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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_103V6.1
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|208362322|gb|DC954568.1|DC954568
EST:     TCATGAAGTGTGATGTTATTGCTGCTGGAATTGTGGCTGCTGCTAAACAG                         GTGAATTTGAAAGTTCCACTAGTAGTACGTTTGGAGGGTACGAATGTGGAT
genomic: TCATGAAGTGTGATGTTATTGCTGCTGGAATTGTGGCTGCTGCTAAACAGgtatacttgt ... gaatctgcagGTGAATTTGAAAGTTCCACTAGTAGTACGTTTGGAGGGTACGAATGTGGAT
EST: gi|208364988|gb|DC947130.1|DC947130
EST:     TCATGAAGTGTGATGTTATTGCTGCTGGAATTGTGGCTGCTGCTAAACAG                         GTGAATTTGAAAGTTCCACTAGTAGTACGTTTGGAGGGTACGAATGTGGAT
genomic: TCATGAAGTGTGATGTTATTGCTGCTGGAATTGTGGCTGCTGCTAAACAGgtatacttgt ... gaatctgcagGTGAATTTGAAAGTTCCACTAGTAGTACGTTTGGAGGGTACGAATGTGGAT
EST: gi|208371603|gb|DC952245.1|DC952245
EST:     TCATGAAGTGTGATGTTATTGCTGCTGGAATTGTGGCTGCTGCTAAACAG                         GTGAATTTGAAAGTTCCACTAGTAGTACGTTTGGAGGGTACGAATGTGGAT
genomic: TCATGAAGTGTGATGTTATTGCTGCTGGAATTGTGGCTGCTGCTAAACAGgtatacttgt ... gaatctgcagGTGAATTTGAAAGTTCCACTAGTAGTACGTTTGGAGGGTACGAATGTGGAT
EST: gi|208364115|gb|DC950407.1|DC950407
EST:     TCATGAAGTGTGATGTTATTGCTGCTGGAATTGTGGCTGCTGCTAAACAG                         GTGAATTTGAAAGTTCCACTAGTAGTACGTTTGGAGGGTACGAATGTGGAT
genomic: TCATGAAGTGTGATGTTATTGCTGCTGGAATTGTGGCTGCTGCTAAACAGgtatacttgt ... gaatctgcagGTGAATTTGAAAGTTCCACTAGTAGTACGTTTGGAGGGTACGAATGTGGAT
EST: gi|208366030|gb|DC951125.1|DC951125
EST:     TCATGAAGTGTGATGTTATTGCTGCTGGAATTGTGGCTGCTGCTAAACAG                         GTGAATTTGAAAGTTCCACTAGTAGTACGTTTGGAGGGTACGAATGTGGAT
genomic: TCATGAAGTGTGATGTTATTGCTGCTGGAATTGTGGCTGCTGCTAAACAGgtatacttgt ... gaatctgcagGTGAATTTGAAAGTTCCACTAGTAGTACGTTTGGAGGGTACGAATGTGGAT
EST: gi|37839956|gb|BJ597964.1|BJ597964
EST:     TCATGAAGTGTGATGTTATTGCTGCTGGAATTGTGGCTGCTGCTAAACAG                         GTGAATTTGAAAGTTCCACTAGTAGTACGTTTGGAGGGTACGAATGTGGAT
genomic: TCATGAAGTGTGATGTTATTGCTGCTGGAATTGTGGCTGCTGCTAAACAGgtatacttgt ... gaatctgcagGTGAATTTGAAAGTTCCACTAGTAGTACGTTTGGAGGGTACGAATGTGGAT
EST: gi|37840531|gb|BJ598539.1|BJ598539
EST:     TCATGAAGTGTGATGTTATTGCTGCTGGAATTGTGGCTGCTGCTGAACAG                         GTGAATTTGAAAGTTCCACTAGTAGTACGTTTGGAGGGTACGAATGTGGAT
genomic: TCATGAAGTGTGATGTTATTGCTGCTGGAATTGTGGCTGCTGCTAAACAGgtatacttgt ... gaatctgcagGTGAATTTGAAAGTTCCACTAGTAGTACGTTTGGAGGGTACGAATGTGGAT

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), 30 (downstream exon)
Score: 8

GACTTCCGACACGAGAGTGAAAGCTATTCTGGTGAACATTTTTGGTGGGATCATGAAGTGTGATGTTATTGCTGCTGGAATTGTGGCTGCTGCTAAACAGgtatacttgt ... gaatctgcagGTGAATTTGAAAGTTCCACTAGTAGTACGTTTGGAGGGTACGAATGTGGATGTTGGGAAGACCATCCTGAAG




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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