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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAATAAGAAATGGCGAGAAGGCTTCTACGTTACATCTATGGCCACAGCGGGAAGCCGATGGGGTGTAGTTATGTCGCGAAACGCAGGTTTCTCTGATCAGgtaattagcgctctaagcctacttgatttacgaaaaccgcatactatttttgcttcttcgactcggagcagatatgaagtaaatgaaaatatttgctgaccaatttagaattcctgtcatcggacatcacctgattacattcctctctcttaccgaatgtatttgccctctgcag

Basic information

species Physcomitrella patens
transcript PP1S131_16V6.1
intron # 14
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S131_16V6.1 (Physcomitrella patens), 5'ss of exon 14
lower sequence: LOC_Os01g10150.1 (Oryza sativa), 5'ss of exon 14
CAATAAGAAATGGCGAGAAGGCTTCTACGTTACATCTATGGCCACAGCGGGAAGCCGATGGGGTGTAGTTATGTCGCGAAACGCAGGTTTCTCTGATCAGgtaattagcgctctaagcctacttgatttacgaaaaccgcatactatttttgcttcttcgactcggagcagatatgaagtaaatgaaaatatttgctgaccaatttagaattcctgtcatcggacatcacctgattacattcctctctcttaccgaatgtatttgccctctgcag
|| || || ||| || || ||||| || || | |||||||||| ||||||||||||| ||| |||||||| || ||||| |||||| | |||||||| || | || | | || | ||| | ||||| || | | | ||| || | ||| | | | | | || | | | ||| ||| | || |
AAACAAAAAGTGGAAGGAGGGGTTCTATGTCACTGCCTTGGCCACAGCAGGAAGCCGATGGGCTGTGGTTATGTCCCGGAACGCTGGTTTCACACATCAGgta-----cgtttggagtgtccaagagccttgtaaaattgaattcattttagcagc---aagctacactgactatcaattgaatatgtaaa----------agtcttgagattttattatctcgcatatctcttttgtag-----------------------------------

upper sequence: PP1S131_16V6.1 (Physcomitrella patens), 5'ss of exon 14
lower sequence: LOC_Os01g10150.2 (Oryza sativa), 5'ss of exon 14
CAATAAGAAATGGCGAGAAGGCTTCTACGTTACATCTATGGCCACAGCGGGAAGCCGATGGGGTGTAGTTATGTCGCGAAACGCAGGTTTCTCTGATCAGgtaattagcgctctaagcctacttgatttacgaaaaccgcatactatttttgcttcttcgactcggagcagatatgaagtaaatgaaaatatttgctgaccaatttagaattcctgtcatcggacatcacctgattacattcctctctcttaccgaatgtatttgccctctgcag
|| || || ||| || || ||||| || || | |||||||||| ||||||||||||| ||| |||||||| || ||||| |||||| | |||||||| || | || | | || | ||| | ||||| || | | | ||| || | ||| | | | ||| |||| | | || ||| | ||| | | || |
AAACAAAAAGTGGAAGGAGGGGTTCTATGTCACTGCCTTGGCCACAGCAGGAAGCCGATGGGCTGTGGTTATGTCCCGGAACGCTGGTTTCACACATCAGgta-----cgtttggagtgtccaagagccttgtaaaattgaattcattttagcagc---aagctacactgactatcaattgaatatgtaaaagtcttga--gattt-----tattatc-tcgcatatctcttttgtaggtag---------------------------------

upper sequence: PP1S131_16V6.1 (Physcomitrella patens), 5'ss of exon 14
lower sequence: LOC_Os01g56580.1 (Oryza sativa), 5'ss of exon 15
CAATAAGAAATGGCGAGAAGGCTTCTACGTTACATCTATGGCCACAGCGGGAAGCCGATGGGGTGTAGTTATGTCGCGAAACGCAGGTTTCTCTGATCAGgtaattagcgctctaagcctacttgatttacgaaaaccgcatactatttttgcttcttcg-actcggagcagatatgaagtaaatgaaaatatttgctgaccaatttagaattcctgtcatcggacatcacctgattacattcctctctcttaccgaatgtatttgccctctgcag
||| ||||||||| |||||| || | |||||||| ||| |||| || |||||||| ||||||||||||||||| | || | || || ||||| |||||| || || || | | || ||||||| ||| | | | | ||| | | ||| || ||||| |||||| || || ||| || |
CAACAAGAAATGGAAAGAAGGATTTCATGTTACATCAATGACCACTGCAGGAAGCCGCTGGGGTGTAGTTATGTCAAGGAATTCTGGATTTTCTGAACAGgtatttg----------------tggttattg------gtgtaatatttttttttcctggtgtgcaaatcagttgcaatctaagcgatggtattt------caattttt--tttttggcatgtgaaaaag----------------------------------------------

upper sequence: PP1S131_16V6.1 (Physcomitrella patens), 5'ss of exon 14
lower sequence: LOC_Os07g07560.2 (Oryza sativa), 5'ss of exon 15
CAATAAGAAATGGCGAGAAGGCTTCTACGTTACATCTATGGCCACAGCGGGAAGCCGATGGGGTGTAGTTATGTCGCGAAACGCAGGTTTCTCTGATCAGgtaattagcgct-ctaagcctacttgatttacgaaaaccgcat---actatttttgcttcttcgactcggagcagatatgaagtaaatgaaaatatttgctgaccaatttagaattcctgtcatcggacatcacctgattacattcctctctcttaccgaatgtatttgccctctgcag
|||||| || ||| |||||| || | || |||||||||||||| || |||| || ||||||||||||||||| | ||| |||||| |||||| ||||| | | | || |||| || || | | | || | |||| | | || || | ||| | | | ||| |||| | || | || || || | |||| | | | |
CAATAAAAAGTGGAAAGAAGGTTTTCATGTGACATCTATGGCCACCGCTGGAAATCGCTGGGGTGTAGTTATGTCAAGGAACTCAGGTTACTCTGAACAGgttagaataattgcttgacctagttcatattcagtccacaaatttggcaatttatattcctgtgagc--attccattatttactgta-gaatatatctacttatgaagctaacctttttctcat--gccctttttag------------------------------------------

upper sequence: PP1S131_16V6.1 (Physcomitrella patens), 5'ss of exon 14
lower sequence: AT3G13670.1 (Arabidopsis thaliana), 5'ss of exon 14
CAATAAGAAATGGCGAGAAGGCTTCTACGTTACATCTATGGCCACAGCGGGAAGCCGATGGGGTGTAGTTATGTCGCGAAACGCAGGTTTCTCTGATCAGgtaattagcgctctaagcctacttgatttacgaaaaccgcatactatttttgcttcttcgactcggagcagatatgaagtaaatgaaaatatttgctgaccaatttagaattcctgtcatcggacatcacctgattacattcctctctcttaccgaatgtatttgccctctgcag
|| ||||||||| ||||||||||| | || || || ||||| ||||| |||| ||||||||||| |||||||| || || | || | | ||| ||||| || | | ||| || || | | | || | | || | || | | || || | | | ||| | || | | |
AAACAAGAAATGGAGAGAAGGCTTCCATGTAACCTCAATGGCAACAGCTGGAAATCGATGGGGTGTTGTTATGTCCCGCAATTCTGGCTACAGTGAACAGgt-----------tagacttcaccgatatagatgaatttcttccgtttccttcagttttggatc--------tgtcgcgttgatttctaattctcctgttttcgcttatatctcctctacag-----------------------------------------------------

Mapped 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|162228109|gb|FC405691.1|FC405691
EST:     GAAGCCGATGGGGTGTAGTTATGTCGCGAAACGCAGGTTTCTCTGATCAG                         GTCGTTGAGCTTGATTTCTTGTATCCCAGTGAAGGTATTCATAGACGATGG
genomic: GAAGCCGATGGGGTGTAGTTATGTCGCGAAACGCAGGTTTCTCTGATCAGgtaattagcg ... ccctctgcagGTCGTTGAGCTTGATTTCTTGTATCCCAGTGAAGGTATTCATAGACGATGG
EST: gi|162257791|gb|FC433989.1|FC433989
EST:     GAAGCCGATGGGGTGTAGTTATGTCGCGAAACGCAGGTTTCTCTGATCAG                         GTCGTTGAGCTTGATTTCTTGTATCCCAGTGAAGGTATTCATAGACGATGG
genomic: GAAGCCGATGGGGTGTAGTTATGTCGCGAAACGCAGGTTTCTCTGATCAGgtaattagcg ... ccctctgcagGTCGTTGAGCTTGATTTCTTGTATCCCAGTGAAGGTATTCATAGACGATGG
EST: gi|162185156|gb|FC362290.1|FC362290
EST:     GAAGCCGATGGGGTGTAGTTATGTCGCGAAACGCAGGTTTCTCTGATCAG                         GTCGTTGAGCTTGATTTC
genomic: GAAGCCGATGGGGTGTAGTTATGTCGCGAAACGCAGGTTTCTCTGATCAGgtaattagcg ... ccctctgcagGTCGTTGAGCTTGATTTC
EST: gi|162252530|gb|FC427339.1|FC427339
EST:     TAGTTATGTCGCGAAACGCAGGTTTCTCTGATCAG                         GTCGTTGAGCTTGATTTCTTGTATCCCAGTGAAGGTATTCATAGACGATGG
genomic: TAGTTATGTCGCGAAACGCAGGTTTCTCTGATCAGgtaattagcg ... ccctctgcagGTCGTTGAGCTTGATTTCTTGTATCCCAGTGAAGGTATTCATAGACGATGG
EST: gi|100448451|gb|CJ972750.1|CJ972750
EST:     GAAGCCGATGGGGTGTAGTTATGTCGCGAAACGCAGGTTTCTCTGATCAG                         GTCGTTGAGCTTGATTTCTTGTATCCCAGTGAAGGTATTCATAGACGATGG
genomic: GAAGCCGATGGGGTGTAGTTATGTCGCGAAACGCAGGTTTCTCTGATCAGgtaattagcg ... ccctctgcagGTCGTTGAGCTTGATTTCTTGTATCCCAGTGAAGGTATTCATAGACGATGG
EST: gi|37831666|gb|BJ589678.1|BJ589678
EST:     GAAGCCGATGGGGTGTAGTTATGTCGCGAAACGCAGGTTTCTCTGATCAG                         GTCGTTGAGCTTGATTTCTTGTATCCCAGTGAAGGTATTCATAGACGATGG
genomic: GAAGCCGATGGGGTGTAGTTATGTCGCGAAACGCAGGTTTCTCTGATCAGgtaattagcg ... ccctctgcagGTCGTTGAGCTTGATTTCTTGTATCCCAGTGAAGGTATTCATAGACGATGG
EST: gi|162157367|gb|FC333170.1|FC333170
EST:     GAAGCCGATGGGGTGTAGTTATGTCGCGAAACGCAGGTTTCTCTGATCAG                         GTCGTTGAGCTTGATTTCTTGTATCCCAGTGAAGGTATTCATAGACGATGG
genomic: GAAGCCGATGGGGTGTAGTTATGTCGCGAAACGCAGGTTTCTCTGATCAGgtaattagcg ... ccctctgcagGTCGTTGAGCTTGATTTCTTGTATCCCAGTGAAGGTATTCATAGACGATGG

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), 35 (downstream exon)
Score: 22

CAATAAGAAATGGCGAGAAGGCTTCTACGTTACATCTATGGCCACAGCGGGAAGCCGATGGGGTGTAGTTATGTCGCGAAACGCAGGTTTCTCTGATCAGgtaattagcg ... ccctctgcagGTCGTTGAGCTTGATTTCTTGTATCCCAGTGAAGGTATTCATAGACGATGGGACAGTGGATACCGCATAACCTCTACTGCTGCGACTTGGGATCAGGCAG




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