Sequence
atgc intronic sequence ATGC exonic sequenceGCTAGTGGTGCGGTCCCATGAGGTCAAGGATGAGGGCTATGAAGTGGACCATGGCGGCAAACTCATTACTGTCTTCTCTGCACCAAATTACTGTGATCAGgtaaatcatattggacaagcttgtagctttgacccagaatgtccatgcggtttgaaaacacggcatcttttgtgctaagttgtactgatcttttacatcatcttatgtctgcag
Basic information
species | Physcomitrella patens |
transcript | PP1S87_139V6.1 |
intron # | 11 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S87_139V6.1 (Physcomitrella patens), 5'ss of exon 11
lower sequence: GLYMA08G42380.1 (Glycine max), 5'ss of exon 11
GCTAGTGGTGCGGTCCCATGAGGTCAAGGATGAGGGCTATGAAGTGGACCATGGCGGCAAACTCATTACTGTCTTCTCTGCACCAAATTACTGTGATCAGgtaaatcatattggacaagcttgtagctttgacccagaatgtccatgcggtttgaaaacacggcatcttttgtgctaagttgtactgatcttttacatcatcttatgtctgcag
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TTTAGTTGTGAGATCTCACGAAGTAAAGGATGAGGGTTATGAGATTGAACATGAGGGTAAACTCATAACTGTGTTTTCTGCTCCAAATTACTGTGACCAGgtaa-ccatatcccttctgct-atattctttttt----atttttatggcatttgcttacttg--attgtcttggaagatttgagaggagggagaaagggggctggggg------
upper sequence: PP1S87_139V6.1 (Physcomitrella patens), 5'ss of exon 11
lower sequence: GLYMA18G12440.1 (Glycine max), 5'ss of exon 11
GCTAGTGGTGCGGTCCCATGAGGTCAAGGATGAGGGCTATGAAGTGGACCATGGCGGCAAACTCATTACTGTCTTCTCTGCACCAAATTACTGTGATCAGgtaaatcatattggacaagct-tgtagctttgacccagaatgtccatgcggtttgaaaacacggcatcttttgtgctaagttgtactgatcttttacatcatcttatgtctgcag
|||| ||||| || ||||| || ||||| ||||| ||||| | || |||| || |||||||| ||||| || ||||| |||||||||||||| ||||||| ||||| ||| | ||| | | ||||| | | |||| | || | || |
-TTAGTTGTGCGATCTCATGAAGTAAAGGACGAGGGTTATGAGATTGAACATGATGGTAAACTCATAACTGTGTTTTCTGCTCCAAATTACTGTGACCAGGtaacacatatcccttttgctacattcttttctattatggcatttgctta-tttgattgtcttggaagatttgagaggagcgaaggggggctgggggaatgg-------------
upper sequence: PP1S87_139V6.1 (Physcomitrella patens), 5'ss of exon 11
lower sequence: AT2G42810.2 (Arabidopsis thaliana), 5'ss of exon 12
GCTAGTGGTGCGGTCCCATGAGGTCAAGGATGAGGGCTATGAAGTGGACCATGGCGGCAAACTCATTACTGTCTTCTCTGCACCAAATTACTGTGATCAGgtaaatcatattggacaagcttgtagctttgacccagaatgtccatgcggtttgaaaacacggcatcttttgtgctaagttgtactgatctt-ttacatcatcttatgtctgcag
| |||| ||||| ||||| || || ||||| || ||||| || || |||| ||| |||||||| |||||||||||||| |||||||||||||||||||||| ||| |||| | ||| || || || | | | ||| || || ||| ||| || |||| | || || |
TTTGTTGGTCCGGTCACATGAAGTAAAAGATGAAGGTTATGAGGTTGAACATGACGGTAAACTCATAACTGTCTTCTCTGCGCCAAATTACTGTGATCAGgtaactca-----gacactcctgtcttcttatttcaaaacagc-acccagtt-------acttgattctttac-ttaacatggactggtattgttgtag----------------
upper sequence: PP1S87_139V6.1 (Physcomitrella patens), 5'ss of exon 11
lower sequence: Vv12s0142g00720.t01 (Vitis vinifera), 5'ss of exon 5
GCTAGTGGTGCGGTCCCATGAGGTCAAGGATGAGGGCTATGAAGTGGACCATGGCGGCAAACTCATTACTGTCTTCTCTGCACCAAATTACTGTGATCAGgtaaatcatattggacaagcttgtagctttgacccagaatgtccatgcggtttgaaaacacggca-tcttttgtgctaagttgtactgatcttttacatcatcttatgtctgcag
|||| ||||| || ||||| || |||||||| |||||||| | || |||| ||||| || |||||||| || ||||| ||||| || |||||||||||| | | | || ||| ||| | || | | | ||||||| | | | || | | | | ||| || | |||| || | | |
TTTAGTTGTGCGATCTCATGAAGTAAAGGATGAAGGCTATGAGATTGAACATGATGGCAAGCTTATTACTGTGTTTTCTGCTCCAAACTATTGTGATCAGgtatgtgaggcttaac---ctt-----tttaata------gttccttggatttgaaagcttagaactcgtgtacattcgactaaactcctccagggga-catcacatatgtatatMapped 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|37821905|gb|BJ579971.1|BJ579971EST: ATGGCGGCAAACTCATTACTGTCTTCTCTGCACCAAATTACTGTGATCAG ATGGGTAATAAAGGAGCTTTTATCCGATTTGGGGCGCCAGATATGAAGCCT
genomic: ATGGCGGCAAACTCATTACTGTCTTCTCTGCACCAAATTACTGTGATCAGgtaaatcata ... atgtctgcagATGGGTAATAAAGGAGCTTTTATCCGATTTGGGGCGCCAGATATGAAGCCT
EST:
gi|208390866|gb|DC945897.1|DC945897EST: ATGGCGGCAAACTCATTACTGTCTTCTCTGCACCAAATTACTGTGATCAG ATGGGTAATAAAGGAGCTTTTATCCGATTTGGGGCGCCAGATATGAAGCCT
genomic: ATGGCGGCAAACTCATTACTGTCTTCTCTGCACCAAATTACTGTGATCAGgtaaatcata ... atgtctgcagATGGGTAATAAAGGAGCTTTTATCCGATTTGGGGCGCCAGATATGAAGCCT
EST:
gi|22132216|gb|BQ827040.1|BQ827040EST: ATGGCGGCAAACTCATTACTGTCTTCTCTGCACCAAATTACTGTGATCAG ATGGGTAATAAAGGAGCTTTTATCCGATTTGGGGCGCCAGATATGAAGCCT
genomic: ATGGCGGCAAACTCATTACTGTCTTCTCTGCACCAAATTACTGTGATCAGgtaaatcata ... atgtctgcagATGGGTAATAAAGGAGCTTTTATCCGATTTGGGGCGCCAGATATGAAGCCT
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:
32 (upstream exon),
22 (downstream exon)
Score:
4GCTAGTGGTGCGGTCCCATGAGGTCAAGGATGAGGGCTATGAAGTGGACCATGGCGGCAAACTCATTACTGTCTTCTCTGCACCAAATTACTGTGATCAGgtaaatcata ... atgtctgcagATGGGTAATAAAGGAGCTTTTATCCGATTTGGGGCGCCAGATATGAAGCCTGAGTTCACGAAGTTTGGTTCAGTG
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