Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGGCCTGACCTGAATGCTGGCACTGCTGCGGAGTTGTTAGACGAGGCATACGTTCGCTGCGGCGAGGTGTGTGCTGAGTATGCGAAGACCTTCTACTTGGgtaagctttcctcggcttcgatctctttagtgtcttctgtagcccccccccccccccccccaaaaaaaaaannnnnnnnnnnnnnnnnnnnnnnnnnnnn...

Basic information

species Physcomitrella patens
transcript PP1S196_120V6.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S196_120V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: Vv12s0028g00960.t01 (Vitis vinifera), 5'ss of exon 1
-CGGCCTGACCTGAATGCTGGCACTGCTGCGGAGTTGTTAGACGAGGCATACGTTCGCTGCGGCGAGGTGTGTGCTGAGTATGCGAAGACCTTCTACTTGGgtaagctttc---ctcggcttcgatctctttagtgtcttctgtagcccccccccccccccccccaaaaaaaaaannnnnnnnnnnnnnnnnnnnnnnnnnnnn
 | |    | ||||  |   |     ||| |||  ||||  | | ||| || | | | ||||| ||||| ||||||||||| || |||||||||||||||||||   | ||    | | ||  | |||||  ||   |     || ||    |   | |    |      | |                               
CCTGTTGAAACTGATGGTATGGTGAACTG-GGATCTGTTGAATGGGGCTTATGATAGGTGCGGTGAGGTCTGTGCTGAGTACGCCAAGACCTTCTACTTGGgtactttctcatttttgcctctgctctctccag---ccataatacccatatcagtcactgttcttgtgtacatgttttcacactgaataatttcttttttcag
















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|162172355|gb|FC348296.1|FC348296
EST:     CGTTCGCTGCGGCGAGGTGTGTGCTGAGTATGCGAAGACCTTCTACTTGG                         GAACAAAGCTCATGACTCCGGAGAGGCAACGTGCCATATGGGCTATATATG
genomic: CGTTCGCTGCGGCGAGGTGTGTGCTGAGTATGCGAAGACCTTCTACTTGGgtaagctttc ... ttctttgcagGAACAAAGCTCATGACTCCGGAGAGGCAACGTGCCATATGGGCTATATATG
EST: gi|208366062|gb|DC935851.1|DC935851
EST:     CGTTCGCTGCGGCGAGGTGTGTGCTGAGTATGCGAAGACCTTCTACTTGG                         GAACAAAGCTCATGACTCCGGAGAGGCAACGTGCCATATGGGCTATATATG
genomic: CGTTCGCTGCGGCGAGGTGTGTGCTGAGTATGCGAAGACCTTCTACTTGGgtaagctttc ... ttctttgcagGAACAAAGCTCATGACTCCGGAGAGGCAACGTGCCATATGGGCTATATATG
EST: gi|100431995|gb|BY978612.1|BY978612
EST:     GTTCGCTGCGGCCGAG-TGTGTGCTGAGTATGCGAAGACCTTCTACTGGG                         GACCAA-GCTCATGA
genomic: GTTCGCTGCGGC-GAGGTGTGTGCTGAGTATGCGAAGACCTTCTACTTGGgtaagctttc ... ttctttgcagGAACAAAGCTCATGA
EST: gi|100419167|gb|BY975871.1|BY975871
EST:     CGTTCGCTGCGGCGAGGTGTGTGCTGAGTATGCGAAGACCTTCTACTTGG                         GAACAAAGCTCATGACTCCGGAGAGGCAACGTGCCATATGGGCTATATATG
genomic: CGTTCGCTGCGGCGAGGTGTGTGCTGAGTATGCGAAGACCTTCTACTTGGgtaagctttc ... ttctttgcagGAACAAAGCTCATGACTCCGGAGAGGCAACGTGCCATATGGGCTATATATG
EST: gi|162167052|gb|FC342514.1|FC342514
EST:     CGTTCGCTGCGGCGAGGTGTGTGCTGAGTATGCGAAGACCTTCTACTTGG                         GAACAAAGCTCATGACTCCGGAGAGGCAACGTGCCATATGGGCTATATATG
genomic: CGTTCGCTGCGGCGAGGTGTGTGCTGAGTATGCGAAGACCTTCTACTTGGgtaagctttc ... ttctttgcagGAACAAAGCTCATGACTCCGGAGAGGCAACGTGCCATATGGGCTATATATG
EST: gi|162214019|gb|FC390426.1|FC390426
EST:     CGTTCGCTGCGGCGAGGTGTGTGCTGAGTATGCGAAGACCTTCTACTTGG                         GAACAAAGCTCATGACTCCGGAGAGGCAACGTGCCATATGGGCTATATATG
genomic: CGTTCGCTGCGGCGAGGTGTGTGCTGAGTATGCGAAGACCTTCTACTTGGgtaagctttc ... ttctttgcagGAACAAAGCTCATGACTCCGGAGAGGCAACGTGCCATATGGGCTATATATG
EST: gi|162173386|gb|FC349557.1|FC349557
EST:     CGTTCGCTGCGGCGAGGTGTGTGCTGAGTATGCGAAGACCTTCTACTTGG                         GAACAAAGCTCATGACTCCGGAGAGGCAACGTGCCATATGGGCTATATATG
genomic: CGTTCGCTGCGGCGAGGTGTGTGCTGAGTATGCGAAGACCTTCTACTTGGgtaagctttc ... ttctttgcagGAACAAAGCTCATGACTCCGGAGAGGCAACGTGCCATATGGGCTATATATG
EST: gi|162245355|gb|FC421257.1|FC421257
EST:     CGTTCGCTGCGGCGAGGTGTGTGCTGAGTATGCGAAGACCTTCTACTTGG                         GAACAAAGCTCATGACTCCGGAGAGGCAACGTGCCATATGGGCTATATATG
genomic: CGTTCGCTGCGGCGAGGTGTGTGCTGAGTATGCGAAGACCTTCTACTTGGgtaagctttc ... ttctttgcagGAACAAAGCTCATGACTCCGGAGAGGCAACGTGCCATATGGGCTATATATG
EST: gi|162269612|gb|FC445571.1|FC445571
EST:     CGTTCGCTGCGGCGAGGTGTGTGCTGAGTATGCGAAGACCTTCTACTTGG                         GAACAAAGCTCATGACTCCGGAGAGGCAACGTGCCATATGGGCTATATATG
genomic: CGTTCGCTGCGGCGAGGTGTGTGCTGAGTATGCGAAGACCTTCTACTTGGgtaagctttc ... ttctttgcagGAACAAAGCTCATGACTCCGGAGAGGCAACGTGCCATATGGGCTATATATG
EST: gi|100452821|gb|CJ975460.1|CJ975460
EST:     CGTTCGCTGCGGCNAGGTGTGTGCTGANTATGCNAAAACCTTCTACTTGG                         -AACAAAGCTCATGACT
genomic: CGTTCGCTGCGGCGAGGTGTGTGCTGAGTATGCGAAGACCTTCTACTTGGgtaagctttc ... ttctttgcagGAACAAAGCTCATGACT
EST: gi|100444172|gb|BY964070.1|BY964070
EST:     CGTTCGCTGCGGCGAGGTGTGTGCTGAGTATGCGAAGACCTTCTACTTGG                         GGAACAA-GCTCATGACTCC
genomic: CGTTCGCTGCGGCGAGGTGTGTGCTGAGTATGCGAAGACCTTCTACTTGGgtaagctttc ... ttctttgcagG-AACAAAGCTCATGACTCC
EST: gi|162175016|gb|FC351123.1|FC351123
EST:     CGTTCGCTGCGGCGAGGTGTGTGCTGAGTATGCGAAGACCTTCTACTTGG                         GAACAAAGCTCATGACTCCGGAGAGGCAACGTGCCATATGGGCTATATATG
genomic: CGTTCGCTGCGGCGAGGTGTGTGCTGAGTATGCGAAGACCTTCTACTTGGgtaagctttc ... ttctttgcagGAACAAAGCTCATGACTCCGGAGAGGCAACGTGCCATATGGGCTATATATG
EST: gi|100393933|gb|BY953555.1|BY953555
EST:     CGTTCGCTGCGGCGAGGTGTGTGCTGAGTATGCGAAGACCTTCTACTTGG                         GAACAAAGCTCATGACTCCGGAGAGGCAACGTGCCATATGGGCTATATATG
genomic: CGTTCGCTGCGGCGAGGTGTGTGCTGAGTATGCGAAGACCTTCTACTTGGgtaagctttc ... ttctttgcagGAACAAAGCTCATGACTCCGGAGAGGCAACGTGCCATATGGGCTATATATG

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: 32 (upstream exon), 35 (downstream exon)
Score: 25

CGGCCTGACCTGAATGCTGGCACTGCTGCGGAGTTGTTAGACGAGGCATACGTTCGCTGCGGCGAGGTGTGTGCTGAGTATGCGAAGACCTTCTACTTGGgtaagctttc ... ttctttgcagGAACAAAGCTCATGACTCCGGAGAGGCAACGTGCCATATGGGCTATATATG




<











<


<









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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGGCCTGACCTGAATGCTGGCACTGCTGCGGAGTTGTTAGACGAGGCATACGTTCGCTGCGGCGAGGTGTGTGCTGAGTATGCGAAGACCTTCTACTTGGgtaagctttcctcggcttcgatctctttagtgtcttctgtagcccccccccccccccccccaaaaaaaaaannnnnnnnnnnnnnnnnnnnnnnnnnnnn

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caaaaaaa