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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGGATAGAGAGAAGCTAATGAAGATGGCTAGTGCAGTGCGCACTGGTGGGAAGGGCAGTGTCAGGAGgttagtgatgatcctttattcttcacgtccccgtgattgaaacccgtgtccttgcgtgtgttgtatgcacctccaaggatcttgctcagtcttggttctc...

Basic information

species Physcomitrella patens
transcript PP1S479_10V6.2
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S479_10V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: Vv17s0053g00620.t01 (Vitis vinifera), 5'ss of exon 2
ATGGATAGAGAGAAGCTAATGAAGATGGCTAGTGCAGTGCGCACTGGTGGGAAGGGCAGTGTCAGGAGgt---tagtgatgatcctttattcttcacgtccccgtgattgaaacccgtgtccttgcgtgtgttgtatgcacctccaaggatcttgctcagtcttggttctc
||| |||| |||||||| |||||||||||| ||||||| ||||| ||||| ||||| ||  | || ||||    |    || |||  | | |  |  |||| |   ||   ||  | |    ||    |  |||  |          || |   |    |    ||     
ATGAATAGGGAGAAGCTTATGAAGATGGCTGGTGCAGTTCGCACCGGTGGAAAGGGTAGCATGAGAAGgtgcaaaaccctgttccagtgtcccacttgtccactcaat---aattcattcttttattgggtttgggttgtttggggggggtgggggggggggggggggggg

upper sequence: PP1S479_10V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: EFJ08565 (Selaginella moellendorffii), 5'ss of exon 1
--------------------------------ATGGATAGAGAGAAGCTAATGAAGATGGCTAGTGCAGTGCGCACTGGTGGGAAGGGCAGTGTCAGGAGgttagtgatgatcctttattcttcacgtccccgtgattgaaacccgtgtccttgcgtgtgttgtatgcacctccaaggatcttgctcagtcttggttctc
                                ||| || |||||||||| ||||||||||||||||| |||||||| ||||| |||||||  || |||||||   |      | ||        | |    |||  ||  | |   ||   ||  || |  ||   |||                               
ATTTCTCACTCGTTTGCTGCGGATTTTGCTAGATGAATCGAGAGAAGCTGATGAAGATGGCTAGTGCTGTGCGCACCGGTGGAAAGGGCACAGTGAGGAGgtatttcggcggcattgg------atgatttcgttgtttgagctgatggatttttgttttctg-gcgcag------------------------------

upper sequence: PP1S479_10V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: EFJ19629 (Selaginella moellendorffii), 5'ss of exon 1
--------------------------------ATGGATAGAGAGAAGCTAATGAAGATGGCTAGTGCAGTGCGCACTGGTGGGAAGGGCAGTGTCAGGAGgttagtgatgatcctttattcttcacgtccccgtgattgaaacccgtgtccttgcgtgtgttgtatgcacctccaaggatcttgctcagtcttggttctc
                                ||| || |||||||||| ||||||||||||||||| |||||||| ||||| |||||||  || |||||||         | |       ||   |    |||  ||  | |   ||   ||  || |  ||   |||                               
TTTCTCACTCATTTGCCGCGGGATTTTGCCAGATGAATCGAGAGAAGCTGATGAAGATGGCTAGTGCTGTGCGCACCGGTGGAAAGGGCACAGTGAGGAGgt-------atttcggcggcattggtgatttcgttgtttgagctgatggatttttgttttctg-gcgcag------------------------------

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|162235488|gb|FC411311.1|FC411311
EST:     ATGAAGATGGCTAGTGCAGTGCGCACTGGTGGGAAGGGCAGTGTCAGGAG                         GAAGAAGAAAGCTGTGCATAAGACCACCTCAACTGACGACAAGAGGTTGCA
genomic: ATGAAGATGGCTAGTGCAGTGCGCACTGGTGGGAAGGGCAGTGTCAGGAGgttagtgatg ... cgtctaacagGAAGAAGAAAGCTGTGCATAAGACCACCTCAACTGACGACAAGAGGTTGCA
EST: gi|162244328|gb|FC421006.1|FC421006
EST:     ATGAAGATGGCTAGTGCAGTGCGCACTGGTGGGAAGGGCAGTGTCAGGAG                         GAAGAAGAAAGCTGTGCATAAGACCACCTCAACTGACGACAAGAGGTTGCA
genomic: ATGAAGATGGCTAGTGCAGTGCGCACTGGTGGGAAGGGCAGTGTCAGGAGgttagtgatg ... cgtctaacagGAAGAAGAAAGCTGTGCATAAGACCACCTCAACTGACGACAAGAGGTTGCA
EST: gi|162279458|gb|FC455574.1|FC455574
EST:     ATGAAGATGGCTAGTGCAGTGCGCACTGGTGGGAAGGGCAGTGTCAGGAG                         GAAGAAGAAAGCTGTGCATAAGACCACCTCAACTGACGACAAGAGGTTGCA
genomic: ATGAAGATGGCTAGTGCAGTGCGCACTGGTGGGAAGGGCAGTGTCAGGAGgttagtgatg ... cgtctaacagGAAGAAGAAAGCTGTGCATAAGACCACCTCAACTGACGACAAGAGGTTGCA
EST: gi|162274368|gb|FC450395.1|FC450395
EST:     ATGAAGATGGCTAGTGCAGTGCGCACTGGTGGGAAGGGCAGTGTCAGGAG                         GAAGAAGAAAGCTGTGCATAAGACCACCTCAACTGACGACAAGAGGTTGCA
genomic: ATGAAGATGGCTAGTGCAGTGCGCACTGGTGGGAAGGGCAGTGTCAGGAGgttagtgatg ... cgtctaacagGAAGAAGAAAGCTGTGCATAAGACCACCTCAACTGACGACAAGAGGTTGCA
EST: gi|37835358|gb|BJ593370.1|BJ593370
EST:     ATGAAGAAGGCTAGTGCAGTGCGCACTGGTGGGAAGGGCAGTGTCAGGAG                         GAAGAAGAAAGCTGTGCATAAGACCACCTCAACTGACGACAAGAGGTTGCA
genomic: ATGAAGATGGCTAGTGCAGTGCGCACTGGTGGGAAGGGCAGTGTCAGGAGgttagtgatg ... cgtctaacagGAAGAAGAAAGCTGTGCATAAGACCACCTCAACTGACGACAAGAGGTTGCA
EST: gi|67579122|gb|BJ951273.1|BJ951273
EST:     ATGAAGATGGCTAGTGCAGTGCGCACTGGTGGGAAGGGCAGTGTCAGGAG                         GAAGAAGAAAGCTGTGCATAAGACCACCTCAACTGACGACAAGAGGTTGCA
genomic: ATGAAGATGGCTAGTGCAGTGCGCACTGGTGGGAAGGGCAGTGTCAGGAGgttagtgatg ... cgtctaacagGAAGAAGAAAGCTGTGCATAAGACCACCTCAACTGACGACAAGAGGTTGCA
EST: gi|162235489|gb|FC411312.1|FC411312
EST:     ATGAAGATGGCTAGTGCAGTGCGCACTGGTGGGAAGGGCAGTGTCAGGAG                         GAAGAAGAAAGCTGTGCATAAGACCACCTCAACTGACGACAAGAGGTTGCA
genomic: ATGAAGATGGCTAGTGCAGTGCGCACTGGTGGGAAGGGCAGTGTCAGGAGgttagtgatg ... cgtctaacagGAAGAAGAAAGCTGTGCATAAGACCACCTCAACTGACGACAAGAGGTTGCA
EST: gi|37837361|gb|BJ595369.1|BJ595369
EST:     ATGAAGATGGCTAGTGCAGTGCGCACTGGTGGGAAGGGCAGTGTCAGGAG                         GAAGAAGAAAGCTGTGCATAAGACCACCTCAACTGACGACAAGAGGTTGCA
genomic: ATGAAGATGGCTAGTGCAGTGCGCACTGGTGGGAAGGGCAGTGTCAGGAGgttagtgatg ... cgtctaacagGAAGAAGAAAGCTGTGCATAAGACCACCTCAACTGACGACAAGAGGTTGCA
EST: gi|18353276|gb|BJ185331.1|BJ185331
EST:     ATGAAGATGGCTAGTGCAGTGCGCACTGGTGGGAAGGGCAGTGTCAGGAG                         GAAGAAGAAAGCTGTGCATAAGACCACCTCAACTGACGACAAGAGGTTGCA
genomic: ATGAAGATGGCTAGTGCAGTGCGCACTGGTGGGAAGGGCAGTGTCAGGAGgttagtgatg ... cgtctaacagGAAGAAGAAAGCTGTGCATAAGACCACCTCAACTGACGACAAGAGGTTGCA
EST: gi|18353886|gb|BJ185941.1|BJ185941
EST:     ATGAAGAAGGCTAGTGCAGTGCGCACTGGTGGGAAGGGCAGTGTCAGGAG                         GAAGAAGAAAGCTGTGCATAAGACCACCTCAACTGACGACAAGAGGTTGCA
genomic: ATGAAGATGGCTAGTGCAGTGCGCACTGGTGGGAAGGGCAGTGTCAGGAGgttagtgatg ... cgtctaacagGAAGAAGAAAGCTGTGCATAAGACCACCTCAACTGACGACAAGAGGTTGCA
EST: gi|18337124|gb|BJ169148.1|BJ169148
EST:     ATGAAGATGGCTAGTGCAGTGCGCACTGATGGGAAGGGCAGTGTCAGGAG                         GAAGAAGAAAGCTGTGCATAAGACCACCTCAACTGACGACAAGAGGTTGCA
genomic: ATGAAGATGGCTAGTGCAGTGCGCACTGGTGGGAAGGGCAGTGTCAGGAGgttagtgatg ... cgtctaacagGAAGAAGAAAGCTGTGCATAAGACCACCTCAACTGACGACAAGAGGTTGCA
EST: gi|162203658|gb|FC379144.1|FC379144
EST:     ATGAAGATGGCTAGTGCAGTGCGCACTGGTGGGAAGGGCAGTGTCAGGAG                         GAAGAAGAAAGCTGTGCATAAGACCACCTCAACTGACGACAAGAGGTTGCA
genomic: ATGAAGATGGCTAGTGCAGTGCGCACTGGTGGGAAGGGCAGTGTCAGGAGgttagtgatg ... cgtctaacagGAAGAAGAAAGCTGTGCATAAGACCACCTCAACTGACGACAAGAGGTTGCA
EST: gi|162241574|gb|FC414696.1|FC414696
EST:     TTGAAGATGGCTAGTGCAGTGCGCACTGGTGGGAAGGGCAGTGTCAGGAG                         GAAGAAGAAAGCTGTGCATAAGACCACCTCAACTGACGTCAAGAGGTTGCA
genomic: ATGAAGATGGCTAGTGCAGTGCGCACTGGTGGGAAGGGCAGTGTCAGGAGgttagtgatg ... cgtctaacagGAAGAAGAAAGCTGTGCATAAGACCACCTCAACTGACGACAAGAGGTTGCA
EST: gi|162279459|gb|FC455575.1|FC455575
EST:     ATGAAGATGGCTAGTGCAGTGCGCACTGGTGGGAAGGGCAGTGTCAGGAG                         GAAGAAGAAAGCTGTGCATAAGACCACCTCAACTGACGACAAGAGGTTGCA
genomic: ATGAAGATGGCTAGTGCAGTGCGCACTGGTGGGAAGGGCAGTGTCAGGAGgttagtgatg ... cgtctaacagGAAGAAGAAAGCTGTGCATAAGACCACCTCAACTGACGACAAGAGGTTGCA
EST: gi|162229541|gb|FC405875.1|FC405875
EST:     ATGAAGATGGCTAGTGCAGTGCGCACTGGTGGGAAGGGCAGTGTCAGGAG                         GAAGAAGAAAGCTGTGCATAAGACCACCTCAACTGACGACAAGAGGTTGCA
genomic: ATGAAGATGGCTAGTGCAGTGCGCACTGGTGGGAAGGGCAGTGTCAGGAGgttagtgatg ... cgtctaacagGAAGAAGAAAGCTGTGCATAAGACCACCTCAACTGACGACAAGAGGTTGCA
EST: gi|37834740|gb|BJ592752.1|BJ592752
EST:     AGGGCAGTGTCAGGAG                         GAAGAAGAAAGCTGTGCATAAGACCACCTCAACTGACGACAAGAGGTTGCA
genomic: AGGGCAGTGTCAGGAGgttagtgatg ... cgtctaacagGAAGAAGAAAGCTGTGCATAAGACCACCTCAACTGACGACAAGAGGTTGCA
EST: gi|162224828|gb|FC400828.1|FC400828
EST:     ATGAAGATGGCTAGTGCAGTGCGCACTGGTGGGAAGGGCAGTGTCAGGAG                         GAAGAAGAAAGCTGTGCATAAGACCACCTCAACTGACGACAAGAGGTTGCA
genomic: ATGAAGATGGCTAGTGCAGTGCGCACTGGTGGGAAGGGCAGTGTCAGGAGgttagtgatg ... cgtctaacagGAAGAAGAAAGCTGTGCATAAGACCACCTCAACTGACGACAAGAGGTTGCA
EST: gi|162224827|gb|FC400827.1|FC400827
EST:     ATGAAGATGGCTAGTGCAGTGCGCACTGGTGGGAAGGGCAGTGTCAGGAG                         GAAGAAGAAAGCTGTGCATAAGACCACCTCAACTGACGACAAGAGGTTGCA
genomic: ATGAAGATGGCTAGTGCAGTGCGCACTGGTGGGAAGGGCAGTGTCAGGAGgttagtgatg ... cgtctaacagGAAGAAGAAAGCTGTGCATAAGACCACCTCAACTGACGACAAGAGGTTGCA
EST: gi|162279226|gb|FC455773.1|FC455773
EST:     ATGAAGATGGCTAGTGCAGTGCGCACTGGTGGGAAGGGCAGTGTCAGGAG                         GAAGAAGAAAGCTGTGCATAAGACCACCTCAACTGACGACAAGAGGTTGCA
genomic: ATGAAGATGGCTAGTGCAGTGCGCACTGGTGGGAAGGGCAGTGTCAGGAGgttagtgatg ... cgtctaacagGAAGAAGAAAGCTGTGCATAAGACCACCTCAACTGACGACAAGAGGTTGCA
EST: gi|37835088|gb|BJ593100.1|BJ593100
EST:     ATGAAGATGGCTAGTGCAGTGCGCACTGGTGGGAAGGGCAGTGTCAGGAG                         GAAGAAGAAAGCTGTGCATAAGACCACCTCAACTGACGACAAGAGGTTGCA
genomic: ATGAAGATGGCTAGTGCAGTGCGCACTGGTGGGAAGGGCAGTGTCAGGAGgttagtgatg ... cgtctaacagGAAGAAGAAAGCTGTGCATAAGACCACCTCAACTGACGACAAGAGGTTGCA
EST: gi|162222208|gb|FC397644.1|FC397644
EST:     ATGAAGATGGCTAGTGCAGTGCGCACTGGTGGGAAGGGCAGTGTCAGGAG                         GAAGAAGAAAGCTGTGCATAAGACCACCTCAACTGACGACAAGAGGTTGCA
genomic: ATGAAGATGGCTAGTGCAGTGCGCACTGGTGGGAAGGGCAGTGTCAGGAGgttagtgatg ... cgtctaacagGAAGAAGAAAGCTGTGCATAAGACCACCTCAACTGACGACAAGAGGTTGCA
EST: gi|67507846|gb|BJ940722.1|BJ940722
EST:     ATGAAGATGGCTAGTGCAGTGCGCACTGGTGGGAAGGGCAGTGTCAGGAG                         GAAGAAGAAAGCTGTGCATAAGACCACCTCAACTGACGACAAGAGGTTGCA
genomic: ATGAAGATGGCTAGTGCAGTGCGCACTGGTGGGAAGGGCAGTGTCAGGAGgttagtgatg ... cgtctaacagGAAGAAGAAAGCTGTGCATAAGACCACCTCAACTGACGACAAGAGGTTGCA

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), 35 (downstream exon)
Score: 212

ATGGATAGAGAGAAGCTAATGAAGATGGCTAGTGCAGTGCGCACTGGTGGGAAGGGCAGTGTCAGGAGgttagtgatg ... cgtctaacagGAAGAAGAAAGCTGTGCATAAGACCACCTCAACTGACGACAAGAGGTTGCAGAGCACCTTGAAACGACTTGGAGTGAATACCGTTCCTGGAATTGAGGAG




<











<


<









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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATGGATAGAGAGAAGCTAATGAAGATGGCTAGTGCAGTGCGCACTGGTGGGAAGGGCAGTGTCAGGAGgttagtgatgatcctttattcttcacgtccccgtgattgaaacccgtgtccttgcgtgtgttgtatgcacctccaaggatcttgctcagtcttggttctc

- - - - - - - - -  TGAAGA
- - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - TGGTGG