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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AATCACTGAGGCTGGAGCCAATAGAGTGCTGGCTTGTGATCTTCATTCAGGGCAGTCAATGGGATATTTTGACATTTCCGTTGATCACGTTTATGGTCAGgtgagtatgattcttagctcgtacttttaccaagtgcattatgtatgggtcgtgcaacgaggtaactttattcttttcgctttgaatgacctttgattaatctcggagccttgtgtgcag

Basic information

species Physcomitrella patens
transcript PP1S42_193V6.3
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S42_193V6.2 (Physcomitrella patens), 5'ss of exon 4
lower sequence: GRMZM2G038791_T01 (Zea mays), 5'ss of exon 4
AATCACTGAGGCTGGAGCCAATAGAGTGCTGGCTTGTGATCTTCATTCAGGGCAGTCAATGGGATATTTTGACATTTCCGTTGATCACGTTTATGGTCAGgtgagta---tgattcttagctcgtacttttaccaagtgcattatgtatgggt-cgtgcaacgaggt--aactttattcttttcgctttgaatgacctttgattaatctcggagccttgtgtgcag
 || || || ||||| |||||  | || || | |||||||||||||||  | ||  |||||||||| ||||||||  | || |||||||||||||| |||||   |    |||  | |    | ||  | ||  || | | ||| |  |  ||   |   | |   |  | | || || |  | | |||  ||      || || |||   ||             
GATTACCGAAGCTGGTGCCAACCGTGTCCTTGTTTGTGATCTTCATTCTAGTCAAGCAATGGGATACTTTGACATCCCAGTAGATCACGTTTATGGCCAGgtatatgtactgaagcatgctacttaaatctattaattcctttaagacttagtgtttatgatggtattcatccttcttataattgttttctatttttcctgtttgatccgtgaag-----------

upper sequence: PP1S42_193V6.2 (Physcomitrella patens), 5'ss of exon 4
lower sequence: GLYMA05G06110.1 (Glycine max), 5'ss of exon 4
AATCACTGAGGCTGGAGCCAATAGAGTGCTGGCTTGTGATCTTCATTCAGGGCAGTCAATGGGATATTTTGACATTTCCGTTGATCACGTTTATGGTCAGgtgagtatgattcttagctcgtacttttaccaagtgcattatgtatgggtcgtgcaacgaggtaactttattcttttcgctttgaatgacctttgattaatctcggagccttgtgtgcag
 || ||  | ||||| ||  |  | || || |||||||| ||||||||||||||||| ||||| || ||||| ||| | |||||||| ||  |  ||||||| |||| | ||||||     |  || ||     |  |||    |   ||     ||     |   |||||  | | | ||                                       
TATTACAAAAGCTGGGGCAGACCGTGTTCTCGCTTGTGACCTTCATTCAGGGCAGTCCATGGGTTACTTTGATATTCCTGTTGATCATGTACACTGTCAGgtaagta-ggttcttaa----tggttgtagtttatttattggtaacatgtttcctaatactattg-tttatgatgtccactag-------------------------------------

upper sequence: PP1S42_193V6.2 (Physcomitrella patens), 5'ss of exon 4
lower sequence: AT2G35390.3 (Arabidopsis thaliana), 5'ss of exon 3
AATCACTGAGGCTGGAGCCAATAGAGTGCTGGCTTGTGATCTTCATTCAGGGCAGTCAATGGGATATTTTGACATTTCCGTTGATCACGTTTATGGTCAGgtgagtatgattcttagctcgtacttttaccaagtgcattatgtatgggtcgtgcaacgaggtaactttattcttttcgctttgaatgacctttgattaatctcggagccttgtgtgcag
 |||||||| ||||| ||  || |||| || |||||||||||||||||||| ||||| ||||| |||||||||||| | || || || || ||  | |||||         ||| |   |    | ||   |    |  | | ||||  | |||     | |   |||| |   |    | || |    |  || |||  | || |              
TATCACTGAAGCTGGTGCAGATCGAGTTCTTGCTTGTGATCTTCATTCAGGACAGTCGATGGGTTATTTTGACATTCCAGTCGACCATGTGTACTGCCAGgttcac----ctctaaagccacgttcttgatac---ccctctttatgcattgtgtgt--atgctcctttgtgtataatacctttatctgc--ttaattg-tttcag--------------

upper sequence: PP1S42_193V6.2 (Physcomitrella patens), 5'ss of exon 4
lower sequence: AT1G32380.1 (Arabidopsis thaliana), 5'ss of exon 4
AATCACTGAGGCTGGAGCCAATAGAGTGCTGGCTTGTGATCTTCATTCAGGGCAGTCAATGGGATATTTTGACATTTCCGTTGATCACGTTTATGGTCAGgtgagtatgattcttagctcgtacttttaccaag--tgcattatgtatgggtcgtgcaacgaggtaactttattcttttcgctttgaatgacctttgattaatctcggagccttgtgtgcag
 || || || || || ||  |||| || ||||||||||||||||||||||| || || ||||| |||||||||||  | || ||||| || ||| | |||||   | | | | | | |   |    |   ||||  |  | | | ||||   | |  ||  |  | ||   ||| |  |  | ||  |                                  
TATAACAGAAGCCGGTGCAGATAGGGTTCTGGCTTGTGATCTTCATTCAGGACAATCCATGGGTTATTTTGACATACCAGTGGATCATGTCTATTGCCAGgtatct-taagtttcaacctttttgatagacaagcctctactttttatgcaacctttaa-aatcttacacaattgtgattacatttcag---------------------------------

upper sequence: PP1S42_193V6.2 (Physcomitrella patens), 5'ss of exon 4
lower sequence: Vv15s0021g00460.t01 (Vitis vinifera), 5'ss of exon 4
AATCACTGAGGCTGGAGCCAATAGAGTGCTGGCTTGTGATCTTCATTCAGGGCAGTCAATGGGATATTTTGACATTTCCGTTGATCACGTTTATGGTCAGgtgagtatgattcttagctcgtacttttaccaagtgcattatgtatgggtcgtgcaacgaggtaactttattcttttcgctttgaatgacctttgattaatctcggagccttgtgtgcag
 || || || || || || ||  |||| || ||||||||||||||||| |||||||| ||||| |||||||| ||| | |||||||| || ||||| ||||| |  | |  |  |||||  || |  | | | ||| || ||     | |     |  || |  | |    |  || |   ||  |     |  |  | |  | || |            
CATTACAGAAGCGGGTGCAAACCGAGTTCTTGCTTGTGATCTTCATTCTGGGCAGTCTATGGGTTATTTTGATATTCCAGTTGATCATGTGTATGGACAGgtaataagg--tgatagcttctagtggt-caatgtgtatgat---cagatttcaaactgatgctattggggttcttccatgttataca---tcagcatgactttggtgt-----------

upper sequence: PP1S42_193V6.2 (Physcomitrella patens), 5'ss of exon 4
lower sequence: Vv02s0012g00530.t01 (Vitis vinifera), 5'ss of exon 4
AATCACTGAGGCTGGAGCCAATAGAGTGCTGGCTTGTGATCTTCATTCAGGGCAGTCAATGGGATATTTTGACATTTCCGTTGATCACGTTTATGGTCAGgtgagtatgattcttagctcgtacttttaccaagtgcattatgtatgggtcgtgcaacgaggtaactttattcttttcgctttgaatgacctttgattaatctcggagccttgtgtgcag
 |||||  | || || ||  |  | || || ||||||||||||||||| |||||||| ||||| || ||||| ||| | || |||||| | ||| ||||||| | ||  ||| |||   | |  ||| | |     | || | |      | |   ||    | |  ||| | |||    | || |                                  
TATCACCAAAGCAGGTGCGGACCGTGTTCTTGCTTGTGATCTTCATTCTGGGCAGTCCATGGGTTACTTTGATATTCCTGTGGATCACATATATTGTCAGgtaatta--atttttaagccattgtttgatccttatctttttctg-actccatatcactgaatgaaattactgtttgttttgtgcacacaag----------------------------

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|100383515|gb|BY950299.1|BY950299
EST:     CAGTNCA-TGGGATATTTTGACATTTCCGTTGATNCACGTT-ATGGGCAG                         CCTGTAATACTCGACTACCTGGCAAGTAAAATGATATCATCAAACGACTTG
genomic: CAGT-CAATGGGATATTTTGACATTTCCGTTGAT-CACGTTTATGGTCAGgtgagtatga ... ttgtgtgcagCCTGTAATACTCGACTACCTGGCAAGTAAAATGATATCATCAAACGACTTG
EST: gi|100356373|gb|BY946332.1|BY946332
EST:     GGCAGTCAATGGGATATTTTGACATTTCCGTTGATCACGTTTATGGTCAG                         CCTGTAAAACTCGACTACCTGGCAAGTAAA-TGATATCATCAAACGACTTG
genomic: GGCAGTCAATGGGATATTTTGACATTTCCGTTGATCACGTTTATGGTCAGgtgagtatga ... ttgtgtgcagCCTGTAATACTCGACTACCTGGCAAGTAAAATGATATCATCAAACGACTTG
EST: gi|100399937|gb|BY990696.1|BY990696
EST:     GGCAGTCAATGGGATATTTTGACATTTCCGTTGATCACGTTTATGGTCAG                         CCTGTAATACTCGACTACCTGGCAAGTAAAATGATATCATCAAACGACTTG
genomic: GGCAGTCAATGGGATATTTTGACATTTCCGTTGATCACGTTTATGGTCAGgtgagtatga ... ttgtgtgcagCCTGTAATACTCGACTACCTGGCAAGTAAAATGATATCATCAAACGACTTG
EST: gi|162261958|gb|FC436817.1|FC436817
EST:     GGCAGTCAATGGGATATTTTGACATTTCCGTTGATCACGTTTATGGTCAG                         CCTGTAATACTCGACTACCTGGCAAGTANAATGATATCATCAAACGACTTG
genomic: GGCAGTCAATGGGATATTTTGACATTTCCGTTGATCACGTTTATGGTCAGgtgagtatga ... ttgtgtgcagCCTGTAATACTCGACTACCTGGCAAGTAAAATGATATCATCAAACGACTTG
EST: gi|100353033|gb|BY945573.1|BY945573
EST:     GGCAGTCAATGGGATATTTTGACATTTCCGTTGATCACGTTTATGGTCAG                         CCTGTAATACTCGACTACCTGGCA-GTAAAATGATATCATCAAACGACTT
genomic: GGCAGTCAATGGGATATTTTGACATTTCCGTTGATCACGTTTATGGTCAGgtgagtatga ... ttgtgtgcagCCTGTAATACTCGACTACCTGGCAAGTAAAATGATATCATCAAACGACTT
EST: gi|208380333|gb|DC907658.1|DC907658
EST:     GGCAGTCAATGGGATATTTTGACATTTCCGTTGATCACGTTTATGGTCAG                         CCTGTAATACTCGACTACCTGGCAAGTAAAATGATATCATCAACCGACTNG
genomic: GGCAGTCAATGGGATATTTTGACATTTCCGTTGATCACGTTTATGGTCAGgtgagtatga ... ttgtgtgcagCCTGTAATACTCGACTACCTGGCAAGTAAAATGATATCATCAAACGACTTG
EST: gi|100372888|gb|BY948750.1|BY948750
EST:     GCAGTCAATGGGATATTTTGACATTTCCCGT-GATCACGTTTATGGTCAG                         CCTGGTA-TACTCGACTACCCTGGCA-GTAAA-TGATATCATCAAACGACT
genomic: GCAGTCAATGGGATATTTTGACATTTCC-GTTGATCACGTTTATGGTCAGgtgagtatga ... ttgtgtgcagCCTG-TAATACTCGACTACC-TGGCAAGTAAAATGATATCATCAAACGACT
EST: gi|37850549|gb|BJ608557.1|BJ608557
EST:     GGCAGTCAATGGGATATTTTGACATTTCCGTTGATCACGTTTATGGTCAG                         CCTGTAATACTCGACTACCTGGCAAGTAAAATGATATCATCAAACGACTTG
genomic: GGCAGTCAATGGGATATTTTGACATTTCCGTTGATCACGTTTATGGTCAGgtgagtatga ... ttgtgtgcagCCTGTAATACTCGACTACCTGGCAAGTAAAATGATATCATCAAACGACTTG
EST: gi|100353317|gb|BY964745.1|BY964745
EST:     GGCAGTCAATGGGATATTTTGACATTTCCGTTGATCACGTTTATGGTCAG                         CCTGTAATACTCGACTACCTGGCAAGTAAAATGATATCATC
genomic: GGCAGTCAATGGGATATTTTGACATTTCCGTTGATCACGTTTATGGTCAGgtgagtatga ... ttgtgtgcagCCTGTAATACTCGACTACCTGGCAAGTAAAATGATATCATC
EST: gi|37851276|gb|BJ609284.1|BJ609284
EST:     GGCAGTCAATGGGATATTTTGACATTTCCGTTGATCACGTTTATGGTCAG                         CCTGTAATACTCGACTACCTGGCAAGTAAAATGATATCATCAAACGACTTG
genomic: GGCAGTCAATGGGATATTTTGACATTTCCGTTGATCACGTTTATGGTCAGgtgagtatga ... ttgtgtgcagCCTGTAATACTCGACTACCTGGCAAGTAAAATGATATCATCAAACGACTTG
EST: gi|162258694|gb|FC434389.1|FC434389
EST:     GGCAGTCAATGGGATATTTTGACATTTCCGTTGATCACGTTTATGGTCAG                         CCTGTAATACTCGACTACCTGGCAAGTAAAATGATATCATCAAACGACTTG
genomic: GGCAGTCAATGGGATATTTTGACATTTCCGTTGATCACGTTTATGGTCAGgtgagtatga ... ttgtgtgcagCCTGTAATACTCGACTACCTGGCAAGTAAAATGATATCATCAAACGACTTG