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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagccagtgctctttcgttttcatacatgtgcttccacactctctagtttatgcatttcatagtgggagctcctgcagcttgtgcatttcagtatattagattatctgtggcatttttacggctgctgaaggttctttccatgactaaataaactgttggcttttgtgcattttagGAGTTGCGAAAGCAATATGGAAGTGGACACCAGACTCAACTTGCTTCTAAATTTGTGCTTCATGCTATGAACCAAGCTTTACAGTTTTTGCAGGAAAACT

Basic information

species Physcomitrella patens
transcript PP1S79_254V6.2
intron # 8
splice site 3'
intron type U2

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|162158020|gb|FC334954.1|FC334954
EST:     ACCTTGAACGACCAGCAGATTTATTTTCTGGAACTTTTAATGGGATTGAA                         GAGTTGCGAAAGCAATATGGAAGTGGACACCAGACTCAACTTGCTTCTAAA
genomic: ACCTTGAACGACCAGCAGATTTATTTTCTGGAACTTTTAATGGGATTGAAgtaagccagt ... tgcattttagGAGTTGCGAAAGCAATATGGAAGTGGACACCAGACTCAACTTGCTTCTAAA
EST: gi|37841176|gb|BJ599184.1|BJ599184
EST:     ACCTTGAACGACCAGCAGATTTATTTTCTGGAACTTTTAATGGGATTGAA                         GAGTTGCGAAAGCAATATGGAAGTGGACACCAGACTCAACTTGCTTCTAAA
genomic: ACCTTGAACGACCAGCAGATTTATTTTCTGGAACTTTTAATGGGATTGAAgtaagccagt ... tgcattttagGAGTTGCGAAAGCAATATGGAAGTGGACACCAGACTCAACTTGCTTCTAAA
EST: gi|162269549|gb|FC445105.1|FC445105
EST:     ACCTTGAACGACCAGCAGATTTATTTTCTGGAACTTTTAATGGGATTGAA                         GAGTTGCGAAAGCAATATGGAAGTGGACACCAGACTCAACTTGCTTCTAAA
genomic: ACCTTGAACGACCAGCAGATTTATTTTCTGGAACTTTTAATGGGATTGAAgtaagccagt ... tgcattttagGAGTTGCGAAAGCAATATGGAAGTGGACACCAGACTCAACTTGCTTCTAAA
EST: gi|37836542|gb|BJ594550.1|BJ594550
EST:     ACCTTGAACGACCAGCAGATTTATTTTCTGGAACTTTTAATGGGATTGAA                         GAGTTGCGAAAGCAATATGGAAGTGGACACCAGACTCAACTTGCTTCTAAA
genomic: ACCTTGAACGACCAGCAGATTTATTTTCTGGAACTTTTAATGGGATTGAAgtaagccagt ... tgcattttagGAGTTGCGAAAGCAATATGGAAGTGGACACCAGACTCAACTTGCTTCTAAA
EST: gi|208354680|gb|DC918706.1|DC918706
EST:     ACCTTGAACGACCAGCAGATTTATTTTCTGGAACTTTTAATGGGATTGAA                         GAGTTGCGAAAGCAATATGGAAGTGGACACCAGACTCAACTTGCTTCTAAA
genomic: ACCTTGAACGACCAGCAGATTTATTTTCTGGAACTTTTAATGGGATTGAAgtaagccagt ... tgcattttagGAGTTGCGAAAGCAATATGGAAGTGGACACCAGACTCAACTTGCTTCTAAA
EST: gi|208347734|gb|DC925607.1|DC925607
EST:     ACCTTGAACGACCAGCAGATTTATTTTCTGGAACTTTTAATGGGATTGAA                         GAGTTGCGAAAGCAATATGGAAGTGGACACCAGACTCAACTTGCTTCTAAA
genomic: ACCTTGAACGACCAGCAGATTTATTTTCTGGAACTTTTAATGGGATTGAAgtaagccagt ... tgcattttagGAGTTGCGAAAGCAATATGGAAGTGGACACCAGACTCAACTTGCTTCTAAA
EST: gi|208366175|gb|DC955276.1|DC955276
EST:     ACCTTGAACGACCAGCAGATTTATTTTCTGGAACTTTTAATGGGATTGAA                         GAGTTGCGAAAGCAATATGGAAGTGGACACCAGACTCAACTTGCTTCTAAA
genomic: ACCTTGAACGACCAGCAGATTTATTTTCTGGAACTTTTAATGGGATTGAAgtaagccagt ... tgcattttagGAGTTGCGAAAGCAATATGGAAGTGGACACCAGACTCAACTTGCTTCTAAA
EST: gi|162238634|gb|FC418997.1|FC418997
EST:     ACCTTGAACGACCAGCAGATTTATTTTCTGGAACTTTTAATGGGATTGAA                         GAGTTGCGAAAGCAATATGGAAGTGGACACCAGACTCAACTTGCTTCTAAA
genomic: ACCTTGAACGACCAGCAGATTTATTTTCTGGAACTTTTAATGGGATTGAAgtaagccagt ... tgcattttagGAGTTGCGAAAGCAATATGGAAGTGGACACCAGACTCAACTTGCTTCTAAA
EST: gi|37833353|gb|BJ591365.1|BJ591365
EST:     AATGGGATTGAA                         GAGTTGCGAAAGCAATATGGAAGTGGACACCAGACTCAACTTGCTTCTAAA
genomic: AATGGGATTGAAgtaagccagt ... tgcattttagGAGTTGCGAAAGCAATATGGAAGTGGACACCAGACTCAACTTGCTTCTAAA
EST: gi|37845130|gb|BJ603138.1|BJ603138
EST:     ACCTTGAACGACCAGCAGATTTATTTTCTGGAACTTTTAATGGGATTGAA                         GAGTTGCGAAAGCAATATGGAAGTGGACACCAGACTCAACTTGCTTCTAAA
genomic: ACCTTGAACGACCAGCAGATTTATTTTCTGGAACTTTTAATGGGATTGAAgtaagccagt ... tgcattttagGAGTTGCGAAAGCAATATGGAAGTGGACACCAGACTCAACTTGCTTCTAAA
EST: gi|37850186|gb|BJ608194.1|BJ608194
EST:     ACCTTGAACGACCAGCAGATTTATTTTCTGGAACTTTTAATGGGATTGAA                         GAGTTGCGAAAGCAATATGGAAGTGGACACCAGACTCAACTTGCTTCTAAA
genomic: ACCTTGAACGACCAGCAGATTTATTTTCTGGAACTTTTAATGGGATTGAAgtaagccagt ... tgcattttagGAGTTGCGAAAGCAATATGGAAGTGGACACCAGACTCAACTTGCTTCTAAA
EST: gi|37844185|gb|BJ602193.1|BJ602193
EST:     ACCTTGAACGACCAGCAGATTTATTTTCTGGAACTTTTAATGGGATTGAA                         GAGTTGCGAAAGCAATATGGAAGTGGACACCAGACTCAACTTGCTTCTAAA
genomic: ACCTTGAACGACCAGCAGATTTATTTTCTGGAACTTTTAATGGGATTGAAgtaagccagt ... tgcattttagGAGTTGCGAAAGCAATATGGAAGTGGACACCAGACTCAACTTGCTTCTAAA
EST: gi|37843376|gb|BJ601384.1|BJ601384
EST:     ACCTTGAACGACCAGCAGATTTATTTTCTGGAACTTTTAATGGGATTGAA                         GAGTTGCGAAAGCAATATGGAAGTGGACACCAGACTCAACTTGCTTCTAAA
genomic: ACCTTGAACGACCAGCAGATTTATTTTCTGGAACTTTTAATGGGATTGAAgtaagccagt ... tgcattttagGAGTTGCGAAAGCAATATGGAAGTGGACACCAGACTCAACTTGCTTCTAAA
EST: gi|208381754|gb|DC928417.1|DC928417
EST:     ACCTTGAACGACCAGCAGATTTATTTTCTGGGACTTTTAATGGGANTGAA                         GAGTTGCGAAAGCAATATGGAAGTGGACACCAGACTCAACTTGCTTCTAAA
genomic: ACCTTGAACGACCAGCAGATTTATTTTCTGGAACTTTTAATGGGATTGAAgtaagccagt ... tgcattttagGAGTTGCGAAAGCAATATGGAAGTGGACACCAGACTCAACTTGCTTCTAAA
EST: gi|37835860|gb|BJ593872.1|BJ593872
EST:     ACCTTGAACGACCAGCAGATTTATTTTCTGGAACTTTTAATGGGATTGAA                         GAGTTGCGAAAGCAATATGGAAGTGGACACCAGACTCAACTTGCTTCTAAA
genomic: ACCTTGAACGACCAGCAGATTTATTTTCTGGAACTTTTAATGGGATTGAAgtaagccagt ... tgcattttagGAGTTGCGAAAGCAATATGGAAGTGGACACCAGACTCAACTTGCTTCTAAA
EST: gi|37843420|gb|BJ601428.1|BJ601428
EST:     ACCTTGAACGACCAGCAGATTTATTTTCTGGAACTTTTAATGGGATTGAA                         GAGTTGCGAAAGCAATATGGAAGTGGACACCAGACTCAACTTGCTTCTAAA
genomic: ACCTTGAACGACCAGCAGATTTATTTTCTGGAACTTTTAATGGGATTGAAgtaagccagt ... tgcattttagGAGTTGCGAAAGCAATATGGAAGTGGACACCAGACTCAACTTGCTTCTAAA
EST: gi|162192771|gb|FC369622.1|FC369622
EST:     ACCTTGAACGACCAGCAGATTTATTTTCTGGAACTTTTAATGGGATTGAA                         GAGTTGCGAAAGCAATATGGAAGTGGACACCAGACTCAACTTGCTTCTAAA
genomic: ACCTTGAACGACCAGCAGATTTATTTTCTGGAACTTTTAATGGGATTGAAgtaagccagt ... tgcattttagGAGTTGCGAAAGCAATATGGAAGTGGACACCAGACTCAACTTGCTTCTAAA
EST: gi|67699119|gb|BJ959352.1|BJ959352
EST:     ACCTTGAACGACCAGCAGATTTATTTTCTGGAACTTTTAATGGGATTGAA                         GAGTTGCGAAAGCAATATGGAAGTGGACACCAGACTCAACTTGCTTCTAAA
genomic: ACCTTGAACGACCAGCAGATTTATTTTCTGGAACTTTTAATGGGATTGAAgtaagccagt ... tgcattttagGAGTTGCGAAAGCAATATGGAAGTGGACACCAGACTCAACTTGCTTCTAAA
EST: gi|37842304|gb|BJ600312.1|BJ600312
EST:     ACCTTGAACGACCAGCAGATTTATTTTCTGGAACTTTTAATGGGATTGAA                         GAGTTGCGAAAGCAATATGGAAGTGGACACCAGACTCAACTTGCTTCTAAA
genomic: ACCTTGAACGACCAGCAGATTTATTTTCTGGAACTTTTAATGGGATTGAAgtaagccagt ... tgcattttagGAGTTGCGAAAGCAATATGGAAGTGGACACCAGACTCAACTTGCTTCTAAA
EST: gi|37824362|gb|BJ582428.1|BJ582428
EST:     ACCTTGAACGACCAGCAGATTTATTTTCTGGAACTTTTAATGGGATTGAA                         GAGTTGCGAAAGCAATATGGAAGTGGACACCAGACTCAACTTGCTTCTAAA
genomic: ACCTTGAACGACCAGCAGATTTATTTTCTGGAACTTTTAATGGGATTGAAgtaagccagt ... tgcattttagGAGTTGCGAAAGCAATATGGAAGTGGACACCAGACTCAACTTGCTTCTAAA
EST: gi|18340062|gb|BJ172090.1|BJ172090
EST:     ACCTTGAACGACCAGCAGATTTATTTTCTGGAACTTTTAATGGGATTGAA                         GAGTTGCGAAAGCAATATGGAAGTGGACACCAGACTCAACTTGCTTCTAAA
genomic: ACCTTGAACGACCAGCAGATTTATTTTCTGGAACTTTTAATGGGATTGAAgtaagccagt ... tgcattttagGAGTTGCGAAAGCAATATGGAAGTGGACACCAGACTCAACTTGCTTCTAAA
EST: gi|208380520|gb|DC915422.1|DC915422
EST:     ACCTTGAACGACCAGCAGATTTATTTTCTGGAACTTTTAATGGGATTGAA                         GAGTTGCGAAAGCAATATGGAAGTGGACACCAGACTCAACTTGCTTCTAAA
genomic: ACCTTGAACGACCAGCAGATTTATTTTCTGGAACTTTTAATGGGATTGAAgtaagccagt ... tgcattttagGAGTTGCGAAAGCAATATGGAAGTGGACACCAGACTCAACTTGCTTCTAAA
EST: gi|162276878|gb|FC452560.1|FC452560
EST:     ACCTTGAACGACCAGCAGATTTATTTTCTGGAACTTTTAATGGGATTGAA                         GAGTTGCGAAAGCAATATGGAAGTGGACACCAGACTCAACTTGCTTCTAAA
genomic: ACCTTGAACGACCAGCAGATTTATTTTCTGGAACTTTTAATGGGATTGAAgtaagccagt ... tgcattttagGAGTTGCGAAAGCAATATGGAAGTGGACACCAGACTCAACTTGCTTCTAAA
EST: gi|208348822|gb|DC925894.1|DC925894
EST:     ACCTTGAACGACCAGCAGATTTATTTTCTGGAACTTTTAATGGGATTGAA                         GAGTTGCGAAAGCAATATGGAAGTGGACACCAGACTCAACTTGCTTCTAAA
genomic: ACCTTGAACGACCAGCAGATTTATTTTCTGGAACTTTTAATGGGATTGAAgtaagccagt ... tgcattttagGAGTTGCGAAAGCAATATGGAAGTGGACACCAGACTCAACTTGCTTCTAAA
EST: gi|162191817|gb|FC367966.1|FC367966
EST:     ACCTTGAACGACCAGCAGATTTATTTTCTGGAACTTTTAATGGGATTGAA                         GAGTTGCGAAAGCAATATGGAAGTGGACACCAGACTCAACTTGCTTCTAAA
genomic: ACCTTGAACGACCAGCAGATTTATTTTCTGGAACTTTTAATGGGATTGAAgtaagccagt ... tgcattttagGAGTTGCGAAAGCAATATGGAAGTGGACACCAGACTCAACTTGCTTCTAAA
EST: gi|208382347|gb|DC919335.1|DC919335
EST:     ACCTTGAACGACCAGCAGATTTATTTTCTGGAACTTTTAATGGGATTGAA                         GAGTTGCGAAAGCAATATGGAAGTGGACACCAGACTCAACTTGCTTCTAAA
genomic: ACCTTGAACGACCAGCAGATTTATTTTCTGGAACTTTTAATGGGATTGAAgtaagccagt ... tgcattttagGAGTTGCGAAAGCAATATGGAAGTGGACACCAGACTCAACTTGCTTCTAAA
EST: gi|37822622|gb|BJ580688.1|BJ580688
EST:     ACCTTGAACGACCAGCAGATTTATTTTCTGGAACTTTTAATGGGATTGAA                         GAGTTGCGAAAGCAATATGGAAGTGGACACCAGACTCAACTTGCTTCTAAA
genomic: ACCTTGAACGACCAGCAGATTTATTTTCTGGAACTTTTAATGGGATTGAAgtaagccagt ... tgcattttagGAGTTGCGAAAGCAATATGGAAGTGGACACCAGACTCAACTTGCTTCTAAA
EST: gi|162164830|gb|FC341345.1|FC341345
EST:     ACCTTGAACGACCAGCAGATTTATTTTCTGGAACTTTTAATGGGATTGAA                         GAGTTGCGAAAGCAATATGGAAGTGGACACCAGACTCAACTTGCTTCTAAA
genomic: ACCTTGAACGACCAGCAGATTTATTTTCTGGAACTTTTAATGGGATTGAAgtaagccagt ... tgcattttagGAGTTGCGAAAGCAATATGGAAGTGGACACCAGACTCAACTTGCTTCTAAA
EST: gi|37834032|gb|BJ592044.1|BJ592044
EST:     ACCTTGAACGACCAGCAGATTTATTTTCTGGAACTTTTAATGGGATTGAA                         GAGTTGCGAAAGCAATATGGAAGTGGACACCAGACTCAACTTGCTTCTAAA
genomic: ACCTTGAACGACCAGCAGATTTATTTTCTGGAACTTTTAATGGGATTGAAgtaagccagt ... tgcattttagGAGTTGCGAAAGCAATATGGAAGTGGACACCAGACTCAACTTGCTTCTAAA
EST: gi|162162092|gb|FC338883.1|FC338883
EST:     ACCTTGAACGACCAGCAGATTTATTTTCTGGAACTTTTAATGGGATTGAA                         GAGTTGCGAAAGCAATATGGAAGTGGACACCAGACTCAACTTGCTTCTAAA
genomic: ACCTTGAACGACCAGCAGATTTATTTTCTGGAACTTTTAATGGGATTGAAgtaagccagt ... tgcattttagGAGTTGCGAAAGCAATATGGAAGTGGACACCAGACTCAACTTGCTTCTAAA
EST: gi|162195496|gb|FC369353.1|FC369353
EST:     ACCTTGAACGACCAGCAGATTTATTTTCTGGAACTTTTAATGGGATTGAA                         GAGTTGCGAAAGCAATATGGAAGTGGACACCAGACTCAACTTGCTTCTAAA
genomic: ACCTTGAACGACCAGCAGATTTATTTTCTGGAACTTTTAATGGGATTGAAgtaagccagt ... tgcattttagGAGTTGCGAAAGCAATATGGAAGTGGACACCAGACTCAACTTGCTTCTAAA

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: 28 (upstream exon), 33 (downstream exon)
Score: 10

GGGCTTATTCAGAAATATGAAGCGAGCAGTCTCTTCACACCAAGTTGTAGACCTTGAACGACCAGCAGATTTATTTTCTGGAACTTTTAATGGGATTGAAgtaagccagt ... tgcattttagGAGTTGCGAAAGCAATATGGAAGTGGACACCAGACTCAACTTGCTTCTAAATTTGTGCTTCATGCTATGAACCAAGCTTTACAGTTTTTGCAGGAAAACT




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gctgctgaaggttctttccatgactaaataaactgttggcttttgtgcattttagGAGTTGCGAAAGCAATATGGAAGTGGACACCAGACTCAACTTGCTTCTAAATTTGTGCTTCATGCTATGAACCAAGCTTTACAGTTTTTGCAGGAAAACT
                     gactaaa  putative branch site (score: 10)
                                       cttttgt  putative PPT
                      actaaataaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagccagtgctctttcgttttcatacatgtgcttccacactctctagtttatgcatttcatagtgggagctcctgcagcttgtgcatttcagtatattagattatctgtggcatttttacggctgctgaaggttctttccatgactaaataaactgttggcttttgtgcattttagGAGTTGCGAAAGCAATATGGAAGTGGACACCAGACTCAACTTGCTTCTAAATTTGTGCTTCATGCTATGAACCAAGCTTTACAGTTTTTGCAGGAAAACT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT