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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaatcgcacattatcaccatgtcgaagtgatccctctaatttaatgcctgacgtattgaatgtactgagtctgcattaccgtctttacatatggtcacgcacggcgtgctaatgatatcgttggatatgaaaccagGAAATGCCGGCAGCGTTTCAAAGCTTGGACCAAATCAAAGGATCCTTGAGGCGTTGAGCGCCACACAGCCCAGCAAGTATTCCGAGTCCATGTTTGCCAA

Basic information

species Physcomitrella patens
transcript PP1S98_113V6.4
intron # 2
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|18369530|gb|BJ201617.1|BJ201617
EST:     GCCGGTCCAAGGTATTTCGGTGATGGGAGCTCTCAAGAATGTAGCTACTG                         GAAATGCCGGCAGCGTTTCAAAGCTTGGACCAAATCAAAGGATCCTTGAGG
genomic: GCCGGTCCAAGGTATTTCGGTGATGGGAGCTCTCAAGAATGTAGCTACTGgtaaaatcgc ... atgaaaccagGAAATGCCGGCAGCGTTTCAAAGCTTGGACCAAATCAAAGGATCCTTGAGG
EST: gi|18349339|gb|BJ181388.1|BJ181388
EST:     GCCGGTCCAAGGTATTTCGGTGATGGGAGCTCTCAAGAATGTAGCTACTG                         GAAATGCCGGCAGCGTTTCAAAGCTTGGACCAAATCAAAGGATCCTTGAGG
genomic: GCCGGTCCAAGGTATTTCGGTGATGGGAGCTCTCAAGAATGTAGCTACTGgtaaaatcgc ... atgaaaccagGAAATGCCGGCAGCGTTTCAAAGCTTGGACCAAATCAAAGGATCCTTGAGG
EST: gi|18367740|gb|BJ199823.1|BJ199823
EST:     GCCGGTCCAAGGTATTTCGGTGATGGGAGCTCTCAAGAATGTAGCTACTG                         GAAATGCCGGCAGCGTTTCAAAGCTTGGACCAAATCAAAGGATCCTTGAGG
genomic: GCCGGTCCAAGGTATTTCGGTGATGGGAGCTCTCAAGAATGTAGCTACTGgtaaaatcgc ... atgaaaccagGAAATGCCGGCAGCGTTTCAAAGCTTGGACCAAATCAAAGGATCCTTGAGG
EST: gi|18349121|gb|BJ181170.1|BJ181170
EST:     GCCGGTCCAAGGTATTTCGGTGATGGGAGCTCTCAAGAATGTAGCTACTG                         GAAATGCCGGCAGCGTTTCAAAGCTTGGACCAAATCAAAGGATCCTTGAGG
genomic: GCCGGTCCAAGGTATTTCGGTGATGGGAGCTCTCAAGAATGTAGCTACTGgtaaaatcgc ... atgaaaccagGAAATGCCGGCAGCGTTTCAAAGCTTGGACCAAATCAAAGGATCCTTGAGG
EST: gi|18366901|gb|BJ198981.1|BJ198981
EST:     GCCGGTCCAAGGTATTTCGGTGATGGGAGCTCTCAAGAATGTAGCTACTG                         GAAATGCCGGCAGCGTTTCAAAGCTTGGACCAAATCAAAGGATCCTTGAGG
genomic: GCCGGTCCAAGGTATTTCGGTGATGGGAGCTCTCAAGAATGTAGCTACTGgtaaaatcgc ... atgaaaccagGAAATGCCGGCAGCGTTTCAAAGCTTGGACCAAATCAAAGGATCCTTGAGG
EST: gi|18360688|gb|BJ192751.1|BJ192751
EST:     GCCGGTCCAAGGTATTTCGGTGATGGGAGCTCTCAAGAATGTAGCTACTG                         GAAATGCCGGCAGCGTTTCAAAGCTTGGACCAAATCAAAGGATCCTTGAGG
genomic: GCCGGTCCAAGGTATTTCGGTGATGGGAGCTCTCAAGAATGTAGCTACTGgtaaaatcgc ... atgaaaccagGAAATGCCGGCAGCGTTTCAAAGCTTGGACCAAATCAAAGGATCCTTGAGG
EST: gi|18375213|gb|BJ206791.1|BJ206791
EST:     GCCGGTCCAAGGTATTTCGGTGATGGGAGCTCTCAAGAATGTAGCTACTG                         GAAATGCCGGCAGCGTTTCAAAGCTTGGACCAAATCAAAGGATCCTTGAGG
genomic: GCCGGTCCAAGGTATTTCGGTGATGGGAGCTCTCAAGAATGTAGCTACTGgtaaaatcgc ... atgaaaccagGAAATGCCGGCAGCGTTTCAAAGCTTGGACCAAATCAAAGGATCCTTGAGG
EST: gi|18362274|gb|BJ194344.1|BJ194344
EST:     GCCGGTCCAAGGTATTTCGGTGATGGGAGCTCTCAAGAATGTAGCTACTG                         GAAATGCCGGCAGCGTTTCAAAGCTTGGACCAAATCAAAGGATCCTTGAGG
genomic: GCCGGTCCAAGGTATTTCGGTGATGGGAGCTCTCAAGAATGTAGCTACTGgtaaaatcgc ... atgaaaccagGAAATGCCGGCAGCGTTTCAAAGCTTGGACCAAATCAAAGGATCCTTGAGG
EST: gi|18357632|gb|BJ189691.1|BJ189691
EST:     GCCGGTCCAAGGTATTTCGGTGATGGGAGCTCTCAAGAATGTAGCTACTG                         GAAATGCCGGCAGCGTTTCAAAGCTTGGACCAAATCAAAGGATCCTTGAGG
genomic: GCCGGTCCAAGGTATTTCGGTGATGGGAGCTCTCAAGAATGTAGCTACTGgtaaaatcgc ... atgaaaccagGAAATGCCGGCAGCGTTTCAAAGCTTGGACCAAATCAAAGGATCCTTGAGG
EST: gi|18343578|gb|BJ175616.1|BJ175616
EST:     GCCGGTCCAAGGTATTTCGGTGATGGGAGCTCTCAAGAATGTAGCTACTG                         GAAATGCCGGCAGCGTTTCAAAGCTTGGACCAAATCAAAGGATCCTTGAGG
genomic: GCCGGTCCAAGGTATTTCGGTGATGGGAGCTCTCAAGAATGTAGCTACTGgtaaaatcgc ... atgaaaccagGAAATGCCGGCAGCGTTTCAAAGCTTGGACCAAATCAAAGGATCCTTGAGG
EST: gi|18366730|gb|BJ198809.1|BJ198809
EST:     GCCGGTCCAAGGTATTTCGGTGATGGGAGCTCTCAAGAATGTAGCTACTG                         GAAATGCCGGCAGCGTTTCAAAGCTTGGACCAAATCAAAGGATCCTTGAGG
genomic: GCCGGTCCAAGGTATTTCGGTGATGGGAGCTCTCAAGAATGTAGCTACTGgtaaaatcgc ... atgaaaccagGAAATGCCGGCAGCGTTTCAAAGCTTGGACCAAATCAAAGGATCCTTGAGG
EST: gi|18372800|gb|BJ204402.1|BJ204402
EST:     GCCGGTCCAAGGTATTTCGGTGATGGGAGCTCTCAAGAATGTAGCTACTG                         GAAATGCCGGCAGCGTTTCAAAGCTTGGACCAAATCAAAGGATCCTTGAGG
genomic: GCCGGTCCAAGGTATTTCGGTGATGGGAGCTCTCAAGAATGTAGCTACTGgtaaaatcgc ... atgaaaccagGAAATGCCGGCAGCGTTTCAAAGCTTGGACCAAATCAAAGGATCCTTGAGG
EST: gi|18366664|gb|BJ198743.1|BJ198743
EST:     GCCGGTCCAAGGTATTTCGGTGATGGGAGCTCTCAAGAATGTAGCTACTG                         GAAATGCCGGCAGCGTTTCAAAGCTTGGACCAAATCAAAGGATCCTTGAGG
genomic: GCCGGTCCAAGGTATTTCGGTGATGGGAGCTCTCAAGAATGTAGCTACTGgtaaaatcgc ... atgaaaccagGAAATGCCGGCAGCGTTTCAAAGCTTGGACCAAATCAAAGGATCCTTGAGG
EST: gi|18351125|gb|BJ183176.1|BJ183176
EST:     GCCGGTCCAAGGTATTTCGGTGATGGGAGCTCTCAAGAATGTAGCTACTG                         GAAATGCCGGCAGCGTTTCAAAGCTTGGACCAAATCAAAGGATCCTTGAGG
genomic: GCCGGTCCAAGGTATTTCGGTGATGGGAGCTCTCAAGAATGTAGCTACTGgtaaaatcgc ... atgaaaccagGAAATGCCGGCAGCGTTTCAAAGCTTGGACCAAATCAAAGGATCCTTGAGG

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: 34 (upstream exon), 35 (downstream exon)
Score: 38

GGGGCAATCTCTAAAGAGACTAACAAGCCGGTCCAAGGTATTTCGGTGATGGGAGCTCTCAAGAATGTAGCTACTGgtaaaatcgc ... atgaaaccagGAAATGCCGGCAGCGTTTCAAAGCTTGGACCAAATCAAAGGATCCTTGAGGCGTTGAGCGCCACACAGCCCAGCAAGTATTCCGAGTCCATGTTTGCCAA




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctttacatatggtcacgcacggcgtgctaatgatatcgttggatatgaaaccagGAAATGCCGGCAGCGTTTCAAAGCTTGGACCAAATCAAAGGATCCTTGAGGCGTTGAGCGCCACACAGCCCAGCAAGTATTCCGAGTCCATGTTTGCCAA
                         tgctaat  putative branch site (score: 38)
                            taatgatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaaatcgcacattatcaccatgtcgaagtgatccctctaatttaatgcctgacgtattgaatgtactgagtctgcattaccgtctttacatatggtcacgcacggcgtgctaatgatatcgttggatatgaaaccagGAAATGCCGGCAGCGTTTCAAAGCTTGGACCAAATCAAAGGATCCTTGAGGCGTTGAGCGCCACACAGCCCAGCAAGTATTCCGAGTCCATGTTTGCCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG