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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtatttgcaatgtgggattggtgttggtaacactggcagcactgcttatctttgtacactgggatgtattctaacgtttttatgaaatgcacaatggaagGTGGCATTGGCGCACACGATTGGACACGTGGCAGCGACTGTGAGTATGTCCAAGGTCGCAGTATCCTTCACGCACATCATCAAGAGCGCAGAACCCGCGT

Basic information

species Physcomitrella patens
transcript PP1S70_177V6.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S70_177V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: LOC_Os07g33910.2 (Oryza sativa), 3'ss of exon 1
---------------gtatttgcaatgtgggattggtgttggtaacactggcagcactgcttatctttgtacactgggatgtattctaa----cgtttttatgaaatgcacaatg-gaagGTGGCATTGGCGCACACGATTGGACACGTGGCAGCGACTGTGAGTATGTCCAAGGTCGCAGTATCCTTCACGCACATCATCAAGAGCGCAGAACCCGCGT
|| || | | | || | | ||| | | |||| || | | || ||| ||||||| || | | | ||||||| | |||||||| || || |||||||| ||||| ||||| ||| | ||||| || || || ||||| |||||||||||||||| || || ||||
gtgagatcgcattgaccatggacaccatcgtctcctccttcttgattctgttc-tattctgaatctctgacgcgttcgttggatttggggattcgtttttgctcgttgtgggacgagcagGTGGCGATCGCGCACACCATCGGGCACGTGGCGGCGACGGTGAGCATGGCGAAGGTGGCGGTGTCGTTCACCCACATCATCAAGAGCGGCGAGCCGGCGT

upper sequence: PP1S70_177V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GRMZM2G009223_T01 (Zea mays), 3'ss of exon 1
gtatttgcaatgtgggattggtgttggtaacactggcagcactgcttatctttgtaca-ctgggatgtattctaacgtttttatgaaatg-cacaatggaagGTGGCATTGGCGCACACGATTGGACACGTGGCAGCGACTGTGAGTATGTCCAAGGTCGCAGTATCCTTCACGCACATCATCAAGAGCGCAGAACCCGCGT
| | | | || | | | | || || | ||| | | || | | | | | | ||| | | | | |||| || | ||||||||||| || |||||||| ||||| ||||| ||| ||||||| || || || |||||||||||||||||||||| || || || |
--gtgagtatcatcggcgccgattaattcctccctaaagatctcttcttctagatgcggctctgtctcggtgtggtgctgatgcgaatcgtctcgttctcagGTTGCGATCGCGCACACGATCGGGCACGTGGCGGCGACGGTGAGCATGGCCAAGGTGGCCGTGTCGTTCACGCACATCATCAAGAGCGGGGAGCCGGCAT

upper sequence: PP1S70_177V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA07G38830.1 (Glycine max), 3'ss of exon 1
---gtatttgcaatgtgggattggtgttggtaacactggcagcactgcttatctttgtacactgggatgtattctaacgtttttatgaaatgcacaatggaagGTGGCATTGGCGCACACGATTGGACACGTGGCAGCGACTGTGAGTATGTCCAAGGTCGCAGTATCCTTCACGCACATCATCAAGAGCGCAGAACCCGCGT
| | | || | | || || | | | | || ||| | | | | | | ||| || | | | |||| || || || || ||||| || || ||||| || |||||||||||||| || ||||| || || || |||||||||||||| |||||||| || |
ggcaaaatagtaaagagattagggggtaaaagaaatcataatcgtcaagcattaatgtcaattagtactcaatggggaatttg---aaactttgggagtgcagGTCGCGGTGTTACATACAATTGGGCATGTTGCAGCTACGGTGAGTATGTCCAAAGTTGCAGTTTCATTTACCCACATCATCAAGAGTGCAGAACCTGCAT

upper sequence: PP1S70_177V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA13G27680.1 (Glycine max), 3'ss of exon 1
-------gtatttgcaatgtgggattggtgttggtaacactggcagcactgcttatctttgtacactgggatgtattctaacgtttttatgaaatgcacaatggaagGTGGCATTGGCGCACACGATTGGACACGTGGCAGCGACTGTGAGTATGTCCAAGGTCGCAGTATCCTTCACGCACATCATCAAGAGCGCAGAACCCGCGT
| ||| || | ||||| ||| | || || | | | || | | | | | | | | ||| | ||| | |||| || |||| ||||| ||||| || || || || |||||||| ||||||||||| || || || ||||| |||||||||||||| | ||| || || |
aagtaacgcgtttatggtggtcaaatggtg--ggtgagtttga-agtaaggaa-aggttgatttagtagtactcactaaagaaatttca---aatttttttgtgcagGTTGCGGTGGCACACACAATTGGGCATGTTGCTGCAACTGTGAGCATGTCCAAGGTTGCTGTTTCATTCACTCACATCATCAAGAGTGGAGAGCCAGCTT

upper sequence: PP1S70_177V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA15G11270.1 (Glycine max), 3'ss of exon 1
-----gtatttgcaatgtgggattggtgttggtaacactggcagcactgcttatctttgtacactgggatgtattctaacgtttttatgaaatgcacaatggaagGTGGCATTGGCGCACACGATTGGACACGTGGCAGCGACTGTGAGTATGTCCAAGGTCGCAGTATCCTTCACGCACATCATCAAGAGCGCAGAACCCGCGT
| |||| || | |||||| || | || || | | | || | | | | | | | | ||| | || | | || | ||| || |||| ||||| ||||| || || || || |||||||| ||||||||||| || || || ||||| |||||||||||||| | ||| || || |
gcaatgcatttatggtggtcaaatggtgtgagtgagtttga-agtaaggaa-aggttgattgagtagtactcacttgagaaatttca--aattttattgtgca-gGTTGCGGTGGCACACACAATTGGGCATGTTGCTGCAACTGTGAGCATGTCCAAGGTTGCTGTTTCATTCACTCACATCATCAAGAGTGGAGAGCCAGCTT

upper sequence: PP1S70_177V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA17G01890.1 (Glycine max), 3'ss of exon 1
---gtatttgcaatgtgggattggtgttggtaacactggcagcactgcttatctttgtacactgggatgtattctaacgtttttatgaaatgcacaatggaagGTGGCATTGGCGCACACGATTGGACACGTGGCAGCGACTGTGAGTATGTCCAAGGTCGCAGTATCCTTCACGCACATCATCAAGAGCGCAGAACCCGCGT
| | | | | | || || | | | | || | | | | | |||| | ||| || | | | |||| || || || || ||||| || || ||||| || |||||||||||||| || ||||| || || || |||||||||||||| ||||| || || |
tacaaaatagtgaagagattagggggtaaaagaaattataatagtcaaacattaatctcaattaatacttattgggaaatttg---aaattttgggagtgcagGTTGCGGTGTTACATACAATTGGGCATGTTGCAGCTACCGTGAGTATGTCCAAAGTTGCAGTTTCATTTACCCACATCATCAAGAGTGCAGAGCCTGCAT

upper sequence: PP1S70_177V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: AT1G61800.1 (Arabidopsis thaliana), 3'ss of exon 1
gtatttgcaatgtgggattggtgttggtaacactggcagcactgcttatctttgtacactggga---tgtattctaac----gtttttatgaaatgc-acaatggaagGTGGCATTGGCGCACACGATTGGACACGTGGCAGCGACTGTGAGTATGTCCAAGGTCGCAGTATCCTTCACGCACATCATCAAGAGCGCAGAACCCGCGT
|| ||| || | | | | | || || | | | | || | ||| || | | ||| | | | | ||||| || | || |||||||| |||||||| ||||| || ||||||||||| || || ||||| |||||||| |||||||| || || | ||||| || |
--------ttcatgatgttgttgcttgatggatttataattttgtttgttgtctgataatgaaagagtgtgttttgatcgatgttcccgttttttcttattcttcaagGTCGCTGTAGCACACACGATAGGACACGTTGCAGCAACAGTGAGTATGTCAAAAGTAGCAGTTTCCTTCACACACATCATTAAAAGTGGTGAACCAGCTT

upper sequence: PP1S70_177V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: AT5G54800.1 (Arabidopsis thaliana), 3'ss of exon 1
gtatttgcaatgtgggat-tggtgttggtaacactggca-gcactgcttatctttgt-acactgggatgtattctaacgtttttatgaaatgcacaatggaagGTGGCATTGGCGCACACGATTGGACACGTGGCAGCGACTGTGAGTATGTCCAAGGTCGCAGTATCCTTCACGCACATCATCAAGAGCGCAGAACCCGCGT
| | || | | | | || || | | || | | | | | |||| | | | | | |||| | || |||||| || | ||| || |||| ||||| ||||| || ||||| || || ||||||||||| ||||| || || || ||||| |||||||||||||| | ||||| ||||
cttgtcattatatagcttctagtatt--tcattctagtttaaagtattgaactttttgatattttgttgtactgaaagtggtttatgttgaattgcatata-gGTTGCTGTGGCACACACAATTGGTCATGTGGCTGCAACGGTGAGTATGTCAAAGGTTGCTGTTTCTTTCACTCACATCATCAAGAGTGGTGAACCTGCGT

upper sequence: PP1S70_177V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: EFJ15098 (Selaginella moellendorffii), 3'ss of exon 1
gtatttgcaatgtgggattggtgttggtaacactggcagcact-gcttat-ctttgtacactgggatgtattctaacgtttttatgaaatgcacaatggaagGTGGCATTGGCGCACACGATTGGACACGTGGCAGCGACTGTGAGTATGTCCAAGGTCGCAGTATCCTTCACGCACATCATCAAGAGCGCAGAACCCGCGT
| ||| || ||| || ||| | | | || || | | | ||| | | | |||| || ||||| || || ||||| ||||| |||||||| ||||| ||||||||||| || || |||||||||||||| ||||||||| | ||||| || |
----------------------------------gtaagctctcgctcatgcttggctaaacgagaaata----acaatctctattgtgttctcctgtacagGTAGCCTTGGCCCATACCATTGGTCACGTAGCAGCGACGGTGAGCATGTCCAAGGTGGCTGTCTCCTTCACGCACATTATCAAGAGCTCGGAACCGGCAT

upper sequence: PP1S70_177V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: EFJ15095 (Selaginella moellendorffii), 3'ss of exon 1
gtatttgcaatgtgggattggtgttggtaacactggcagcactgcttatctttgtacactgggatgtattctaacgtttttatgaaatgcacaatggaagGTGGCATTGGCGCACACGATTGGACACGTGGCAGCGACTGTGAGTATGTCCAAGGTCGCAGTATCCTTCACGCACATCATCAAGAGCGCAGAACCCGCGT
| | | || ||| || ||| ||| ||| ||| | ||||||| |||| || || ||||| ||||| || || || ||||| ||||||||||| || || |||||||| || |||||||||||||| || || || |
--------------------------------------------gtaagtcctccac-ctgcga---gctcttgactttccgctaaaaccacga--acagGTGGCGCTGGCTCATACCATTGGGCACGTTGCCGCCACGGTGAGCATGTCCAAGGTTGCCGTCTCCTTCACTCATATCATCAAGAGCGCGGAGCCAGCCT

upper sequence: PP1S70_177V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: EFJ37591 (Selaginella moellendorffii), 3'ss of exon 1
gtatttgcaatgtgggattggtgttggtaacactggcagcact-gcttat-ctttgtacactgggatgtattctaacgtttttatgaaatgcacaatggaagGTGGCATTGGCGCACACGATTGGACACGTGGCAGCGACTGTGAGTATGTCCAAGGTCGCAGTATCCTTCACGCACATCATCAAGAGCGCAGAACCCGCGT
| ||| || ||| || ||| | | | || || | | | ||| ||| | |||| || ||||| || || ||||| ||||| |||||||| ||||| ||||||||||| || || |||||||||||||| ||||||||| | ||||| || |
----------------------------------gtaagctctcgctcatgcttagctaaacgagaaata----acaatctctattgtgtgctcctgtacagGTAGCTTTGGCCCATACCATTGGTCACGTAGCAGCGACGGTGAGCATGTCCAAGGTGGCTGTCTCCTTCACGCACATTATCAAGAGCTCGGAACCGGCAT

upper sequence: PP1S70_177V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: EFJ37594 (Selaginella moellendorffii), 3'ss of exon 1
gtatttgcaatgtgggattggtgttggtaacactggcagcactgcttatctttgtacactgggatgtattctaacgtttttatgaaatgcacaatggaagGTGGCATTGGCGCACACGATTGGACACGTGGCAGCGACTGTGAGTATGTCCAAGGTCGCAGTATCCTTCACGCACATCATCAAGAGCGCAGAACCCGCGT
| | | || ||| || ||| ||| ||| ||| | |||| || |||| || || ||||| ||||| || || || ||||| ||||||||||| || || |||||||| ||||||||||||||||| || || || |
--------------------------------------------gtaagtcctccac-ctgcga---gctcttgactttccgctaaaaccacga--acagGTTGCGCTGGCTCATACCATTGGTCACGTTGCCGCCACGGTGAGCATGTCCAAGGTTGCCGTCTCCTTCACTCACATCATCAAGAGCGCGGAGCCAGCCT

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|208355127|gb|DC926750.1|DC926750
EST:     TCGTGCCGGCACCAGACGTAGACGCGGAGTTCTGGAAGGGACTTTTTCCG                         GTGGCATTGGCGCACACGATTGGACACGTGGCAGCGACTGTGAGTATGTCC
genomic: TCGTGCCGGCACCAGACGTAGACGCGGAGTTCTGGAAGGGACTTTTTCCGgtacgccact ... acaatggaagGTGGCATTGGCGCACACGATTGGACACGTGGCAGCGACTGTGAGTATGTCC
EST: gi|67726624|gb|BJ976883.1|BJ976883
EST:     TCGTGCCGGCACCAGACGTAGACGCNGAGTTCTGGAAGGGACTTTTTCCG                         GTGGCATTGGCGCACACGATTNGGACACGTGGCAGCGACTGTGAGTATGTC
genomic: TCGTGCCGGCACCAGACGTAGACGCGGAGTTCTGGAAGGGACTTTTTCCGgtacgccact ... acaatggaagGTGGCATTGGCGCACACGATT-GGACACGTGGCAGCGACTGTGAGTATGTC
EST: gi|162196937|gb|FC375188.1|FC375188
EST:     TCGTGCCGGCACCAGACGTAGACGCGGAGTTCTGGAAGGGACTTTTTCCG                         GTGGCATTGGCGCACACGATTGGACACGTGGCAGCGACTGTGAGTATGTCC
genomic: TCGTGCCGGCACCAGACGTAGACGCGGAGTTCTGGAAGGGACTTTTTCCGgtacgccact ... acaatggaagGTGGCATTGGCGCACACGATTGGACACGTGGCAGCGACTGTGAGTATGTCC

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: 27 (upstream exon), 35 (downstream exon)
Score: 15

GTCCCTTGCCGCGGGTTCAGCGATCATGCTGATTTCATGGGCCCTGCGGATCGTGCCGGCACCAGACGTAGACGCGGAGTTCTGGAAGGGACTTTTTCCGgtacgccact ... acaatggaagGTGGCATTGGCGCACACGATTGGACACGTGGCAGCGACTGTGAGTATGTCCAAGGTCGCAGTATCCTTCACGCACATCATCAAGAGCGCAGAACCCGCGT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttatctttgtacactgggatgtattctaacgtttttatgaaatgcacaatggaagGTGGCATTGGCGCACACGATTGGACACGTGGCAGCGACTGTGAGTATGTCCAAGGTCGCAGTATCCTTCACGCACATCATCAAGAGCGCAGAACCCGCGT
                       ttctaac  putative branch site (score: 15)
 tttttatgaaat  TA-rich tract