Sequence
atgc intronic sequence ATGC exonic sequenceAGATGGCACAGATGACCAGAAGAAGGGCACGCAGCTGCTGGAAGTTTATGCGATTGAAATTCAGATGTATACAGAGACTAAGAACAACAAAAAACTTAAGgttagttcaagtgaaaccttcaattgaaattctgtgacctaagctctgctaccagatctagtggaactaaaaaaattaattattcattcttgacattgtagcaataggatctcgaagtcgttagtgttggaatctcgtatattggtataagagttagtatttattctttttagcgtgaaccttgcag
Basic information
species | Physcomitrella patens |
transcript | PP1S105_216V6.1 |
intron # | 6 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S105_216V6.1 (Physcomitrella patens), 5'ss of exon 6
lower sequence: GLYMA05G14170.1 (Glycine max), 5'ss of exon 6
AGATGGCACAGATGACCAGAAGAAGGGCACGCAGCTGCTGGAAGTTTATGCGATTGAAATTCAGATGTATACAGAGACTAAGAACAACAAAAAACTTAAGgttagttcaagtgaaaccttcaattgaaattctgtgacctaagctctgctaccagatctagtggaactaaaaaaattaattattcattcttgacattgtagcaataggatctcgaagtcgttagtgttggaatctcgtatattggtataagagttagtatttattctttttagcgtgaaccttgcag
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AGATGGCACAGATGACCACAAAAAAGGAACTCAACTTTTGGAGGTATATGCTGTAGAGATTCAAATGTACACAGAGACCAAGAACAACAAAAAACTTAAGgtcag-------gatttcttttacagaag-----------aaactcttgt------tcttgcatgacttaagtaattatgtcttttcaattgcttttagtgtgtttg--cctgcaatttatcattg-------------------------------------------------------------
upper sequence: PP1S105_216V6.1 (Physcomitrella patens), 5'ss of exon 6
lower sequence: GLYMA19G30100.1 (Glycine max), 5'ss of exon 6
AGATGGCACAGATGACCAGAAGAAGGGCACGCAGCTGCTGGAAGTTTATGCGATTGAAATTCAGATGTATACAGAGACTAAGAACAACAAAAAACTTAAGgttag--ttcaagtgaaaccttcaattgaaattctgtgacctaagctctgctaccagatctagtggaactaaaaaaatta--attattcattcttgacattgtagcaataggatctcgaagtcgttagtgttggaatctcgtatattggtataagagttagtatttattctttttagcgtgaaccttgcag
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AGATGGTACAGATGATCACAAGAAAGGAACCCAACTTTTGGAGGTTTATGCAATAGAAATTCAAATGTACACAGAGATGAAGAACAACAAAAAACTCAAGgtcagcatttgttttagaaaataaattcttattatgcaacttgca------taggagtaataatgtgcctttccaatttattactgtcttttcctacaattttagc-------------------------------------------------------------------------------------
upper sequence: PP1S105_216V6.1 (Physcomitrella patens), 5'ss of exon 6
lower sequence: GLYMA19G17660.3 (Glycine max), 5'ss of exon 6
AGATGGCACAGATGACCAGAAGAAGGGCACGCAGCTGCTGGAAGTTTATGCGATTGAAATTCAGATGTATACAGAGACTAAGAACAACAAAAAACTTAAGgttag--ttcaagtgaaaccttcaattgaaattct---gtgacctaagctctgctaccagatctagtggaactaaaaaaattaattattcattcttgacattgtagcaataggatctcgaagtcgttagtgttggaatctcgtatattggtataagagttagtatttattctttttagcgtgaaccttgcag
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AGATGGCACAGATGACCATAAGAAAGGAACCCAACTTTTGGAGGTATATGCTGTAGAGATTCAAATGTACACTGAGACCAAGAACAACAAAAAACTTAAGgtcaggatttgttttatagaagaaattcttgttcttgcatgacttaagta--gttaagtaattatgtcttttcaaattcttttattgtgtttgcctgcaatt------------------------------------------------------------------------------------------
upper sequence: PP1S105_216V6.1 (Physcomitrella patens), 5'ss of exon 6
lower sequence: GLYMA03G00670.1 (Glycine max), 5'ss of exon 6
AGATGGCACAGATGACCAGAAGAAGGGCACGCAGCTGCTGGAAGTTTATGCGATTGAAATTCAGATGTATACAGAGACTAAGAACAACAAAAAACTTAAGgttagttcaagtgaaaccttcaattgaaattctgtgacctaagctctgctaccagatctagtggaactaaaaaaattaattattcattcttg-acattgtagcaataggatctcgaagtcgttagtgttggaatctcgtatattggtataagagttagtatttattctttttagcgtgaaccttgcag
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AGATGGTACAGATGACCATAAGAAAGGAACCCAACTTTTAGAGGTTTATGCAATAGAAATCCAAATGTACACAGAGACAAAAAACAACAAAAAACTCAAGgtcagc----attgatttttgaaataaattcttattatgcaacttgca-taagactaataatgagcctttccaatatattactgcttttttgtacaatttagctt-----------------------------------------------------------------------------------
upper sequence: PP1S105_216V6.1 (Physcomitrella patens), 5'ss of exon 6
lower sequence: AT2G26990.1 (Arabidopsis thaliana), 5'ss of exon 6
AGATGGCACAGATGACCAGAAGAAGGGCACGCAGCTGCTGGAAGTTTATGCGATTGAAATTCAGATGTATACAGAGACTAAGAACAACAAAAAACTTAAGgttagttc---aagtgaaaccttcaattgaaattctgtgacctaagctctgctaccagatctagtggaactaaaaaaattaattattcattcttgacattgtagcaataggatctcgaagtcgttagtgttggaatctcgtatattggtataagagttagtatttattctttttagcgtgaaccttgcag
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AGATGGAACTGATGATCAGAAGAAAGGAAGTCAGCTGCTTGAGGTTTATGCAATTGAAATTCAGATTTACACTGAAACGAAGGACAACAAAAAGCTTAAGgtaaatgtcataagctacatggtttcttacaattttgagat------tctgcaat----tttattg---ctgcatactttcttctggcttttgtgactgagactcaacaacactcttgaatggatgcag-------------------------------------------------------------
upper sequence: PP1S105_216V6.1 (Physcomitrella patens), 5'ss of exon 6
lower sequence: Vv08s0040g00430.t01 (Vitis vinifera), 5'ss of exon 6
AGATGGCACAGATGACCAGAAGAAGGGCACGCAGCTGCTGGAAGTTTATGCGATTGAAATTCAGATGTATACAGAGACTAAGAACAACAAAAAACTTAAGgttagttcaagtgaaaccttcaattgaaattctgtgacctaagctctgctaccag--atctagtggaa--ctaaaaaaattaattattcattcttgacattgtagcaataggatctcgaagtcgttagtgttggaatctcgtatattggtataagagttagtatttattctttttagcgtgaaccttgcag
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AGATGGTACAGATGATCAAAAGAAAGGAACCCAACTTTTGGAAGTATATGCAATTGAGATTCAAATGTATACTGAGACCAAGAATAACAAAAAACTCAAGgtcagggtttcttgaatgtttgtttccatattgatttgtaaatcatttttttcagtaattttgtatatttctatagtatttaagt-tccatgagttaaaat------------------------------------------------------------------------------------------
upper sequence: PP1S105_216V6.1 (Physcomitrella patens), 5'ss of exon 6
lower sequence: EFJ29478 (Selaginella moellendorffii), 5'ss of exon 6
AGATGGCACAGATGACCAGAAGAAGGGCACGCAGCTGCTGGAAGTTTATGCGATTGAAATTCAGATGTATACAGAGACTAAGAACAACAAAAAACTTAAGgttagttcaagtgaaaccttcaattgaaattctgtgacctaagctctgctaccagatctagtggaactaaaaaaattaattattcattcttgacattgtagcaataggatctcgaagtcgttagtgttggaatctcgtatattggtataagagttagtatttattctttttagcgtgaaccttgcag
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AGATGGCTCTGATGATCAGAAGAAAGGAACTCAGCTTCTGGAAGTATACGCCATTGAGATTCAGATGTACACGGAGACAAAGAACAACAAGAAGCTAAAGgt--atctatgcagttctttttat-gatattttg----ctgaacctcggcctcag------------------------------------------------------------------------------------------------------------------------------------
upper sequence: PP1S105_216V6.1 (Physcomitrella patens), 5'ss of exon 6
lower sequence: EFJ28052 (Selaginella moellendorffii), 5'ss of exon 6
AGATGGCACAGATGACCAGAAGAAGGGCACGCAGCTGCTGGAAGTTTATGCGATTGAAATTCAGATGTATACAGAGACTAAGAACAACAAAAAACTTAAGgttagttcaagtgaaaccttcaattgaaattctgtgacctaagctctgctaccagatctagtggaactaaaaaaattaattattcattcttgacattgtagcaataggatctcgaagtcgttagtgttggaatctcgtatattggtataagagttagtatttattctttttagcgtgaaccttgcag
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AGATGGCTCTGATGATCAGAAGAAAGGAACTCAGCTTCTGGAAGTATACGCCATTGAGATTCAGATGTACACGGAGACAAAGAACAACAAGAAGCTAAAGgt--atctatgcagttttttttat-gatattcta----ctgaacctcggcctcag------------------------------------------------------------------------------------------------------------------------------------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|208386927|gb|DC941603.1|DC941603EST: CGATTGAAATTCANATGTATACNGAGACTAANAACACCAAAAA-CTTAAG CANCTATACCTGAA-GCGCTGAACATAA-GTCTGCTATTCCGCATC
genomic: CGATTGAAATTCAGATGTATACAGAGACTAAGAACAACAAAAAACTTAAGgttagttcaa ... aaccttgcagCAACTATACCTGAAAGCGCTGAACATAAAGTCTGCTATTCCGCATC
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
AGATGGCACAGATGACCAGAAGAAGGGCACGCAGCTGCTGGAAGTTTATGCGATTGAAATTCAGATGTATACAGAGACTAAGAACAACAAAAAACTTAAGgttagttcaagtgaaaccttcaattgaaattctgtgacctaagctctgctaccagatctagtggaactaaaaaaattaattattcattcttgacattgtagcaataggatctcgaagtcgttagtgttggaatctcgtatattggtataagagttagtatttattctttttagcgtgaaccttgcag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC