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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agatttagttttgcttatgagatcctgttgtgcttttgtcactttgttatttatgtttgttaccaatggttgtattttttatgcatttggaacatttcagTATTTATGGTGTGCATGATGAGGCCAAGGACAAGGCCTTTGAGCTGGAGATGAGCTGGATTTGTGACGAGTCAAACCGTGAGCATCAACGA

Basic information

species Physcomitrella patens
transcript PP1S72_57V6.4
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S72_57V6.1 (Physcomitrella patens), 3'ss of exon 10
lower sequence: GRMZM2G445100_T01 (Zea mays), 3'ss of exon 9
agatttagttttgcttatgagatcctgttgtg-cttttgtcactttgttatttatgtttgttaccaatggttgtattttttatgcatttggaacatttcagTATTTATGGTGTGCATGATGAGGCCAAGGACAAGGCCTTTGAGCTGGAGATGAGCTGGATTTGTGACGAGTCAAACCGTGAGCATCAACGA
  | ||  ||||   | |  |  | |  | || |     | |   ||  |    |  |  |   ||| | ||   || |  |   |    |  || ||||| |||||||  ||||||||||| || |||||||| || |||||| ||||| |||||||||| ||||| || || || ||  |||||||    
caagttgcttttatattttcgtgctttatatgacgccaatgaacctgaaaaggctactgctcttcaaagtttacgttctg-acaaaacgtgcccaattcagAATTTATGCAGTGCATGATGAAGCTAAGGACAAAGCTTTTGAGTTGGAGTTGAGCTGGATCTGTGAGGAATCGAAGCGCCAGCATCAGAAG

upper sequence: PP1S72_57V6.1 (Physcomitrella patens), 3'ss of exon 10
lower sequence: GLYMA05G14330.1 (Glycine max), 3'ss of exon 8
---agatttagttttgcttatgagatcctgttgtgcttttgtcactttgttatttatgtttgttaccaatggttgtattttttatgcatttggaacatttcagTATTTATGGTGTGCATGATGAGGCCAAGGACAAGGCCTTTGAGCTGGAGATGAGCTGGATTTGTGACGAGTCAAACCGTGAGCATCAACGA---------
      |||| ||     |  | ||  || || |          ||||| |||         || |  |      | ||||  ||   ||||   ||   |||||| ||||| || ||||||||||| |||||||| |  |||||||| || ||||||||| | ||||| |||||||||||  | ||| |             
ggggcttttaattcaaaatgggtgaatcttttataagaca--tgctttgatataataagacattccttacaagaattttttgcatttgtttgtgccaag-cagTATATATGGAGTTCATGATGAGGCAAAGGACAAAGATTTTGAGCTAGAAATGAGCTGGGTGTGTGATGAGTCAAACCGCCAACATGAGAAGGTAAGGCTG

upper sequence: PP1S72_57V6.1 (Physcomitrella patens), 3'ss of exon 10
lower sequence: GLYMA05G14330.2 (Glycine max), 3'ss of exon 8
---agatttagttttgcttatgagatcctgttgtgcttttgtcactttgttatttatgtttgttaccaatggttgtattttttatgcatttggaacatttcagTATTTATGGTGTGCATGATGAGGCCAAGGACAAGGCCTTTGAGCTGGAGATGAGCTGGATTTGTGACGAGTCAAACCGTGAGCATCAACGA
      |||| ||     |  | ||  || || |          ||||| |||         || |  |      | ||||  ||   ||||   ||   |||||| ||||| || ||||||||||| |||||||| |  |||||||| || ||||||||| | ||||| |||||||||||  | ||| |    
ggggcttttaattcaaaatgggtgaatcttttataagaca--tgctttgatataataagacattccttacaagaattttttgcatttgtttgtgccaag-cagTATATATGGAGTTCATGATGAGGCAAAGGACAAAGATTTTGAGCTAGAAATGAGCTGGGTGTGTGATGAGTCAAACCGCCAACATGAGAAG

upper sequence: PP1S72_57V6.1 (Physcomitrella patens), 3'ss of exon 10
lower sequence: AT2G27020.1 (Arabidopsis thaliana), 3'ss of exon 8
------agatttagttttgcttatg-agatcctgttgtgcttttgtcactttgttatttatgtttgttaccaatggttgtattttttatgcatttggaacatttcagTATTTATGGTGTGCATGATGAGGCCAAGGACAAGGCCTTTGAGCTGGAGATGAGCTGGATTTGTGACGAGTCAAACCGTGAGCATCAACGA
      ||   | | ||  | | |  |  |  | | || ||  |||   ||   ||   | |||  ||    || |    || |  | |   |||   |  |  ||| || ||     | || ||||| |||||||||||||| |||||  |||||||||||||||| || || |||||||| || ||||||||    
gtgagtagtgcttgcttctcatgtacatgttttctggttctcatgtgctttctataaccaggttcatttt--atagcaagatgtgatgttactttttcatgtg-cagCATCTACAAGCTACACGATGAAGCCAAGGACAAGGCTTTTGAATTGGAGATGAGCTGGATATGCGAGGAGTCAAAACGAGAGCATCAGAAG

upper sequence: PP1S72_57V6.1 (Physcomitrella patens), 3'ss of exon 10
lower sequence: Vv08s0040g00410.t01 (Vitis vinifera), 3'ss of exon 8
agatttagttt---tgcttatgagatcctgttgtgcttttgtcactttgttatttatgtttgttaccaatggttgtattttttatgcatttggaacatttcagTATTTATGGTGTGCATGATGAGGCCAAGGACAAGGCCTTTGAGCTGGAGATGAGCTGGATTTGTGACGAGTCAAACCGTGAGCATCAACGA
  ||||  |||   || |    |  |    |  ||  | |   | |||    ||||| ||| | ||| | | |  |  || || | ||||      |   ||| |||||||| || || |||||||||||||||||||| |||||| |||| ||||||||| ||||||| |||||||||||  |||||||    
-tatttgttttccatgttctgaaacttacataatggatcttcaaattttcattttatttttctgaccca-gttcatggttattttacattaatggtaag-cagCATTTATGGGGTACACGATGAGGCCAAGGACAAGGCATTTGAGTTGGAAATGAGCTGGGTTTGTGAGGAGTCAAACCGCCAGCATCAGAAG

upper sequence: PP1S72_57V6.1 (Physcomitrella patens), 3'ss of exon 10
lower sequence: EFJ26741 (Selaginella moellendorffii), 3'ss of exon 9
agatttagttttgcttatgagatcctgttgtgcttttgtcactttgttatttatgtttgttaccaatggttgtattttttatgcatttggaacattt-cagTATTTATGGTGTGCATGATGAGGCCAAGGACAAGGCCTTTGAGCTGGAGATGAGCTGGATTTGTGACGAGTCAAACCGTGAGCATCAACGA
                                          |  ||| |||   ||  |  |   ||| || ||| |||   | | || ||  |   ||| || || || || || || || ||||||||||| |||||||| ||||| |||||||||||||| |||||||| |||   ||||| |||   
-----------------------------------------gtaagttttttcgtttcctccctgttggatggattctttgaacttgtgaaaactaaacagCATCTACGGAGTTCACGACGAAGCCAAGGACAAAGCCTTTGAACTGGAAATGAGCTGGATTTGCGACGAGTCGAACAAGGAGCACCAAAAG

upper sequence: PP1S72_57V6.1 (Physcomitrella patens), 3'ss of exon 10
lower sequence: EFJ26434 (Selaginella moellendorffii), 3'ss of exon 9
agatttagttttgcttatgagatcctgttgtgcttttgtcactttgttatttatgtttgttaccaatggttgtattttttatgcatttggaacattt---cagTATTTATGGTGTGCATGATGAGGCCAAGGACAAGGCCTTTGAGCTGGAGATGAGCTGGATTTGTGACGAGTCAAACCGTGAGCATCAACGA
                                  |  ||   || |||   |   | |   |   ||  ||  |  ||   | ||  ||  | |  |   ||| || || || || || || || ||||||||||| |||||||| ||||| |||||||||||||| |||||||| |||   ||||| |||   
---------------------------------gtaagttttttggtttcctccctgttggatggattctttgaacttccttccacctgtgaaaactaaacagCATCTACGGAGTTCACGACGAAGCCAAGGACAAAGCCTTTGAACTGGAAATGAGCTGGATTTGCGACGAGTCGAACAAGGAGCACCAAAAG

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|18335635|gb|BJ167655.1|BJ167655
EST:     AATTTGTCAGAGATGACCTGCAGGCAAGGAGTGATTGCAATTGCGAAGAT                         TATTTATGGTGTGCATGATGAGGCCAAGGACAAGGCCTTTGAGCTGGAGAT
genomic: AATTTGTCAGAGATGACCTGCAGGCAAGGAGTGATTGCAATTGCGAAGATgtaagccaaa ... aacatttcagTATTTATGGTGTGCATGATGAGGCCAAGGACAAGGCCTTTGAGCTGGAGAT
EST: gi|37840289|gb|BJ598297.1|BJ598297
EST:     AATTTGTCAGAGATGACCTGCAGGCAAGGAGTGATTGCAATTGCGAAGAT                         TATTTATGGTGTGCATGATGAGGCCAAGGACAAGGCCTTTGAGCTGGAGAT
genomic: AATTTGTCAGAGATGACCTGCAGGCAAGGAGTGATTGCAATTGCGAAGATgtaagccaaa ... aacatttcagTATTTATGGTGTGCATGATGAGGCCAAGGACAAGGCCTTTGAGCTGGAGAT
EST: gi|208346631|gb|DC916897.1|DC916897
EST:     AATTTGTCAGAGATGACCTGCAGGCAAGGAGTGATTGCAATTGCGAAGAT                         TATTTATGGTGTGCATGATGAGGCCAAGGACAAGGCCTTTGAGCTGGAGAT
genomic: AATTTGTCAGAGATGACCTGCAGGCAAGGAGTGATTGCAATTGCGAAGATgtaagccaaa ... aacatttcagTATTTATGGTGTGCATGATGAGGCCAAGGACAAGGCCTTTGAGCTGGAGAT
EST: gi|37844839|gb|BJ602847.1|BJ602847
EST:     AATTTGTCAGAGATGACCTGCAGGCAAGGAGTGATTGCAATTGCGAAGAT                         TATTTATGGTGTGCATGATGAGGCCAAGGACAAGGCCTTTGAGCTGGAGAT
genomic: AATTTGTCAGAGATGACCTGCAGGCAAGGAGTGATTGCAATTGCGAAGATgtaagccaaa ... aacatttcagTATTTATGGTGTGCATGATGAGGCCAAGGACAAGGCCTTTGAGCTGGAGAT
EST: gi|208367520|gb|DC954952.1|DC954952
EST:     AATTTGTCAGAGATGACCTGCAGGCAAGGAGTGATTGCAATTGCGAAGAT                         TATTTATGGTGTGCATGATGAGGCCAAGGACAAGGCCTTTGAGCTGGAGAT
genomic: AATTTGTCAGAGATGACCTGCAGGCAAGGAGTGATTGCAATTGCGAAGATgtaagccaaa ... aacatttcagTATTTATGGTGTGCATGATGAGGCCAAGGACAAGGCCTTTGAGCTGGAGAT
EST: gi|67693091|gb|BJ953324.1|BJ953324
EST:     AATTTGTCAGAGATGACCTGCAGGCAAGGAGTGATTGCAATTGCGAAGAT                         TATTTATGGTGTGCATGATGAGGCCAAGGACAAGGCCTTTGAGCTGGAGAT
genomic: AATTTGTCAGAGATGACCTGCAGGCAAGGAGTGATTGCAATTGCGAAGATgtaagccaaa ... aacatttcagTATTTATGGTGTGCATGATGAGGCCAAGGACAAGGCCTTTGAGCTGGAGAT
EST: gi|37823229|gb|BJ581295.1|BJ581295
EST:     AATTTGTCAGAGATGACCTGCAGGCAAGGAGTGATTGCAATTGCGAAGAT                         TATTTATGGTGTGCATGATGAGGCCAAGGACAAGGCCTTTGAGCTGGAGAT
genomic: AATTTGTCAGAGATGACCTGCAGGCAAGGAGTGATTGCAATTGCGAAGATgtaagccaaa ... aacatttcagTATTTATGGTGTGCATGATGAGGCCAAGGACAAGGCCTTTGAGCTGGAGAT
EST: gi|162272069|gb|FC447863.1|FC447863
EST:     AATTTGTCAGAGATGACCTGCAGGCAAGGAGTGATTGCAATTGCGAAGAT                         TATTTATGGTGTGCATGATGAGGCCAAGGACAAGGCCTTTGAGCTGGAGAT
genomic: AATTTGTCAGAGATGACCTGCAGGCAAGGAGTGATTGCAATTGCGAAGATgtaagccaaa ... aacatttcagTATTTATGGTGTGCATGATGAGGCCAAGGACAAGGCCTTTGAGCTGGAGAT
EST: gi|162272070|gb|FC447864.1|FC447864
EST:     AATTTGTCAGAGATGACCTGCAGGCAAGGAGTGATTGCAATTGCGAAGAT                         TATTTATGGTGTGCATGATGAGGCCAAGGACAAGGCCTTTGAGCTGGAGAT
genomic: AATTTGTCAGAGATGACCTGCAGGCAAGGAGTGATTGCAATTGCGAAGATgtaagccaaa ... aacatttcagTATTTATGGTGTGCATGATGAGGCCAAGGACAAGGCCTTTGAGCTGGAGAT
EST: gi|162267459|gb|FC444210.1|FC444210
EST:     AATTTGTCAGAGATGACCTGCAGGCAAGGAGTGATTGCAATTGCGAAGAT                         TATTTATGGTGTGCATGATGAGGCCAAGGACAAGGCCTTTGAGCTGGAGAT
genomic: AATTTGTCAGAGATGACCTGCAGGCAAGGAGTGATTGCAATTGCGAAGATgtaagccaaa ... aacatttcagTATTTATGGTGTGCATGATGAGGCCAAGGACAAGGCCTTTGAGCTGGAGAT
EST: gi|208371637|gb|DC932466.1|DC932466
EST:     AATTTGTCANAAATGACCTGCANGCAAGGANTGATTGCAATTGCNAAAAT                         AATTTATGGTGTGCATGATGAG
genomic: AATTTGTCAGAGATGACCTGCAGGCAAGGAGTGATTGCAATTGCGAAGATgtaagccaaa ... aacatttcagTATTTATGGTGTGCATGATGAG
EST: gi|208369160|gb|DC956035.1|DC956035
EST:     AATTTGTCAGAGATGACCTGCAGGCAAGGAGTGATTGCAATTGCGAAGAT                         TATTTATGGTGTGCATGATGAGGCCAAGGACAAGGCCTTTGAGCTGGAGAT
genomic: AATTTGTCAGAGATGACCTGCAGGCAAGGAGTGATTGCAATTGCGAAGATgtaagccaaa ... aacatttcagTATTTATGGTGTGCATGATGAGGCCAAGGACAAGGCCTTTGAGCTGGAGAT
EST: gi|37823184|gb|BJ581250.1|BJ581250
EST:     AATTTGTCAGAGATGACCTGCAGGCAAGGAGTGATTGCAATTGCGAAGAT                         TATTTATGGTGTGCATGATGAGGCCAAGGACAAGGCCTTTGAGCTGGAGAT
genomic: AATTTGTCAGAGATGACCTGCAGGCAAGGAGTGATTGCAATTGCGAAGATgtaagccaaa ... aacatttcagTATTTATGGTGTGCATGATGAGGCCAAGGACAAGGCCTTTGAGCTGGAGAT
EST: gi|208394276|gb|DC904096.1|DC904096
EST:     AATTTGTCAGAGATGACCTGCAGGCAAGGAGTGATTGCAATTGCGAAAAT                         TATTTATGGTGTGCATGATGA
genomic: AATTTGTCAGAGATGACCTGCAGGCAAGGAGTGATTGCAATTGCGAAGATgtaagccaaa ... aacatttcagTATTTATGGTGTGCATGATGA
EST: gi|208390148|gb|DC941955.1|DC941955
EST:     AATTTGTCANAGATGACCTGCAGGCAAGAAGTGATNGCAATTGCGAAAAT                         -ATTTATGGTGTGCATGATGAG
genomic: AATTTGTCAGAGATGACCTGCAGGCAAGGAGTGATTGCAATTGCGAAGATgtaagccaaa ... aacatttcagTATTTATGGTGTGCATGATGAG
EST: gi|208374326|gb|DC948386.1|DC948386
EST:     AATTTGTCAGAGATGACCTGCAGGCAAGGAGTGATTGCAATTGCGAAGAT                         TATTTATGGTGTGCATGATGAGGCCAAGGACAAGGCCTTTGAGCTGGAGAT
genomic: AATTTGTCAGAGATGACCTGCAGGCAAGGAGTGATTGCAATTGCGAAGATgtaagccaaa ... aacatttcagTATTTATGGTGTGCATGATGAGGCCAAGGACAAGGCCTTTGAGCTGGAGAT
EST: gi|208363378|gb|DC946976.1|DC946976
EST:     AATTTGTCAGAGATGACCTGCAGGCAAGGAGTGATTGCAATTGCGAAGAT                         TATTTATGGTGTGCATGATGAGGCCAAGGACAAGGCCTTTGAGCTGGAGAT
genomic: AATTTGTCAGAGATGACCTGCAGGCAAGGAGTGATTGCAATTGCGAAGATgtaagccaaa ... aacatttcagTATTTATGGTGTGCATGATGAGGCCAAGGACAAGGCCTTTGAGCTGGAGAT
EST: gi|208399219|gb|DC916574.1|DC916574
EST:     AATTTGTCAGAGATGACCTGCAGGCAAGGAGTGATTGCAATTGCGAAGAT                         TATTTATGGTGTGCATGATGAGGCCAAGGACAAGGCCTTTGAGCTGGAGAT
genomic: AATTTGTCAGAGATGACCTGCAGGCAAGGAGTGATTGCAATTGCGAAGATgtaagccaaa ... aacatttcagTATTTATGGTGTGCATGATGAGGCCAAGGACAAGGCCTTTGAGCTGGAGAT
EST: gi|18336615|gb|BJ168638.1|BJ168638
EST:     AATTTGTCAGAGATAACCTGCAGGCAAGGAGTTATTGCAATTGNGAAGAT                         TATTTATGGTGTGCATGATGAGGCCAAGGACAAGGCCTTTGAGCTGGAGAT
genomic: AATTTGTCAGAGATGACCTGCAGGCAAGGAGTGATTGCAATTGCGAAGATgtaagccaaa ... aacatttcagTATTTATGGTGTGCATGATGAGGCCAAGGACAAGGCCTTTGAGCTGGAGAT
EST: gi|162209436|gb|FC386069.1|FC386069
EST:     AATTTGTCAGAGATGACCTGCAGGCAAGGAGTGATTGCAATTGCGAAGAT                         TATTTATGGTGTGCATGATGAGGCCAAGGACAAGGCCTTTGAGCTGGAGAT
genomic: AATTTGTCAGAGATGACCTGCAGGCAAGGAGTGATTGCAATTGCGAAGATgtaagccaaa ... aacatttcagTATTTATGGTGTGCATGATGAGGCCAAGGACAAGGCCTTTGAGCTGGAGAT
EST: gi|37847181|gb|BJ605189.1|BJ605189
EST:     AATTTGTCAGAGATGACCTGCAGGCAAGGAGTGATTGCAATTGCGAAGAT                         TATTTATGGTGTGCATGATGAGGCCAAGGACAAGGCCTTTGAGCTGGAGAT
genomic: AATTTGTCAGAGATGACCTGCAGGCAAGGAGTGATTGCAATTGCGAAGATgtaagccaaa ... aacatttcagTATTTATGGTGTGCATGATGAGGCCAAGGACAAGGCCTTTGAGCTGGAGAT
EST: gi|208349231|gb|DC917995.1|DC917995
EST:     AATTTGTCAGAGATGACCTGCAGGCAAGGAGTGATTGCAATTGCGAAGAT                         TATTTATGGTGTGCATGATGAGGCCAAGGACAAGGCCTTTGAGCTGGAGAT
genomic: AATTTGTCAGAGATGACCTGCAGGCAAGGAGTGATTGCAATTGCGAAGATgtaagccaaa ... aacatttcagTATTTATGGTGTGCATGATGAGGCCAAGGACAAGGCCTTTGAGCTGGAGAT
EST: gi|208357921|gb|DC943047.1|DC943047
EST:     AATTTGTCAGAGATGACCTGCAGGCAAGGAGTGATTGCAATTGCGAAAAT                         -ATTTATGGTGTGCATGATGAGGCCAAGGACAAG
genomic: AATTTGTCAGAGATGACCTGCAGGCAAGGAGTGATTGCAATTGCGAAGATgtaagccaaa ... aacatttcagTATTTATGGTGTGCATGATGAGGCCAAGGACAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttatttatgtttgttaccaatggttgtattttttatgcatttggaacatttcagTATTTATGGTGTGCATGATGAGGCCAAGGACAAGGCCTTTGAGCTGGAGATGAGCTGGATTTGTGACGAGTCAAACCGTGAGCATCAACGA
                           tattttttatgcattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agatttagttttgcttatgagatcctgttgtgcttttgtcactttgttatttatgtttgttaccaatggttgtattttttatgcatttggaacatttcagTATTTATGGTGTGCATGATGAGGCCAAGGACAAGGCCTTTGAGCTGGAGATGAGCTGGATTTGTGACGAGTCAAACCGTGAGCATCAACGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA