Sequence
atgc intronic sequence ATGC exonic sequence...tggatcagaagtccacagggatttgtttagattacctgatagaatccaggtgataaaaagtggggccacacttacaatgaaccggatgtgggatgtgtagATGCACATGTGGGGCCATGGATCCCAATATAGGAAAGGCCCTGAATCGCTTCGAGGAACCCAACCCACTGCCATGCTGAGGCTGGCATGCTACTGTTGCT
Basic information
species | Physcomitrella patens |
transcript | PP1S359_44V6.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S359_44V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GLYMA03G29610.1 (Glycine max), 3'ss of exon 1
tggatcagaagtccacagggatttgtttagattacctgatagaatccaggtgataaaaagtggggccacacttacaatgaaccggatgtgggatgtg-----tagATGCACATGTGGGGCCATGGATCCCAATATAGGAAAGGCCCTGAATCGCTTCGAGGAACCCAACCCACTGCCATGCTGAGGCTGGCATGCTACTGTTGCT
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---atctcc-gtgtatgatagcttaatttgtttgcttaatgtaacctttaattttttggg-gtgtccataattttatttaattttttttgggttgggggtttcagATGCACATGTGGGGGCATGGATCACAGTACAGAAAAGGACCTGAATCTCTGAGGGGAACCCAACCAACAGGAATGTTGAGGCTTCCTTGCTATTGTTGTG
upper sequence: PP1S359_44V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GLYMA12G06080.1 (Glycine max), 3'ss of exon 1
-tggatcagaagtccacagggatttgtttagattacctgatagaatccaggtgataaaaagtggggccacacttacaatgaac-cggatgtggga-tgtgtagATGCACATGTGGGGCCATGGATCCCAATATAGGAAAGGCCCTGAATCGCTTCGAGGAACCCAACCCACTGCCATGCTGAGGCTGGCATGCTACTGTTGCT
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gtatgtgtgagtgtgtcaatggcttccaaattcttcttcatctaatt---attctatgctgttacgtgataataataaataacattggtgcaaaaataaacagATGCATATGTGGGGGCATGGATCTCAATATAGGAAGGGACCAGAGTCTCTAAGGGGAACACAACCCACGGCTATGCTAAGACTTCCTTGCTATTGCTGTG
upper sequence: PP1S359_44V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GLYMA11G14100.1 (Glycine max), 3'ss of exon 1
tggatcagaagtccacagggatttgtttagattacctg-atagaatccaggtgataaaaagtggggccacac-ttacaatgaaccggatgtggga---tgtgtagATGCACATGTGGGGCCATGGATCCCAATATAGGAAAGGCCCTGAATCGCTTCGAGGAACCCAACCCACTGCCATGCTGAGGCTGGCATGCTACTGTTGCT
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----ttattcatgtatgtgtgagtgtgtcaatggcttccaaattcttcatctaattattc-tatgctcttacgtgataataatattggtgcaaaaatctacacagATGCATATGTGGGGGCATGGATCTCAATATAGGAAGGGACCAGAGTCTCTAAGGGGAACACAACCAACAGCAATGCTAAGACTCCCTTGCTATTGCTGTG
upper sequence: PP1S359_44V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GLYMA19G32430.1 (Glycine max), 3'ss of exon 1
tggatcagaagtccacagggatttgtttagattacctgatag-aatccaggtgataaaaagtggggccaca----cttacaatgaaccggatgtgggatgtgtagATGCACATGTGGGGCCATGGATCCCAATATAGGAAAGGCCCTGAATCGCTTCGAGGAACCCAACCCACTGCCATGCTGAGGCTGGCATGCTACTGTTGCT
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-----tttaactcggtgtataatagcttaaattgtttgctcgtaacctttaatttttatggggtgtccataattttttttttttttttgggttggggggtttcagATGCATATGTGGGGGCATGGATCACAGTACAGAAAAGGACCTGAATCTCTGAGGGGAACCCAACCAACAGGCATGTTGAGGCTTCCTTGCTATTGTTGTGMapped 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|162181817|gb|FC357416.1|FC357416EST: TTTCCTGCCCTGTTTGCAACAAGACTTTCAATCGCTACAACAACATGCAG ATGCACATGTGGGGCCATGGATCCCAATATAGGAAAGGCCCTGAATCGCTT
genomic: TTTCCTGCCCTGTTTGCAACAAGACTTTCAATCGCTACAACAACATGCAGgtgggtagct ... ggatgtgtagATGCACATGTGGGGCCATGGATCCCAATATAGGAAAGGCCCTGAATCGCTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ccaggtgataaaaagtggggccacacttacaatgaaccggatgtgggatgtgtagATGCACATGTGGGGCCATGGATCCCAATATAGGAAAGGCCCTGAATCGCTTCGAGGAACCCAACCCACTGCCATGCTGAGGCTGGCATGCTACTGTTGCT
cacttac putative branch site (score: 2)
tgataaaaa TA-rich tract
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tggatcagaagtccacagggatttgtttagattacctgatagaatccaggtgataaaaagtggggccacacttacaatgaaccggatgtgggatgtgtagATGCACATGTGGGGCCATGGATCCCAATATAGGAAAGGCCCTGAATCGCTTCGAGGAACCCAACCCACTGCCATGCTGAGGCTGGCATGCTACTGTTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG