Sequence
atgc intronic sequence ATGC exonic sequencegtatagcacgtgtttttttgtctttgtcttgggtacgccctcttgaaaagatgcttaacaagatgcagaattgtttagactgtcagtatacttgcaatatacttgcaatcatgagaaaatggaagtcttgctgatcgttagagaagcagttttagttaatgttgatttttttactgttggttcgttgctttacacagGTACTGTTAGGTAAAATATCAACAGGTGCACAGAATGACTTGGAGAAAGTTACGAAAATGACTTATGCACAAGTTGCAGTATATGGGTTTAGTGAAAAAG
Basic information
species | Physcomitrella patens |
transcript | PP1S346_22V6.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S346_22V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: LOC_Os01g62500.1 (Oryza sativa), 3'ss of exon 7
gtatagcacgtgtttttttgtctttgtcttgggtacgccctcttgaaaagatgcttaacaagatgcagaattgtttagactgtcagtatacttgcaatatacttgcaatcatgagaaaatggaagtcttgctgatcgttagagaagcagttttagttaatgttgatttttttactgttggttcgttgctttacacagGTACTGTTAGGTAAAATATCAACAGGTGCACAGAATGACTTGGAGAAAGTTACGAAAATGACTTATGCACAAGTTGCAGTATATGGGTTTAGTGAAAAAG
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--------------------------------------------------------------------------------------------------------------------gtacacaacattttctaac--ttatcagtagagtttattcttaagcaaatgacttaattatgtgatttttttt-----cagGTCTTGATTGGAAAGATCTCGACTGGTGCACAGAATGATCTGGAGAAAGTTACTAAGATGACTTATGCCCAGGTTGCAGTATATGGCTTCAGCGAAAAGG
upper sequence: PP1S346_22V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: LOC_Os05g38400.2 (Oryza sativa), 3'ss of exon 7
gtatagcacgtgtttttttgtctttgtcttgggtacgccctcttgaaaagatgcttaacaagatgcagaattgtttagactgtcagtatacttgcaatatacttgcaatcatgagaaaatggaagtcttgctgatcgttagagaagcagttttagttaatgttgatttttttactgttggttcgttgctttacacagGTACTGTTAGGTAAAATATCAACAGGTGCACAGAATGACTTGGAGAAAGTTACGAAAATGACTTATGCACAAGTTGCAGTATATGGGTTTAGTGAAAAAG
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-------------------------------------------------------------------------------------atttgttcattccatatttcca-tgattacgctgtcaaatcgttcacaat-gttggcagtggaatgatacctaatgtagatGTTTTGATTGC----------CTTGTTACAGGTTTTGATTGGAAGGATCTCCACTGGTGCTCAGAATGACCTGGAGAAAGTTACCAAAATGACCTATGCGCAGGTTGCTGTATACGGTTTCAGCGAAAAGG
upper sequence: PP1S346_22V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: GRMZM2G038401_T01 (Zea mays), 3'ss of exon 7
gtatagcacgtgtttttttgtctttgtcttgggtacgccctcttgaaaagatgcttaacaagatgcagaattgtttagactgtcagtatacttgcaatatacttgcaatcatgagaaaatggaagtcttgctgatcgttagagaagcagttttagt-taatgttgatttttttactgttggttcgttgctttacacagGTACTGTTAGGTAAAATATCAACAGGTGCACAGAATGACTTGGAGAAAGTTACGAAAATGACTTATGCACAAGTTGCAGTATATGGGTTTAGTGAAAAAG
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--------------------------------------------------------------------------------------tccaat-gtcatatgttggggtacccgtttatttcacagtattc----tcaccaga-aattggtataagcatattgttgaaatgc--gctaattgagctttgttt----cagGTTTTGATTGGCAAAATCTCAACTGGTGCTCAGAATGACCTGGAGAAAGTTACCAAAATGACATATGCACAGGTCGCCGTGTATGGTTTTAGTGAAAAGG
upper sequence: PP1S346_22V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: GLYMA12G06580.1 (Glycine max), 3'ss of exon 4
gtatagcacgtgtttttttgtctttgtcttgggtacgccctcttgaaaagatgcttaacaagatgcagaattgtttagactgtcagtatacttgcaatatacttgcaatcatgagaaaatggaagtcttgctgatcgttagagaagcagttttagttaatgttgatttttttactgttggttcgttgctttacacagGTACTGTTAGGTAAAATATCAACAGGTGCACAGAATGACTTGGAGAAAGTTACGAAAATGACTTATGCACAAGTTGCAGTATATGGGTTTAGTGAAAAAG
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-----------------------------------------------------------------------------------tgttatgttt--aatggattttcc-ttatctgatgtttgaatgtttgatacttcccaaagttcaaaggcatgaaaatgatgtttcccttcct-------tgtcact----gcagGTTCTTATAGGGAGAATCTCAACAGGAGCACAAAATGACTTGGAAAAAGTGACCAAGATGACGTATGCCCAAGTAGCAGTTTATGGTTTTAGCGACAAAG
upper sequence: PP1S346_22V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: GLYMA11G14640.1 (Glycine max), 3'ss of exon 4
gtatagcacgtgtttttttgtctttgtcttgggtacgccctcttgaaaagatgcttaacaagatgcagaattgtttagactgtcagtatacttgcaatatacttgcaatcatgagaaaatggaagtcttgctgatcgttagagaagcagttttagttaatgttgatttttttactgttggttcgttgctttacacagGTACTGTTAGGTAAAATATCAACAGGTGCACAGAATGACTTGGAGAAAGTTACGAAAATGACTTATGCACAAGTTGCAGTATATGGGTTTAGTGAAAAAG
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--------------------------------------------------------------------------tatgtttttcagt----tgtaaatgttattttccttatctgcggtttgata-cttcccaaacttcaaag--gca--------tgaaaatgatatttccc-------ttcattgccac-tgcagGTTCTTATAGGGAGAATCTCAACAGGAGCACAAAATGACTTGGAAAAAGTGACCAAGATGACGTATGCCCAAGTAGCAGTTTATGGTTTTAGCGACAAAG
upper sequence: PP1S346_22V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: GLYMA12G06530.1 (Glycine max), 3'ss of exon 7
gtatagcacgtgtttttttgtctttgtcttgggtacgccctcttgaaaagatgcttaacaagatgcagaattgtttagactgtcagtatacttgcaatatacttgcaatcatgagaaaatggaagtcttgctgatcgttagagaagcagttttagttaatgttgatttttttactgttggttcgttgctttacacagGTACTGTTAGGTAAAATATCAACAGGTGCACAGAATGACTTGGAGAAAGTTACGAAAATGACTTATGCACAAGTTGCAGTATATGGGTTTAGTGAAAAAG
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-----------------------------------------------------------------------------tactgctttgttatgtttaatggattttcc-ttatctgatgtttgata-cttcccaaagttcaaag-----gtatgaa--aatgatgtttcccttcct-------tgtcact----gcagGTTCTTATAGGGAGAATCTCAACAGGAGCACAAAATGACTTGGAAAAAGTGACCAAGCTGACGTATGCCCAAGTAGCAGTTTATGGTTTTAGCGACAAAG
upper sequence: PP1S346_22V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: Vv08s0007g00550.t01 (Vitis vinifera), 3'ss of exon 1
gtatagcacgtgtttttttgtctttgtcttgggtacgccctcttgaaaagatgcttaacaagatgcagaattgtttagactgtcagtatacttgcaatatacttgcaatcatgagaaaatggaagtcttgctgatcgttagagaagcagttttagttaatgttgatttttttactgttggttcgttgctttaca--cagGTACTGTTAGGTAAAATATCAACAGGTGCACAGAATGACTTGGAGAAAGTTACGAAAATGACTTATGCACAAGTTGCAGTATATGGGTTTAGTGAAAAAG
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------------------------------------------------------------------------------------------------cttttgatgtgattttggacaaat---aatctgttatgaaaacagaaaagcaattagaatctatcgtaatccatttggtgttcaaatgaaaatctggaagtagGTATTATTGGGGAAGATCTCAACTGGAGCCCAGAATGACTTGGAGAAAGTGACAAAGATGATCTATGCCCAAGTAGCAGTCTATGGTTTCAGTGAGAAGGMapped 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|162176716|gb|FC352769.1|FC352769EST: AGCTTTTGGACATGACATGTATGACACTTGGAGGTCGTGCCGCTGAGCAG GTACTGTTAGGTAAAATATCAACAGGTGCACAGAATGACTTGGAGAAAGTT
genomic: AGCTTTTGGACATGACATGTATGACACTTGGAGGTCGTGCCGCTGAGCAGgtatagcacg ... ctttacacagGTACTGTTAGGTAAAATATCAACAGGTGCACAGAATGACTTGGAGAAAGTT
RNA-Seq data
ATGC Supported by RNA-Seq exonic block that spans over the splice site
atgs Truncated intron sequence
Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.
Found data for 1 RNA-Seqlibrary.
Block sizes:
24 (upstream exon),
32 (downstream exon)
Score:
5AGGTTTTGCTCAGTATTTACCAAATGAGAATCTGCTTATGACAAAGGAGCAGCTTTTGGACATGACATGTATGACACTTGGAGGTCGTGCCGCTGAGCAGgtatagcacg ... ctttacacagGTACTGTTAGGTAAAATATCAACAGGTGCACAGAATGACTTGGAGAAAGTTACGAAAATGACTTATGCACAAGTTGCAGTATATGGGTTTAGTGAAAAAG
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atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gaagcagttttagttaatgttgatttttttactgttggttcgttgctttacacagGTACTGTTAGGTAAAATATCAACAGGTGCACAGAATGACTTGGAGAAAGTTACGAAAATGACTTATGCACAAGTTGCAGTATATGGGTTTAGTGAAAAAG
tgttgat putative branch site (score: 5)
ttgcttt putative PPT
ttttagttaatgttga TA-rich tract