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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATATGCAAGTGCCTTTTACGGGCCCTTCAGAGAAGCACTGGACTCCAATCCCCGTTTTGGTGACAAGAAGACgtaagttccaagtacaatctcttgtccggtattatgtcagtactagccaggattcaccaaaaggaatataattgcaattcatggggttttttacgaggtccttacctatgtggtgttatcag

Basic information

species Physcomitrella patens
transcript PP1S450_21V6.2
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S450_21V6.2 (Physcomitrella patens), 5'ss of exon 9
lower sequence: Vv18s0001g02550.t01 (Vitis vinifera), 5'ss of exon 9
ATATGCAAGTGCCTTTTACGGGCCCTTCAGAGAAGCACTGGACTCCAATCCCCGTTTTGGTGACAAGAAGACgtaagttccaagtacaatctcttgtccggtattatgtcagtactagccaggattcaccaaaaggaatataattgca-attcatggggttttttacgaggtccttacctatgtggtgttatcag
 ||||||||||| ||||| || || ||| |||||||| ||||||| ||||| || ||||| ||||| || ||||| |       |  ||  |    |      |||  |   || | |  |  | |         |   |   ||||| |||  || |||     || |                          
GTATGCAAGTGCATTTTATGGTCCATTCCGAGAAGCATTGGACTCAAATCCACGCTTTGGAGACAAAAAAACgtatgcagtccatgaaagttgaactttatggttaatttcttattcgatattactgct------gctcacttttgcatattattgtggtggcaaacaaaag-----------------------

upper sequence: PP1S450_21V6.2 (Physcomitrella patens), 5'ss of exon 9
lower sequence: EFJ25898 (Selaginella moellendorffii), 5'ss of exon 9
ATATGCAAGTGCCTTTTACGGGCCCTTCAGAGAAGCACTGGACTCCAATCCCCGTTTTGGTGACAAGAAGACgtaagttccaagtacaatctcttgtccggtattatgtcagtactagccaggattcaccaaaaggaatataattgcaattcatggggttttttacgaggtccttacctatgtggtgttatcag
 |||||||| || || || || || |||||||||||  ||||||| |||||||||||||| || ||||| |||||||   ||  | |  | | |   |   | || ||      ||    || ||     ||||  |                                                         
GTATGCAAGCGCGTTCTATGGTCCATTCAGAGAAGCTTTGGACTCAAATCCCCGTTTTGGAGATAAGAAAACgtaag---cagttcctctttttctccaactcttttgctcactctctggagaatg----aaaaccag--------------------------------------------------------

upper sequence: PP1S450_21V6.2 (Physcomitrella patens), 5'ss of exon 9
lower sequence: EFJ10919 (Selaginella moellendorffii), 5'ss of exon 9
ATATGCAAGTGCCTTTTACGGGCCCTTCAGAGAAGCACTGGACTCCAATCCCCGTTTTGGTGACAAGAAGACgtaagttccaagtacaatctcttgtccggtattatgtcagtactagccaggattcaccaaaaggaatataattgcaattcatggggttttttacgaggtccttacctatgtggtgttatcag
 |||||||| || || || || || ||||||||||| |||||||| |||||||||||||| || ||||| |||||||   ||  | |  | | |   |   | || ||      ||    || ||     ||||  |                                                         
GTATGCAAGCGCGTTCTATGGTCCATTCAGAGAAGCTCTGGACTCAAATCCCCGTTTTGGAGATAAGAAAACgtaag---cagttcctctttatctccaactcttttgctcactctctggagaatg----aaaaccag--------------------------------------------------------

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|208357191|gb|DC926538.1|DC926538
EST:     CCCTTCAGAGAAGCACTGGACTCCAATCCCCGTTTTGGTGACAAGAAGAC                         GTATCAAATGAACCCCGCAAATTACCGCGAGGCTCTGATCGAGACAAGGTT
genomic: CCCTTCAGAGAAGCACTGGACTCCAATCCCCGTTTTGGTGACAAGAAGACgtaagttcca ... gtgttatcagGTATCAAATGAACCCCGCAAATTACCGCGAGGCTCTGATCGAGACAAGGTT
EST: gi|162234870|gb|FC410643.1|FC410643
EST:     CCCTTCAGAGAAGCACTGGACTCCNATCCCCGTTTTGGTGACAAGAAGAC                         GTATCAAATGAACCCCGC
genomic: CCCTTCAGAGAAGCACTGGACTCCAATCCCCGTTTTGGTGACAAGAAGACgtaagttcca ... gtgttatcagGTATCAAATGAACCCCGC
EST: gi|162218487|gb|FC395064.1|FC395064
EST:     CCCTTCAGAGAAGCACTGGACTCCAATCCCCGTTTTGGTGACAAGAAGAC                         GTATCAAATGAACCCCGCAAATTACCGCGAGGCTCTGATCGAGACAAGGTT
genomic: CCCTTCAGAGAAGCACTGGACTCCAATCCCCGTTTTGGTGACAAGAAGACgtaagttcca ... gtgttatcagGTATCAAATGAACCCCGCAAATTACCGCGAGGCTCTGATCGAGACAAGGTT
EST: gi|208353431|gb|DC918487.1|DC918487
EST:     CCCTTCAGAGAAGCACTGGACTCCAATCCCCGTTTTGGTGACAAGAAGAC                         GTATCAAATGAACCCCGCAAATTACCGCGAGGCTCTGATCGAGACAAGGTT
genomic: CCCTTCAGAGAAGCACTGGACTCCAATCCCCGTTTTGGTGACAAGAAGACgtaagttcca ... gtgttatcagGTATCAAATGAACCCCGCAAATTACCGCGAGGCTCTGATCGAGACAAGGTT
EST: gi|162234869|gb|FC410642.1|FC410642
EST:     CCCTTCAGAGAAGCACTGGACTCCAATCCCCGTTTTGGTGACAAGAAGAC                         GTATCAAATGAACCCCGCAAATTACCGCGAGGCTCTGATCGAGACAAGGTT
genomic: CCCTTCAGAGAAGCACTGGACTCCAATCCCCGTTTTGGTGACAAGAAGACgtaagttcca ... gtgttatcagGTATCAAATGAACCCCGCAAATTACCGCGAGGCTCTGATCGAGACAAGGTT
EST: gi|37828958|gb|BJ586970.1|BJ586970
EST:     CCCTTCAGAGAAGCACTGGACTCCAATCCCCGTTTTGGTGACAAGAAGAC                         GAATCAAATGAACCCCGCAAATTACCGCGAGGCTCTGATCGAGACAAGGTT
genomic: CCCTTCAGAGAAGCACTGGACTCCAATCCCCGTTTTGGTGACAAGAAGACgtaagttcca ... gtgttatcagGTATCAAATGAACCCCGCAAATTACCGCGAGGCTCTGATCGAGACAAGGTT
EST: gi|162185929|gb|FC361029.1|FC361029
EST:     CCCTTCAGAGAAGCACTGGACTCCAATCCCCGTTTTGGTGACAAGAAGAC                         GTATCAAATGAACCCCGCAAATTACCGCGAGGCTCTGATCGAGACAAGGTT
genomic: CCCTTCAGAGAAGCACTGGACTCCAATCCCCGTTTTGGTGACAAGAAGACgtaagttcca ... gtgttatcagGTATCAAATGAACCCCGCAAATTACCGCGAGGCTCTGATCGAGACAAGGTT
EST: gi|37852710|gb|BJ610718.1|BJ610718
EST:     CCCTTCAGAGAAGCACTGGACTCCAATCCCCGTTTTGGTGACAAGAAGAC                         GTATCAAATGAACCCCGCAAATTACCGCGAGGCTCTGATCGAGACAAGGTT
genomic: CCCTTCAGAGAAGCACTGGACTCCAATCCCCGTTTTGGTGACAAGAAGACgtaagttcca ... gtgttatcagGTATCAAATGAACCCCGCAAATTACCGCGAGGCTCTGATCGAGACAAGGTT
EST: gi|162268622|gb|FC443676.1|FC443676
EST:     CCCTTCAGAGAAGCACTGGACTCCAATCCCCGTTTTGGTGACAAGAAGAC                         GTATCAAATGAACCCCGCAAATTACCGCGAGGCTCTGATCGAGACAAGGTT
genomic: CCCTTCAGAGAAGCACTGGACTCCAATCCCCGTTTTGGTGACAAGAAGACgtaagttcca ... gtgttatcagGTATCAAATGAACCCCGCAAATTACCGCGAGGCTCTGATCGAGACAAGGTT
EST: gi|162232564|gb|FC408400.1|FC408400
EST:     CCCTTCAGAGAAGCACTGGACTCCAATCCCCGTTTTGGTGACAAGAAGAC                         GTATCAAATGAACCCCGCAAATTACCGCGAGGCTCTGATCGAGACAAGGTT
genomic: CCCTTCAGAGAAGCACTGGACTCCAATCCCCGTTTTGGTGACAAGAAGACgtaagttcca ... gtgttatcagGTATCAAATGAACCCCGCAAATTACCGCGAGGCTCTGATCGAGACAAGGTT
EST: gi|162184165|gb|FC359639.1|FC359639
EST:     CCCTTCAGAGAAGCACTGGACTCCAATCCCCGTTTTGGTGACAAGAAGAC                         GTATCAAATGAACCCCGCAAATTACCGCGAGGCTCTGATCGAGACAAGGTT
genomic: CCCTTCAGAGAAGCACTGGACTCCAATCCCCGTTTTGGTGACAAGAAGACgtaagttcca ... gtgttatcagGTATCAAATGAACCCCGCAAATTACCGCGAGGCTCTGATCGAGACAAGGTT
EST: gi|162176322|gb|FC353507.1|FC353507
EST:     CCCTTCAGAGAAGCACTGGACTCCAATCCCCGTTTTGGTGACAAGAAGAC                         GTATCAAATGAACCCCGCAAATTACCGCGAGGCTTTGATCGAGACAAGGTT
genomic: CCCTTCAGAGAAGCACTGGACTCCAATCCCCGTTTTGGTGACAAGAAGACgtaagttcca ... gtgttatcagGTATCAAATGAACCCCGCAAATTACCGCGAGGCTCTGATCGAGACAAGGTT
EST: gi|208397366|gb|DC916320.1|DC916320
EST:     CCCTTCAGAGAAGCACTGGACTCCAATCCCCGTTTTGGTGACAAGAAGAC                         GTATCAAATGAACCCCGCAAATTACCGCGAGGCTCTGATCGAGACAAGGTT
genomic: CCCTTCAGAGAAGCACTGGACTCCAATCCCCGTTTTGGTGACAAGAAGACgtaagttcca ... gtgttatcagGTATCAAATGAACCCCGCAAATTACCGCGAGGCTCTGATCGAGACAAGGTT
EST: gi|37827165|gb|BJ585177.1|BJ585177
EST:     CCCTTCAGAGAAGCACTGGACTCCAATCCCCGTTTTGGTGACAAGAAGAC                         GTATCAAATGAACCCCGCAAATTACCGCGAGGCTCTGATCGAGACAAGGTT
genomic: CCCTTCAGAGAAGCACTGGACTCCAATCCCCGTTTTGGTGACAAGAAGACgtaagttcca ... gtgttatcagGTATCAAATGAACCCCGCAAATTACCGCGAGGCTCTGATCGAGACAAGGTT
EST: gi|37822149|gb|BJ580215.1|BJ580215
EST:     CCCTTCAGAGAAGCACTGGACTCCAATCCCCGTTTTGGTGACAAGAAGAC                         GTATCAAATGAACCCCGCAAATTACCGCGAGGCTCTGATCGAGACAGGGTT
genomic: CCCTTCAGAGAAGCACTGGACTCCAATCCCCGTTTTGGTGACAAGAAGACgtaagttcca ... gtgttatcagGTATCAAATGAACCCCGCAAATTACCGCGAGGCTCTGATCGAGACAAGGTT
EST: gi|208380828|gb|DC923310.1|DC923310
EST:     CCCTTCAGAGAAGCACTGGACTCCAATCCCCGTTTTGGTGACAAGAAGAC                         GTATCAAATGAACCCCGCAAATTACCGCGAGGCTCTGATCGAGACAAGGTT
genomic: CCCTTCAGAGAAGCACTGGACTCCAATCCCCGTTTTGGTGACAAGAAGACgtaagttcca ... gtgttatcagGTATCAAATGAACCCCGCAAATTACCGCGAGGCTCTGATCGAGACAAGGTT
EST: gi|67727441|gb|BJ977700.1|BJ977700
EST:     CCCTTCAGAGAAGCACTGGACTCCAATCCCCGTTTTGGTGACAAGAAGAC                         GTATCAAATGAACCCCGCAAATTACCGCGAGGCTCTGATCGAGACAAGGTT
genomic: CCCTTCAGAGAAGCACTGGACTCCAATCCCCGTTTTGGTGACAAGAAGACgtaagttcca ... gtgttatcagGTATCAAATGAACCCCGCAAATTACCGCGAGGCTCTGATCGAGACAAGGTT
EST: gi|162265940|gb|FC442943.1|FC442943
EST:     CCCTTCAGAGAAGCACTGGACTCCAATCCCCGTTTTGGTGACAAGAAGAC                         GTATCAAATGAACCCCGCAAATTACCGCGAGGCTCTGATCGAGACAAGGTT
genomic: CCCTTCAGAGAAGCACTGGACTCCAATCCCCGTTTTGGTGACAAGAAGACgtaagttcca ... gtgttatcagGTATCAAATGAACCCCGCAAATTACCGCGAGGCTCTGATCGAGACAAGGTT
EST: gi|208388243|gb|DC945575.1|DC945575
EST:     CCCTTCAGAGAAGCACTGGACTCCAATCCCCGTTTTGGTGACAAGAAGAC                         GTATCAAATGAACCCCGCAAATTACCGCGAGGCTCTGATCGAGACAAGGTT
genomic: CCCTTCAGAGAAGCACTGGACTCCAATCCCCGTTTTGGTGACAAGAAGACgtaagttcca ... gtgttatcagGTATCAAATGAACCCCGCAAATTACCGCGAGGCTCTGATCGAGACAAGGTT
EST: gi|162232563|gb|FC408399.1|FC408399
EST:     CCCTTCAGAGAAGCACTGGACTCCAATCCCCGTTTTGGTGACAAGAAGAC                         GTATCAAATGAACCCCGCAAATTACCGCGAGGCTCTGATCGAGACAAGGTT
genomic: CCCTTCAGAGAAGCACTGGACTCCAATCCCCGTTTTGGTGACAAGAAGACgtaagttcca ... gtgttatcagGTATCAAATGAACCCCGCAAATTACCGCGAGGCTCTGATCGAGACAAGGTT
EST: gi|37821562|gb|BJ579628.1|BJ579628
EST:     CCCTTCAGAGAAGCACTGGACTCCAATCCCCGTTTTGGTGACAAGAAGAC                         GTATCAAATGAACCCCGCAAATTACCGCGAGGCTCTGATCGAGACAAGGTT
genomic: CCCTTCAGAGAAGCACTGGACTCCAATCCCCGTTTTGGTGACAAGAAGACgtaagttcca ... gtgttatcagGTATCAAATGAACCCCGCAAATTACCGCGAGGCTCTGATCGAGACAAGGTT
EST: gi|162227004|gb|FC403361.1|FC403361
EST:     CCCTTCAGAGAAGCACTGGACTCCAATCCCCGTTTTGGTGACAAGAAGAC                         GTATCAAATGAACCCCGCAAATTACCGCGAGGCTCTGATCGAGACAAGGTT
genomic: CCCTTCAGAGAAGCACTGGACTCCAATCCCCGTTTTGGTGACAAGAAGACgtaagttcca ... gtgttatcagGTATCAAATGAACCCCGCAAATTACCGCGAGGCTCTGATCGAGACAAGGTT

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: 16 (upstream exon), 35 (downstream exon)
Score: 7

ATATGCAAGTGCCTTTTACGGGCCCTTCAGAGAAGCACTGGACTCCAATCCCCGTTTTGGTGACAAGAAGACgtaagttcca ... gtgttatcagGTATCAAATGAACCCCGCAAATTACCGCGAGGCTCTGATCGAGACAAGGTTGGACGAAGCTGAAGGTGCTGACATTCTCATG




<











<


<









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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATATGCAAGTGCCTTTTACGGGCCCTTCAGAGAAGCACTGGACTCCAATCCCCGTTTTGGTGACAAGAAGACgtaagttccaagtacaatctcttgtccggtattatgtcagtactagccaggattcaccaaaaggaatataattgcaattcatggggttttttacgaggtccttacctatgtggtgttatcag

- - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG