Sequence
atgc intronic sequence ATGC exonic sequenceGATTGAGCAGATCGCTGGGCGGGACAACATTTTGAACCATAATAGCGTACCAGCGGCTTGTTTCACGCACCCTGAGATCAGCATGGTCGGCTTGACTGAGgtatagcaatccttttgtttcacaatttactttttaataacttgatttgaacctctttgtaatgtagctcttgtgactggaaagcttcacagcctaatccatttttcaggtgaaagttaatttctttttattctctggcag
Basic information
species | Physcomitrella patens |
transcript | PP1S112_186V6.1 |
intron # | 11 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S112_186V6.1 (Physcomitrella patens), 5'ss of exon 11
lower sequence: GRMZM2G145595_T01 (Zea mays), 5'ss of exon 11
GATTGAGCAGATCGCTGGGCGGGACAACATTTTGAACCATAATAGCGTACCAGCGGCTTGTTTCACGCACCCTGAGATCAGCATGGTCGGCTTGACTGAGgtata-gcaatccttttgtttcacaatttactttttaat-aacttgatttgaacctctttgtaatgtagctcttgtgactggaaagcttcacagcctaatccatttttcaggtgaaagttaatttct--ttttattctctggcag-----------------------------------------
| ||||| ||| |||| ||||||||||||| || || ||| | ||||| ||||||||||| |||||||||||||| ||||| |||||||| |||||| | || | || | | | | | | | | | ||| | || || || ||| | || | | ||||| | | ||| || | | || | || | | ||| || || |||
TGTGGAGCAAATCAGTGGGAGGGACAACATTTTAAATCACCTAAGCATCCCAGCTGCTTGTTTCACTCACCCTGAGATCAGTATGGTTGGCTTGACAGAGgtaagtgagataccattctccaatattacattctctgttcaacatagttgaaatctgcttg--gtaaagttaatttgactagtacactttcttaagta--taaaatcacaacttgtttccaactcttgctttgcttggctagcaaaccaatctttacgactctaatcattgttcctgcttttgcag
upper sequence: PP1S112_186V6.1 (Physcomitrella patens), 5'ss of exon 11
lower sequence: GLYMA09G04270.1 (Glycine max), 5'ss of exon 6
GATTGAGCAGATCGCTGGGCGGGACAACATTTTGAACCATAATAGCGTACCAGCGGCTTGTTTCACGCACCCTGAGATCAGCATGGTCGGCTTGACTGAGgtatagcaatccttttgtttcacaatttactttttaataacttgatttgaacctctttgtaatgtagctcttgtgactggaaagcttcacagcctaatccatttttcaggtgaaagttaatttctttttattctctggcag
| |||| || || |||| | || || | | || ||| ||| ||||||| ||||||||||| || ||||| ||||||||||| || |||||||||||||| || | ||| |||| | | || | || | || || | | | |||| || | ||| || | | ||| | |
GGTTGAACAAGTCACTGGAAGAGATCACGTGCTCAATCATTTAAGCATACCAGCTGCTTGTTTCACTCATCCTGAAATCAGCATGGTTGGATTGACTGAGgtatatca-tattttcttttcgttgatgtttcttctcttcctccaccc--actgctgcatgtttca-ttcttctgtgcacatggcta-actgtcccttcctctgt------------------------------------
upper sequence: PP1S112_186V6.1 (Physcomitrella patens), 5'ss of exon 11
lower sequence: GLYMA15G15310.1 (Glycine max), 5'ss of exon 11
GATTGAGCAGATCGCTGGGCGGGACAACATTTTGAACCATAATAGCGTACCAGCGGCTTGTTTCACGCACCCTGAGATCAGCATGGTCGGCTTGACTGAGgtatagcaatccttttgtttcacaatttactttttaataacttgatttgaacctctttgtaatgtagctcttgtgactggaaagcttcacagcctaatccatttttcaggtgaaagttaatttctttttattctctggcag
| |||| || | | || | || || | | || ||| ||| ||||||| ||||||||||| || ||||| ||||||||||| || ||||| |||||||| || |||| ||| |||| ||| | || | || || || | | | || | || | ||| || | ||| | || ||
GGTTGAACAAGTGACCGGAAGAGATCACGTGCTCAATCATTTAAGCATACCAGCTGCTTGTTTCACTCATCCTGAAATCAGCATGGTTGGATTGACAGAGgtatatcatatattttttttttttgtttatgtttcatc--ctccacctgctgcttgtttcattctt-ctgtacagatggctaagtgtcccctcct---ctgttctt-----------------------------------
upper sequence: PP1S112_186V6.1 (Physcomitrella patens), 5'ss of exon 11
lower sequence: GLYMA07G37050.1 (Glycine max), 5'ss of exon 11
GATTGAGCAGATCGCTGGGCGGGACAACATTTTGAACCATAATAGCGTACCAGCGGCTTGTTTCACGCACCCTGAGATCAGCATGGTCGGCTTGACTGAGgtatagcaatccttttgtttcacaatttactttttaataacttgatttgaacctctttgtaatgtagctcttgtgactggaaagcttcacagcctaatccatttttcaggtgaaagttaatttctttttattctctggcag
| |||| || || |||| | || | | | || ||| ||| | ||||| ||||||||||| || ||||| ||||||||||| || ||||| |||||||| ||| ||||| |||| ||||| || || || || | || || || || | ||||| ||| | | |||| | |||||
GGTTGAACAAGTCACTGGAAGAGATCTCGTGCTCAATCATTTAAGCATCCCAGCTGCTTGTTTCACTCATCCTGAAATCAGCATGGTTGGATTGACAGAGgtata--------------tcataattttatttt-----gtttgatgtgtcattcactgcaacat----tttacaacaaatgagttt--------------tctttcatgtgtggttaaccttctctccattcttct----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|208366234|gb|DC943808.1|DC943808EST: CAGCGGCTTGTTTCACGCACCCTGAGATCAGCATGGTCGGCTTGACTGAG CCACAAGCAAGAGCACTGGGAGAGAAAGAGGGTTTCAAAGTTAGTGTTGCC
genomic: CAGCGGCTTGTTTCACGCACCCTGAGATCAGCATGGTCGGCTTGACTGAGgtatagcaat ... tctctggcagCCACAAGCAAGAGCACTGGGAGAGAAAGAGGGTTTCAAAGTTAGTGTTGCC
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GATTGAGCAGATCGCTGGGCGGGACAACATTTTGAACCATAATAGCGTACCAGCGGCTTGTTTCACGCACCCTGAGATCAGCATGGTCGGCTTGACTGAGgtatagcaatccttttgtttcacaatttactttttaataacttgatttgaacctctttgtaatgtagctcttgtgactggaaagcttcacagcctaatccatttttcaggtgaaagttaatttctttttattctctggcag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA