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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GACTCTCGAGCACGATGCTATGAAGGAAAAAATTAATGAGAATCAGGAGAAGATCAAACTCAATAAACAGCTGCCTTACCTAGTTGGAAACATTGTGGAGgttggtgttgtccacttgtcatttattggatgcatcagtagctttgaatttatttggcaagcaatgtgtcaaggctggggttaacatgcttttgtttcgt...

Basic information

species Physcomitrella patens
transcript PP1S340_7V6.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S340_7V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: LOC_Os02g56000.1 (Oryza sativa), 5'ss of exon 2
-GACTCTCGAGCACGATGCTATGAAGGAAAAAATTAATGAGAATCAGGAGAAGATCAAACTCAATAAACAGCTGCCTTACCTAGTTGGAAACATTGTGGAGgttggtgttgtccacttgtcatttattggatgcatcagt--agctttgaatttatttggcaagcaatgtg--tcaaggctggggttaacatgcttttgtttcgt
  ||  |   |    || |||  ||||| || || || ||||| |||||||||||||||||||| || |||||||||||||| || || ||||| || |||||| |||  |  |||   |  || | ||| |  | ||||  |  ||    || | ||      | | ||   |  |   || ||  | |     |     ||| 
GAACCTTGAGGTGGAATCCTAC-AAGGAGAAGATCAAGGAGAACCAGGAGAAGATCAAACTCAACAAGCAGCTGCCTTACCTTGTCGGCAACATCGTCGAGgtttgtgc-gcgcaccact--ttgactgggt-taccagtgaaatttcatgttcaatttaaggcccaagtagttttaatgtgcggagatcggttctggacatcga

upper sequence: PP1S340_7V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: GLYMA20G38030.1 (Glycine max), 5'ss of exon 2
GACTCTCGAGCACGATGCTATGAAGGAAAAAATTAATGAGAATCAGGAGAAGATCAAACTCAATAAACAGCTGCCTTACCTAGTTGGAAACATTGTGGAGgt--tggtgttgtccacttgtcatttattggat---gcatcagtagctttgaatttatt-tggcaagcaatgtgtcaaggctggggttaacatgctt-ttgtttcgt--------------------------------------------
 | | | ||    ||  |    ||||| || || || ||||||||||||||||| || |||||||| ||| |||| ||||| ||||| |||||||| |||||     | ||||    || ||  || ||||||   | ||  | |  |||| | || |  |    |    | ||  | || |||    ||  || || ||| ||  |                                            
CAATTTGGAATTGGAATCGTACAAGGACAAGATCAAGGAGAATCAGGAGAAGATTAAGCTCAATAAGCAGTTGCCCTACCTCGTTGGCAACATTGTTGAGgtacctatattgtttgtttctctgtt-ttggatattgtattgggatttttggacttttaattctgaatcttctggaatggatggaaaaaagttgtttcttgatttttaaacatttttcattgattatgacgtgataattttttgcatttag

upper sequence: PP1S340_7V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: GLYMA10G29250.1 (Glycine max), 5'ss of exon 2
GACTCTCGAGCACGATGCTATGAAGGAAAAAATTAATGAGAATCAGGAGAAGATCAAACTCAATAAACAGCTGCCTTACCTAGTTGGAAACATTGTGGAGgttggtg--ttgtccacttgtcatttattg--gatgcatcagtagcttt--gaatttatttggcaagcaatgtgtcaaggctggggttaacatgctt-ttgtttcgt--------------------------------------------
 | | | |||   ||  |    ||||| || || || ||||||||||||||||| || |||||||| ||| |||| ||||| ||||| ||||| || ||||| | |   ||||    || ||  || | |  | || ||  |    |||  |  |||   |    |    ||||  | || |||    ||  || || ||| ||  |                                            
CAATTTGGAGTTGGAATCGTACAAGGACAAGATCAAGGAGAATCAGGAGAAGATTAAGCTCAATAAGCAGTTGCCCTACCTCGTTGGGAACATCGTTGAGgtagctacattgtttgtttctctgttttggatgttgtatttgggatttttgggctttgaattctgaatcttgtggaatggatggaaaaaagttgtttcttgattttttctcattgttcttggattatgacgtgataactttttgcatttag

upper sequence: PP1S340_7V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: AT3G05530.1 (Arabidopsis thaliana), 5'ss of exon 2
GACTCTCGAGCACGATGCTATGAAGGAAAAAATTAATGAGAATCAGGAGAAGATCAAACTCAATAAACAGCTGCCTTACCTAGTTGGAAACATTGTGGAGg--ttggtgttgtccacttgtc--atttattggatgcatcagtagctttgaatttatttggcaagcaatgtgtcaaggctggggttaacatgcttttgtttcgt
 | ||| ||    ||| ||   ||||| || ||||| ||||||||||||||||| |||||||| || |||||||||||| | ||||| |||||||| ||||  ||    | ||   ||| ||  |||| | | ||    |   ||  |   |  ||||||    | | | |  |     | | |||| |||    |  | |   
AAATCTAGAATGTGATTCTTACAAGGAGAAGATTAAGGAGAATCAGGAGAAGATTAAACTCAACAAGCAGCTGCCTTACTTGGTTGGCAACATTGTCGAGgtattcaactagttttcttatcttatttttggtattttcctacagagtcttacctatttgatttgaattctaactg---ttgtgttaccatatcatgctattag

upper sequence: PP1S340_7V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: AT1G09100.1 (Arabidopsis thaliana), 5'ss of exon 2
GACTCTCGAGCACGATGCTATGAAGGAAAAAATTAATGAGAATCAGGAGAAGATCAAACTCAATAAACAGCTGCCTTACCTAGTTGGAAACATTGTGGAGgttggtgttgtccacttgtcatttattggatgcatcagtagctttgaatttatttggcaagcaatgtgtcaaggctggggttaacatgcttttgtttcgt------------
 |  || ||    ||  |  ||||||| ||||| || ||||| ||||||||||| || || || |||||||| |||||| ||||||| || || || |||||   | |     |||  ||  ||   || ||  |||    | ||    |||| |||   ||  |  ||   || |  |  |||||| | ||| | | |             
AAACCTTGATTTGGAATCAGTGAAGGAGAAAATAAAGGAGAACCAGGAGAAGATTAAGCTTAACAAACAGCTTCCTTACTTAGTTGGCAATATCGTTGAGgt-actttcactgactcttctcttg--gggtgtttca----cattc--cttatatgg--ggcttttggttttgg-tatgtataacattcctttttgttgagtgacacaattg

upper sequence: PP1S340_7V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: Vv05s0020g01180.t01 (Vitis vinifera), 5'ss of exon 3
GACTCTCGAGCACGATGCTATGAAGGAAAAAATTAATGAGAATCAGGAGAAGATCAAACTCAATAAACAGCTGCCTTACCTAGTTGGAAACATTGTGGAGgttggtgttgtccacttgtcatttattggatgcatcagtagctttgaatttatttggcaagcaatgtgtcaaggctggggttaacatgcttttgtttcgt----
|| ||| |||   ||  |  | || |||||||| || |||||||| ||||||||||| ||||| || ||||| || ||||| ||||| ||||| || |||||   | || |   ||     | | |||  || |    |   |||     |||  |   ||  ||       ||| | |    | |  ||| | ||| |     
GAATCTGGAGTTGGAATCGTTCAAAGAAAAAATAAAGGAGAATCAAGAGAAGATCAAGCTCAACAAGCAGCTACCCTACCTTGTTGGGAACATCGTTGAGgtgatttttcttggctccgtttgttttgactgaaaagtttattttcgtaatatcagtggag--ataaaatggggcagtg--cgaaaaacttctattttgaaaca

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|100446734|gb|CJ971033.1|CJ971033
EST:     AGATCAAACTCAATAAACAGCTGCCTTACCTAGTTGGAAACATTGTGGAG                         ATATTGGACGTCAATCCAGAAGATGAAGCTGAAGAGGATGGTGCTAATGTT
genomic: AGATCAAACTCAATAAACAGCTGCCTTACCTAGTTGGAAACATTGTGGAGgttggtgttg ... tgccctgcagATATTGGACGTCAATCCAGAAGATGAAGCTGAAGAGGATGGTGCTAATGTT
EST: gi|208366108|gb|DC935869.1|DC935869
EST:     AGATCAAACTCAATAAACAGCTGCCTTACCTAGTTGGAAACATTGTGGAG                         ATATTGGACGTCAATCCAGAAGATGAAGCTGAAGAGGATGGTGCTAATGTT
genomic: AGATCAAACTCAATAAACAGCTGCCTTACCTAGTTGGAAACATTGTGGAGgttggtgttg ... tgccctgcagATATTGGACGTCAATCCAGAAGATGAAGCTGAAGAGGATGGTGCTAATGTT
EST: gi|208373535|gb|DC941104.1|DC941104
EST:     AGATCAAACTCAATAAACAGCTGCCTTACCTAGTTGGAAACATTGTGGAG                         ATATTGGACGTCGATCCAGAAGATGAAGCTGAAGAGGATGGTGCTAATGTT
genomic: AGATCAAACTCAATAAACAGCTGCCTTACCTAGTTGGAAACATTGTGGAGgttggtgttg ... tgccctgcagATATTGGACGTCAATCCAGAAGATGAAGCTGAAGAGGATGGTGCTAATGTT
EST: gi|208382087|gb|DC914776.1|DC914776
EST:     AGATCAAACTCAATAAACAGCTGCCTTACCTAGTTGGAAACATTGTGGAG                         ATATTGGACGTCAATCCAGAAGATGAAGCTGAAGAGGATGGTGCTAATGTT
genomic: AGATCAAACTCAATAAACAGCTGCCTTACCTAGTTGGAAACATTGTGGAGgttggtgttg ... tgccctgcagATATTGGACGTCAATCCAGAAGATGAAGCTGAAGAGGATGGTGCTAATGTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GACTCTCGAGCACGATGCTATGAAGGAAAAAATTAATGAGAATCAGGAGAAGATCAAACTCAATAAACAGCTGCCTTACCTAGTTGGAAACATTGTGGAGgttggtgttgtccacttgtcatttattggatgcatcagtagctttgaatttatttggcaagcaatgtgtcaaggctggggttaacatgcttttgtttcgt

- - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG