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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactgtctgttgttagagttctattagcagcacgactatgatgtaacttacaacttttagacgaggtttctcttctctggctgtttttaaggtcttcgaccatgtggccgtgaggtagaaaatctgtggatgattaatgaaaagtgtttgtggcgattgcagGGAGGCGGAGATGCGTGACTTGAATGAACTAACGAACTCAAGAGTGGCATGGTTTGGGATTATGTCTCTCTTCGTGTGCCTAGGAGTAGCAGGATGGCAG

Basic information

species Physcomitrella patens
transcript PP1S78_15V6.1
intron # 3
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|162279030|gb|FC454769.1|FC454769
EST:     GAGGAAGCTGTGGGTTCAATCCACAGTGAGATGCTGTATTTTCGAGAGAG                         GGAGGCGGAGATGCGTGACTTGAATGAACTAACGAACTCAAGAGTGGCATG
genomic: GAGGAAGCTGTGGGTTCAATCCACAGTGAGATGCTGTATTTGCGAGAGAGgtactgtctg ... gcgattgcagGGAGGCGGAGATGCGTGACTTGAATGAACTAACGAACTCAAGAGTGGCATG
EST: gi|67724104|gb|BJ974363.1|BJ974363
EST:     GAGGAAGCTGTGGGTTCAATCCACAGTGAGATGCTGTATTTGCGAGAGAG                         GGAGGCGGAGATGCGTGACTTGAATGAACTAACGAACTCAAGAGTGGCATG
genomic: GAGGAAGCTGTGGGTTCAATCCACAGTGAGATGCTGTATTTGCGAGAGAGgtactgtctg ... gcgattgcagGGAGGCGGAGATGCGTGACTTGAATGAACTAACGAACTCAAGAGTGGCATG
EST: gi|18350261|gb|BJ182312.1|BJ182312
EST:     GAGGAAGCTGTGGGTTCAATCCACAGTGAGATGCTGTATTTGCGAGAGAG                         GGAGGCGGAGATGCGTGACTTGAATGAACTA
genomic: GAGGAAGCTGTGGGTTCAATCCACAGTGAGATGCTGTATTTGCGAGAGAGgtactgtctg ... gcgattgcagGGAGGCGGAGATGCGTGACTTGAATGAACTA
EST: gi|67699533|gb|BJ959766.1|BJ959766
EST:     CAGTGAGATGCTGTATTTNCGAGAGAA                         GGAGGCGGAGATGCGTGACTTGAATGAACTAACGAACTCAAGAGTGGCATG
genomic: CAGTGAGATGCTGTATTTGCGAGAGAGgtactgtctg ... gcgattgcagGGAGGCGGAGATGCGTGACTTGAATGAACTAACGAACTCAAGAGTGGCATG
EST: gi|162211706|gb|FC387994.1|FC387994
EST:     GAGGAAGCTGTGGGTTCAATCCACAGTGAGATGCTGTATTTGCGAGAGAG                         GGAGGCGGAGATGCGTGACTTGAATGAACTAACGAACTCAAGAGTGGCATG
genomic: GAGGAAGCTGTGGGTTCAATCCACAGTGAGATGCTGTATTTGCGAGAGAGgtactgtctg ... gcgattgcagGGAGGCGGAGATGCGTGACTTGAATGAACTAACGAACTCAAGAGTGGCATG
EST: gi|37829234|gb|BJ587246.1|BJ587246
EST:     GAGGAAGCTGTGGGTTCAATCCACAGTGAGATGCTGTATTTGCGAGAGAG                         GGAGGCGGAGATGCGTGACTTGAATGAACTAACGAACTCAAGAGTGGCATG
genomic: GAGGAAGCTGTGGGTTCAATCCACAGTGAGATGCTGTATTTGCGAGAGAGgtactgtctg ... gcgattgcagGGAGGCGGAGATGCGTGACTTGAATGAACTAACGAACTCAAGAGTGGCATG
EST: gi|67701137|gb|BJ961370.1|BJ961370
EST:     GAGGAAGCTGTGGGTTCAATCCACAGTGAGATGCTGTATTTGCGAGAGAG                         GGAGGCGGAGATGCGTGACTTGAATGAACTAACGAACTCAAGAGTGGCATG
genomic: GAGGAAGCTGTGGGTTCAATCCACAGTGAGATGCTGTATTTGCGAGAGAGgtactgtctg ... gcgattgcagGGAGGCGGAGATGCGTGACTTGAATGAACTAACGAACTCAAGAGTGGCATG
EST: gi|162261140|gb|FC436975.1|FC436975
EST:     GAGGAAGCTGTGGGTTCAATCCACAGTGAGATGCTGTATTTGCGAGAGAG                         GGAGGCGGAGATGCGTGACTTGAATGAACTAACGAACTCAAGAGTGGCATG
genomic: GAGGAAGCTGTGGGTTCAATCCACAGTGAGATGCTGTATTTGCGAGAGAGgtactgtctg ... gcgattgcagGGAGGCGGAGATGCGTGACTTGAATGAACTAACGAACTCAAGAGTGGCATG
EST: gi|37847109|gb|BJ605117.1|BJ605117
EST:     GAGGAAGCTGTGGGTTCAATCCACAGTGAGATGCTGTATTTGCGAGAGAG                         GGAGGCGGAGATGCGTGACTTGAATGAACTAACGAACTCAAGAGTGGCATG
genomic: GAGGAAGCTGTGGGTTCAATCCACAGTGAGATGCTGTATTTGCGAGAGAGgtactgtctg ... gcgattgcagGGAGGCGGAGATGCGTGACTTGAATGAACTAACGAACTCAAGAGTGGCATG
EST: gi|37842290|gb|BJ600298.1|BJ600298
EST:     GAGGAAGCTGTGGGTTCAATCCACAGTGAGATGCTGTATTTGCGAGAGAG                         GGAGGCGGAGATGCGTGACTTGAATGAACTAACGAACTCAAGAGTGGCATG
genomic: GAGGAAGCTGTGGGTTCAATCCACAGTGAGATGCTGTATTTGCGAGAGAGgtactgtctg ... gcgattgcagGGAGGCGGAGATGCGTGACTTGAATGAACTAACGAACTCAAGAGTGGCATG
EST: gi|162261139|gb|FC436974.1|FC436974
EST:     GAGGAAGCTGTGGGTTCAATCCACAGTGAGATGCTGTATTTGCGAGAGAG                         GGAGGCGGAGATGCGTGACTTGAATGAACTAACGAACTCAAGAGTGGCATG
genomic: GAGGAAGCTGTGGGTTCAATCCACAGTGAGATGCTGTATTTGCGAGAGAGgtactgtctg ... gcgattgcagGGAGGCGGAGATGCGTGACTTGAATGAACTAACGAACTCAAGAGTGGCATG
EST: gi|162279031|gb|FC454770.1|FC454770
EST:     GAGGAAGCTGTGGGTTCAATCCACAGTGAGATGCTGTATTTGCGAGAGAG                         GGAGGCGGAGATGCGTGACTTGAATGAACTAACGAACTCAAGAGTGGCATG
genomic: GAGGAAGCTGTGGGTTCAATCCACAGTGAGATGCTGTATTTGCGAGAGAGgtactgtctg ... gcgattgcagGGAGGCGGAGATGCGTGACTTGAATGAACTAACGAACTCAAGAGTGGCATG
EST: gi|22133340|gb|BQ827684.1|BQ827684
EST:     GAGGAAGCTGTGGGTTCAATCCACAGTGAGATGCTGTATTTGCGAGAGAG                         GGAGGCGGAGATGCGTGACTTGAATGAACTAACGAACTCAAGAGTGGCATG
genomic: GAGGAAGCTGTGGGTTCAATCCACAGTGAGATGCTGTATTTGCGAGAGAGgtactgtctg ... gcgattgcagGGAGGCGGAGATGCGTGACTTGAATGAACTAACGAACTCAAGAGTGGCATG

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: 25 (upstream exon), 34 (downstream exon)
Score: 2

GGAATGGAGCTTGAGTTGAGAAAGTTGGAGGAAGCTGTGGGTTCAATCCACAGTGAGATGCTGTATTTGCGAGAGAGgtactgtctg ... gcgattgcagGGAGGCGGAGATGCGTGACTTGAATGAACTAACGAACTCAAGAGTGGCATGGTTTGGGATTATGTCTCTCTTCGTGTGCCTAGGAGTAGCAGGATGGCAG




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccgtgaggtagaaaatctgtggatgattaatgaaaagtgtttgtggcgattgcagGGAGGCGGAGATGCGTGACTTGAATGAACTAACGAACTCAAGAGTGGCATGGTTTGGGATTATGTCTCTCTTCGTGTGCCTAGGAGTAGCAGGATGGCAG
                        gattaat  putative branch site (score: 2)
                      atgattaatgaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtactgtctgttgttagagttctattagcagcacgactatgatgtaacttacaacttttagacgaggtttctcttctctggctgtttttaaggtcttcgaccatgtggccgtgaggtagaaaatctgtggatgattaatgaaaagtgtttgtggcgattgcagGGAGGCGGAGATGCGTGACTTGAATGAACTAACGAACTCAAGAGTGGCATGGTTTGGGATTATGTCTCTCTTCGTGTGCCTAGGAGTAGCAGGATGGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG