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

gtatgattccatactgataattgaagaggaccttgccgtgttttttacgaaaaactttgattaatttgctactcaatttttctttgacgagtacaatattcagtgcctcaaattactattgtcgcatttttccagAACATCCTGGTGGTTTCAAAGTACTACTCAAGAATCACATTGAAGAGGCTCTCAGAATTGTTGTGCCTCACTGGCCAG

Basic information

species Physcomitrella patens
transcript PP1S58_256V6.1
intron # 9
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|162189223|gb|FC366732.1|FC366732
EST:     CCCTCGGAGATCGAGCAGCTGAAGATCTTCGCCTGCGAGTTATTGAGCAT                         AACATCCTGGTGGTTTCNAAGTACTACTCAAGAATCACATTGAAGAGGCTC
genomic: CCCTCGGAGATCGAGCAGCTGAAGATCTTCGCCTGCGAGTTATTGAGCATgtatgattcc ... atttttccagAACATCCTGGTGGTTTCAAAGTACTACTCAAGAATCACATTGAAGAGGCTC
EST: gi|37823682|gb|BJ581748.1|BJ581748
EST:     CCCTCGGAGATCGAGCAGCTGAAGATCTTCGCCTGCGAGTTATTGAGCAT                         AACATCCTGGTGGTTTCAAAGTACTACTCAAGAATCACATTGAAGAGGCTC
genomic: CCCTCGGAGATCGAGCAGCTGAAGATCTTCGCCTGCGAGTTATTGAGCATgtatgattcc ... atttttccagAACATCCTGGTGGTTTCAAAGTACTACTCAAGAATCACATTGAAGAGGCTC
EST: gi|19784261|gb|BQ040146.1|BQ040146
EST:     CCCTCGGAGATCGAGCAGCTGAAGATCTTCGCCTGCGAGTTATTGAGCAT                         AACATCCTGGTGGTTTCAAAGTACTACTCAAGAATCACATTGAAGAGGCTC
genomic: CCCTCGGAGATCGAGCAGCTGAAGATCTTCGCCTGCGAGTTATTGAGCATgtatgattcc ... atttttccagAACATCCTGGTGGTTTCAAAGTACTACTCAAGAATCACATTGAAGAGGCTC
EST: gi|162269558|gb|FC445114.1|FC445114
EST:     CCCTCGGAGATCGAGCAGCTGAAGATCTTCGCCTGCGAGTTATTGAGCAT                         AACATCCTGGTGGTTTCAAAGTACTACTCAAGAATCACATTGAAGAGGCTC
genomic: CCCTCGGAGATCGAGCAGCTGAAGATCTTCGCCTGCGAGTTATTGAGCATgtatgattcc ... atttttccagAACATCCTGGTGGTTTCAAAGTACTACTCAAGAATCACATTGAAGAGGCTC
EST: gi|162156857|gb|FC332803.1|FC332803
EST:     CCCTCGGAGATCGAGCAGCTGAAGATCTTCGCCTGCGAGTTATTGAGCAT                         AACATCCTGGTGGTTTCAAAGTACTACTCAAGAATCACATTGAAGAGGCTC
genomic: CCCTCGGAGATCGAGCAGCTGAAGATCTTCGCCTGCGAGTTATTGAGCATgtatgattcc ... atttttccagAACATCCTGGTGGTTTCAAAGTACTACTCAAGAATCACATTGAAGAGGCTC
EST: gi|162226295|gb|FC403003.1|FC403003
EST:     CCCTCGGAGATCGAGCAGCTGAAGATCTTCGCCTGCGAGTTATTGAGCAT                         AACATCCTGGTGGTTTCAAAGTACTACTCAAGAATCACATTGAAGAGGCTC
genomic: CCCTCGGAGATCGAGCAGCTGAAGATCTTCGCCTGCGAGTTATTGAGCATgtatgattcc ... atttttccagAACATCCTGGTGGTTTCAAAGTACTACTCAAGAATCACATTGAAGAGGCTC
EST: gi|162225702|gb|FC401844.1|FC401844
EST:     CCCTCGGAGATCGAGCAGCTGAAGATCTTCGCCTGCGAGTTATTGAGCAT                         AACATCCTGGTGGTTTCAAAGTACTACTCAAGAATCACATTGAAGAGGCTC
genomic: CCCTCGGAGATCGAGCAGCTGAAGATCTTCGCCTGCGAGTTATTGAGCATgtatgattcc ... atttttccagAACATCCTGGTGGTTTCAAAGTACTACTCAAGAATCACATTGAAGAGGCTC
EST: gi|37822290|gb|BJ580356.1|BJ580356
EST:     CCCTCGGAGATCGAGCAGCTGAAGATCTTCGCCTGCGAGTTATTGAGCAT                         AACATCCTGGTGGTTTCAAAGTACTACTCAAGAATCACATTGAAGAGGCTC
genomic: CCCTCGGAGATCGAGCAGCTGAAGATCTTCGCCTGCGAGTTATTGAGCATgtatgattcc ... atttttccagAACATCCTGGTGGTTTCAAAGTACTACTCAAGAATCACATTGAAGAGGCTC

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: 33 (upstream exon), 33 (downstream exon)
Score: 15

GGAAGATTACAAGATTGAGTTTGAGGAGGAGGCTAATCTTCCTGGTGGGGCCCTCGGAGATCGAGCAGCTGAAGATCTTCGCCTGCGAGTTATTGAGCATgtatgattcc ... atttttccagAACATCCTGGTGGTTTCAAAGTACTACTCAAGAATCACATTGAAGAGGCTCTCAGAATTGTTGTGCCTCACTGGCCAG




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctttgacgagtacaatattcagtgcctcaaattactattgtcgcatttttccagAACATCCTGGTGGTTTCAAAGTACTACTCAAGAATCACATTGAAGAGGCTCTCAGAATTGTTGTGCCTCACTGGCCAG
 ctttgac  putative branch site (score: 15)
                                            catttttcc  putative PPT
                             aaattactatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgattccatactgataattgaagaggaccttgccgtgttttttacgaaaaactttgattaatttgctactcaatttttctttgacgagtacaatattcagtgcctcaaattactattgtcgcatttttccagAACATCCTGGTGGTTTCAAAGTACTACTCAAGAATCACATTGAAGAGGCTCTCAGAATTGTTGTGCCTCACTGGCCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG