.1|FC331767
EST:     ATCCCGAGATCACTGACATCATTGAACACGAGAAGAATCGTCAATGGAAG                         GGACTTGAGCTGATCCCGTCAGAGAATTTTACGTCCGTATCAGTTATGCAG
genomic: ATCCCGAGATCACTGACATCATTGAACACGAGAAGAATCGTCAATGGAAGgtatgaacat ... cgctttccagGGACTTGAGCTGATCCCGTCAGAGAATTTTACGTCCGTATCAGTTATGCAG
EST: gi|18356126|gb|BJ188185.1|BJ188185
EST:     ATCCCGAGATCACTGACATCATTGAACACGAGAAGAATCGTCAATGGAAG                         GGACTTGAGCTGATCCCGTCAGAGAATTTTACGTCCGTATCAGTTATGCAG
genomic: ATCCCGAGATCACTGACATCATTGAACACGAGAAGAATCGTCAATGGAAGgtatgaacat ... cgctttccagGGACTTGAGCTGATCCCGTCAGAGAATTTTACGTCCGTATCAGTTATGCAG
EST: gi|18366816|gb|BJ198896.1|BJ198896
EST:     ATCCCGAGATCACTGACATCATTGAACACGAGAAGAATCGTCAATGGAAG                         GGACTTGAGCTGATCCCGTCAGAGAATTTTACGTCCGTATCAGTTATGCAG
genomic: ATCCCGAGATCACTGACATCATTGAACACGAGAAGAATCGTCAATGGAAGgtatgaacat ... cgctttccagGGACTTGAGCTGATCCCGTCAGAGAATTTTACGTCCGTATCAGTTATGCAG
EST: gi|100392460|gb|BY953374.1|BY953374
EST:     ATCCCGAGATCACTGACATCATTGAACACGAGAAGAATCGTCAATGGAAG                         GGACTTGAGCTGATCCCGTCAGAGAATTTTACGTCCGTATCAGTTATGCAG
genomic: ATCCCGAGATCACTGACATCATTGAACACGAGAAGAATCGTCAATGGAAGgtatgaacat ... cgctttccagGGACTTGAGCTGATCCCGTCAGAGAATTTTACGTCCGTATCAGTTATGCAG
EST: gi|18370401|gb|BJ202003.1|BJ202003
EST:     ATCCCGAGATCACTGACATCATTGAACACGAGAAGAATCGTCAATGGAAG                         GGACTTGAGCTGATCCCGTCAGAGAATTTTACGTCCGTATCAGTTATGCAG
genomic: ATCCCGAGATCACTGACATCATTGAACACGAGAAGAATCGTCAATGGAAGgtatgaacat ... cgctttccagGGACTTGAGCTGATCCCGTCAGAGAATTTTACGTCCGTATCAGTTATGCAG

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: 18 (upstream exon), 29 (downstream exon)
Score: 4

TGGCCGAAGCAGCTCAATGCCGACATCTCCGAGGTTGATCCCGAGATCACTGACATCATTGAACACGAGAAGAATCGTCAATGGAAGgtatgaacat ... cgctttccagGGACTTGAGCTGATCCCGTCAGAGAATTTTACGTCCGTATCAGTTATGCAGGCAGTGGGTTCAGTCATGACCAATAAGTACAGTGAAGGTTACCCCGGTG




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgaatgaacttatctagggctgggtgataattctaagttgcgttgcgctttccagGGACTTGAGCTGATCCCGTCAGAGAATTTTACGTCCGTATCAGTTATGCAGGCAGTGGGTTCAGTCATGACCAATAAGTACAGTGAAGGTTACCCCGGTG
                                             cgctttcc  CT-rich tract
                          ataattctaa  TA-rich tract