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

...gcttggtatgaaggactctctcgtgttcactgatgcctgtttatttgaaattgatgttccgcttacttttgactccaacatctactggtttgtgtaccagAGATATCAAACCGGACAACTTGCTGTTAGATAAGAATGGGCACATGAAGTTATCTGATTTTGGCCTCTGTAAGCCTTTGGACTGCTCCAACTTGCCTGCC

Basic information

species Physcomitrella patens
transcript PP1S22_429V6.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S22_429V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GLYMA10G00830.1 (Glycine max), 3'ss of exon 4
-------------------------------------gcttggtatgaaggactctctcg-tgttcactgatgcctgtttatttgaaattgatgttccgcttacttttgactccaaca-tctactggtt---tgtgtaccagAGATATCAAACCGGACAACTTGCTGTTAGATAAGAATGGGCACATGAAGTTATCTGATTTTGGCCTCTGTAAGCCTTTGGACTGCTCCAACTTGCCTGCC
                                     |     | ||    ||| |   |   |  |   |||  |  |||||      |  |  |      |   || | | ||| | |||  |  ||   ||  | ||||||||||||| || |||||||||||| ||||||  ||||| |||||||| ||||| ||||||||  | ||||| ||  | ||||||   ||| | |  |  
gtaagctcaaagctgtaaaaaataacgtcaaatgatggtaaattttgctatacttttatgacatggatcaatga-tacttattgcggtcttcttctggatcaatacttaatttcaataatctgatttttaaatgcattccagAGATATCAAGCCTGACAACTTGCTGCTAGATAGAAATGGCCACATGAAATTATCAGATTTTGGATTATGTAAACCGCTAGACTGCAGTAACCTTCAAGAA

upper sequence: PP1S22_429V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GLYMA02G00580.2 (Glycine max), 3'ss of exon 5
-------------------------gcttggtatgaagg-actctctcgtgttcactgatgcc-tgtttatttgaaattgatgttccgcttacttttgact--ccaacatcta-------ctggttt------gtgtaccagAGATATCAAACCGGACAACTTGCTGTTAGATAAGAATGGGCACATGAAGTTATCTGATTTTGGCCTCTGTAAGCCTTTGGACTGCTCCAACTTGCCTGCC
                          | |   |||| || |   | | || | |  | ||| |  |  |   ||| | | |||     |||  | | ||      || || |        ||| |||      |  | ||||||||||||| || |||||||||||| ||||||  ||||| |||||||| ||||| ||||||||  | ||||| ||  | ||||||   ||  | |  |  
gtaagctcaaagctgtaaaaaaataacgtcaaatgatggtaaattttggtatgcttttatgacacggatcaatgatacttatggcggtcttcgtctggatcaataaatatttttaataatctgatttttaaatgcattccagAGATATCAAGCCTGACAACTTGCTGCTAGATAGAAATGGCCACATGAAATTATCAGATTTTGGATTATGTAAACCGCTAGACTGCAGTAATCTTCAAGAA

upper sequence: PP1S22_429V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GLYMA20G35110.1 (Glycine max), 3'ss of exon 4
-------------------------gct-tggtatgaaggactctctcgtgttcactgatg--cctgtttatttgaaattgatgttccgcttacttttgactccaacatctactggtttgtgtaccagAGATATCAAACCGGACAACTTGCTGTTAGATAAGAATGGGCACATGAAGTTATCTGATTTTGGCCTCTGTAAGCCTTTGGACTGCTCCAACTTGCCTGCC
                         | |     |||||   ||        |    || ||  | |||||  ||| |  | |          |  |   | || ||  |    || | ||  | ||||||||||||| || |||||||||||| ||||||  ||||| |||||||| ||||| || |||||  | ||||| ||  | ||||||   ||  | |  |  
gtaagctcaagctgcaaatagtcatgttacaccatgaaaatcttatattaatcttatggtggtcttgttttcttgcacataaaaaaaaaaagatataatattctaattt----tgatatgcattccagAGATATCAAGCCTGACAACTTGCTGCTAGATAGAAATGGTCACATGAAATTATCAGACTTTGGATTATGTAAACCACTAGACTGCAGTAATCTTCAGGAA

upper sequence: PP1S22_429V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GLYMA10G32480.1 (Glycine max), 3'ss of exon 4
----gcttg-gtatgaaggactctctcgtgttcactgatgcctgtttatttgaaatt---gatgttccgcttacttttgactccaaca---------------tctactggtttgtgtaccagAGATATCAAACCGGACAACTTGCTGTTAGATAAGAATGGGCACATGAAGTTATCTGATTTTGGCCTCTGTAAGCCTTTGGACTGCTCCAACTTGCCTGCC
    |||   |  | ||  | ||         ||   |   ||  |||| | ||  |   | || ||   ||   ||  ||  ||| |               | |  || | ||  | ||||||||||||| || ||||| |||||| ||||||  ||||| |||||||| ||||| || |||||  | ||||| ||  ||||||||   ||  | |  |  
gtaagctcaagcttcaaatagtcatgttacaccatgaaaatcttattatattaatcttatggtggtctttttttcttgcacatcaaaaaaggtataatattcttattttgatatgcattccagAGATATCAAGCCTGACAATTTGCTGCTAGATAGAAATGGTCACATGAAATTATCAGACTTTGGATTATGTAAACCACTGGACTGCAGTAATCTTCAGGAA

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|162170612|gb|FC347108.1|FC347108
EST:     CAATGTGTTCTGGCTATCGAGTCAATTCACAAACACAACTACATTCATAG                         AGATATCANACCGGACAACTTTGCTGT-AGATAAGAATGGGCACATGAAGT
genomic: CAATGTGTTCTGGCTATCGAGTCAATTCACAAACACAACTACATTCATAGgtacttgaga ... tgtgtaccagAGATATCAAACCGGACAACTT-GCTGTTAGATAAGAATGGGCACATGAAGT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgaaattgatgttccgcttacttttgactccaacatctactggtttgtgtaccagAGATATCAAACCGGACAACTTGCTGTTAGATAAGAATGGGCACATGAAGTTATCTGATTTTGGCCTCTGTAAGCCTTTGGACTGCTCCAACTTGCCTGCC
                     ttttgac  putative branch site (score: 3)
                 ttactttt  TA-rich tract