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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GACTTCCGACACGAGAGTGAAAGCTATTCTGGTGAACATTTTTGGTGGGATCATGAAGTGTGATGTTATTGCTGCTGGAATTGTGGCTGCTGCTAAACAGgtatacttgtctaagtgtggcagaagaatgttttgctgagttttgttccttcaatactcgtaacattctgatatggaagtctatacataagcatgttcat...

Basic information

species Physcomitrella patens
transcript PP1S9_103V6.2
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S9_103V6.1 (Physcomitrella patens), 5'ss of exon 10
lower sequence: LOC_Os02g40830.1 (Oryza sativa), 5'ss of exon 10
GACTTCCGACACGAGAGTGAAAGCTATTCTGGTGAACATTTTTGGTGGGATCATGAAGTGTGATGTTATTGCTGCTGGAATTGTGGCTGCTGCTAAACAGgtatacttgtctaagtgtggcagaagaatgt-tttgctgagttttgttccttcaatactcgtaacattctgatatggaagtctatacataagcatgttcat--
||||||||| |||||||| |||||||| ||||||||||||||||| |||||||| |||||||| || || |||||| ||| ||| || |||||||| | | || || | || | || | ||| ||| | | ||| || | || | | || | | || | | || ||
GACTTCCGATGATAGAGTGAAGGCTATTCTAGTGAACATTTTTGGTGGTATCATGAAATGTGATGTGATAGCAAGTGGAATAGTGAATGCAGCAAAACAGgtttgtct-tcaaattttgtatgtagttttcatttaatgactaaagcagctt--attgtggttccctcttgcttcaaattaataaattacaatatacctattg

upper sequence: PP1S9_103V6.1 (Physcomitrella patens), 5'ss of exon 10
lower sequence: GRMZM2G064695_T02 (Zea mays), 5'ss of exon 10
GACTTCCGACACGAGAGTGAAAGCTATTCTGGTGAACATTTTTGGTGGGATCATGAAGTGTGATGTTATTGCTGCTGGAATTGTGGCTGCTGCTAAACAGgtatacttgtctaagtgtggcagaagaatgttttgctgagttttgttccttcaatactcgtaacattctgatatggaagtctatacataagcatgttcat----
|||||| || |||||||| || ||||| ||||||||||||||||| || ||||| |||||||| || || ||||||||| |||||| ||||||||| | || | | | || |||| | | || || | |||| | | | | | | || | || ||
GACTTCAGATGATAGAGTGAAGGCAATTCTAGTGAACATTTTTGGTGGCATTATGAAATGTGATGTGATAGCAAGTGGAATTGTTAATGCTGCCAAACAGgtacattt-ttagcctttcttagctttatgtataacataggttc---ctgacaatgttggcataccccccacccccctccccccccaacaacaacaacagaatc

upper sequence: PP1S9_103V6.1 (Physcomitrella patens), 5'ss of exon 10
lower sequence: GLYMA10G04480.1 (Glycine max), 5'ss of exon 10
GACTTCCGACACGAGAGTGAAAGCTATTCTGGTGAACATTTTTGGTGGGATCATGAAGTGTGATGTTATTGCTGCTGGAATTGTGGCTGCTGCTAAACAGgtatacttgtctaagtgtggcagaagaatgttttgctgagttttgttccttcaatactcgt--aacattctgatatggaagtctatacataagcatgttcat
|||| | || | |||||| || ||| |||| |||||||||||||| || ||||||||||||||||| || |||||| ||| |||||| ||| |||| || | | ||| || ||| | | |||||| | || | || |||| | || ||| | | | |
GACTGCTGATGACAAAGTGAAGGCAATTTTGGTTAACATTTTTGGTGGTATAATGAAGTGTGATGTTATAGCAAGTGGAATAGTGAATGCTGCAAAAGAGgt-tagtcaagaacatgtaaattctttatatttgatcccatgtaagat-ttcaatttttgtttacgatgttgatgtaattgttgatattacaatttctgaaa

upper sequence: PP1S9_103V6.1 (Physcomitrella patens), 5'ss of exon 10
lower sequence: GLYMA13G18730.1 (Glycine max), 5'ss of exon 10
GACTTCCGACACGAGAGTGAAAGCTATTCTGGTGAACATTTTTGGTGGGATCATGAAGTGTGATGTTATTGCTGCTGGAATTGTGGCTGCTGCTAAACAGgtatacttgtctaagtgtggcaga-agaatgttttgctgagttttgttccttcaatactcgtaacattctgatatggaagtctatacataagcatgttcat---
|||| | || | |||||| || ||| |||| ||||||||||| || || ||||||||||||||||| || |||||| ||| |||||| ||| |||| ||| ||| | | || | | | | | ||| | | | | | | | | | | | | | |||
GACTGCTGATGACAAAGTGAAGGCAATTTTGGTTAACATTTTTGGGGGTATAATGAAGTGTGATGTTATAGCAAGTGGAATAGTGAATGCTGCAAAAGAGgttagtttgcctattcccccctcccacaaaaaataaataaatgaaaaaacagaaatctt----atgtctttacaaccagttttcttcctttgtccaaccatata

upper sequence: PP1S9_103V6.1 (Physcomitrella patens), 5'ss of exon 10
lower sequence: AT2G20420.1 (Arabidopsis thaliana), 5'ss of exon 10
GACTTCCGACACGAGAGTGAAAGCTATTCTGGTGAACATTTTTGGTGGGATCATGAAGTGTGATGTTATTGCTGCTGGAATTGTGGCTGCTGCTAAACAGgtatacttgtc-taagtgtggcagaagaatgttttgctgagttttgttccttcaatactcgtaacattctgatatggaagtctatacataagcatgttcat
||| || ||| | ||||||||| || |||||||||| ||||||||||| ||||| |||||||| |||||| |||||| ||| ||||| ||| |||| | || || | | ||| ||| | | || | | | || | || | ||||| | |
GACATCGGACGATAAAGTGAAAGCAATCTTGGTGAACATATTTGGTGGGATAATGAAATGTGATGTGATTGCTAGTGGAATCGTGAACGCTGCAAAAGAGgtgagtgagaaacaaccttgttaccataatatttcatatattcatgattgaaaataaatccgagtgttt--gtgtggaatggcgaggacag----------

upper sequence: PP1S9_103V6.1 (Physcomitrella patens), 5'ss of exon 10
lower sequence: EFJ19055 (Selaginella moellendorffii), 5'ss of exon 10
GACTTCCGACACGAGAGTGAAAGCTATTCTGGTGAACATTTTTGGTGGGATCATGAAGTGTGATGTTATTGCTGCTGGAATTGTGGCTGCTGCTAAACAGgtatacttgtctaagtgtggcagaagaatgttttgctgagttttgttccttcaatactcgtaacattctgatatggaagtctatacataagcatgttcat
|| || |||| || ||||| || |||||||||||||| || ||||| |||||||||||| | || || || ||| ||||| ||||| || ||| | ||| | || || || ||| | | || ||| |||| | || ||| | |
CACGTCTGACAAGAAGGTGAAGGCCATTCTGGTGAACATCTTCGGTGGAATCATGAAGTGTAACGTGATCGCGAGTGGTATTGTCAACGCTGCCAAGACGgtgcgtctttctcttcctcttggacatgtg-------gatgcatgtggatgaagtaaaaagaactctctgctctg---gtccttgtag------------

upper sequence: PP1S9_103V6.1 (Physcomitrella patens), 5'ss of exon 10
lower sequence: EFJ13492 (Selaginella moellendorffii), 5'ss of exon 10
GACTTCCGACACGAGAGTGAAAGCTATTCTGGTGAACATTTTTGGTGGGATCATGAAGTGTGATGTTATTGCTGCTGGAATTGTGGCTGCTGCTAAACAGgtatacttgtctaagtgtggcagaagaatgttttgctgagttttgttccttcaatactcgtaacattctgatatggaagtctatacataagcatgttcat
|| || |||| || ||||| || |||||||||||||| || ||||| |||||||||||| | || || || ||| ||||| ||||| || ||| | ||| | | || || ||| | | || ||| |||| | || ||| | |
CACGTCTGACAAGAAGGTGAAGGCCATTCTGGTGAACATCTTCGGTGGAATCATGAAGTGTAACGTGATCGCGAGTGGTATTGTCAACGCTGCCAAGACGgtgcgtctttctcttcctcttgt-------tcatgtggatgcatgtggatgaagtaaaaagaactctctgctctg---gtccttgtag------------

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|18338652|gb|BJ170676.1|BJ170676
EST:     TCATGAAGTGTGATGTTATTGCTGCTGGAATTGTGGCTGCTGCTAAACAG                         GTGAATTTGAAAGTTCCACTAGTAGTACGTTTGGAGGGTACGAATGTGGAT
genomic: TCATGAAGTGTGATGTTATTGCTGCTGGAATTGTGGCTGCTGCTAAACAGgtatacttgt ... gaatctgcagGTGAATTTGAAAGTTCCACTAGTAGTACGTTTGGAGGGTACGAATGTGGAT
EST: gi|208365272|gb|DC946817.1|DC946817
EST:     TCATGAAGTGTGATGTTATTGCTGCTGGAATTGTGGCTGCTGCTAAACAG                         GTGAATTTGAAAGTTCCACTAGTAGTACGTTTGGAGGGTACGAATGTGGAT
genomic: TCATGAAGTGTGATGTTATTGCTGCTGGAATTGTGGCTGCTGCTAAACAGgtatacttgt ... gaatctgcagGTGAATTTGAAAGTTCCACTAGTAGTACGTTTGGAGGGTACGAATGTGGAT
EST: gi|208352527|gb|DC918236.1|DC918236
EST:     TCATGAAGTGTGATGTTATTGCTGCTGGAATTGTGGCTGCTGCTAAACAG                         GTGAATTTGAAAGTTCCACTAGTAGTACGTTTGGAGGGTACGAATGTGGAT
genomic: TCATGAAGTGTGATGTTATTGCTGCTGGAATTGTGGCTGCTGCTAAACAGgtatacttgt ... gaatctgcagGTGAATTTGAAAGTTCCACTAGTAGTACGTTTGGAGGGTACGAATGTGGAT
EST: gi|67724647|gb|BJ974906.1|BJ974906
EST:     TCATGAAGTGTGATGTTATTGCTGCTGGAATTGTGGCTGCTGCTAAACAG                         GTGAATTTGAAAGTTCCACTAGTAGTACGTTTGGAGGGTACGAATGTGGAT
genomic: TCATGAAGTGTGATGTTATTGCTGCTGGAATTGTGGCTGCTGCTAAACAGgtatacttgt ... gaatctgcagGTGAATTTGAAAGTTCCACTAGTAGTACGTTTGGAGGGTACGAATGTGGAT
EST: gi|18334936|gb|BJ166954.1|BJ166954
EST:     TCATGAAGTGTGATGTTATTGCTGCTGGAATTGTGGCTGCTGCTAAACAG                         GTGAATTTGAAAGTTCCACTAGTAGTACGTTTGGAGGGTACGAATGTGGAT
genomic: TCATGAAGTGTGATGTTATTGCTGCTGGAATTGTGGCTGCTGCTAAACAGgtatacttgt ... gaatctgcagGTGAATTTGAAAGTTCCACTAGTAGTACGTTTGGAGGGTACGAATGTGGAT
EST: gi|67691893|gb|BJ952126.1|BJ952126
EST:     TCATGAAGTGTGATGTTATTGCTGCTGGAATTGTGGCTGCTGCTAAACAG                         GTGAATTTGAAAGTTCCACTAGTAGTACGTTTGGAGGGTACGAATGTGGAT
genomic: TCATGAAGTGTGATGTTATTGCTGCTGGAATTGTGGCTGCTGCTAAACAGgtatacttgt ... gaatctgcagGTGAATTTGAAAGTTCCACTAGTAGTACGTTTGGAGGGTACGAATGTGGAT
EST: gi|67727713|gb|BJ977972.1|BJ977972
EST:     TCATGAAGTGTGATGTTATTGCTGCTGGAATTGTGGCTGCTGCTAAACAG                         GTGAATTTGAAAGTTCCACTAGTAGTACGTTTGGAGGGTACGAATGTGGAT
genomic: TCATGAAGTGTGATGTTATTGCTGCTGGAATTGTGGCTGCTGCTAAACAGgtatacttgt ... gaatctgcagGTGAATTTGAAAGTTCCACTAGTAGTACGTTTGGAGGGTACGAATGTGGAT
EST: gi|208397427|gb|DC916353.1|DC916353
EST:     TCATGAAGTGTGATGTTATTGCTGCTGGAATTGTGGCTGCTGCTAAACAG                         GTGAATTTGAAAGTTCCACTAGTAGTACGTTTGGAGGGTACGAATGTGGAT
genomic: TCATGAAGTGTGATGTTATTGCTGCTGGAATTGTGGCTGCTGCTAAACAGgtatacttgt ... gaatctgcagGTGAATTTGAAAGTTCCACTAGTAGTACGTTTGGAGGGTACGAATGTGGAT
EST: gi|37829801|gb|BJ587813.1|BJ587813
EST:     TCATGAAGTGTGATGTTATTGCTGCTGGAATTGTGGCTGCTGCTAAACAG                         GTGAATTTGAAAGTTCCACTAGTAGTACGTTTGGAGGGTACGAATGTGGAT
genomic: TCATGAAGTGTGATGTTATTGCTGCTGGAATTGTGGCTGCTGCTAAACAGgtatacttgt ... gaatctgcagGTGAATTTGAAAGTTCCACTAGTAGTACGTTTGGAGGGTACGAATGTGGAT
EST: gi|67695119|gb|BJ955352.1|BJ955352
EST:     TCATGAAGTGTGATGTTATTGCTGCTGGAATTGTGGCTGCTGCTAAACAG                         GTGAATTTGAAAGTTCCACTAGTAGTACGTTTGGAGGGTACGAATGTGGAT
genomic: TCATGAAGTGTGATGTTATTGCTGCTGGAATTGTGGCTGCTGCTAAACAGgtatacttgt ... gaatctgcagGTGAATTTGAAAGTTCCACTAGTAGTACGTTTGGAGGGTACGAATGTGGAT

Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GACTTCCGACACGAGAGTGAAAGCTATTCTGGTGAACATTTTTGGTGGGATCATGAAGTGTGATGTTATTGCTGCTGGAATTGTGGCTGCTGCTAAACAGgtatacttgtctaagtgtggcagaagaatgttttgctgagttttgttccttcaatactcgtaacattctgatatggaagtctatacataagcatgttcat

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT