Sequence
atgc intronic sequence ATGC exonic sequenceGTGAGGTTATGCCGAGAGAAATCAAGTACAACTGTGTATGCCATGAAGAAGCTGAAGAAGTCCGAGATGCTTCGGAGAGGCCAGgtacgtcacgtgtatatatgtggaagttgtttatagaattgtatctgtctttatttgccgtttgccaaaatcatataactctgaagaatcgactgaaggtcaaatctggagttattgttatgttttgttactcactttagtaatcgaaatctgaaggggattactttaccattttaatcaatggataaacactattgcag
Basic information
species | Physcomitrella patens |
transcript | PP1S22_429V6.1 |
intron # | 3 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S22_429V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: GLYMA13G18670.1 (Glycine max), 5'ss of exon 3
GTGAGGTTATGCCGAGAGAAATCAAGTACAACTGTGTATGCCATGAAGAAGCTGAAGAAGTCCGAGATGCTTCGGAGAGGCCAGgtacgtcacgtgtatatatgtggaagttgtttatagaattgtatctgtctttatttgccgtttgccaaaatcatataactctgaagaatcgactgaaggtcaaatctggagttattgttatgttttgttactcactttagtaatcgaaatctgaaggggattactttaccattttaatcaatggataaacactattgcag
|| || | || | |||||| | ||| ||| ||||| |||||||||||||| || || ||||||||||| ||||||||||| | || || || || ||| | | || | || | | | | || || || ||| || |||| | ||||| ||| |||||| | || ||
GTCAGAGTCTGTAGGGAGAAAACTAGTGATCATGTATATGCAATGAAGAAGCTGAAAAAATCAGAGATGCTTCGTAGAGGCCAGgt---ttacaatcattgat----------cttgccagattatgttattccagtccagatattagt--agtttaaatgcctatggtcaat------aaagtca---tcatacttattcctat---ttgttaatattttcag------------------------------------------------------------
upper sequence: PP1S22_429V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: GLYMA10G32480.1 (Glycine max), 5'ss of exon 3
GTGAGGTTATGCCGAGAGAAATCAAGTACAACTGTGTATGCCATGAAGAAGCTGAAGAAGTCCGAGATGCTTCGGAGAGGCCAGgtacgtcacgtgtatatatgtggaagttgtttatagaattgtatctgtctttatttgccgtttgccaaaatcatataactctgaagaatcgactgaaggtcaaatctggagttattgttatgttttgttactcactttagtaatcgaaatctgaaggggattactttaccattttaatcaatggataaacactattgcag
|| || | |||||||||||| ||| | ||| ||||| |||||||| || ||||| || ||||||||||| |||||||||||| | | | | | | ||| || ||| |||||| | | ||| | | ||| || | ||
GTCAGAGTCTGCCGAGAGAAAACAACTGGTCATGTATATGCTATGAAGAAACTTAAGAAATCAGAGATGCTTCGCAGAGGCCAGgta-acaaaataagcaggacttgctctcatttttaaaatgaatattgtcttgttatattcattgattactttttatccctgtttag------------------------------------------------------------------------------------------------------------------
upper sequence: PP1S22_429V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: GLYMA02G00580.2 (Glycine max), 5'ss of exon 4
GTGAGGTTATGCCGAGAGAAATCAAGTACAACTGTGTATGCCATGAAGAAGCTGAAGAAGTCCGAGATGCTTCGGAGAGGCCAGgtacgtcacgtgtatatatgtggaagttgtttatagaat-tgtatctgtctttatttgccgtttgccaaaatcatataactctgaagaatcgactgaaggtcaaatctggagttattgttatgttttgttactcactttagtaatcgaaatctgaaggggattactttaccattttaatcaatggataaacactattgcag
|| || | ||||| ||||| | | | ||| ||||| ||||||||||| ||||| || |||||||| || ||||||||||| || | || | || |||| | | | | | | ||||| | |
GTTAGAATCTGCCGGGAGAAGGCCACTGGTCATGTATATGCTATGAAGAAGCTTAAGAAATCAGAGATGCTACGTAGAGGCCAGgtgaaattatcacattgttagagacttagtgtatatattgttttcttatacttattggatacactttcag-----------------------------------------------------------------------------------------------------------------------------------
upper sequence: PP1S22_429V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: GLYMA10G00830.1 (Glycine max), 5'ss of exon 3
GTGAGGTTATGCCGAGAGAAATCAAGTACAACTGTGTATGCCATGAAGAAGCTGAAGAAGTCCGAGATGCTTCGGAGAGGCCAGgtacgtcacgtgtatatatgtggaagttgtttatagaattgtatctgtctttatttgccgtttgccaaaatcatataactctgaagaatcgactgaaggtcaaatctggagttattgttatgttttgttactcactttagtaatcgaaatctgaaggggattactttaccattttaatcaatggataaacactattgcag
|| || | ||||| ||||| | | | ||| ||||| ||||||||||| ||||| || |||||||| || ||||||||||| || ||| || | | ||| | | | | ||| | | | | | | | |
GTTAGAATCTGCCGGGAGAAGGCCACTGGCCATGTTTATGCTATGAAGAAGCTTAAGAAATCAGAGATGCTACGAAGAGGCCAGgtgaaattatcacat---tgttagagacttagagtaaatattgttttcttatatgtattggatac--acttttttcag--------------------------------------------------------------------------------------------------------------------------
upper sequence: PP1S22_429V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: GLYMA20G35110.1 (Glycine max), 5'ss of exon 3
GTGAGGTTATGCCGAGAGAAATCAAGTACAACTGTGTATGCCATGAAGAAGCTGAAGAAGTCCGAGATGCTTCGGAGAGGCCAGgtacgtcacgtgtatatatgtggaagttgtttatagaattgtatctgtctttatttgccgtttgccaaaatcatataactctgaagaatcgactgaaggtcaaatctggagttattgttatgttttgttactcactttagtaatcgaaatctgaaggggattactttaccattttaatcaatggataaacactattgcag
|| || | |||||||||||| ||| ||| ||||| |||||||| || ||||| || ||||||||||| ||||||||||| | | | | | | || || ||| |||||| | ||| | | ||| || | ||
GTCAGAGTCTGCCGAGAGAAAGCAACCGGTCATGTATATGCTATGAAGAAACTTAAGAAATCAGAGATGCTTCGCAGAGGCCAGgt-tacaaaatcatcaggacttgctctcattgttaaaatgaatattgtcttgttaaattcattggttactttctatccctgtttag------------------------------------------------------------------------------------------------------------------
upper sequence: PP1S22_429V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: GLYMA10G04410.2 (Glycine max), 5'ss of exon 4
GTGAGGTTATGCCGAGAGAAATCAAGTACAACTGTGTATGCCATGAAGAAGCTGAAGAAGTCCGAGATGCTTCGGAGAGGCCAGgtacgtcacgtgtatatatgtggaagttgtttatagaattgtatctgtctttatttgccgtttgccaaaatcatataactctgaagaatcgactgaaggtcaaatctggagttattgttatgttttgttactcactttagtaatcgaaatctgaaggggattactttaccattttaatcaatggataaacactattgcag
|| || | || | |||||| | || || ||||| ||||| |||||||| || || ||||||||||| ||||||||||| || | | || ||| | ||| | | || | || | | | | || || || ||| | | | | | | | ||||| | | |||||| | || ||
GTCAGAGTCTGTAGGGAGAAAACTAGCGGTCACGTATATGCAATGAAAAAGCTGAAAAAATCAGAGATGCTTCGCAGAGGCCAGgt----------tacaatcattgatcttgct----agattatgttattccagtccagatattagt--agtttaaatgcctatggtcaataaggtcatcat--actttatacttattcctgt---ttgttaatattttcag------------------------------------------------------------
upper sequence: PP1S22_429V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: AT4G14350.3 (Arabidopsis thaliana), 5'ss of exon 4
GTGAGGTTATGCCGAGAGAAATCAAGTACAACTGTGTATGCCATGAAGAAGCTGAAGAAGTCCGAGATGCTTCGGAGAGGCCAGgtacgtcacgtgtatatatgtggaagttgtttatagaattgtatctgtctttatttgccgtttgccaaaatcatataactctgaagaatcgactgaaggtcaaatctggagttattgttatgttttgttactcactttagtaatcgaaatctgaaggggattactttaccattttaatcaatggataaacactattgcag
|| ||| | || | ||||| || | ||| ||||| ||||||||||| ||||| || ||||||||||| |||||||||||| | | | | | |||| | |||| | | |||| | || ||| || | || | | | | |
GTTAGGATCTGTAGGGAGAAGGGAACAGGCAATGTCTATGCAATGAAGAAGCTTAAGAAATCTGAGATGCTTCGCAGAGGCCAGgtat-ttaaattccttcaagtggctttcgtttg-acatttgtttag----ttggttgatgtgaatgtgga--atctgattttcag-------------------------------------------------------------------------------------------------------------------
upper sequence: PP1S22_429V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: AT2G20470.1 (Arabidopsis thaliana), 5'ss of exon 3
GTGAGGTTATGCCGAGAGAAATCAAGTACAACTGTGTATGCCATGAAGAAGCTGAAGAAGTCCGAGATGCTTCGGAGAGGCCAGgtacgtcacgtgtatatatgtggaagttgtttatagaattgtatctgtct-ttatttgccgtttgccaaaatcatataactctgaagaatcgactgaaggtcaaatctggagttattgttatgttttgttactcactttagtaatcgaaatctgaaggggattactttaccattttaatcaatggataaacactattgcag
|| || | || |||| || | | || ||||| ||||| ||||| |||||| | ||||||||||| ||||||||||| | | ||| ||| || | ||| | | || | | || | || | | | | || || | | | |
GTTAGAGTTTGTAGAGAAAAGACGACAGGTCAAGTTTATGCAATGAAAAAGCTCAAGAAGGCTGAGATGCTTCGCAGAGGCCAGgtgagacttccctatctat-tgctacttgatggtctt-ttctgtgaatcaatcatcttttgacttcataactcgttttttttcaag-------------------------------------------------------------------------------------------------------------------
upper sequence: PP1S22_429V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: Vv10s0003g05720.t01 (Vitis vinifera), 5'ss of exon 4
GTGAGGTTATGCCGAGAGAAATCAAGTACAACTGTGTATGCCATGAAGAAGCTGAAGAAGTCCGAGATGCTTCGGAGAGGCCAGgtacgtcacgtgtatatatgtggaagttgtttatagaattgtatctgtctttatttgccgtttgccaaaatcatataactctgaagaatcgactgaaggtcaaatctggagttattgttatgttttgttactcactttagtaatcgaaatctgaaggggattactttaccattttaatcaatggataaacactattgcag
||||| | ||| |||| ||| | | | ||||||||||||||| ||||| ||||| || |||||||||||||| |||||||||| | | || || |||| || ||| | | | | ||| | | || | || | | | | | ||| || |||| ||
GTGAGACTTTGCAGAGAAAAAACTACTGGCCATGTGTATGCCATGAAAAAGCTCAAGAAATCAGAGATGCTTCGGAGGGGCCAGgtaccttctgggt-catttgtgctgcttttttcc-----tttgtgaataaatatgatctataaataaataacaagtgatttactgaattgtactcaa---caaagcttt-------------------------------------------------------------------------------------------
upper sequence: PP1S22_429V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: Vv07s0005g03690.t01 (Vitis vinifera), 5'ss of exon 3
GTGAGGTTATGCCGAGAGAAATCAAGTACAACTGTGTATGCCATGAAGAAGCTGAAGAAGTCCGAGATGCTTCGGAGAGGCCAGgtacgtcacgtgtatatatgtggaagttgtttatagaattgtatctgtct-ttatttgccgtttgccaaaatcatataactctgaagaatcgactgaaggtcaaatctggagttattgttatgttttgttactcactttagtaatcgaaatctgaaggggattactttaccattttaatcaatggataaacactattgcag
|| || | || ||||||| ||| | ||||||||| ||||| ||||| |||||||| ||||||||||| ||||||||||| || | | | | || || ||||| || || | | | || ||||| ||| || | | || | | |
GTAAGAGTCTGTAGAGAGAAGACAACGGGTAATGTGTATGCAATGAAAAAGCTTAAGAAGTCAGAGATGCTTCGACGAGGCCAGgtattacatctttctg-gtctgccagatgtttggtgattttgcccaatatgtttgttgccagttgacac--ttaaatgattttag--------------------------------------------------------------------------------------------------------------------
upper sequence: PP1S22_429V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: Vv05s0049g01220.t01 (Vitis vinifera), 5'ss of exon 3
GTGAGGTTATGCCGAGAGAAATCAAGTACAACTGTGTATGCCATGAAGAAGCTGAAGAAGTCCGAGATGCTTCGGAGAGGCCAGgtacgtcacgtgtatatatgtggaagttgtttatagaattgtatctgtctttatttgccgt-ttgccaaaatcatataactctgaagaatcgactgaaggtcaaatctggagttattgttatgttttgttactcactttagtaatcgaaatctgaaggggattactttaccattttaatcaatggataaacactattgcag
|| || | ||| | ||||| || ||| ||||||||||||||||| ||||| || ||||||||||| || ||||||||| | | ||| || | | ||||| | ||| | | | ||||||| | | ||||| | | ||| || | |
GTTAGAGTCTGCAGGGAGAAGAAAACCGGCCATGTATATGCCATGAAGAAGCTTAAGAAATCAGAGATGCTTCGAAGGGGCCAGgtatgacttctgttggcctg-gcagacaatttattg---tgtgt-tatatttatttttcttattgcccgatttgc----ttcttaatatttag------------------------------------------------------------------------------------------------------------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|FC347108EST: TGTATGCCATGAAGAAGCTGAAGAAGTCCGAGATGCTTCGGAGAGGCCAG GTGGAGCATGTAAAGGCAGAGAGAAATTTGCTTGCAGAGGTTGACAGTAAC
genomic: TGTATGCCATGAAGAAGCTGAAGAAGTCCGAGATGCTTCGGAGAGGCCAGgtacgtcacg ... actattgcagGTGGAGCATGTAAAGGCAGAGAGAAATTTGCTTGCAGAGGTTGACAGTAAC
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GTGAGGTTATGCCGAGAGAAATCAAGTACAACTGTGTATGCCATGAAGAAGCTGAAGAAGTCCGAGATGCTTCGGAGAGGCCAGgtacgtcacgtgtatatatgtggaagttgtttatagaattgtatctgtctttatttgccgtttgccaaaatcatataactctgaagaatcgactgaaggtcaaatctggagttattgttatgttttgttactcactttagtaatcgaaatctgaaggggattactttaccattttaatcaatggataaacactattgcag
- - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG