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

...ccaatggtttctccaatttctatctgaattttggacctcgtgaatttcctactcctaccttcttaactgacatagtgatgacttgtgtgggttacttcagTGGTATGGGTCCTGATTCTCGTGTCTTAGTTCGCAAAAGCCGGAAGCAAGCACAAACGTATCAGCGACTTTATCAG

Basic information

species Physcomitrella patens
transcript PP1S61_202V6.1
intron # 4
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|162247556|gb|FC421677.1|FC421677
EST:     CGATAAACAAGATTCAGTCACTGACGCCAAATATCGGAGTCGTCTACAG                         TGGTATGGGTCCTGATTCTCGTGTCTTAGTTCGCAAAAGCCGGAAGCAAGC
genomic: CGATAAACAAGATTCAGTCACTGACGCCAAATATCGGAGTCGTCTACAGgtcagtgctt ... gttacttcagTGGTATGGGTCCTGATTCTCGTGTCTTAGTTCGCAAAAGCCGGAAGCAAGC
EST: gi|162262550|gb|FC439541.1|FC439541
EST:     ATAAACAAGATTCAGTCACTGACGCCAAATATCGGAGTCGTCTACAG                         TGGTATGGGTCCTGATTCTCGTGTCTTAGTTCGCAAAAGCCGGAAGCAAGC
genomic: ATAAACAAGATTCAGTCACTGACGCCAAATATCGGAGTCGTCTACAGgtcagtgctt ... gttacttcagTGGTATGGGTCCTGATTCTCGTGTCTTAGTTCGCAAAAGCCGGAAGCAAGC
EST: gi|18347210|gb|BJ179256.1|BJ179256
EST:     ATAAACAAGATTCAGTCGCTGACGCCAAATATCGGAGTCGTCTACAG                         TGGTATGGGTCCTGATTCTCGTGTCTTAGTTCGCAAAAGCCGGAAGCAAGC
genomic: ATAAACAAGATTCAGTCACTGACGCCAAATATCGGAGTCGTCTACAGgtcagtgctt ... gttacttcagTGGTATGGGTCCTGATTCTCGTGTCTTAGTTCGCAAAAGCCGGAAGCAAGC
EST: gi|162275765|gb|FC451936.1|FC451936
EST:     ATAAACAAGATTCAGTCACTGACGCCAAATATCGGAGTCGTCTACAG                         TGGTATGGGTCCTGATTCTCGTGTCTTAGTTCGCAAAAGCCGGAAGCAAGC
genomic: ATAAACAAGATTCAGTCACTGACGCCAAATATCGGAGTCGTCTACAGgtcagtgctt ... gttacttcagTGGTATGGGTCCTGATTCTCGTGTCTTAGTTCGCAAAAGCCGGAAGCAAGC
EST: gi|162162081|gb|FC338872.1|FC338872
EST:     ATAAACAAGATTCAGTCACTGACGCCAAATATCGGAGTCGTCTACAG                         TGGTATGGGTCCTGATTCTCGTGTCTTAGTTCGCAAAAGCCGGAAGCAAGC
genomic: ATAAACAAGATTCAGTCACTGACGCCAAATATCGGAGTCGTCTACAGgtcagtgctt ... gttacttcagTGGTATGGGTCCTGATTCTCGTGTCTTAGTTCGCAAAAGCCGGAAGCAAGC
EST: gi|37826384|gb|BJ584396.1|BJ584396
EST:     ATAAACAAGATTCAGTCGCTGACGCCAAATATCGGAGTCGTCTACAG                         TGGTATGGGTCCTGATTCTCGTGTCTTAGTTCGCAAAAGCCGGAAGCAAGC
genomic: ATAAACAAGATTCAGTCACTGACGCCAAATATCGGAGTCGTCTACAGgtcagtgctt ... gttacttcagTGGTATGGGTCCTGATTCTCGTGTCTTAGTTCGCAAAAGCCGGAAGCAAGC
EST: gi|162247557|gb|FC421678.1|FC421678
EST:     TCGATAAACAAGATTCAGTCACTGACGCCAAATATCGGAGTCGTCTACAG                         TGGTATGGGTCCTGATTCTCGTGTCTTAGTTCGCAAAAGCCGGAAGCAAGC
genomic: TCGATAAACAAGATTCAGTCACTGACGCCAAATATCGGAGTCGTCTACAGgtcagtgctt ... gttacttcagTGGTATGGGTCCTGATTCTCGTGTCTTAGTTCGCAAAAGCCGGAAGCAAGC
EST: gi|162262536|gb|FC439540.1|FC439540
EST:     ATAAACAAGATTCAGTCACTGACGCCAAATATCGGAGTCGTCTACAG                         TGGTATGGGTCCTGATTCTCGTGTCTTAGTTCGCAAAAGCCGGAAGCAAGC
genomic: ATAAACAAGATTCAGTCACTGACGCCAAATATCGGAGTCGTCTACAGgtcagtgctt ... gttacttcagTGGTATGGGTCCTGATTCTCGTGTCTTAGTTCGCAAAAGCCGGAAGCAAGC
EST: gi|162272506|gb|FC448508.1|FC448508
EST:     ATAAACAAGATTCAGTCACTGACGCCAAATATCGGAGTCGTCTACAG                         TGGTATGGGTCCTGATTCTCGTGTCTTAGTTCGCAAAAGCCGGAAGCAAGC
genomic: ATAAACAAGATTCAGTCACTGACGCCAAATATCGGAGTCGTCTACAGgtcagtgctt ... gttacttcagTGGTATGGGTCCTGATTCTCGTGTCTTAGTTCGCAAAAGCCGGAAGCAAGC
EST: gi|162272507|gb|FC448509.1|FC448509
EST:     ATAAACAAGATTCAGTCACTGACGCCAAATATCGGAGTCGTCTACAG                         TGGTATGGGTCCTGATTCTCGTGTCTTAGTTCGCAAAAGCCGGAAGCAAGC
genomic: ATAAACAAGATTCAGTCACTGACGCCAAATATCGGAGTCGTCTACAGgtcagtgctt ... gttacttcagTGGTATGGGTCCTGATTCTCGTGTCTTAGTTCGCAAAAGCCGGAAGCAAGC

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: 23

ATAAACAAGATTCAGTCACTGACGCCAAATATCGGAGTCGTCTACAGgtcagtgctt ... gttacttcagTGGTATGGGTCCTGATTCTCGTGTCTTAGTTCGCAAAAGCCGGAAGCAAGCACAAACGTATCAGCGACTTTATCAG




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcctactcctaccttcttaactgacatagtgatgacttgtgtgggttacttcagTGGTATGGGTCCTGATTCTCGTGTCTTAGTTCGCAAAAGCCGGAAGCAAGCACAAACGTATCAGCGACTTTATCAG
                   aactgac  putative branch site (score: 23)
                                              ttacttc  putative PPT
              ttcttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ccaatggtttctccaatttctatctgaattttggacctcgtgaatttcctactcctaccttcttaactgacatagtgatgacttgtgtgggttacttcagTGGTATGGGTCCTGATTCTCGTGTCTTAGTTCGCAAAAGCCGGAAGCAAGCACAAACGTATCAGCGACTTTATCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG