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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtataatttctactcttaacccgtcaaattacattaccagcttttctaatcataccgactctgaattggacaaaattcttattgactgctttaactaacttatcttttcatttcagGCCAGGACACCTCAAAACTTGGTCGAGGATCAATGCTCTTAGCTGGTGGTGTTGCTGGAGCGATGTTCTGGGTGTCTGTCTACCCTACAGACGTGATCAA

Basic information

species Physcomitrella patens
transcript PP1S475_26V6.1
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|37828019|gb|BJ586031.1|BJ586031
EST:     CCAACCAGTATCTCGCAGGAG                         GCCAGGACACCTCAAAACTTGGTCGAGGATCAATGCTCTTAGCTGGTGGTG
genomic: CCAAACAGTATCTCGCAGGAGgtataatttc ... ttcatttcagGCCAGGACACCTCAAAACTTGGTCGAGGATCAATGCTCTTAGCTGGTGGTG
EST: gi|162158833|gb|FC335356.1|FC335356
EST:     TGCGGCTATGTTCGGTACTTATGAAGCCACCAAACAGTATCTCGCAGGAG                         GCCAGGACACCTCAAAACTTGGTCGAGGATCAATGCTCTTAGCTGGTGGTG
genomic: TGCGGCTATGTTCGGTACTTATGAAGCCACCAAACAGTATCTCGCAGGAGgtataatttc ... ttcatttcagGCCAGGACACCTCAAAACTTGGTCGAGGATCAATGCTCTTAGCTGGTGGTG
EST: gi|67695823|gb|BJ956056.1|BJ956056
EST:     TGCGGCTATGTTCGGTACTTATGAAGCCACCAAACAGTATCTCGCAGGAG                         GCCAGGACACCTCAAAACTTGGTCGAGGATCAATGCTCTTAGCTGGTGGTG
genomic: TGCGGCTATGTTCGGTACTTATGAAGCCACCAAACAGTATCTCGCAGGAGgtataatttc ... ttcatttcagGCCAGGACACCTCAAAACTTGGTCGAGGATCAATGCTCTTAGCTGGTGGTG
EST: gi|208380180|gb|DC927459.1|DC927459
EST:     TGCGGCTATGTTCGGTACTTATGAAGCCACCAAACAGTATCTCGCAGGAG                         GCCAGGACACCTCAAAACTCGGTCGAGGATCAATGCTCTTAGCTGGTGGTG
genomic: TGCGGCTATGTTCGGTACTTATGAAGCCACCAAACAGTATCTCGCAGGAGgtataatttc ... ttcatttcagGCCAGGACACCTCAAAACTTGGTCGAGGATCAATGCTCTTAGCTGGTGGTG
EST: gi|7647899|gb|AW738889.1|AW738889
EST:     TGCGGCTATGTTCGGTACTTATGAAGCCACCAAACAGTATCTCGCAGGAG                         GCCAGGACACCTCAAAACTTGGTCGAGGATCAATGCTCTTAGCTGGTGGTG
genomic: TGCGGCTATGTTCGGTACTTATGAAGCCACCAAACAGTATCTCGCAGGAGgtataatttc ... ttcatttcagGCCAGGACACCTCAAAACTTGGTCGAGGATCAATGCTCTTAGCTGGTGGTG
EST: gi|162154301|gb|FC330640.1|FC330640
EST:     TGCGGCTATGTTCGGTACTTATGAAGCCACCAAACAGTATCTCGCAGGAG                         GCCAGGACACCTCAAAACTTGGTCGAGGATCAATGCTCTTAGCTGGTGGTG
genomic: TGCGGCTATGTTCGGTACTTATGAAGCCACCAAACAGTATCTCGCAGGAGgtataatttc ... ttcatttcagGCCAGGACACCTCAAAACTTGGTCGAGGATCAATGCTCTTAGCTGGTGGTG
EST: gi|162177171|gb|FC352600.1|FC352600
EST:     TGCGGCTATGTTCGGTACTTATGAAGCCACCAAACAGTATCTCGCAGGAG                         GCCAGGACACCTCAAAACTTGGTCGAGGATCAATGCTCTTAGCTGGTGGTG
genomic: TGCGGCTATGTTCGGTACTTATGAAGCCACCAAACAGTATCTCGCAGGAGgtataatttc ... ttcatttcagGCCAGGACACCTCAAAACTTGGTCGAGGATCAATGCTCTTAGCTGGTGGTG
EST: gi|162158213|gb|FC335256.1|FC335256
EST:     TGCGGCTATGTTCGGTACTTATGAAGCCACCAAACAGTATCTCGCAGGAG                         GCCAGGACACCTCAAAACTTGGTCGAGGATCAATGCTCTTAGCTGGTGGTG
genomic: TGCGGCTATGTTCGGTACTTATGAAGCCACCAAACAGTATCTCGCAGGAGgtataatttc ... ttcatttcagGCCAGGACACCTCAAAACTTGGTCGAGGATCAATGCTCTTAGCTGGTGGTG
EST: gi|208348136|gb|DC920927.1|DC920927
EST:     TGCGGCTATGTTCGGTACTTATGAAGCCACCAAACAGTATCTCGCAGGAG                         GCCAGGACACCTCAAAACTTGGTCGAGGATCAATGCTCTTAGCTGGTGGTG
genomic: TGCGGCTATGTTCGGTACTTATGAAGCCACCAAACAGTATCTCGCAGGAGgtataatttc ... ttcatttcagGCCAGGACACCTCAAAACTTGGTCGAGGATCAATGCTCTTAGCTGGTGGTG
EST: gi|162169498|gb|FC346062.1|FC346062
EST:     TGCGGCTATGTTCGGTACTTATGAAGCCACCAAACAGTATCTCGCAGGAG                         GCCAGGACACCTCAAAACTTGGTCGAGGATCAATGCTCTTAGCTGGTGGTG
genomic: TGCGGCTATGTTCGGTACTTATGAAGCCACCAAACAGTATCTCGCAGGAGgtataatttc ... ttcatttcagGCCAGGACACCTCAAAACTTGGTCGAGGATCAATGCTCTTAGCTGGTGGTG
EST: gi|162184078|gb|FC358824.1|FC358824
EST:     TGCGGCTATGTTCGGTACTTATGAAGCCACCAAACAGTATCTCGCAGGAG                         GCCAGGACACCTCAAAACTTGGTCGAGGATCAATGCTCTTAGCTGGTGGTG
genomic: TGCGGCTATGTTCGGTACTTATGAAGCCACCAAACAGTATCTCGCAGGAGgtataatttc ... ttcatttcagGCCAGGACACCTCAAAACTTGGTCGAGGATCAATGCTCTTAGCTGGTGGTG
EST: gi|37826531|gb|BJ584543.1|BJ584543
EST:     TGCGGCTATGTTCGGTACTTATGAAGCCACCAAACAGTATCTCGCAGGAG                         GCCAGGACACCTCAAAACTTGGTCGAGGATCAATGCTCTTAGCTGGTGGTG
genomic: TGCGGCTATGTTCGGTACTTATGAAGCCACCAAACAGTATCTCGCAGGAGgtataatttc ... ttcatttcagGCCAGGACACCTCAAAACTTGGTCGAGGATCAATGCTCTTAGCTGGTGGTG
EST: gi|208378793|gb|DC927495.1|DC927495
EST:     TGCGGCTATGTTCGGTACTTATGAAGCCACCAAACAGTATCTCGCAGGAG                         GCCAGGACACCTCAAAACTTGGTCGAGGATCAATGCTCTTAGCTGGTGGTG
genomic: TGCGGCTATGTTCGGTACTTATGAAGCCACCAAACAGTATCTCGCAGGAGgtataatttc ... ttcatttcagGCCAGGACACCTCAAAACTTGGTCGAGGATCAATGCTCTTAGCTGGTGGTG
EST: gi|208370451|gb|DC952154.1|DC952154
EST:     TGCGGCTATGTTCGGTACTTATGAAGCCACCAAACAGTATCTCGCAGGAG                         GCCAGGACACCTCAAAACTTGGTCGAGGATCAATGCTCTTAGCTGGTGGTG
genomic: TGCGGCTATGTTCGGTACTTATGAAGCCACCAAACAGTATCTCGCAGGAGgtataatttc ... ttcatttcagGCCAGGACACCTCAAAACTTGGTCGAGGATCAATGCTCTTAGCTGGTGGTG
EST: gi|162164665|gb|FC340712.1|FC340712
EST:     TGCGGCTATGTTCGGTACTTATGAAGCCACCAAACAGTATCTCGCAGGAG                         GCCAGGACACCTCAAAACTTGGTCGAGGATCAATGCTCTTAGCTGGTGGTG
genomic: TGCGGCTATGTTCGGTACTTATGAAGCCACCAAACAGTATCTCGCAGGAGgtataatttc ... ttcatttcagGCCAGGACACCTCAAAACTTGGTCGAGGATCAATGCTCTTAGCTGGTGGTG
EST: gi|162158212|gb|FC335255.1|FC335255
EST:     ATGTTCGGTATTTATGAAGCCACCAAACAGTATCTCGCAGGAG                         GCCAGGACACCTCAAAACTTGGTCGAGGATCAATGCTCTTAGCTGGTGGTG
genomic: ATGTTCGGTACTTATGAAGCCACCAAACAGTATCTCGCAGGAGgtataatttc ... ttcatttcagGCCAGGACACCTCAAAACTTGGTCGAGGATCAATGCTCTTAGCTGGTGGTG
EST: gi|162167489|gb|FC343686.1|FC343686
EST:     TGCGGCTATGTTCGGTACTTATGAAGCCACCAAACAGTATCTCGCAGGAG                         GCCAGGACACCTCAAAACTTGGTCGAGGATCAATGCTCTTAGCTGGTGGTG
genomic: TGCGGCTATGTTCGGTACTTATGAAGCCACCAAACAGTATCTCGCAGGAGgtataatttc ... ttcatttcagGCCAGGACACCTCAAAACTTGGTCGAGGATCAATGCTCTTAGCTGGTGGTG
EST: gi|162214874|gb|FC391009.1|FC391009
EST:     TGCGGCTATGTTCGGTACTTATGAAGCCACCAAACAGTATCTCGCAGGAG                         GCCAGGACACCTCAAAACTTGGTCGAGGATCAATGCTCTTAGCTGGTGGTG
genomic: TGCGGCTATGTTCGGTACTTATGAAGCCACCAAACAGTATCTCGCAGGAGgtataatttc ... ttcatttcagGCCAGGACACCTCAAAACTTGGTCGAGGATCAATGCTCTTAGCTGGTGGTG
EST: gi|18334541|gb|BJ166558.1|BJ166558
EST:     TGCGGCTATGTTCGGTACTTATGAAGCCACCAAACAGTATCTCGCAGGAG                         GCCAGGACACCTCAAAACTTGGTCGAGGATCAATGCTCTTAGCTGGTGGTG
genomic: TGCGGCTATGTTCGGTACTTATGAAGCCACCAAACAGTATCTCGCAGGAGgtataatttc ... ttcatttcagGCCAGGACACCTCAAAACTTGGTCGAGGATCAATGCTCTTAGCTGGTGGTG
EST: gi|162158834|gb|FC335357.1|FC335357
EST:     TGCGGCTATGTTCGGTACTTATGAAGCCACCAAACAGTATCTCGCAGGAG                         GCCAGGACACCTCAAAACTTGGTCGAGGATCAATGCTCTTAGCTGGTGGTG
genomic: TGCGGCTATGTTCGGTACTTATGAAGCCACCAAACAGTATCTCGCAGGAGgtataatttc ... ttcatttcagGCCAGGACACCTCAAAACTTGGTCGAGGATCAATGCTCTTAGCTGGTGGTG

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: 160

GGATTATACAAGGGACTTACTCCCACCCTCATGCGTGAGGTGCCCGGTAATGCGGCTATGTTCGGTACTTATGAAGCCACCAAACAGTATCTCGCAGGAGgtataatttc ... ttcatttcagGCCAGGACACCTCAAAACTTGGTCGAGGATCAATGCTCTTAGCTGGTGGTGTTGCTGGAGCGATGTTCTGGGTGTCTGTCTACCCTACAGACGTGATCAA




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgaattggacaaaattcttattgactgctttaactaacttatcttttcatttcagGCCAGGACACCTCAAAACTTGGTCGAGGATCAATGCTCTTAGCTGGTGGTGTTGCTGGAGCGATGTTCTGGGTGTCTGTCTACCCTACAGACGTGATCAA
                               aactaac  putative branch site (score: 160)
                                     cttatcttttcatttc  CT-rich tract
        acaaaattcttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtataatttctactcttaacccgtcaaattacattaccagcttttctaatcataccgactctgaattggacaaaattcttattgactgctttaactaacttatcttttcatttcagGCCAGGACACCTCAAAACTTGGTCGAGGATCAATGCTCTTAGCTGGTGGTGTTGCTGGAGCGATGTTCTGGGTGTCTGTCTACCCTACAGACGTGATCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA