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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtggatatgccttttgtcccggtacaatttgcgtaattttattgcattgtacttttgatgatattttggaatttagcacaattatttcgtcaacactactgaaaaatttgggtcgagacgttgagatgttgagacacctgcataaccaagcagatcttttgattggcagGTGAAGCGAAAGAAGGCCGCACATGCTGGCATGTTTGAGTTAGCACGGACACAGAATAGGCCAATGGTTCACATTGGTGGGTGATACGGAAGTGCATCTA

Basic information

species Physcomitrella patens
transcript PP1S23_46V6.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S23_46V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: EFJ36608 (Selaginella moellendorffii), 3'ss of exon 4
gtaagtggatatgccttttgtcccggtacaatttgcgtaattttattgcattgtacttttgatgatattttggaatttagcacaattatttcgtcaacactactgaaaaatttgggtcgagacgttgagatgttgagacacctgcataaccaagcagatcttttgattggcagGTGAAGCGAAAGAAGGCCGCACATGCTGGCATGTTTGAGTTAGCACGGACACAGAATAGGCCAATGGTTCACATTGGTGGGTGATACGGAAGTGCATCTA
                                                                                                              ||   |   |  | |    |||    || |  |   ||  |       | |  |   |||||||| ||| ||||||| || || |||||||| ||||||||| | |||  |||||  || ||||| ||||| ||||||||||| |||                
---------------------------------------------------------------------------------------------------------gtgggttctcgagtatccataagaatggcttgatatgtatctattcg------tttcctccctggcagGTTAAGAGAAAGAAAGCAGCTCATGCTGGGATGTTTGAGCTTGCAAAGACACCAAACAGGCCCATGGTCCACATTGGTGGATGA----------------
















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|37841690|gb|BJ599698.1|BJ599698
EST:     TTCGCAGTGGCATGCAGGAATTGGACTTGCAGCAGGTCATCAGTGATGCA                         GTGAAGCGAAAGAAGGCCGCACATGCTGGCATGTTTGAGTTAGCACGGACA
genomic: TTCGCAGTGGCATGCAGGAATTGGACTTGCAGCAGGTCATCAGTGATGCAgtaagtggat ... tgattggcagGTGAAGCGAAAGAAGGCCGCACATGCTGGCATGTTTGAGTTAGCACGGACA
EST: gi|162165937|gb|FC340962.1|FC340962
EST:     CATGCTGGAATTGGACTTGCAGCAGGTCATCAGTGATGCA                         GTGAAGCGAAAGAAGGCCGCACATGCTGGCATGTTTGAGTTAGCACGGACA
genomic: CATGCAGGAATTGGACTTGCAGCAGGTCATCAGTGATGCAgtaagtggat ... tgattggcagGTGAAGCGAAAGAAGGCCGCACATGCTGGCATGTTTGAGTTAGCACGGACA
EST: gi|162193399|gb|FC368911.1|FC368911
EST:     TTCGCAGTGGCATGCAGGAATTGGACTTGCAGCAGGTCATCAGTGATGCA                         GTGAAGCGAAAGAAGGCCGCACATGCTGGCATGTTTGAGTTAGCACGGACA
genomic: TTCGCAGTGGCATGCAGGAATTGGACTTGCAGCAGGTCATCAGTGATGCAgtaagtggat ... tgattggcagGTGAAGCGAAAGAAGGCCGCACATGCTGGCATGTTTGAGTTAGCACGGACA
EST: gi|162260719|gb|FC435371.1|FC435371
EST:     TTCGCAGTGGCATGCAGGAATTGGACTTGCAGCAGGTCATCAGTGATGCA                         GTGAAGCGAAAGAAGGCCGCACATGCTGGCATGTTTGAGTTAGCACGGACA
genomic: TTCGCAGTGGCATGCAGGAATTGGACTTGCAGCAGGTCATCAGTGATGCAgtaagtggat ... tgattggcagGTGAAGCGAAAGAAGGCCGCACATGCTGGCATGTTTGAGTTAGCACGGACA
EST: gi|162161664|gb|FC339079.1|FC339079
EST:     TTCGCAGTGGCATGCAGGAATTGGACTTGCAGCAGGTCATCAGTGATGCA                         GTGAAGCGAAAGAAGGCCGCACATGCTGGCATGTTTGAGTTAGCACGGACA
genomic: TTCGCAGTGGCATGCAGGAATTGGACTTGCAGCAGGTCATCAGTGATGCAgtaagtggat ... tgattggcagGTGAAGCGAAAGAAGGCCGCACATGCTGGCATGTTTGAGTTAGCACGGACA
EST: gi|162263880|gb|FC438668.1|FC438668
EST:     TTCGCAGTGGCATGCAGGAATTGGACTTGCAGCAGGTCATCAGTGATGCA                         GTGAAGCGAAAGAAGGCCGCACATGCTGGCATGTTTGAGTTAGCACGGACA
genomic: TTCGCAGTGGCATGCAGGAATTGGACTTGCAGCAGGTCATCAGTGATGCAgtaagtggat ... tgattggcagGTGAAGCGAAAGAAGGCCGCACATGCTGGCATGTTTGAGTTAGCACGGACA
EST: gi|162205182|gb|FC381280.1|FC381280
EST:     TTCGCAGTGGCATGCAGGAATTGGACTTGCAGCAGGTCATCAGTGATGCA                         GTGAAGCGAAAGAAGGCCGCACATGCTGGCATGTTTGAGTTAGCACGGACA
genomic: TTCGCAGTGGCATGCAGGAATTGGACTTGCAGCAGGTCATCAGTGATGCAgtaagtggat ... tgattggcagGTGAAGCGAAAGAAGGCCGCACATGCTGGCATGTTTGAGTTAGCACGGACA
EST: gi|162196916|gb|FC373308.1|FC373308
EST:     TTCGCAGTGGCATGCAGGAATTGGACTTGCAGCAGGTCATCAGTGATGCA                         GTGAAGCGAAAGAAGGCCGCACATGCTGGCATGTTTGAGTTAGCACGGACA
genomic: TTCGCAGTGGCATGCAGGAATTGGACTTGCAGCAGGTCATCAGTGATGCAgtaagtggat ... tgattggcagGTGAAGCGAAAGAAGGCCGCACATGCTGGCATGTTTGAGTTAGCACGGACA
EST: gi|162165470|gb|FC340581.1|FC340581
EST:     TCGCAGTGGCATGCAGGAATTGGAC-TGNCAGCAGGTCATCAGTGATGCA                         GTGAAGCGAAAGAAGGCCGCACATGCTGGCATGTTTGAGTTAGCACGGACA
genomic: TCGCAGTGGCATGCAGGAATTGGACTTG-CAGCAGGTCATCAGTGATGCAgtaagtggat ... tgattggcagGTGAAGCGAAAGAAGGCCGCACATGCTGGCATGTTTGAGTTAGCACGGACA
EST: gi|162191850|gb|FC367999.1|FC367999
EST:     TTCGCAGTGGCATGCAGGAATTGGACTTGCAGCAGGTCATCAGTGATGCA                         GTGAAGCGAAAGAAGGCCGCACATGCTGGCATGTTTGAGTTAGCACGGACA
genomic: TTCGCAGTGGCATGCAGGAATTGGACTTGCAGCAGGTCATCAGTGATGCAgtaagtggat ... tgattggcagGTGAAGCGAAAGAAGGCCGCACATGCTGGCATGTTTGAGTTAGCACGGACA
EST: gi|162260718|gb|FC435370.1|FC435370
EST:     TTCGCAGTGGCATGCAGGAATTGGACTTGCAGCAGGTCATCAGTGATGCA                         GTGAAGCGAAAGAAGGCCGCACATGCTGGCATGTTTGAGTTAGCACGGACA
genomic: TTCGCAGTGGCATGCAGGAATTGGACTTGCAGCAGGTCATCAGTGATGCAgtaagtggat ... tgattggcagGTGAAGCGAAAGAAGGCCGCACATGCTGGCATGTTTGAGTTAGCACGGACA
EST: gi|162174387|gb|FC350458.1|FC350458
EST:     CATCAGTGATGCA                         GTGAAGCGAAAGAAGGCCGCACATGCTGGCATGTTTGAGTTAGCACGGACA
genomic: CATCAGTGATGCAgtaagtggat ... tgattggcagGTGAAGCGAAAGAAGGCCGCACATGCTGGCATGTTTGAGTTAGCACGGACA
EST: gi|162193398|gb|FC368910.1|FC368910
EST:     TTCGCAGTGGCATGCAGGAATTGGACTTGCAGCAGGTCATCAGTGATGCA                         GTGAAGCGAAAGAAGGCCGCACATGCTGGCATGTTTGAGTTAGCACGGACA
genomic: TTCGCAGTGGCATGCAGGAATTGGACTTGCAGCAGGTCATCAGTGATGCAgtaagtggat ... tgattggcagGTGAAGCGAAAGAAGGCCGCACATGCTGGCATGTTTGAGTTAGCACGGACA
EST: gi|162205183|gb|FC381281.1|FC381281
EST:     TTCGCAGTGGCATGCAGGAATTGGACTTGCAGCAGGTCATCAGTGATGCA                         GTGAAGCGAAAG
genomic: TTCGCAGTGGCATGCAGGAATTGGACTTGCAGCAGGTCATCAGTGATGCAgtaagtggat ... tgattggcagGTGAAGCGAAAG
EST: gi|6102178|gb|AW126648.1|AW126648
EST:     TTCGCAGTGGCATGCAGGAATTGGACTTGCAGCAGGTCATCAGTGATGCA                         GTGAAGCGAAAGAAGGCCGCACATGCTGGCATGTTNTGAGTTAGCACGGAC
genomic: TTCGCAGTGGCATGCAGGAATTGGACTTGCAGCAGGTCATCAGTGATGCAgtaagtggat ... tgattggcagGTGAAGCGAAAGAAGGCCGCACATGCTGGCATGTT-TGAGTTAGCACGGAC
EST: gi|162161663|gb|FC339078.1|FC339078
EST:     CAGTGGCATGCAGGAATTGGACTTGCAGCAGGTCATCAGTGATGCA                         GTGAAGCGAAAGAAGGCCGCACATGCTGGCATGTTTGAGTTAGCACGGACA
genomic: CAGTGGCATGCAGGAATTGGACTTGCAGCAGGTCATCAGTGATGCAgtaagtggat ... tgattggcagGTGAAGCGAAAGAAGGCCGCACATGCTGGCATGTTTGAGTTAGCACGGACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gagacgttgagatgttgagacacctgcataaccaagcagatcttttgattggcagGTGAAGCGAAAGAAGGCCGCACATGCTGGCATGTTTGAGTTAGCACGGACACAGAATAGGCCAATGGTTCACATTGGTGGGTGATACGGAAGTGCATCTA
                                        tctttt  CT-rich tract
                                          ttttgatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtggatatgccttttgtcccggtacaatttgcgtaattttattgcattgtacttttgatgatattttggaatttagcacaattatttcgtcaacactactgaaaaatttgggtcgagacgttgagatgttgagacacctgcataaccaagcagatcttttgattggcagGTGAAGCGAAAGAAGGCCGCACATGCTGGCATGTTTGAGTTAGCACGGACACAGAATAGGCCAATGGTTCACATTGGTGGGTGATACGGAAGTGCATCTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG