Sequence
atgc intronic sequence ATGC exonic sequence...gaatttttttctgtaagcggttgtttatttcatttggaattataagcttcctttgacggatattgtcacgcgagcaccctttgtacttgccattttgcagCGTGAGGACGCCCCTATCGATGCAGTTCTTTCCTCGCTTCTTTTTTCTCTATTTCATGGCTTTCCACATTTACTTCTTCTCTTATACCTACG
Basic information
species | Physcomitrella patens |
transcript | PP1S96_202V6.1 |
intron # | 12 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S96_202V6.1 (Physcomitrella patens), 3'ss of exon 12
lower sequence: LOC_Os03g45770.2 (Oryza sativa), 3'ss of exon 10
gaatttttttctgtaagcggtt-gtttatttcatttggaattataagcttcctttgacggatattgtcacgcgagcaccctttgtacttgccat--tttgcagCGTGAGGACGCCCCTATCGATGCAGTTCTTTCCTCGCTTCTTTTTTCTCTATTTCATGGCTTTCCACATTTACTTCTTCTCTTATACCTACG
| || | || || | | | || ||||| | | | | | | | || ||| | | | || | || | ||||||| |||||||| | |||| ||||||||||| || ||||| || || || |||||| ||| ||||||||||||||||||||| || || || |
catttaacatttgcaactttcaagcatgcattatc-agaattgttgtcatgcatag-caaattcggtc-tgtctgaatttactgaattttgtgtcctttgcagTGTGAGGACATCTATATCAATGCAGTTCTTCCCGCGCTTTTTCTTGCTGTATTTCTTGGTTTTCCACATTTACTTCTTCTCGTACACATATG
upper sequence: PP1S96_202V6.1 (Physcomitrella patens), 3'ss of exon 12
lower sequence: GRMZM5G814310_T02 (Zea mays), 3'ss of exon 2
--gaatttttttctgtaagcggttgtttatttcatttggaattataagcttcctttgacggatattgtcacgcgagcaccctttgtacttgccattttgcagCGTGAGGACGCCCCTATCGATGCAGTTCTTTCCTCGCTTCTTTTTTCTCTATTTCATGGCTTTCCACATTTACTTCTTCTCTTATACCTACG--------
| | | | | | || || | | | | || | ||| | | | |||| ||| ||| ||| ||| |||| || ||||||||||||||||||| |||||||| || || ||||| ||| |||||| || ||||||||||| |||||||| |
gcgggtagcatgaatgcatctatcagaaatgatcttgtgtaggacgaaattttcaagctaatcattcttaaatacttatccttaaatctt--tgcttttcagTGTGCGGACATCCATATCGATGCAGTTCTTTCCACGCTTCTTCTTGCTGTATTTTTTGGTTTTCCATATCTACTTCTTCTCATATACCTATGGTATGTGT
upper sequence: PP1S96_202V6.1 (Physcomitrella patens), 3'ss of exon 12
lower sequence: GRMZM5G814310_T01 (Zea mays), 3'ss of exon 2
--gaatttttttctgtaagcggttgtttatttcatttggaattataagcttcctttgacggatattgtcacgcgagcaccctttgtacttgccattttgcagCGTGAGGACGCCCCTATCGATGCAGTTCTTTCCTCGCTTCTTTTTTCTCTATTTCATGGCTTTCCACATTTACTTCTTCTCTTATACCTACG
| | | | | | || || | | | | || | ||| | | | |||| ||| ||| ||| ||| |||| || ||||||||||||||||||| |||||||| || || ||||| ||| |||||| || ||||||||||| |||||||| |
gcgggtagcatgaatgcatctatcagaaatgatcttgtgtaggacgaaattttcaagctaatcattcttaaatacttatccttaaatctt--tgcttttcagTGTGCGGACATCCATATCGATGCAGTTCTTTCCACGCTTCTTCTTGCTGTATTTTTTGGTTTTCCATATCTACTTCTTCTCATATACCTATG
upper sequence: PP1S96_202V6.1 (Physcomitrella patens), 3'ss of exon 12
lower sequence: GLYMA15G05080.1 (Glycine max), 3'ss of exon 11
gaatttttttctgtaagcggttgtttatttcatttggaattataagcttcctttgacggatattgtcacgcg---agcaccctttgtacttgccat--tttgcagCGTGAGGACGCCCCTATCGATGCAGTTCTTTCCTCGCTTCTTTTTTCTCTATTTCATGGCTTTCCACATTTACTTCTTCTCTTATACCTACG
| ||| || || ||| | | | || | || || || | | ||| ||| | ||| | | |||||| || | || || |||| ||| |||||||||||||||||||||| || |||||| ||| |||||||| || |||||||||||| | ||||
-----tcttttaatatctggaccagtatctgttacacattttcatgcacatttgtggggttgtggtccagcgtatgataatgagtgtgttcattgtaacttgcagTGTCCGAACACCAATATCAATGAAGTTCTTTCCTCGCTTCTTTTTGCTGTATTTCCTGGTCTTCCACATATATTTCTTCTCTTATGCTTACG
upper sequence: PP1S96_202V6.1 (Physcomitrella patens), 3'ss of exon 12
lower sequence: GLYMA08G19970.1 (Glycine max), 3'ss of exon 11
gaatttttttctgtaagcggttgtttatttcatttggaattataagcttcctttgacggatattgtcacgcg---agcaccctttgtacttgccattttgcagCGTGAGGACGCCCCTATCGATGCAGTTCTTTCCTCGCTTCTTTTTTCTCTATTTCATGGCTTTCCACATTTACTTCTTCTCTTATACCTACG
|| ||| || || ||| | | | | || | || || | || | | ||| ||| | || | | |||||| || | || || |||| ||| |||||||||||||||||||||| || |||||| ||| |||||||| || |||||||||||| | || |
---gttcttttaatatctggaccagtatctattatacattttcatgcacatttgtagggttgtggtccagcgtatgataatacaagtgtattgtaacttgcagTGTCCGAACACCAATATCAATGAAGTTCTTTCCTCGCTTCTTTTTGCTGTATTTCCTGGTCTTCCACATATATTTCTTCTCTTATGCTTATG
upper sequence: PP1S96_202V6.1 (Physcomitrella patens), 3'ss of exon 12
lower sequence: Vv12s0034g02140.t01 (Vitis vinifera), 3'ss of exon 11
--------------------------------------------------------------------gaatttttttctgtaagcggttgtttat-ttcatttggaattataagcttcctttgacggatattgtcacgcgagcaccct----------ttgtacttgccattt---tgcagCGTGAGGACGCCCCTATCGATGCAGTTCTTTCCTCGCTTCTTTTTTCTCTATTTCATGGCTTTCCACATTTACTTCTTCTCTTATACCTACG
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gtctctctctctttctctctctatgatatatgtttatatatatatatctatatatatatatatatattatgtatgtttgtgtatgtgtatatgtatatacacatgcataaatattatatatctgtttg-tatttttatataagtctcctactaatattattatacttggcatttgcttgcagTGTCCGCACTCCTATATCGATGAAGTTCTTTCCTCGCTTCTTTTTGCTCTATTTTCTGGTTTTCCACATCTATTTCTTTTCTTATGCTTATGMapped 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|162162209|gb|FC337991.1|FC337991EST: TTTCTGGTCCTCACACTGGTCTGGCTTTGCGAGCTCTTCACTATGATAAG CGTGAGGACGCCCCTATCGATGCAGTTCTTTCCTCGCTTCTTTTTTCTCTA
genomic: TTTCTGGTCCTCACACTGGTCTGGCTTTGCGAGCTCTTCACTATGATAAGgtattgtgct ... cattttgcagCGTGAGGACGCCCCTATCGATGCAGTTCTTTCCTCGCTTCTTTTTTCTCTA
EST:
gi|162153810|gb|FC329941.1|FC329941EST: TTTCTGGTCCTCACACTGGTCTGGCTTTGCGAGCTCTTCACTATGATAAG CGTGAGGACGCCCCTATCGATGCAGTTCTTTCCTCGCTTCTTTTTTCTCTA
genomic: TTTCTGGTCCTCACACTGGTCTGGCTTTGCGAGCTCTTCACTATGATAAGgtattgtgct ... cattttgcagCGTGAGGACGCCCCTATCGATGCAGTTCTTTCCTCGCTTCTTTTTTCTCTA
EST:
gi|162167081|gb|FC342543.1|FC342543EST: TTTCTGGTCCTCACACTGGTCTGGCTTTGCGAGCTCTTCACTATGATAAG CGTGAGGACGCCCCTATCGATGCAGTTCTTTCCTCGCTTCTTTTTTCTCTA
genomic: TTTCTGGTCCTCACACTGGTCTGGCTTTGCGAGCTCTTCACTATGATAAGgtattgtgct ... cattttgcagCGTGAGGACGCCCCTATCGATGCAGTTCTTTCCTCGCTTCTTTTTTCTCTA
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:
34 (upstream exon),
23 (downstream exon)
Score:
4TTGGGATACTCTTTTTCCTGTTCGAGTTTTTCGATGACCAGCTGCTTGCGTTTCTGGTCCTCACACTGGTCTGGCTTTGCGAGCTCTTCACTATGATAAGgtattgtgct ... cattttgcagCGTGAGGACGCCCCTATCGATGCAGTTCTTTCCTCGCTTCTTTTTTCTCTATTTCATGGCTTTCCACATTTACTTCTTCTCTTATACCTACG
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atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gcttcctttgacggatattgtcacgcgagcaccctttgtacttgccattttgcagCGTGAGGACGCCCCTATCGATGCAGTTCTTTCCTCGCTTCTTTTTTCTCTATTTCATGGCTTTCCACATTTACTTCTTCTCTTATACCTACG
ctttgac putative branch site (score: 4)
ccatttt putative PPT
atattgt TA-rich tract