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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taggctataactggtacaaagttcgtcgggattagttttgtctcgagtgcagtttattgtcattggaattaggaatctcatgtattatttgctctcgcagAAGCGGTATGATGTTCGTGCAATGATGCTGGAGACCGTGGCGGCTGTTCCTGGAATGGTCGGCGGAATGCTGCTCCATTGCAAATCATTGCGTAAATTTC

Basic information

species Physcomitrella patens
transcript PP1S183_11V6.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S183_11V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: LOC_Os04g51150.1 (Oryza sativa), 3'ss of exon 2
taggctataactggtacaa--agttcgtcgggattagttttgtctcgagtgcagtttattgtcattgg-aattaggaatctcatgtattatttgctctcgcagAAGCGGTATGATGTTCGTGCAATGATGCTGGAGACCGTGGCGGCTGTTCCTGGAATGGTCGGCGGAATGCTGCTCCATTGCAAATCATTGCGTAAATTTC
 |    ||| |   | | |  |||  || |  || |  | |   |||   ||   ||  ||| | ||  |||    ||        |||   |    | ||||| | ||||||     || || |||||||||||||| |||||||| || || || ||||| ||||| |||||||||||   |   ||  | ||    ||  
-acatgatatccatttctagtagtatgtggaaatgatctctag-tcggtcgctaattgctgtaactgtcaatggttaacactgcaaattgggttgggt-gcagAGGAGGTATGGCTGCCGCGCGATGATGCTGGAGACGGTGGCGGCGGTGCCGGGGATGGTGGGCGGCATGCTGCTCCACCTCCGGTCCCTCCGGCGCTTCG

upper sequence: PP1S183_11V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: LOC_Os02g47200.1 (Oryza sativa), 3'ss of exon 2
taggctataactggtacaaagttcgtcgggattagttttgtctcgagtgcagtttattgtcattggaattaggaatctcatgtattatttgctctcgcagAAGCGGTATGATGTTCGTGCAATGATGCTGGAGACCGTGGCGGCTGTTCCTGGAATGGTCGGCGGAATGCTGCTCCATTGCAAATCATTGCGTAAATTTC
       ||||       || |   |    || |    |    | | |  | |||  ||  || | |||  |||     ||  ||     | | | ||||| | |||| |     || || |||||||||||||| |||||||| || || || ||||| ||||| |||||||| ||   |   ||  | ||    ||  
------gtaaccaaccacaactaattttccatcaaagatcatgccaatctattttgctg--atcgaaat--ggatgggaatcaatggaacgattttgcagAGGAGGTACGGGTGCCGCGCGATGATGCTGGAGACGGTGGCGGCGGTGCCGGGGATGGTGGGCGGCATGCTGCTGCACCTCCGGTCGCTCCGCCGCTTCG

upper sequence: PP1S183_11V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GRMZM2G125669_T01 (Zea mays), 3'ss of exon 2
-taggctataactgg-tacaaagttcgtcggga---ttagttttgtctcgagtgcagtttattgtca-ttggaattaggaatctcatgtattatttgctctcgcagAAGCGGTATGATGTTCGTGCAATGATGCTGGAGACCGTGGCGGCTGTTCCTGGAATGGTCGGCGGAATGCTGCTCCATTGCAAATCATTGCGTAAATTTC
  | |    ||     | || | || |  || |   | |    |   ||          | |||| |  ||    |  ||||     | ||| | |||      ||| ||||||||     || || ||||||||||| |||||||| || || ||||| ||||| ||||| |||||||||||       ||| | ||    ||  
gcatgtcgaaatgatctgcatattttgaaggaaggttgaaaggtcgatcattcatgtgctgttgtaagctgaccctgtgaattgggcgaattgtctgc------agAGGCGGTATGGCTGCCGGGCGATGATGCTGGAAACCGTGGCTGCGGTGCCTGGGATGGTGGGCGGCATGCTGCTCCACCTGCGCTCACTCCGCCGCTTCG

upper sequence: PP1S183_11V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: Vv12s0142g00430.t01 (Vitis vinifera), 3'ss of exon 3
-taggctataactggtacaaagttcgtcgggatt-agttttgtctcgagtgcagtttattgtcattggaattaggaatctcatgtattatttgctctcgcagAAGCGGTATGATGTTCGTGCAATGATGCTGGAGACCGTGGCGGCTGTTCCTGGAATGGTCGGCGGAATGCTGCTCCATTGCAAATCATTGCGTAAATTTC
  |     |  ||| ||   | |      |  || |  ||  | |    | ||   || ||    | |    |  |  |  |||  | |  |    | |||||   | ||||    |||||||||||||||||| || ||||| ||||||||||| ||||| || || ||||| || |||   | |||  | || || ||| 
gcatatggtgcctgctattgattatactagtttttaagttaatttttcttccatcatactggttcttggtccaaca--ccgatggttgaaattacattgcagAGAAGATATGGGTGTCGTGCAATGATGCTGGAAACAGTGGCAGCTGTTCCTGGTATGGTGGGAGGGATGCTACTGCATCTAAGATCTCTCCGCAAGTTTG

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|162232061|gb|FC407468.1|FC407468
EST:     CTTACTGGCTGGTGAAGTCGTTACGTGTACCTTCGGATATGTTCTTTAAG                         AAGCGGTATGATGTTCGTGCAATGATGCTGGAGACCGTGGCGGCTGTTCCT
genomic: CTTACTGGCTGGTGAAGTCGTTACGTGTACCTTCGGATATGTTCTTTAAGgtacgagatt ... gctctcgcagAAGCGGTATGATGTTCGTGCAATGATGCTGGAGACCGTGGCGGCTGTTCCT
EST: gi|100403550|gb|BY954982.1|BY954982
EST:     TTACTGGCTGGTGAAGTCGTTACGTGTACCTTNCG-ATATGTTCTTTAAG                         AAGCGGTATGATGTTCGTGCAATGATGCTGGAGACCGTGNCGGCTGTTCCC
genomic: TTACTGGCTGGTGAAGTCGTTACGTGTACCTT-CGGATATGTTCTTTAAGgtacgagatt ... gctctcgcagAAGCGGTATGATGTTCGTGCAATGATGCTGGAGACCGTGGCGGCTGTTCC-
EST: gi|100384733|gb|BY950723.1|BY950723
EST:     CTTACTGGCTGGTGAAGTCGTTACGTGTACCTTCGGATAAGTTCTTTAAG                         AAGCGGTATGATGTTCGTGCAATGATGCTGGAGACCGTGGCGGCTGTTCCT
genomic: CTTACTGGCTGGTGAAGTCGTTACGTGTACCTTCGGATATGTTCTTTAAGgtacgagatt ... gctctcgcagAAGCGGTATGATGTTCGTGCAATGATGCTGGAGACCGTGGCGGCTGTTCCT
EST: gi|100430350|gb|BY959825.1|BY959825
EST:     CTTACTGGCTGGTGAAGTCGTTACGTGTACCTTCGGATATGTTCTTTAAG                         AAGCGGTATGATGTTCGTGCAATGATGCTGGAGACCGTGGCGGCTGT-CCN
genomic: CTTACTGGCTGGTGAAGTCGTTACGTGTACCTTCGGATATGTTCTTTAAGgtacgagatt ... gctctcgcagAAGCGGTATGATGTTCGTGCAATGATGCTGGAGACCGTGGCGGCTGTTCC-
EST: gi|100399415|gb|BY954360.1|BY954360
EST:     TTACTGGCTGGTGAAGTCGTTACGTGTACCTTNCGGATATGT-CTTTANG                         AAAGCG-TATGATGTTCGTGCAATGATGCTGGAGAC
genomic: TTACTGGCTGGTGAAGTCGTTACGTGTACCTT-CGGATATGTTCTTTAAGgtacgagatt ... gctctcgcagAA-GCGGTATGATGTTCGTGCAATGATGCTGGAGAC
EST: gi|162168864|gb|FC345338.1|FC345338
EST:     CTTACTGGCTGGTGAAGTCGTTACGTGTACCTTCGGATATGTTCTTTAAG                         AAGCGGTATGATGTTCGTGCAATGATGCTGGAGACCGTGGCGGCTGTTCCT
genomic: CTTACTGGCTGGTGAAGTCGTTACGTGTACCTTCGGATATGTTCTTTAAGgtacgagatt ... gctctcgcagAAGCGGTATGATGTTCGTGCAATGATGCTGGAGACCGTGGCGGCTGTTCCT
EST: gi|162275512|gb|FC451579.1|FC451579
EST:     CTTACTGGCTGGTGAAGTCGTTACGTGTACCTTCGGATATGTTCTTTAAG                         AAGCGGTATGATGTTCGTGCAATGATGCTGGAGACCGTGGCGGCTGTTCCT
genomic: CTTACTGGCTGGTGAAGTCGTTACGTGTACCTTCGGATATGTTCTTTAAGgtacgagatt ... gctctcgcagAAGCGGTATGATGTTCGTGCAATGATGCTGGAGACCGTGGCGGCTGTTCCT
EST: gi|100355861|gb|BY946075.1|BY946075
EST:     CTTACTGGCTGGTGAAGTCGTTACGTGTACCTTCGAA-ATGTTCTTTAAG                         AAGCGGTATGATGTTCGTGCAATGATGCTGGAGA
genomic: CTTACTGGCTGGTGAAGTCGTTACGTGTACCTTCGGATATGTTCTTTAAGgtacgagatt ... gctctcgcagAAGCGGTATGATGTTCGTGCAATGATGCTGGAGA
EST: gi|162228517|gb|FC404141.1|FC404141
EST:     CTTACTGGCTGGTGAAGTCGTTACGTGTACCTTCGGATATGTTCTTTAAG                         AAGCGGTATGATGTTCGTGCAATGATGCTGGAGACCGTGGCGGCTGTTCCT
genomic: CTTACTGGCTGGTGAAGTCGTTACGTGTACCTTCGGATATGTTCTTTAAGgtacgagatt ... gctctcgcagAAGCGGTATGATGTTCGTGCAATGATGCTGGAGACCGTGGCGGCTGTTCCT
EST: gi|100410681|gb|BY992216.1|BY992216
EST:     CT-ACTGGCTGGTGAAGTCGTTACGTGTACCTTCGGATATGTTCTTTTAG                         AAGCGGTATGATGTTCGTGGCA-TGATGCTGGAGACGGTGGCGGC
genomic: CTTACTGGCTGGTGAAGTCGTTACGTGTACCTTCGGATATGTTCTTTAAGgtacgagatt ... gctctcgcagAAGCGGTATGATGTTCGTG-CAATGATGCTGGAGACCGTGGCGGC
EST: gi|100389101|gb|BY952305.1|BY952305
EST:     TTACTGGCTGGTGAAGTCGTTACGTGTACCTTCGGATATGTTTCTTTA-G                         AAGCGGTATGATGTTCGTGCAATGATGCTGGAGACCGTGGGCG-CTGTTC
genomic: TTACTGGCTGGTGAAGTCGTTACGTGTACCTTCGGATATGTT-CTTTAAGgtacgagatt ... gctctcgcagAAGCGGTATGATGTTCGTGCAATGATGCTGGAGACCGTGG-CGGCTGTTC
EST: gi|162172123|gb|FC347986.1|FC347986
EST:     CTTACTGGCTGGTGAAGTCGTTACGTGTACCTTCGGATATGTTCTTTAAG                         AAGCGGTATGATGTTCGTGCAATGATGCTGGAGACCGTGGCGGCTGTTCCT
genomic: CTTACTGGCTGGTGAAGTCGTTACGTGTACCTTCGGATATGTTCTTTAAGgtacgagatt ... gctctcgcagAAGCGGTATGATGTTCGTGCAATGATGCTGGAGACCGTGGCGGCTGTTCCT
EST: gi|162197805|gb|FC373599.1|FC373599
EST:     CTTACTGGCTGGTGAAGTCGTTACGTGTACCTTCGGATATGTTCTTTAAG                         AAGCGGTATGATGTTCGTGCAATGATGCTGGAGACCGTGGCGGCTGTTCCT
genomic: CTTACTGGCTGGTGAAGTCGTTACGTGTACCTTCGGATATGTTCTTTAAGgtacgagatt ... gctctcgcagAAGCGGTATGATGTTCGTGCAATGATGCTGGAGACCGTGGCGGCTGTTCCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtgcagtttattgtcattggaattaggaatctcatgtattatttgctctcgcagAAGCGGTATGATGTTCGTGCAATGATGCTGGAGACCGTGGCGGCTGTTCCTGGAATGGTCGGCGGAATGCTGCTCCATTGCAAATCATTGCGTAAATTTC
                                          tttgctctc  CT-rich tract
                                  atgtattattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taggctataactggtacaaagttcgtcgggattagttttgtctcgagtgcagtttattgtcattggaattaggaatctcatgtattatttgctctcgcagAAGCGGTATGATGTTCGTGCAATGATGCTGGAGACCGTGGCGGCTGTTCCTGGAATGGTCGGCGGAATGCTGCTCCATTGCAAATCATTGCGTAAATTTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT