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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagtaatcccgtctctacgtttttctgcatttagtatttttctttttttcttcttttttttttctgcttgatatgatttcctattgctttatttattttctgtgaattgccattatgcatcatgtgatgcaatttttgttacctgatgtattctttgaccggattatggttatacgtctgtagAGCGAATGCCCAGCAGCCCAAGCTCTTCGTTGGTATGATTTTGATCCTCATTTTTGCCGAGGCGCTTGCTTTGTATGGACTTATCGTCGGCATCATCTTG

Basic information

species Physcomitrella patens
transcript PP1S1_66V6.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S1_66V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA11G07980.1 (Glycine max), 3'ss of exon 1
gtagtaatcccgtctctacgtttttctgcatttagtatttttctttttttcttcttttttttttctgcttgatatgatttcctattgctttatttattttctgtgaattgccattatgcatcatgtgatgcaatttttgttacctgatgtattctttgaccggattatggttatacgtctgtagAGCGAATGCCCAGCAGCCCAAGCTCTTCGTTGGTATGATTTTGATCCTCATTTTTGCCGAGGCGCTTGCTTTGTATGGACTTATCGTCGGCATCATCTTG
| | || | || | | || | | | | || || ||| || | | | | ||||| |||| || ||| | || ||| || | |||||||| |||||||| ||||| ||||| || ||||| |||||| | || ||||| ||||| |||||| | || ||||||||||| || || ||||||||| |
--------------------------------------------------------------------acgctttgttaaccaagagattgttcaactcttactggatg---attgtgtctaactt----ctattttagttat----tgaatttgacatgctgaaaatgttt-----tttgtagAGCAAATGCCCAACAGCCAAAGCTTTTTGTTGGGATGATTCTCATTCTCATCTTTGCTGAGGCGTTGGCATTGTATGGACTCATTGTTGGCATCATCCTC

upper sequence: PP1S1_66V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA01G37320.1 (Glycine max), 3'ss of exon 1
gtagtaatcccgtctctacgtttttctgcatttagtatttttctttttttcttcttttttttttctgcttgatatgatttcctattgctttatttattttctgtgaattgccattatgcatcatgtgatgcaatttttgttacctgatgtattctttgaccggattatggttatacgtctgtagAGCGAATGCCCAGCAGCCCAAGCTCTTCGTTGGTATGATTTTGATCCTCATTTTTGCCGAGGCGCTTGCTTTGTATGGACTTATCGTCGGCATCATCTTG
||| | || ||| | || | | | | | ||| | | | ||||| |||| || | || | | | | | | | | |||||||| |||||||| ||||| ||||| || ||||| |||||| | || ||||| ||||| |||||| | || ||||||||||| || || ||||||||| |
-----------------------------------------------------------------------------tttttaactgagagattgctcaactcttactggataa-atgtgtttaat--ctcgattttagttattgaatatgacct---gctgaaattggactgttt-tttgtagAGCAAATGCCCAACAGCCAAAGCTTTTTGTTGGGATGATTCTCATTCTCATCTTTGCTGAGGCGTTGGCATTGTATGGACTCATTGTTGGCATCATCCTC

upper sequence: PP1S1_66V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA02G05630.1 (Glycine max), 3'ss of exon 2
gtagtaatcccgtctctacgtttttctgcatttagtatttttctttttttcttcttttttttttctgcttgatatgatttcctattgctttatt--tattttctgtgaattgccattatgcatcatgtgatgcaatttttgttacctgatgtattctttgaccggattatggttatacgtctgtagAGCGAATGCCCAGCAGCCCAAGCTCTTCGTTGGTATGATTTTGATCCTCATTTTTGCCGAGGCGCTTGCTTTGTATGGACTTATCGTCGGCATCATCTTG
| || | ||| || | | | || | |||||| | | || | | | |||||| | ||| ||| ||| | ||| | | | || ||||| ||||| |||||||| || || || ||||| |||||| | |||||||||||||| ||||| | || || ||||| || ||||| ||||||||| |
----------------------------------------------------------------------------acgtcatgttggttcactcctgttgattatgaatttactaatggtattttaagct-taattttaacaaattga-atatgacttgcc--------ggtaactcttttgcagAGCAAATGCTCAGCAGCCTAAACTTTTTGTTGGAATGATTCTCATCCTCATTTTTGCTGAGGCATTGGCATTATATGGTCTCATCGTTGGCATCATCCTC

upper sequence: PP1S1_66V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA14G23990.1 (Glycine max), 3'ss of exon 2
gtagtaatcccgtctctacgtttttctgcatttagtatttttctttttttcttcttttttttttctgcttgatatgatttcctattgctttatttatttt--ctgtgaattgccattatgcatc-atgtgatgcaatttttgttacctgatgtattctttgac-cggattatggttatacgtctgt----agAGCGAATGCCCAGCAGCCCAAGCTCTTCGTTGGTATGATTTTGATCCTCATTTTTGCCGAGGCGCTTGCTTTGTATGGACTTATCGTCGGCATCATCTTG
|||||| | | | | | ||| | || ||| |||| ||| || || ||| |||| || ||| ||| | || || ||| || | | | | || || |||||||||||||| ||||| || |||||||||||| | ||| | ||||| || || || |||||| ||||||| || || || || |||||| |
-------------------------------------------------------------------------------------tgcttttctcagctaaattatagtttgtt-tcatagatctatgtaatg---ttattattaactga---atacttggacgctgagtaaggtaattccttttttgtcagGGCTAATGCCCAGCAGCCGAAGCTGTTTGTTGGTATGATTCTTATCTTGATTTTCGCTGAAGCTCTTGCTCTGTATGGCCTCATTGTGGGTATCATCCTC

upper sequence: PP1S1_66V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA16G24220.1 (Glycine max), 3'ss of exon 2
gtagtaatcccgtctctacgtttttctgcatttagtatttttctttttttcttcttttttttttctgcttgatatgatttcctattgctttatttattttctgtgaattgccattatgcatcatgtgatgcaatttttgttacctgatgtattctttgaccggattatggttatacgtctgtagAGCGAATGCCCAGCAGCCCAAGCTCTTCGTTGGTATGATTTTGATCCTCATTTTTGCCGAGGCGCTTGCTTTGTATGGACTTATCGTCGGCATCATCTTG
| |||| || | |||| ||| | | | | || || || || || ||| | ||| | | || ||| | | | || ||||| ||||| |||||||| ||||| || ||||| ||||| | |||||||||||||| |||||| | || || || || || || || ||||||||| |
---------------------------------------------------------------------------------atgcatttttagttcactcctgttgattatgaatttactaatagtaatttaagcttcatt--ttgacgaattgaat-atgacatgccggtaactcttttgcagAGCAAATGCTCAGCAGCCAAAGCTTTTTGTTGGAATGATACTCATCCTCATTTTTGCTGAGGCGTTGGCATTATACGGTCTCATTGTTGGCATCATCCTC

upper sequence: PP1S1_66V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: AT4G38920.1 (Arabidopsis thaliana), 3'ss of exon 2
gtagtaatcccgtctctacgtttttctgcatttagtatttttctttttttcttcttttttttttctgcttgatatgatttcctattgctttatttattttctgtgaattgccattatgcatcatgtgatgcaatttttgttacctgatgtatt-ctttgac-cggattatggttatacgtctgtagAGCGAATGCCCAGCAGCCCAAGCTCTTCGTTGGTATGATTTTGATCCTCATTTTTGCCGAGGCGCTTGCTTTGTATGGACTTATCGTCGGCATCATCTTG
| || | | | | ||| | ||| | || | || || | | | | | |||| | ||| ||||| || | | || | | || || ||||| || ||||| ||||| ||||||||||||||| | ||||||||||| || || || |||||| | || || || |||||||| ||||| |||
-------------------------------------------------------------------------------ttctctaggatgaaatataatggaagaaatatcaattca-attgtg------agtgtctatcccctgttatatcattttgatacgcaaatttgtggtttgatgacagGGCCAATGCTCAACAGCCAAAGCTTTTCGTTGGTATGATTCTTATCCTCATTTTCGCTGAAGCTCTTGCTCTATACGGTCTCATCGTCGGGATCATTTTG

upper sequence: PP1S1_66V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: Vv18s0001g02650.t01 (Vitis vinifera), 3'ss of exon 2
gtagtaatcccgtctctacgtttttctgcatttagtatttttctttttttcttcttttttttttctgcttgatatgatttcctattgctttatttattttctgtgaattgccattatgcatcatgtgatgcaatttttgttacctgatgtattctttgaccggattatggttatacgtctgtagAGCGAATGCCCAGCAGCCCAAGCTCTTCGTTGGTATGATTTTGATCCTCATTTTTGCCGAGGCGCTTGCTTTGTATGGACTTATCGTCGGCATCATCTTG
| | | | | | |||| || | ||| | || | |||| | || | | ||| || || | |||| | || || ||||| |||||||| ||||| || || ||||||||| | |||||||| ||||| || ||||||||| | ||||| || || ||||||||||| |
-------------------------------------------------------------------------------acttctctcccctcccccctcatttgaaatgaaacatcaaatcctccattgatggtgttgt-atatgtttaccttttttcccctgttgggattat----tttcagGGCTAATGCACAGCAGCCAAAGCTGTTTGTGGGTATGATTCTCATCCTCATCTTTGCTGAAGCGCTTGCTCTTTATGGCCTGATTGTCGGCATCATTCTT

upper sequence: PP1S1_66V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: Vv18s0001g13630.t01 (Vitis vinifera), 3'ss of exon 2
gtagtaatcccgtctctacgtttttctgcatttagtatttttctttttttcttcttttttttttctgcttgatatgatttcctattgctttatttattttctgtgaattgccattatgcatc-atgtgatgcaatttttgttacctgat-gtat-tctttgaccggattatggttatacgtctgtagAGCGAATGCCCAGCAGCCCAAGCTCTTCGTTGGTATGATTTTGATCCTCATTTTTGCCGAGGCGCTTGCTTTGTATGGACTTATCGTCGGCATCATCTTG
|||| |||| | | | || |||| || | |||| || || | |||| | | | | |||| | |||| | | ||| | |||||| | || ||||| ||||| |||||||| ||||| |||||||| ||||| | || ||||| ||||| || || ||||| ||||||||||||| || ||||||||| |
-----------------------------------------------------------------------------tttcatattaggatttctgcctt--------tgcctttttacatctattcaattctatttatttcctttaagagtatgtttttgtctgaattgttgttata--tttgcagAGCCAATGCTCAGCAGCCAAAGCTTTTCGTTGGAATGATCCTCATTCTCATCTTTGCTGAAGCTCTTGCCCTGTATGGACTTATTGTTGGCATCATCCTA

upper sequence: PP1S1_66V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: EFJ37480 (Selaginella moellendorffii), 3'ss of exon 2
gtagtaatcccgtctctacgtttttctgcatttagtatttttctttttttcttcttttttttttctgcttgatatgatttcctattgctttatttattttctgtgaattgccattatgcatcatgtgatgcaatttttgttacctgatgtattctttgaccggattatggttatacgtct--gtagAGCGAATGCCCAGCAGCCCAAGCTCTTCGTTGGTATGATTTTGATCCTCATTTTTGCCGAGGCGCTTGCTTTGTATGGACTTATCGTCGGCATCATCTTG
|| ||| || | | | | | | || || || | | ||| | | |||| || | | | | ||| | || || || || || ||||| ||||||||||| || ||||| ||||||||||| || ||||||||||| ||| | || ||| | ||||| || ||||| |
-----------------------------------------------------------------------------------atca-tttgaagatcgcgagcttggtcctcacaagatttccctgctggaaactccact--ctgttttcttctctggctttctcactttccatcgttttcacagGGCCAACGCTCAACAGCCAAAGCTCTTCGTGGGCATGATCTTGATCCTCATCTTCGCCGAGGCGCTGGCTCTCTACGGATTGATCGTGGGGATCATTCTT

upper sequence: PP1S1_66V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: EFJ33972 (Selaginella moellendorffii), 3'ss of exon 2
gtagtaatcccgtctctacgtttttctgcatttagtatttttctttttttcttcttttttttttctgcttgatatgatttcctattgctttatttattttctgtgaattgccattatgcatcatgtgatgcaatttttgttacctgatgtattctttgaccggattatggttatacgtct--gtagAGCGAATGCCCAGCAGCCCAAGCTCTTCGTTGGTATGATTTTGATCCTCATTTTTGCCGAGGCGCTTGCTTTGTATGGACTTATCGTCGGCATCATCTTG
|| ||| || | | | | | | || || || | | ||| | | |||| || | | | | ||| | || || || || || ||||| ||||||||||| || ||||| ||||||||||| || ||||||||||| ||| | || ||| | ||||| || ||||| |
-----------------------------------------------------------------------------------atca-tttgaagatcgggagcttggtcctcacaagatttccctgctggaaactccact--ctgttttcttctctggctttctcactttccatcgttttcacagGGCCAACGCTCAACAGCCAAAGCTCTTCGTGGGCATGATCTTGATCCTCATCTTCGCCGAGGCGCTGGCTCTCTACGGATTGATCGTGGGGATCATTCTT

upper sequence: PP1S1_66V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: EFJ26016 (Selaginella moellendorffii), 3'ss of exon 2
gtagtaatcccgtctctacgtttttctgcatttagtatttttctttttttcttcttttttttttctgcttgatatgatttcctattgctttatttattttctgtgaattgccattatgcatcatgtgatgcaatttttgttacctgatgtattctttgaccggattatggttatacgtctgtagAGCGAATGCCCAGCAGCCCAAGCTCTTCGTTGGTATGATTTTGATCCTCATTTTTGCCGAGGCGCTTGCTTTGTATGGACTTATCGTCGGCATCATCTTG
| | | | || | | || ||| || ||| | | | |||| || || | || | || || |||||||| ||||| |||||||| || ||||| ||||| |||| ||||| ||||||||||| | ||| | || || || || || || |||||| ||
-------------------------------------------------------------------------------------------------------------gtaagttcgatcgatcaaaaaccatcttt-ttcttcgatatctccattgattggtttgtttttc----tttgcagGGCGAATGCGCAGCAACCCAAGCTTTTTGTTGGAATGATCCTGATTCTCATCTTTGCCGAGGCTTTGGCTCTATACGGTCTCATTGTGGGAATCATCCTG

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|67507548|gb|BJ940430.1|BJ940430
EST:     GGCCTGTCCGCAGGCATGGCGATTGGCATCGTTGGAGATGCTGGTGTCAG                         AGCGAATGCCCAGCAGCCCAAGCTCTTCGTTGGTATGATTTTGATCCTCAT
genomic: GGCCTGTCCGCAGGCATGGCGATTGGCATCGTTGGAGATGCTGGTGTCAGgtagtaatcc ... acgtctgtagAGCGAATGCCCAGCAGCCCAAGCTCTTCGTTGGTATGATTTTGATCCTCAT
EST: gi|37830648|gb|BJ588660.1|BJ588660
EST:     GGCCTGTCCGCAGGCATGGCGATTGGCATCGTTGGAGATGCTGGTGTCAG                         AGCGAATGCCCAGCAGCCCAAGCTCTTCGTTGGTATGATTTTGATCCTCAT
genomic: GGCCTGTCCGCAGGCATGGCGATTGGCATCGTTGGAGATGCTGGTGTCAGgtagtaatcc ... acgtctgtagAGCGAATGCCCAGCAGCCCAAGCTCTTCGTTGGTATGATTTTGATCCTCAT
EST: gi|18336166|gb|BJ168188.1|BJ168188
EST:     GGCCTGTCCGCAGGCATGGCGATTGGCATCGTTGGAGATGCTGGTGTCAG                         AGCGAATGCCCAGCAGCCCAAGCTCTTCGTTGGTATGATTTTGATCCTCAT
genomic: GGCCTGTCCGCAGGCATGGCGATTGGCATCGTTGGAGATGCTGGTGTCAGgtagtaatcc ... acgtctgtagAGCGAATGCCCAGCAGCCCAAGCTCTTCGTTGGTATGATTTTGATCCTCAT
EST: gi|162219761|gb|FC395965.1|FC395965
EST:     GGCCTGTCCGCAGGCATGGCGATTGGCATCGTTGGAGATGCTGGTGTCAG                         AGCGAATGCCCAGCAGCCCAAGCTCTTCGTTGGTATGATTTTGATCCTCAT
genomic: GGCCTGTCCGCAGGCATGGCGATTGGCATCGTTGGAGATGCTGGTGTCAGgtagtaatcc ... acgtctgtagAGCGAATGCCCAGCAGCCCAAGCTCTTCGTTGGTATGATTTTGATCCTCAT
EST: gi|208344620|gb|DC909179.1|DC909179
EST:     GGCCTGTCCGCAGGCATGGCGATTGGCATCGTTGGAGATGCTGGTGTCAG                         AGCGAATGCCCAGCAGCCCAAGCTCTTCGTTGGTATGATTTTGATCCTCAT
genomic: GGCCTGTCCGCAGGCATGGCGATTGGCATCGTTGGAGATGCTGGTGTCAGgtagtaatcc ... acgtctgtagAGCGAATGCCCAGCAGCCCAAGCTCTTCGTTGGTATGATTTTGATCCTCAT
EST: gi|208393998|gb|DC946152.1|DC946152
EST:     GGCCTGTCCGCAGGCATGGCGATTGGCATCGTTGGAGATGCTGGTGTCAG                         AGCGAATGCCCAGCAGCCCAAGCTCTTCGTTGGTATGATTTTGATCCTCAT
genomic: GGCCTGTCCGCAGGCATGGCGATTGGCATCGTTGGAGATGCTGGTGTCAGgtagtaatcc ... acgtctgtagAGCGAATGCCCAGCAGCCCAAGCTCTTCGTTGGTATGATTTTGATCCTCAT
EST: gi|208378400|gb|DC923043.1|DC923043
EST:     GGCCTGTCCGCAGGCATGGCGATTGGCATCGTTGGAGATGCTGGTGTCAG                         AGCGAATGCCCAGCAGCCCAAGCTCTTCGTTGGTATGATTTTGATCCTCAT
genomic: GGCCTGTCCGCAGGCATGGCGATTGGCATCGTTGGAGATGCTGGTGTCAGgtagtaatcc ... acgtctgtagAGCGAATGCCCAGCAGCCCAAGCTCTTCGTTGGTATGATTTTGATCCTCAT
EST: gi|37829947|gb|BJ587959.1|BJ587959
EST:     GGCCTGTCCGCAGGCATGGCGATTGGCATCGTTGGAGATGCTGGTGTCAG                         AGCGAATGCCCAGCAGCCCAAGCTCTTCGTTGGTATGATTTTGATCCTCAT
genomic: GGCCTGTCCGCAGGCATGGCGATTGGCATCGTTGGAGATGCTGGTGTCAGgtagtaatcc ... acgtctgtagAGCGAATGCCCAGCAGCCCAAGCTCTTCGTTGGTATGATTTTGATCCTCAT
EST: gi|18327933|gb|BJ159937.1|BJ159937
EST:     GGCCTGTCCGCAGGCATGGCGATTGGCATCGTTGGAGATGCTGGTGTCAG                         AGCGAATGCCCAGCAGCCCAAGCTCTTCGTTGGTATGATTTTGATCCTCAT
genomic: GGCCTGTCCGCAGGCATGGCGATTGGCATCGTTGGAGATGCTGGTGTCAGgtagtaatcc ... acgtctgtagAGCGAATGCCCAGCAGCCCAAGCTCTTCGTTGGTATGATTTTGATCCTCAT
EST: gi|22133405|gb|BQ827717.1|BQ827717
EST:     GGCCTGTCCGCAGGCATGGCGATTGGCATCGTTGGAGATGCTGGTGTCAG                         AGCGAATGCCCAGCAGCCCAAGCTCTTCGTTGGTATGATTTTGATCCTCAT
genomic: GGCCTGTCCGCAGGCATGGCGATTGGCATCGTTGGAGATGCTGGTGTCAGgtagtaatcc ... acgtctgtagAGCGAATGCCCAGCAGCCCAAGCTCTTCGTTGGTATGATTTTGATCCTCAT
EST: gi|37845441|gb|BJ603449.1|BJ603449
EST:     GGCCTGTCCGCAGGCATGGCGATTGGCATCGTTGGAGATGCTGGTGTCAG                         AGCGAATGCCC--CAGCCCAAGCTCTTCGTTGGTATGATTTTGATCCTCAT
genomic: GGCCTGTCCGCAGGCATGGCGATTGGCATCGTTGGAGATGCTGGTGTCAGgtagtaatcc ... acgtctgtagAGCGAATGCCCAGCAGCCCAAGCTCTTCGTTGGTATGATTTTGATCCTCAT
EST: gi|100415451|gb|BY992850.1|BY992850
EST:     GGCCTGTCCGCAGGCATGGCGATTGGCATCGTTGGAGATGCTGGTGTCAG                         AGCGAATGCCCAGCAGCCCAAGCTCTTCGTTGGTATGATTTTGATCCTCAT
genomic: GGCCTGTCCGCAGGCATGGCGATTGGCATCGTTGGAGATGCTGGTGTCAGgtagtaatcc ... acgtctgtagAGCGAATGCCCAGCAGCCCAAGCTCTTCGTTGGTATGATTTTGATCCTCAT
EST: gi|162208936|gb|FC385280.1|FC385280
EST:     GGCCTGTCCGCAGGCATGGCGATTGGCATCGTTGGAGATGCTGGTGTCAG                         AGCGAATGCCCAGCAGCCCAAGCTCTTCGTTGGTATGATTTTGATCCTCAT
genomic: GGCCTGTCCGCAGGCATGGCGATTGGCATCGTTGGAGATGCTGGTGTCAGgtagtaatcc ... acgtctgtagAGCGAATGCCCAGCAGCCCAAGCTCTTCGTTGGTATGATTTTGATCCTCAT

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: 33 (upstream exon), 29 (downstream exon)
Score: 16

TGTTTGACGGCTATGCGCATCTTTCATCTGGTCTGTCATGTGGGTTAGCCGGCCTGTCCGCAGGCATGGCGATTGGCATCGTTGGAGATGCTGGTGTCAGgtagtaatcc ... acgtctgtagAGCGAATGCCCAGCAGCCCAAGCTCTTCGTTGGTATGATTTTGATCCTCATTTTTGCCGAGGCGCTTGCTTTGTATGGACTTATCGTCGGCATCATCTTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcaatttttgttacctgatgtattctttgaccggattatggttatacgtctgtagAGCGAATGCCCAGCAGCCCAAGCTCTTCGTTGGTATGATTTTGATCCTCATTTTTGCCGAGGCGCTTGCTTTGTATGGACTTATCGTCGGCATCATCTTG
                        ctttgac  putative branch site (score: 16)
 ttttgtta  TA-rich tract