Sequence
atgc intronic sequence ATGC exonic sequenceGCCCTGGAGTTTGGGAAGTCTGGCAAGGACCGGATCACCACGTCTTCTGCTTTCAATGCCTTCAAGAACAACTACCTGGTCGTCTACTCGCTTATGATGGgtaacaaaccgttttgcaacttagcctgggattcgcgtcttccctctgtctttctttttcttttcttttctctttgtttttctgtaccgtccgtaaactgtataagaattgttcaccgtgtagtctaccctacgcatatgaccag
Basic information
species | Physcomitrella patens |
transcript | PP1S18_8V6.1 |
intron # | 1 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S18_8V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: GLYMA06G13760.2 (Glycine max), 5'ss of exon 1
GCCCTGGAGTTTGGGAAGTCTGGCAAGGACCGGATCACCACGTCTTCTGCTTTCAATGCCTTCAAGAACAACTACCTGGTCGTCTACTCGCTTATGATGGgtaacaaaccgttttgcaacttagcctgggattcgcgtcttccctctgtctttctttttcttttcttttctctttgtttttctgtaccgtccgtaaactgtataagaattgttcaccgtgtagtctaccctacgcatatgaccag
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GTGACGGAGCTGAGCAAGAGCAACAAGGACCGAATCAACACCTCTTCCGCATTCAATTCCTTCAAGAACAACTACCTCATCGTCTATTCCCTCATGATGGgtacagatctgtcttctctctcttagatccactcagatctaacctcatttccctctttattccacccattacttcatttctcattttcatttttttatcg---------------------------------------------
upper sequence: PP1S18_8V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: GLYMA04G41090.1 (Glycine max), 5'ss of exon 1
GCCCTGGAGTTTGGGAAGTCTGGCAAGGACCGGATCACCACGTCTTCTGCTTTCAATGCCTTCAAGAACAACTACCTGGTCGTCTACTCGCTTATGATGGgtaacaaaccgttttgcaacttagcctgggattcgcgtcttccctctgtctttctttttcttttcttttctctttgtttttctgtaccgtccgtaaactgtataagaattgttcaccgtgtagtctaccctacgcatatgaccag
| ||||| | | ||| |||||| || |||| ||| ||||| || |||||| ||||||||||||||||||| ||||||| || || |||||||||| | | || | || | || ||||| ||| ||| | | | | ||||| ||| | | | | ||
GTTATGGAGCTGAGCAAGAACAACAAGGATCGAATCAACACCTCTTCCGCATTCAATTCCTTCAAGAACAACTACCTCCTCGTCTATTCCCTCATGATGGgtacagatctgtctcttctctcttagatccactcagatcttctctcattctccttgatctaaccttcctttctttcatttctcatttccattgccagctt---------------------------------------------
upper sequence: PP1S18_8V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: Vv02s0025g02420.t01 (Vitis vinifera), 5'ss of exon 1
GCCCTGGAGTTTGGGAAGTCTGGCAAGGACCGGATCACCACGTCTTCTGCTTTCAATGCCTTCAAGAACAACTACCTGGTCGTCTACTCGCTTATGATGGgtaacaaaccgttttgcaacttagcctgggattcgcgtcttccctctgtctttc-tttttcttttcttttctctttgtttttctgtaccgtccgtaaactgtataagaattgttcaccgtgtagtctaccctacgcatatgaccag
|| ||||| | | || | ||||||| ||||||| |||||| |||| |||| | |||| |||||||| ||||| |||||||||| |||||||||||||| || | | || || || || | |||| | | ||| || || | || || | || || || | |||||
GCGTTGGAGCTCAGCAAAACAAGCAAGGATCGGATCAATACGTCTACTGCCTTCACTTCCTTTAAGAACAATTACCTTCTCGTCTACTCTCTTATGATGGgtaa-------------------gcttagacctcaagttttttcttcatttttcatctggggtttggttattcatggtggaatcacactgaccctacgct-cgtgttgtttgtttgatac--------------------------
upper sequence: PP1S18_8V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: EFJ11977 (Selaginella moellendorffii), 5'ss of exon 1
GCCCTGGAGTTTGGGAAGTCTGGCAAGGACCGGATCACCACGTCTTCTGCTTTCAATGCCTTCAAGAACAACTACCTGGTCGTCTACTCGCTTATGATGGgtaacaaaccgttttgcaacttagcctgggattcgcgtcttccctctgtctttctttttcttttcttttctctttgtttttctgtaccgtccgtaaactgtataagaattgttcaccgtgtagtctaccctacgcatatgaccag
|| || |||||| | |||||||||||||| | || | || || |||||||||||||||||||| |||||||| ||||||||||| ||||||||| | ||| | | || ||| | | || | | | | | | || | | | | | ||| | | | |||| | | | | || ||| ||| |
GCACTCGAGTTTCGCCGTGGCAGCAAGGACCGGATCGTCGCGACATCGGCCTTCAATGCCTTCAAGAACAATTACCTGGTGGTCTACTCGCTCATGATGGgtg---agttctttctcgatttcgcccgcattgcgtgctt----ccagctcctagatctcgccaaatgcgtactcggatctctagatctt-----aactctcttccctctttcttcc------tctcccccag------------
upper sequence: PP1S18_8V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: EFJ21113 (Selaginella moellendorffii), 5'ss of exon 1
GCCCTGGAGTTTGGGAAGTCTGGCAAGGACCGGATCACCACGTCTTCTGCTTTCAATGCCTTCAAGAACAACTACCTGGTCGTCTACTCGCTTATGATGGgtaacaaaccgttttgcaacttagcctgggattcgcgtcttc--cctctgtctttctttttcttttcttttctctttgtttttctgtaccgtccgtaaactgtataagaattgttcaccgtgtagtctaccctacgcatatgaccag
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GCGCTCGAGTTTCGCCGTGGCAGCAAGGACCGGATCGTCGCGACATCGGCCTTCAATGCCTTCAAGAACAATTACCTGGTGGTCTACTCGCTCATGATGGgtg---agttctttctcgatttcgcccgcattgcgtgcttccagctcctagatctcgccaaatgcgcactcggatctctagatcttaactctcttctctctttctttctctcccccag-----------------------------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|100422628|gb|BY976468.1|BY976468EST: TTTCAATGCCTTCAAGAACAACTACCTGGTCGTCTACTCGCTTATGATGG GTCCATCCATGAGCTTACATGACTGCGAACCGTAGTTGGGGGTTTTCTGCG
genomic: TTTCAATGCCTTCAAGAACAACTACCTGGTCGTCTACTCGCTTATGATGGgtaacaaacc ... atatgaccagGTCCATCCATGAGCTTACATGACTGCGAACCGTAGTTGGTGGTTTTCTGCG
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GCCCTGGAGTTTGGGAAGTCTGGCAAGGACCGGATCACCACGTCTTCTGCTTTCAATGCCTTCAAGAACAACTACCTGGTCGTCTACTCGCTTATGATGGgtaacaaaccgttttgcaacttagcctgggattcgcgtcttccctctgtctttctttttcttttcttttctctttgtttttctgtaccgtccgtaaactgtataagaattgttcaccgtgtagtctaccctacgcatatgaccag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC