Sequence
atgc intronic sequence ATGC exonic sequence...acaagtctatgtggtggcttattctactggctgtagggttcatcaccatacgtgctaatatctgtttgtttgtaacgcgttttttatttgtttgttccagGTTATAGCTCAAAATCTGCAAAAAATTGATCCCAAGTCTGATGGAGCGAAGAGAGATTGGGTTGCAATATACGATGAATGTGCAAATGTGCTATATGAG
Basic information
species | Physcomitrella patens |
transcript | PP1S83_45V6.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S83_45V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GLYMA08G14920.1 (Glycine max), 3'ss of exon 5
acaagtctatgtggtggcttattctactggctgt--agggttcatcaccatacgtgctaatatctgtttgtttgtaacgcgttttttatttgtttgttccagGTTATAGCTCAAAATCTGCAAAAAATTGATCCCAAGTCTGATGGAGCGAAGAGAGATTGGGTTGCAATATACGATGAATGTGCAAATGTGCTATATGAG
|| | | | | | ||| | | | | | | | | | | | || | || | || | ||| || |||||||||| ||| || |||| ||||||||||||||||| || ||||| || ||||| ||||||||||| || || ||||| ||||| ||| ||||| ||
ttaaatttttttttta-cttgcatgaaggatttttaataatatgacttcctgcctatgaagacttgcagaatgatacttgggccttt-ttccccccctccagGTTATTGCTGAATATCTTCAAAAAATTGATCCCAAATCAGATGGTGCAAAGAGGGATTGGGTTGCTATTTATGATGAGTGTGCCTCTGTTTTATATCAG
upper sequence: PP1S83_45V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GLYMA06G15070.1 (Glycine max), 3'ss of exon 5
acaagtctatgtggtggcttattctactggctgtagggttcatcaccatacgtgctaatatctgtttgtttgtaacg-cgttttttatttgtttgttccagGTTATAGCTCAAAATCTGCAAAAAATTGATCCCAAGTCTGATGGAGCGAAGAGAGATTGGGTTGCAATATACGATGAATGTGCAAATGTGCTATATGAG
||| ||| | ||| | || || | | || || | || ||| | | || | | || |||| ||| ||||||||| ||| || |||| |||||||| ||||| || || ||||| || ||||| ||||||||||| || || ||||||||||| ||| ||||| ||
----gtcagtgttataaattaaggctttt-ctataatgcttatggtactatgagcaaatctgatataacttctgataatgtcttttcttta---accccagGTTATTGCTGAATATCTTCAAAAAATCGATCCAAAATCAGATGGCGCAAAGAGGGATTGGGTTGCTATTTATGATGAATGTGCCTCTGTCTTATATCAG
upper sequence: PP1S83_45V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GLYMA05G31670.1 (Glycine max), 3'ss of exon 5
-acaagtctatgtggtggcttattctact-ggctgtagggttcatcaccatacgtgctaatatctgtttgtttgtaacgcgttttttatttgtttgttccagGTTATAGCTCAAAATCTGCAAAAAATTGATCCCAAGTCTGATGGAGCGAAGAGAGATTGGGTTGCAATATACGATGAATGTGCAAATGTGCTATATGAG
| | || || || | || | || | | | | | | | | | || | ||| || ||||| |||| ||| || |||| ||||||||||||||||| || ||||| || ||||| || |||||||| || || ||||| ||||| ||| ||||| ||
tttttccttgtatgaaggattttaataataggacttcctgcctgtgaagacttgcagaattgataaaacactgatacttgggccttttttccccc--tccagATTATTGCTGAATATCTTCAAAAAATTGATCCCAAATCAGATGGTGCAAAGAGGGACTGGGTTGCTATTTATGATGAGTGTGCCTCTGTTTTATATCAG
upper sequence: PP1S83_45V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: AT5G64940.2 (Arabidopsis thaliana), 3'ss of exon 5
------------------------------------------------acaagtctatgtggtggcttattctactggctgtagggttcatcaccatacgtgctaatatctgtttgtttgtaacgcgttttttatttgtttgttccagGTTATAGCTCAAAATCTGCAAAAAATTGATCCCAAGTCTGATGGAGCGAAGAGAGATTGGGTTGCAATATACGATGAATGTGCAAATGTGCTATATGAG
| ||| | ||| || | || ||| | | | || | | |||| | | || | ||| |||| | | || |||| || ||| | |||| ||||| | || || || || ||||| || |||||||||||||||||||| || ||||||||||| | ||| | || ||
gttagtgtctctataccacagtcattatagagcttttccatgttgcaagcgtccttatctcgtgattt-tcttatccgctct----tctgaagctatttgcatgatgttctgctgagtc--aatgactttgttatgcttctattt-agGTGATCGCTGAGTATCTCCAAAAGGTGGACCCAAAATCAGATGGTGCAAAGAGAGATTGGGTTGCAATCTATGATGAATGTGCCAGTGTTTTGTACCAG
upper sequence: PP1S83_45V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: EFJ35897 (Selaginella moellendorffii), 3'ss of exon 4
acaagtctatgtggtggcttattctactggctgtagggttcatcaccatacgtgctaatatctgtttgtttgtaacg-cgttttttatttgtttgttccagGTTATAGCTCAAAATCTGCAAAAAATTGATCCCAAGTCTGATGGAGCGAAGAGAGATTGGGTTGCAATATACGATGAATGTGCAAATGTGCTATATGAG
||| | || | | ||| | | | |||| | | | | | |||| || | | ||||| || || | || | ||||| |||||||| ||||||||||| |||||||| ||||||||||| || |||||||| ||||| |||||||| ||| ||
--------------------------------gtaag--tctttgctttactt-----ttcttttttgctcgaactgtcaccttttcttcactgg---cagGTAATCGCAGAGAACTTACAAAAGATTGATCCAAAGTCTGATGGCGCGAAGAGGGATTGGGTTGCCATTTACGATGAGTGTGCCAATGTGCTCTATCAG
upper sequence: PP1S83_45V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: EFJ09480 (Selaginella moellendorffii), 3'ss of exon 6
acaagtctatgtggtggcttattctactggctgtagggttcatcaccatacgtgctaatatctgtttgtttgtaacg-cgttttttatttgtttgttccagGTTATAGCTCAAAATCTGCAAAAAATTGATCCCAAGTCTGATGGAGCGAAGAGAGATTGGGTTGCAATATACGATGAATGTGCAAATGTGCTATATGAG
||| | || | | ||| | | | |||| | | | | | |||| || | | ||||| || || | || | ||||| |||||||| ||||||||||| |||||||| ||||||||||| || |||||||| ||||| |||||||| ||| ||
--------------------------------gtaag--tctttgctttactt-----ttcttttttgctcgaactgtcaccttttcttcactcg---cagGTAATCGCAGAGAACTTACAAAAGATTGATCCAAAGTCTGATGGCGCGAAGAGGGATTGGGTTGCCATTTACGATGAGTGTGCCAATGTGCTCTATCAGMapped 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|162187089|gb|FC362871.1|FC362871EST: AACGCCCAGGCTTGAAAGCACTTTTTGATATTGACCTCAAGAACTTGCGG GTTATAGCTCAAAATCTGCAAAAAATTGATCCCAAGTCTGATGGAGCGAAG
genomic: AACGCCCAGGCTTGAAAGCACTTTTTGATATTGACCTCAAGAACTTGCGGgttagtgctc ... tttgttccagGTTATAGCTCAAAATCTGCAAAAAATTGATCCCAAGTCTGATGGAGCGAAG
EST:
gi|100392147|gb|BY953217.1|BY953217EST: AACGCCCAGGCTTGAAAGCACTTTTTGATATTGACCTCAAGAACTTGCGG GTTATAGCTCAAAATCTGCAAAAAATTGATCCCAAGTCTGATGGAGCGAAG
genomic: AACGCCCAGGCTTGAAAGCACTTTTTGATATTGACCTCAAGAACTTGCGGgttagtgctc ... tttgttccagGTTATAGCTCAAAATCTGCAAAAAATTGATCCCAAGTCTGATGGAGCGAAG
EST:
gi|100390428|gb|BY952836.1|BY952836EST: AACGCCCAGGCTTGAAAGCACTTTTTGATATTGACCTCAAGAACTTGCGG GTTATAGCTCANAATCTGCAAAAAATTGATCCCAAGTCTGATGGAGCGAAG
genomic: AACGCCCAGGCTTGAAAGCACTTTTTGATATTGACCTCAAGAACTTGCGGgttagtgctc ... tttgttccagGTTATAGCTCAAAATCTGCAAAAAATTGATCCCAAGTCTGATGGAGCGAAG
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:
35 (upstream exon),
34 (downstream exon)
Score:
17TCAAGTTCACAGGGCGAAACTTCGTGGTAAGGAAATCGTTGTTAAAGTGCAACGCCCAGGCTTGAAAGCACTTTTTGATATTGACCTCAAGAACTTGCGGgttagtgctc ... tttgttccagGTTATAGCTCAAAATCTGCAAAAAATTGATCCCAAGTCTGATGGAGCGAAGAGAGATTGGGTTGCAATATACGATGAATGTGCAAATGTGCTATATGAG
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atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ccatacgtgctaatatctgtttgtttgtaacgcgttttttatttgtttgttccagGTTATAGCTCAAAATCTGCAAAAAATTGATCCCAAGTCTGATGGAGCGAAGAGAGATTGGGTTGCAATATACGATGAATGTGCAAATGTGCTATATGAG
ttgtaac putative branch site (score: 17)
ttttttatttgttt putative PPT
ttttttatttgtttgt TA-rich tract