Sequence
atgc intronic sequence ATGC exonic sequenceGGAAATAGAGGAGAAGATCAACAAAATAAGATGGTGCCAGACCACCAATGCTGCCCAGTTTCTACTTTCTACAAATGACAAAACTATTAAATCATGGAAGgtactctcagcttaagcaatgtacattgtacctattgtagcttcactttattaaattagaaaaagcattgcgatctgctggctctgagcctgtaattttt...
Basic information
species | Physcomitrella patens |
transcript | PP1S100_124V6.1 |
intron # | 4 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S100_124V6.1 (Physcomitrella patens), 5'ss of exon 4
lower sequence: LOC_Os06g36770.1 (Oryza sativa), 5'ss of exon 4
GGAAATAGAGGAGAAGATCAACAAAATAAGATGGTGCCAGACCACCAATGCTGCCCAGTTTCTACTTTCTACAAATGACAAAACTATTAAATCATGGAAGgtactctcagcttaagcaatgtacattgtacctattgtagcttcactttattaaattagaaaaagcattgcgatctgctg---gctctgagcctgtaattttt--
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GGAAATAGAGGAGAAGATCAACAAGATCAGGTGGTGCCAGACAGCCAATAATTCACTCTCCCTTCTGTCTACAAATGATAAAACAATAAAATACTGGAAGgtatggagaa---aaatatgttaggacccaggaatggt--tttcaagatttctgcatgccaatatctttctaatctaatgtaacatttaagcctgtcttgaccaa
upper sequence: PP1S100_124V6.1 (Physcomitrella patens), 5'ss of exon 4
lower sequence: GLYMA15G02640.1 (Glycine max), 5'ss of exon 4
GGAAATAGAGGAGAAGATCAACAAAATAAGATGGTGCCAGACCACCAATGCTGCCCAGTTTCTACTTTCTACAAATGACAAAACTATTAAATCATGGAAGgtactctcagcttaagcaatgtacattgtacctattgtagcttcactttattaaatta--gaaaaagcat-tgcgatctgctggctctgagcctgtaattttt
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GGAGATTGAAGAGAAAATCAACAAAATCAGATGGTGCCAAACAGCTAATGGTGCCCTGTTCCTTCTTTCTACAAATGATAAAACGATCAAATTTTGGAAGgtatgaaatgaatgatcacctt-tagcatgttttcagtgctgtca-tttatcaattcattgataaattgtgcacaagtttgcacttctgaggaactaagttt-
upper sequence: PP1S100_124V6.1 (Physcomitrella patens), 5'ss of exon 4
lower sequence: GLYMA13G42800.1 (Glycine max), 5'ss of exon 4
GGAAATAGAGGAGAAGATCAACAAAATAAGATGGTGCCAGACCACCAATGCTGCCCAGTTTCTACTTTCTACAAATGACAAAACTATTAAATCATGGAAGgtactctcagcttaagcaatgtacattgtacctattgtagcttcactttattaaatta--gaaaaagcat-tgcgatctgctggctctgagcctgtaattttt
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GGAAATTGAAGAGAAAATCAACAAAATCAGATGGTGCCAAATAGCTAATGGTGCCCTCTTCCTTCTTTCTACAAATGATAAAACAATCAAATTTTGGAAGgtatgaaatgaatgatcacctt-tagcatgcttttagtgctgtca-tttatcaattcattgataaattgtgcacaaggttgcacttctgaggaactaagttt-
upper sequence: PP1S100_124V6.1 (Physcomitrella patens), 5'ss of exon 4
lower sequence: AT1G17720.2 (Arabidopsis thaliana), 5'ss of exon 4
GGAAATAGAGGAGAAGATCAACAAAATAAGATGGTGCCAGACCACCAATGCTGCCCAGTTTCTACTTTCTACAAATGACAAAACTATTAAATCATGGAAGgtactctcagcttaagcaatgtacattgtacctattgtagcttcactttattaaattagaaaaagca-ttgcgatctgctggctctgagcctgtaattttt------
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GGAGATAGAGGAGAAAATCAACAAAATCAGATGGTGTCAGCCAGCTAATGGTGCATTGTTTCTGCTTTCTACAAACGATAAAACCATCAAATATTGGAAGgtg-tgacatctggatggatttttatatcacatgt-----ctgcaaaatat-aggccacttatagcaattcctttctgtgtaactcggttccataatcttgtttcat
upper sequence: PP1S100_124V6.1 (Physcomitrella patens), 5'ss of exon 4
lower sequence: Vv09s0002g02470.t01 (Vitis vinifera), 5'ss of exon 4
GGAAATAGAGGAGAAGATCAACAAAATAAGATGGTGCCAGACCACCAATGCTGCCCAGTTTCTACTTTCTACAAATGACAAAACTATTAAATCATGGAAGgtactctcagc---ttaagcaatgtacattgtacctattgtagcttcactttattaa---attagaaaaagcattgcgatctgctggctctgagcctgtaattttt-----------------------------------------------------------
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GGAAATAGAGGAGAAAATCAATAAGATCAGATGGTGCCAGACAGCAAATGGTGCCCTGTTTCTTCTATCTACGAATGATAAAACCATTAAGTTTTGGAAGgtaggaagggaaaattgtcttatgaaactttaaacttcctgatttttaatttgttgacagattatgctcaacatcaccaact-ccagtttggtttctttaactactgatataatatatatcctgcacatgctgattacatagctgtcttttcgagaatgaaacagMapped 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|162182433|gb|FC358032.1|FC358032EST: CTGCCCAGTTTCTACTTTCTACAAATGACAAAACTATTAAATCATGGAAG GTGACTGAAAAGAAAGTGAAACAGGTGAAGAATCTGAATCTGGATCCTGGA
genomic: CTGCCCAGTTTCTACTTTCTACAAATGACAAAACTATTAAATCATGGAAGgtactctcag ... aatattgcagGTGACTGAAAAGAAAGTGAAACAGGTGAAGAATCTGAATCTGGATCCTGGA
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GGAAATAGAGGAGAAGATCAACAAAATAAGATGGTGCCAGACCACCAATGCTGCCCAGTTTCTACTTTCTACAAATGACAAAACTATTAAATCATGGAAGgtactctcagcttaagcaatgtacattgtacctattgtagcttcactttattaaattagaaaaagcattgcgatctgctggctctgagcctgtaattttt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -agaaaaag