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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gttcgcaattgcaccttcatggctttgatgctcgccagtatggtatcttattcgtctgtctaagtgaattttttcatgattttctattgtgatatgacagGGCTTTGGGAATGTGGGTTCTTGGGCATCGAAACTTATCCACGAAAAGGGTGGAAAAATTAAGGCTGTTAGTGATGTTACTGGAGCCATCAAGAACAACT

Basic information

species Physcomitrella patens
transcript PP1S62_236V6.3
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S62_236V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: AT3G03910.1 (Arabidopsis thaliana), 3'ss of exon 5
gttcgcaattgcaccttcatggctttgatgctcgccagtatggtatcttattcgtctgtctaagtgaattttttcatgattttctattgtgatatgacagGGCTTTGGGAATGTGGGTTCTTGGGCATCGAAACTTATCCACGAAAAGGGTGGAAAAATTAAGGCTGTTAGTGATGTTACTGGAGCCATCAAGAACAACT
                | |  |   | |   |    |||  |  |  ||| |    ||||   ||        |||| | | |||  || | | |   |||||||||| |||||||||||||||||| ||||  | ||    || || ||||| || |||  ||| || |||||||| || ||||| |||||||||||  
---------------gtaaaagaagttacaatgtttagtcagagagattacttcggtgtcagggta------ctcat-actgtct-ctgcgtttt---agGGCTTTGGAAATGTGGGTTCTTGGGCAGCGAAGTTGATAAGTGACAAAGGTGGTAAGATTGTGGCGGTGAGTGATGTCACAGGAGCAATCAAGAACAATA

upper sequence: PP1S62_236V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: Vv08s0007g07400.t01 (Vitis vinifera), 3'ss of exon 7
gttcgcaattgcaccttcatggctttgatgctcgccagtatggtatcttattcgtctgtctaagtgaattttttcatgatt--ttctattgtgatatgacagGGCTTTGGGAATGTGGGTTCTTGGGCATCGAAACTTATCCACGAAAAGGGTGGAAAAATTAAGGCTGTTAGTGATGTTACTGGAGCCATCAAGAACAACT
 |     | || |  |  | ||     |   |    |    | ||  | | || | | | ||   |  ||||| ||| |||  |     | |  |||  ||||| |||||||||||||||||||||||  |  |||| |||   ||| | |||||||| |||   ||||| |||||  | ||||||||||| ||||| | | 
atagaagaatggatgta-agggagaaaaacttgataaactcgataaataaatcatttatttataagc-tttttccattattaatggatcttttttatcccagGGGTTTGGGAATGTGGGTTCTTGGGCTGCCCAACTCATCAGTGAACACGGTGGAAAGATTGTTGCTGTAAGTGACATCACTGGAGCCATTAAGAATAGCA
















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|162176130|gb|FC351079.1|FC351079
EST:     TGCTTAAGGATCATAACCTCAGCATTAGGGGCCAAACGTTCGTTGTCCAA                         GGCTTTGGGAATGTGGGTTCTTGGGCATCGAAACTTATCCACGAAAAGGGT
genomic: TGCTTAAGGATCATAACCTCAGCATTAGGGGCCAAACGTTCGTTGTCCAAgtaagtgccc ... gatatgacagGGCTTTGGGAATGTGGGTTCTTGGGCATCGAAACTTATCCACGAAAAGGGT
EST: gi|19790576|gb|BQ041944.1|BQ041944
EST:     TGCTTAAGGATCATAACCTCAGCATTAGGGGCCAAACGTTCGTTGTCCAA                         GGCTTTGGGAATGTGGGTTCTTGGGCATCGAAACTTATCCACGAAAAGGGT
genomic: TGCTTAAGGATCATAACCTCAGCATTAGGGGCCAAACGTTCGTTGTCCAAgtaagtgccc ... gatatgacagGGCTTTGGGAATGTGGGTTCTTGGGCATCGAAACTTATCCACGAAAAGGGT
EST: gi|162253971|gb|FC430215.1|FC430215
EST:     TGCTTAAGGATCATAACCTCAGCATTAGGGGCCAAACGTTCGTTGTCCAA                         GGCTTTGGGAATGTGGGTTCTTGGGCATCGAAACTTATCCACGA
genomic: TGCTTAAGGATCATAACCTCAGCATTAGGGGCCAAACGTTCGTTGTCCAAgtaagtgccc ... gatatgacagGGCTTTGGGAATGTGGGTTCTTGGGCATCGAAACTTATCCACGA
EST: gi|162194068|gb|FC370243.1|FC370243
EST:     TGCTTAAGGATCATAACCTCAGCATTAGGGGCCAAACGTTCGTTGTCCAA                         GGCTTTGGGAATGTGGGTTCTTGGGCATCGAAACTTATCCACGAAAAGGGT
genomic: TGCTTAAGGATCATAACCTCAGCATTAGGGGCCAAACGTTCGTTGTCCAAgtaagtgccc ... gatatgacagGGCTTTGGGAATGTGGGTTCTTGGGCATCGAAACTTATCCACGAAAAGGGT
EST: gi|162151269|gb|FC327723.1|FC327723
EST:     TGCTTAAGGATCATAACCTCAGCATTAGGGGCCAAACGTTCGTTGTCCAA                         GGCTTTGGGAATGTGGGTTCTTGGGCATCGAAACTTATCCACGAAAAGGGT
genomic: TGCTTAAGGATCATAACCTCAGCATTAGGGGCCAAACGTTCGTTGTCCAAgtaagtgccc ... gatatgacagGGCTTTGGGAATGTGGGTTCTTGGGCATCGAAACTTATCCACGAAAAGGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttattcgtctgtctaagtgaattttttcatgattttctattgtgatatgacagGGCTTTGGGAATGTGGGTTCTTGGGCATCGAAACTTATCCACGAAAAGGGTGGAAAAATTAAGGCTGTTAGTGATGTTACTGGAGCCATCAAGAACAACT
                     aattttttcatgattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttcgcaattgcaccttcatggctttgatgctcgccagtatggtatcttattcgtctgtctaagtgaattttttcatgattttctattgtgatatgacagGGCTTTGGGAATGTGGGTTCTTGGGCATCGAAACTTATCCACGAAAAGGGTGGAAAAATTAAGGCTGTTAGTGATGTTACTGGAGCCATCAAGAACAACT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC