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'   		12  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTTACGACTTCGCCAGCAATTGCCATTCCTAAAGCAATCTCTCGGGCTGGGATTGATCAATCACAAGTGGATTTCTATGAAATCAATGAAGCCTTTGCTgtaagttctgcgattatcactgcaggtctccttagtgctgttctcggctacaaacatgatcattatgtggaaatgcgtcattaatttattttttattttattttatttatttatttttttaattgaatcccttgtcctattttgcag

Basic information

species Physcomitrella patens
transcript PP1S160_44V6.2
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S160_44V6.1 (Physcomitrella patens), 5'ss of exon 10
lower sequence: Vv12s0057g01200.t01 (Vitis vinifera), 5'ss of exon 11
CTTTACGACTTCGCCAGCAATTGCCATTCCTAAAGCAATCTCTCGGGCTGGGATTGATCAATCACAAGTGGATTTCTATGAAATCAATGAAGCCTTTGCTgtaagttctgcgattatcactgcaggtctccttagtgctgttctcggctacaaacatgatcattatgtggaaatgcgtcattaatttattttttattttattttatttatttatttttttaattgaatcccttgtcctattttgcag
 ||||| ||  | |||||  |||| ||||| ||||| || ||    || ||  | ||    || ||| | |||| ||||||||| |||||||||||||||||||||| |     |||    |||    || | |   |  |      ||    |  || ||| | | || |      |||  |  |||||||   |   |||  || |                                       
ATTTACTACAGCTCCAGCCCTTGCAATTCCAAAAGCTATTTCAAATGCAGGCTTGGAGGCTTCTCAAATTGATTACTATGAAATAAATGAAGCCTTTGCTgtaagtttt-----tat----gcattgatcttcaacacaatcacaaactc---atttgttcaatctatgaat-----tcacaatcttatttt--gtcacattggatctgcag-----------------------------------
















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|208362030|gb|DC950479.1|DC950479
EST:     GGATTGATCAATCACAAGTGGATTTCTATGAAATCAATGAAGCCTTTGCT                         GTGGTCTCAGTGGCAAATCAGCAAATATTGAAACTGAAACCG
genomic: GGATTGATCAATCACAAGTGGATTTCTATGAAATCAATGAAGCCTTTGCTgtaagttctg ... tattttgcagGTGGTCTCAGTGGCAAATCAGCAAATATTGAAACTGAAACCG
EST: gi|67728109|gb|BJ978368.1|BJ978368
EST:     GGATTGATCAATCACAAGTGGATTTCTATGAAATCAATGAAGCCTTTGCT                         GTGGTCTCAGTGGCAAATCAGCAAATATTGAAACTGAAACCG
genomic: GGATTGATCAATCACAAGTGGATTTCTATGAAATCAATGAAGCCTTTGCTgtaagttctg ... tattttgcagGTGGTCTCAGTGGCAAATCAGCAAATATTGAAACTGAAACCG
EST: gi|162231216|gb|FC407003.1|FC407003
EST:     GGATTGATCAATCACAAGTGGATTTCTATGAAATCAATGAAGCCTTTGCT                         GTGGTCTCAGTGGCAAATCAGCAAATATTGAAACTGAAACCG
genomic: GGATTGATCAATCACAAGTGGATTTCTATGAAATCAATGAAGCCTTTGCTgtaagttctg ... tattttgcagGTGGTCTCAGTGGCAAATCAGCAAATATTGAAACTGAAACCG
EST: gi|37824997|gb|BJ583063.1|BJ583063
EST:     GGATTGATCAATCACAAGTGGATTTCTATGAAATCAATGAAGCCTTTGCT                         GTGGTCTCAGTGGCAAATCAGCAAATATTGAAACTGAAACCG
genomic: GGATTGATCAATCACAAGTGGATTTCTATGAAATCAATGAAGCCTTTGCTgtaagttctg ... tattttgcagGTGGTCTCAGTGGCAAATCAGCAAATATTGAAACTGAAACCG
EST: gi|18333054|gb|BJ165068.1|BJ165068
EST:     GGATTGATCAATCACAAGTGGATTTCTATGAAATCAATGAAGCCTTTGCT                         GTGGTCTCAGTGGCAAATCAGCAAATATTGAAACTGAAACCG
genomic: GGATTGATCAATCACAAGTGGATTTCTATGAAATCAATGAAGCCTTTGCTgtaagttctg ... tattttgcagGTGGTCTCAGTGGCAAATCAGCAAATATTGAAACTGAAACCG
EST: gi|208372747|gb|DC952634.1|DC952634
EST:     GGATTGATCAATCACAAGTGGATTTCTATGAAATCAATGAAGCCTTTGCT                         GTGGTCTCAGTGGCAAATCAGCAAATATTGAAACTGAAACCG
genomic: GGATTGATCAATCACAAGTGGATTTCTATGAAATCAATGAAGCCTTTGCTgtaagttctg ... tattttgcagGTGGTCTCAGTGGCAAATCAGCAAATATTGAAACTGAAACCG
EST: gi|67724453|gb|BJ974712.1|BJ974712
EST:     GGATTGATCAATCACAAGTGGATTTCTATGAAATCAATGAAGCCTTTGCT                         GTGGTCTCAGTGGCAAATCAGCAAATATTGAAACTGAAACCG
genomic: GGATTGATCAATCACAAGTGGATTTCTATGAAATCAATGAAGCCTTTGCTgtaagttctg ... tattttgcagGTGGTCTCAGTGGCAAATCAGCAAATATTGAAACTGAAACCG
EST: gi|208364951|gb|DC947093.1|DC947093
EST:     GGATTGATCAATCACAAGTGGATTTCTATGAAATCAATGAAGCCTTTGCT                         GTGGTCTCAGTGGCAAATCAGCAAATATTGAAACTGAAACCG
genomic: GGATTGATCAATCACAAGTGGATTTCTATGAAATCAATGAAGCCTTTGCTgtaagttctg ... tattttgcagGTGGTCTCAGTGGCAAATCAGCAAATATTGAAACTGAAACCG
EST: gi|22132646|gb|BQ827270.1|BQ827270
EST:     GGATTGATCAATCACAAGTGGATTTCTATGAAATCAATGAAGCCTTTGCT                         GTGGTCTCAGTGGCAAATCAGCAAATATTGAAACTGAAACCG
genomic: GGATTGATCAATCACAAGTGGATTTCTATGAAATCAATGAAGCCTTTGCTgtaagttctg ... tattttgcagGTGGTCTCAGTGGCAAATCAGCAAATATTGAAACTGAAACCG
EST: gi|208388349|gb|DC949321.1|DC949321
EST:     GGATTGATCAATCACAAGTGGATTTCTATGAAATCAATGAAGCCTTTGCT                         GTGGTCTCAGTGGCAAATCAGCAAATATTGAAACTGAAACCG
genomic: GGATTGATCAATCACAAGTGGATTTCTATGAAATCAATGAAGCCTTTGCTgtaagttctg ... tattttgcagGTGGTCTCAGTGGCAAATCAGCAAATATTGAAACTGAAACCG
EST: gi|208368091|gb|DC947651.1|DC947651
EST:     GGATTGATCAATCACAAGTGGATTTCTATGAAATCAATGAAGCCTTTGCT                         GTGGTCTCAGTGGCAAATCAGCAAATATTGAAACTGAAACCG
genomic: GGATTGATCAATCACAAGTGGATTTCTATGAAATCAATGAAGCCTTTGCTgtaagttctg ... tattttgcagGTGGTCTCAGTGGCAAATCAGCAAATATTGAAACTGAAACCG
EST: gi|162258772|gb|FC434571.1|FC434571
EST:     GGATTGATCAATCACAAGTGGATTTCTATGAAATCAATGAAGCCTTTGCT                         GTGGTCTCAGTGGCAAATCAGCAAATATTGAAACTGAAACCG
genomic: GGATTGATCAATCACAAGTGGATTTCTATGAAATCAATGAAGCCTTTGCTgtaagttctg ... tattttgcagGTGGTCTCAGTGGCAAATCAGCAAATATTGAAACTGAAACCG
EST: gi|22492620|gb|BU052543.1|BU052543
EST:     GGATTGATCAATCACAAGTGGATTTCTATGAAATCAATGAAGCCTTTGCT                         GTGGTCTCAGTGGCAAATCAGCAAATATTGAAACTGAAACCG
genomic: GGATTGATCAATCACAAGTGGATTTCTATGAAATCAATGAAGCCTTTGCTgtaagttctg ... tattttgcagGTGGTCTCAGTGGCAAATCAGCAAATATTGAAACTGAAACCG
EST: gi|15320244|gb|BI488011.1|BI488011
EST:     AATCAATGAAGCCTTTGCT                         GTGGTCTCAGTGGCAAATCAGCAAATATTGAAACTGAAACCG
genomic: AATCAATGAAGCCTTTGCTgtaagttctg ... tattttgcagGTGGTCTCAGTGGCAAATCAGCAAATATTGAAACTGAAACCG
EST: gi|18335246|gb|BJ167264.1|BJ167264
EST:     GGATTGATCAATCACAAGTGGATTTCTATGAAATCAATGAAGCCTTTGCT                         GTGGTCTCAGTGGCAAATCAGCAAATATTGAAACTGAAACCG
genomic: GGATTGATCAATCACAAGTGGATTTCTATGAAATCAATGAAGCCTTTGCTgtaagttctg ... tattttgcagGTGGTCTCAGTGGCAAATCAGCAAATATTGAAACTGAAACCG
EST: gi|67727140|gb|BJ977399.1|BJ977399
EST:     GGATTGATCAATCACAAGTGGATTTCTATGAAATCAATGAAGCCTTTGCT                         GTGGTCTCAGTGGCAAATCAGCAAATATTGAAACTGAAACCG
genomic: GGATTGATCAATCACAAGTGGATTTCTATGAAATCAATGAAGCCTTTGCTgtaagttctg ... tattttgcagGTGGTCTCAGTGGCAAATCAGCAAATATTGAAACTGAAACCG
EST: gi|37828592|gb|BJ586604.1|BJ586604
EST:     GGATTGATCAATCACAAGTGGATTTCTATGAAATCAATGAAGCCTTTGCT                         GTGGTCTCAGTGGCAAATCAGCAAATATTGAAACTGAAACCG
genomic: GGATTGATCAATCACAAGTGGATTTCTATGAAATCAATGAAGCCTTTGCTgtaagttctg ... tattttgcagGTGGTCTCAGTGGCAAATCAGCAAATATTGAAACTGAAACCG
EST: gi|162177571|gb|FC352429.1|FC352429
EST:     GGATTGATCAATCACAAGTGGATTTCTATGAAATCAATGAAGCCTTTGCT                         GTGGTCTCAGTGGCAAATCAGCAAATATTGAAACTGAAACCG
genomic: GGATTGATCAATCACAAGTGGATTTCTATGAAATCAATGAAGCCTTTGCTgtaagttctg ... tattttgcagGTGGTCTCAGTGGCAAATCAGCAAATATTGAAACTGAAACCG
EST: gi|208357273|gb|DC949903.1|DC949903
EST:     GGATTGATCAATCACAAGTGGATTTCTATGAAATCAATGAAGCCTTTGCT                         GTGGTCTCAGTGGCAAATCAGCAAATATTGAAACTGAAACCG
genomic: GGATTGATCAATCACAAGTGGATTTCTATGAAATCAATGAAGCCTTTGCTgtaagttctg ... tattttgcagGTGGTCTCAGTGGCAAATCAGCAAATATTGAAACTGAAACCG
EST: gi|208367940|gb|DC955375.1|DC955375
EST:     GGATTGATCAATCACAAGTGGATTTCTATGAAATCAATGAAGCCTTTGCT                         GTGGTCTCAGTGGCAAATCAGCAAATATTGAAACTGAAACCG
genomic: GGATTGATCAATCACAAGTGGATTTCTATGAAATCAATGAAGCCTTTGCTgtaagttctg ... tattttgcagGTGGTCTCAGTGGCAAATCAGCAAATATTGAAACTGAAACCG
EST: gi|162173639|gb|FC349607.1|FC349607
EST:     GGATTGATCAATCACAAGTGGATTTCTATGAAATCAATGAAGCCTTTGCT                         GTGGTCTCAGTGGCAAATCAGCAAATATTGAAACTGAAACCG
genomic: GGATTGATCAATCACAAGTGGATTTCTATGAAATCAATGAAGCCTTTGCTgtaagttctg ... tattttgcagGTGGTCTCAGTGGCAAATCAGCAAATATTGAAACTGAAACCG
EST: gi|40781593|gb|AJ583523.1|AJ583523
EST:     GGATTGATCAATCACAAGTGGATTTCTATGAAATCAATGAAGCCTTTGCT                         GTGGTCTCAGTGGCAAATCAGCAAATATTGAAACTGAAACCG
genomic: GGATTGATCAATCACAAGTGGATTTCTATGAAATCAATGAAGCCTTTGCTgtaagttctg ... tattttgcagGTGGTCTCAGTGGCAAATCAGCAAATATTGAAACTGAAACCG
EST: gi|208362110|gb|DC943523.1|DC943523
EST:     GGATTGATCAATCACAAGTGGATTTCTATGAAATCAATGAAGCCTTTGCT                         GTGGTCTCAGTGGCAAATCAGCAAATATTGAAACTGAAACCG
genomic: GGATTGATCAATCACAAGTGGATTTCTATGAAATCAATGAAGCCTTTGCTgtaagttctg ... tattttgcagGTGGTCTCAGTGGCAAATCAGCAAATATTGAAACTGAAACCG
EST: gi|208353436|gb|DC922490.1|DC922490
EST:     GGATTGATCAATCACAAGTGGATTTCTATGAAATCAATGAAGCCTTTGCT                         GTGGTCTCAGTGGCAAATCAGCAAATATTGAAACTGAAACCG
genomic: GGATTGATCAATCACAAGTGGATTTCTATGAAATCAATGAAGCCTTTGCTgtaagttctg ... tattttgcagGTGGTCTCAGTGGCAAATCAGCAAATATTGAAACTGAAACCG
EST: gi|162156305|gb|FC332329.1|FC332329
EST:     GGATTGATCAATCACAAGTGGATTTCTATGAAATCAATGAAGCCTTTGCT                         GTGGTCTCAGTGGCAAATCAGCAAATATTGAAACTGAAACCG
genomic: GGATTGATCAATCACAAGTGGATTTCTATGAAATCAATGAAGCCTTTGCTgtaagttctg ... tattttgcagGTGGTCTCAGTGGCAAATCAGCAAATATTGAAACTGAAACCG
EST: gi|208389390|gb|DC953228.1|DC953228
EST:     GGATTGATCAATCACAAGTGGATTTCTATGAAATCAATGAAGCCTTTGCT                         GTGGTCTCAGTGGCAAATCAGCAAATATTGAAACTGAAACCG
genomic: GGATTGATCAATCACAAGTGGATTTCTATGAAATCAATGAAGCCTTTGCTgtaagttctg ... tattttgcagGTGGTCTCAGTGGCAAATCAGCAAATATTGAAACTGAAACCG
EST: gi|208385682|gb|DC952843.1|DC952843
EST:     GGATTGATCAATCACAAGTGGATTTCTATGAAATCAATGAAGCCTTTGCT                         GTGATCTCAGTGGCAAATCAGCAAATATTGAAACTGAAACCG
genomic: GGATTGATCAATCACAAGTGGATTTCTATGAAATCAATGAAGCCTTTGCTgtaagttctg ... tattttgcagGTGGTCTCAGTGGCAAATCAGCAAATATTGAAACTGAAACCG
EST: gi|19782978|gb|BQ039945.1|BQ039945
EST:     GGATTGATCAATCACAAGTGGATTTCTATGAAATCAATGAAGCCTTTGCT                         GTGGTCTCAGTGG
genomic: GGATTGATCAATCACAAGTGGATTTCTATGAAATCAATGAAGCCTTTGCTgtaagttctg ... tattttgcagGTGGTCTCAGTGG
EST: gi|162166658|gb|FC343550.1|FC343550
EST:     GGATTGATCAATCACAAGTGGATTTCTATGAAATCAATGAAGCCTTTGCT                         GTGGTCTCAGTGGCAAATCAGCAAATATTGAAACTGAAACCG
genomic: GGATTGATCAATCACAAGTGGATTTCTATGAAATCAATGAAGCCTTTGCTgtaagttctg ... tattttgcagGTGGTCTCAGTGGCAAATCAGCAAATATTGAAACTGAAACCG
EST: gi|37838686|gb|BJ596694.1|BJ596694
EST:     GGATTGATCAATCACAAGTGGATTTCTATGAAATCAATGAAGCCTTTGCT                         GTGGTCTCAGTGGCAAATCAGCAAATATTGAAACTGAAACCG
genomic: GGATTGATCAATCACAAGTGGATTTCTATGAAATCAATGAAGCCTTTGCTgtaagttctg ... tattttgcagGTGGTCTCAGTGGCAAATCAGCAAATATTGAAACTGAAACCG
EST: gi|208375552|gb|DC945111.1|DC945111
EST:     GGATTGATCAATCACAAGTGGATTTCTATGAAATCAATGAAGCCTTTGCT                         GTGGTCTCAGTGGCAAATCAGCAAATATTGAAACTGAAACCG
genomic: GGATTGATCAATCACAAGTGGATTTCTATGAAATCAATGAAGCCTTTGCTgtaagttctg ... tattttgcagGTGGTCTCAGTGGCAAATCAGCAAATATTGAAACTGAAACCG
EST: gi|37837476|gb|BJ595484.1|BJ595484
EST:     GGATTGATCAATCACAAGTGGATTTCTATGAAATCAATGAAGCCTTTGCT                         GTGGTCTCAGTGGCAAATCAGCAAATATTGAAACTGAAACCG
genomic: GGATTGATCAATCACAAGTGGATTTCTATGAAATCAATGAAGCCTTTGCTgtaagttctg ... tattttgcagGTGGTCTCAGTGGCAAATCAGCAAATATTGAAACTGAAACCG
EST: gi|162177570|gb|FC352428.1|FC352428
EST:     GGATTGATCAATCACAAGTGGATTTCTATGAAATCAATGAAGCCTTTGCT                         GTGGTCTCAGTGGCAAATCAGCAAATATTGAAACTGAAACCG
genomic: GGATTGATCAATCACAAGTGGATTTCTATGAAATCAATGAAGCCTTTGCTgtaagttctg ... tattttgcagGTGGTCTCAGTGGCAAATCAGCAAATATTGAAACTGAAACCG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTTTACGACTTCGCCAGCAATTGCCATTCCTAAAGCAATCTCTCGGGCTGGGATTGATCAATCACAAGTGGATTTCTATGAAATCAATGAAGCCTTTGCTgtaagttctgcgattatcactgcaggtctccttagtgctgttctcggctacaaacatgatcattatgtggaaatgcgtcattaatttattttttattttattttatttatttatttttttaattgaatcccttgtcctattttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC