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'   		11  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcgtgtgacatgatagaaacattcttgtgcgattaatgtttacagtagggtcttgttcttaatccattgcattcatgaggttgccaattgttgtattcagATCAAGAACAACAAGAGATACGCTGGGTCAACTGCTTGGACTGTACAG

Basic information

species Physcomitrella patens
transcript PP1S29_256V6.1
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|162171618|gb|FC347559.1|FC347559
EST:     TGTATCCCTTAGATGCTGTATTCGACACTCCTGAAGATGTGCCTGAGGAT                         ATCAAGAACAACAAGAGATACGCTGGGTCAACTGCTTGGACTGTACAG
genomic: TGTATCCCTTAGATGCTGTATTCGACACTCCTGAAGATGTGCCTGAGGATgtaagtggaa ... ttgtattcagATCAAGAACAACAAGAGATACGCTGGGTCAACTGCTTGGACTGTACAG
EST: gi|18327390|gb|BJ159392.1|BJ159392
EST:     TGTATCCCTTAGATGCTGTATTCGACACTCCTGAAGATGTGCCTGAGGAT                         ATCAAGAACAACAAGAGATACGCTGGGTCAACTGCTTGGACTGTACAG
genomic: TGTATCCCTTAGATGCTGTATTCGACACTCCTGAAGATGTGCCTGAGGATgtaagtggaa ... ttgtattcagATCAAGAACAACAAGAGATACGCTGGGTCAACTGCTTGGACTGTACAG
EST: gi|162182768|gb|FC359515.1|FC359515
EST:     TGTATCCCTTAGATGCTGTATTCGACACTCCTGAAGATGTGCCTGAGGAT                         ATCAAGAACAACAAGAGATACGCTGGGTCAACTGCTTGGACTGTACAG
genomic: TGTATCCCTTAGATGCTGTATTCGACACTCCTGAAGATGTGCCTGAGGATgtaagtggaa ... ttgtattcagATCAAGAACAACAAGAGATACGCTGGGTCAACTGCTTGGACTGTACAG
EST: gi|19777824|gb|BQ039232.1|BQ039232
EST:     TGTATCCCTTAGATGCTGTATTCGACACTCCTGAAGATGTGCCTGAGGAT                         ATCAAGAACAACAAGAGATACGCTGGGTCAACTGCTTGGACTGTACAG
genomic: TGTATCCCTTAGATGCTGTATTCGACACTCCTGAAGATGTGCCTGAGGATgtaagtggaa ... ttgtattcagATCAAGAACAACAAGAGATACGCTGGGTCAACTGCTTGGACTGTACAG
EST: gi|67719586|gb|BJ969845.1|BJ969845
EST:     TGTATCCCTTAGATGCTGTATTCGACACTCCTGAAGATGTGCCTGAGGAT                         ATCAAGAACAACAAGAGATACGCTGGGTCAACTGCTTGGACTGTACAG
genomic: TGTATCCCTTAGATGCTGTATTCGACACTCCTGAAGATGTGCCTGAGGATgtaagtggaa ... ttgtattcagATCAAGAACAACAAGAGATACGCTGGGTCAACTGCTTGGACTGTACAG
EST: gi|67718262|gb|BJ968521.1|BJ968521
EST:     TGTATCCCTTAGATGCTGTATTCGACACTCCTGAAGATGTGCCTGAGGAT                         ATCAAGAACAACAAGAGATACGCTGGGTCAACTGCTTGGACTGTACAG
genomic: TGTATCCCTTAGATGCTGTATTCGACACTCCTGAAGATGTGCCTGAGGATgtaagtggaa ... ttgtattcagATCAAGAACAACAAGAGATACGCTGGGTCAACTGCTTGGACTGTACAG
EST: gi|162176349|gb|FC353534.1|FC353534
EST:     TGTATCCCTTAGATGCTGTATTCGACACTCCTGAAGATGTGCCTGAGGAT                         ATCAAGAACAACAAGAGATACGCTGGGTCAACTGCTTGGACTGTACAG
genomic: TGTATCCCTTAGATGCTGTATTCGACACTCCTGAAGATGTGCCTGAGGATgtaagtggaa ... ttgtattcagATCAAGAACAACAAGAGATACGCTGGGTCAACTGCTTGGACTGTACAG
EST: gi|208359693|gb|DC930283.1|DC930283
EST:     TGTATCCCTTAGATGCTGTATTCGACACTCCTGAAGATGTGCCTGAGGAT                         ATCAAGAACAACAAGAGATACGCTGGGTCAACTGCTTGGACTGTACAG
genomic: TGTATCCCTTAGATGCTGTATTCGACACTCCTGAAGATGTGCCTGAGGATgtaagtggaa ... ttgtattcagATCAAGAACAACAAGAGATACGCTGGGTCAACTGCTTGGACTGTACAG
EST: gi|162167232|gb|FC342797.1|FC342797
EST:     TGTATCCCTTAGATGCTGTATTCGACACTCCTGAAGATGTGCCTGAGGAT                         ATCAAGAACAACAAGAGATACGCTGGGTCAACTGCTTGGACTGTACAG
genomic: TGTATCCCTTAGATGCTGTATTCGACACTCCTGAAGATGTGCCTGAGGATgtaagtggaa ... ttgtattcagATCAAGAACAACAAGAGATACGCTGGGTCAACTGCTTGGACTGTACAG
EST: gi|19789330|gb|BQ041244.1|BQ041244
EST:     TGTATCCCTTAGATGCTGTATTCGACACTCCTGAAGATGTGCCTGAGGAT                         ATCAAGAACAACAAGAGATACGCTGGGTCAACTGCTTGGACTGTACAG
genomic: TGTATCCCTTAGATGCTGTATTCGACACTCCTGAAGATGTGCCTGAGGATgtaagtggaa ... ttgtattcagATCAAGAACAACAAGAGATACGCTGGGTCAACTGCTTGGACTGTACAG
EST: gi|162169758|gb|FC345295.1|FC345295
EST:     TGTATCCCTTAGATGCTGTATTCGACACTCCTGAAGATGTGCCTGAGGAT                         ATCAAGAACAACAAGAGATACGCTGGGTCAACTGCTTGGACTGTACAG
genomic: TGTATCCCTTAGATGCTGTATTCGACACTCCTGAAGATGTGCCTGAGGATgtaagtggaa ... ttgtattcagATCAAGAACAACAAGAGATACGCTGGGTCAACTGCTTGGACTGTACAG
EST: gi|162176594|gb|FC353063.1|FC353063
EST:     TGTATCCCTTAGATGCTGTATTCGACACTCCTGAAGATGTGCCTGAGGAT                         ATCAAGAACAACAAGAGATACGCTGGGTCAACTGCTTGGACTGTACAG
genomic: TGTATCCCTTAGATGCTGTATTCGACACTCCTGAAGATGTGCCTGAGGATgtaagtggaa ... ttgtattcagATCAAGAACAACAAGAGATACGCTGGGTCAACTGCTTGGACTGTACAG
EST: gi|162181164|gb|FC357609.1|FC357609
EST:     TGTATCCCTTAGATGCTGTATTCGACACTCCTGAAGATGTGCCTGAGGAT                         ATCAAGAACAACAAGAGATACGCTGGGTCAACTGCTTGGACTGTACAG
genomic: TGTATCCCTTAGATGCTGTATTCGACACTCCTGAAGATGTGCCTGAGGATgtaagtggaa ... ttgtattcagATCAAGAACAACAAGAGATACGCTGGGTCAACTGCTTGGACTGTACAG
EST: gi|67718833|gb|BJ969092.1|BJ969092
EST:     TGTATCCCTTAGATGCTGTATTCGACACTCCTGAAGATGTGCCTGAGGAT                         ATCAAGAACAACAAGAGATACGCTGGGTCAACTGCTTGGACTGTACAG
genomic: TGTATCCCTTAGATGCTGTATTCGACACTCCTGAAGATGTGCCTGAGGATgtaagtggaa ... ttgtattcagATCAAGAACAACAAGAGATACGCTGGGTCAACTGCTTGGACTGTACAG
EST: gi|100384688|gb|BY950678.1|BY950678
EST:     TGTATCCCTTAGATGCTGTATTCGACACTCCTGAAGATGTGCCTGAGGAT                         ATCAAGAACAACAAGAGATACGCTGGGTCAACTGCTTGGACTGTACAG
genomic: TGTATCCCTTAGATGCTGTATTCGACACTCCTGAAGATGTGCCTGAGGATgtaagtggaa ... ttgtattcagATCAAGAACAACAAGAGATACGCTGGGTCAACTGCTTGGACTGTACAG
EST: gi|100429370|gb|BY978077.1|BY978077
EST:     TGTATCCCTTAGATGCTGTATTCGACACTCCTGAAGATGTGCCTGAGGAT                         ATCAAGAACAACAAGAGATACGCTGGGTGCA-CTGCTTGGACTGTACAG
genomic: TGTATCCCTTAGATGCTGTATTCGACACTCCTGAAGATGTGCCTGAGGATgtaagtggaa ... ttgtattcagATCAAGAACAACAAGAGATACGCTGGGT-CAACTGCTTGGACTGTACAG
EST: gi|100403476|gb|BY991219.1|BY991219
EST:     TGTATCCCTTAGATGCTGTATTCGACACTCCTGAAGATGTGCCTGAGGAT                         ATCAAGAACAACAAGAGATACGCTGGGTCAACTGCTTGGACTGTACAG
genomic: TGTATCCCTTAGATGCTGTATTCGACACTCCTGAAGATGTGCCTGAGGATgtaagtggaa ... ttgtattcagATCAAGAACAACAAGAGATACGCTGGGTCAACTGCTTGGACTGTACAG
EST: gi|162241271|gb|FC416902.1|FC416902
EST:     TGTATCCCTTAGATGCTGTATTCGACACTCCTGAAGATGTGCCTGAGGAT                         ATCAAGAACAACAAGAGATACGCTGGGTCAACTGCTTGGACTGTACAG
genomic: TGTATCCCTTAGATGCTGTATTCGACACTCCTGAAGATGTGCCTGAGGATgtaagtggaa ... ttgtattcagATCAAGAACAACAAGAGATACGCTGGGTCAACTGCTTGGACTGTACAG

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: 29 (upstream exon), 28 (downstream exon)
Score: 9

GCTTCCCACCGGAGGATTACTCGAGATTGCCAAAGTGTATCCCTTAGATGCTGTATTCGACACTCCTGAAGATGTGCCTGAGGATgtaagtggaa ... ttgtattcagATCAAGAACAACAAGAGATACGCTGGGTCAACTGCTTGGACTGTACAG




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagggtcttgttcttaatccattgcattcatgaggttgccaattgttgtattcagATCAAGAACAACAAGAGATACGCTGGGTCAACTGCTTGGACTGTACAG
           tcttaat  putative branch site (score: 9)
          ttcttaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcgtgtgacatgatagaaacattcttgtgcgattaatgtttacagtagggtcttgttcttaatccattgcattcatgaggttgccaattgttgtattcagATCAAGAACAACAAGAGATACGCTGGGTCAACTGCTTGGACTGTACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA