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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCCCTTCTCCAAGAAGGATTGGTATGACATCAAGGCACCCAATACTTTCACTCAAAAGAACTTGGGAAAGACTCTCGTGACCAGGACCGCGGGAACGAAGgtggggggttatgcttctctctctcgctctgtttgtgtgtatctctcgcctccgtcccgtggggatttgattgaagttggacatttatgagagagatggatacgcttttttcttttgtgaagttgtacacggaactgacgcgggtttggatgcgacag

Basic information

species Physcomitrella patens
transcript PP1S46_147V6.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S46_147V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: LOC_Os02g18550.1 (Oryza sativa), 5'ss of exon 2
TCCCTTCTCCAAGAAGGATTGGTATGACATCAAGGCACCCAATACTTTCACTCAAAAGAACTTGGGAAAGACTCTCGTGACCAGGACCGCGGGAACGAAGgtggggggttatgcttctctctctcgctctgtttgtgtgtatctctcgcctccgtcccgtggggatttgattgaagttggacatttatgagagagatggatacgcttttttcttttgtgaagttgtacacggaactgacgcgggtttggatgcgacag
|||||| ||||||||||||||||| ||||||||||| || |     ||| |       ||| | || ||||| |||||  ||||||||  ||| || |||||  |    |  | | | |  || ||| | ||     |  |||      ||  |  || ||    ||| |||     |     | | ||||  | |||       |                                                    
TCCCTTTTCCAAGAAGGATTGGTACGACATCAAGGCGCCGACCGTGTTCTCCGTCCGCAACATCGGCAAGACCCTCGTCTCCAGGACCCAGGGGACCAAGgttcgttcgttcgttccccattcgcgccc-gtcaacctcaatccgcgatct--gatccatgc---tttcattttgtatcactgtctgtgagt-acatgtgcggaatc---------------------------------------------------

upper sequence: PP1S46_147V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: GRMZM2G030915_T08 (Zea mays), 5'ss of exon 2
TCCCTTCTCCAAGAAGGATTGGTATGACATCAAGGCACCCAATACTTTCACTCAAAAGAACTTGGGAAAGACTCTCGTGACCAGGACCGCGGGAACGAAGgtggggggttatgcttctctctctcgctctgtttgtgtgtatctctcgcctccgtcccgtggggatttgattgaagttggacatttatgagagagatggatacgcttttttcttttgtgaagttgtacacggaactgacgcgggtttggatgcgacag
 || ||||| |||||||||||||||||||||||||||||       |||| |      ||| | || |||||||||||  |||||||   ||| || | |||       | |  |||| |   |  |  ||||| |  |||   | |  || | | | |||     |||  |||| |||  ||| ||||      ||| ||| |       |  | || |                                      
CCCTTTCTCTAAGAAGGATTGGTATGACATCAAGGCACCGTCGGTGTTCAGTGTGCGCAACATCGGGAAGACTCTCGTATCCAGGACACAGGGTACCAGGgta------tgtttttctttgattatcgatgtttttccgtactgccc--ctacattctgtg-----ttg--tgaacttgcgcatatatgc-----atgtatatgtagaccgcgctagtca--------------------------------------

upper sequence: PP1S46_147V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: GRMZM2G030915_T07 (Zea mays), 5'ss of exon 2
------TCCCTTCTCCAAGAAGGATTGGTATGACATCAAGGCACCCAATACTTTCACTCAAAAGAACTTGGGAAAGACTCTCGTGACCAGGACCGCGGGAACGAAGgtggggggttatgcttctctctctcgctctgtttgtgtgtatctctcgcctccgtcccgtggggatttgattgaagttggacatttatgagagagatggatacgcttttttcttttgtgaagttgtacacggaactgacgcgggtttggatgcgacag
       || ||||| |||||||||||||||||||||||||||||       |||| |      ||| | || |||||||||||  |||||||   ||| || | |||  |    | |  || |  || ||| | | ||                                                                                                                             
CGTCGACCCTTTCTCTAAGAAGGATTGGTATGACAtcaaggcaccgtcggtgttcagtgtgcgcaacatcgggaagactctcgtatccaggacacagggtaccagggtatg----tttttttttgactatcgatatttt-----------------------------------------------------------------------------------------------------------------------------

upper sequence: PP1S46_147V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: GRMZM2G030915_T03 (Zea mays), 5'ss of exon 2
TCCCTTCTCCAAGAAGGATTGGTATGACATCAAGGCACCCAATACTTTCACTCAAAAGAACTTGGGAAAGACTCTCGTGACCAGGACCGCGGGAACGAAGgtggggggttatgcttctctctctcgctctgtttgtgtgtatctctcgcctccgtcccgtggggatttgattgaagttggacatttatgagagagatggatacgcttttttcttttgtgaagttgtacacggaactgacgcgggtttggatgcgacag
 || ||||| |||||||||||||||||||||||||||||       |||| |      ||| | || |||||||||||  |||||||   ||| || | |||        ||| || | | |  |  ||  | | | |   |    | ||| | |   |||     |||  |||| |||  ||| ||||      |||  || |       |  | || |                                      
CCCTTTCTCTAAGAAGGATTGGTATGACATCAAGGCACCGTCGGTGTTCAGTGTGCGCAACATCGGGAAGACTCTCGTATCCAGGACACAGGGTACCAGGgt--------atgtttttttttgactatcgatattttttcgtactgcccctacattgtgtg-----ttg--tgaacttgcgcatatatgc-----atgtgtatgtagaccgcgctagtca--------------------------------------

upper sequence: PP1S46_147V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: GRMZM2G145258_T01 (Zea mays), 5'ss of exon 2
TCCCTTCTCCAAGAAGGATTGGTATGACATCAAGGCACCCAATACTTTCACTCAAAAGAACTTGGGAAAGACTCTCGTGACCAGGACCGCGGGAACGAAGgtggggggttatgcttctctctctcgctctgtttgtgtgtatctctcgcctccgtcccgtggggatttgattgaagttggacatttatgagagagatggatacgcttttttcttttgtgaagttgtacacggaactgacgcgggtttggatgcgacag
 || ||||| |||||||||||||||||||||||||||||       |||| |      ||| | || |||||||||||  |||||||   ||| || | |||       | |  |||| |   || |  ||||| |  |||   | |  || ||| | |||  ||      |     ||  ||| || ||  | | | |  | | | ||                                                 
CCCTTTCTCTAAGAAGGATTGGTATGACATCAAGGCACCGTCGGTGTTCAGTGTGCGCAACATCGGGAAGACTCTCGTATCCAGGACACAGGGTACCAGGgta------tgtttttctttaattctcgatgttttttcgtactgccc--ctacgttctgtgttgagagatatatgcatgtccatgta-gaccgcgctagcaaggttatt-------------------------------------------------

upper sequence: PP1S46_147V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: GRMZM2G030915_T05 (Zea mays), 5'ss of exon 2
------TCCCTTCTCCAAGAAGGATTGGTATGACATCAAGGCACCCAATACTTTCACTCAAAAGAACTTGGGAAAGACTCTCGTGACCAGGACCGCGGGAACGAAGgtggggggttatgcttctctctctcgctctgtttgtgtgtatctctcgcctccgtcccgtggggatttgattgaagttggacatttatgagagagatggatacgcttttttcttttgtgaagttgtacacggaactgacgcgggtttggatgcgacag
       || ||||| |||||||||||||||||||||||||||||       |||| |      ||| | || |||||||||||  |||||||   ||| || | |||  |    | |  || |  || ||| | | |||  ||    | |   | |  ||    || | | |||                                                                                         
CGTCGACCCTTTCTCTAAGAAGGATTGGTATGACATCAAGGCACCGTCGGTGTTCAGTGTGCGCAACATCGGgaagactctcgtatccaggacacagggtaccagggtatg----tttttttttgactatcgatattttttcgtactgcccctacatt-gtgtgttgtgaacttgcg---------------------------------------------------------------------------------------

upper sequence: PP1S46_147V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: GRMZM2G013457_T01 (Zea mays), 5'ss of exon 2
TCCCTTCTCCAAGAAGGATTGGTATGACATCAAGGCACCCAATACTTTCACTCAAAAGAACTTGGGAAAGACTCTCGTGACCAGGACCGCGGGAACGAAGgtggggggttatgcttctctctctcgctctgtttgtgtgtatctctcgcctccgtcccgtggggatttg-attgaagttggacatttatg-agagagatggatacgcttttttcttttgtgaagttgtacacggaactgacgcgggtttggatgcgacag
||||||||| |||||||| ||||||||||||||||| ||       |||| |      ||| | || |||||||||||| |||||||   ||| || | |||  ||  || |  ||   ||||  | | | |  ||    | | ||    |  ||   |||  |||  |  |  | |||  |  | |||| |||  |  | |                                                          
TCCCTTCTCTAAGAAGGACTGGTATGACATCAAGGCCCCATCGGTCTTCAGTGTGCGCAACATTGGGAAGACTCTCGTGTCCAGGACACAGGGTACCAGGgtatgg--ttttctttaaatctcgaggtttttacgtac-cacccctacgttttgtggtgtgaagatgggcgtataggttctatgtctatgtagaccgccgtag---------------------------------------------------------

upper sequence: PP1S46_147V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: AT4G34670.1 (Arabidopsis thaliana), 5'ss of exon 3
TCCCTTCTCCAAGAAGGATTGGTATGACATCAAGGCACCCAATACTTTCACTCAAAAGAACTTGGGAAAGACTCTCGTGACCAGGACCGCGGGAACGAAGgtggggggttatgcttctctctctcgctctgtttgtgtgtatctctcgcctccgtcccgtggggatttgattgaagttggacattt-atgagagagatggatacgcttttttcttttgtgaagttgtacacggaactgacgcgggtttggatgcgacag
|||||||||||||||||||||||||||| | ||||| ||   | |||||||  | | |||  | || |||||||| ||  |||||||   ||| || |||||   |  |||||  ||| ||| |  || |  | | |      |   || | |         || ||||| |  |  | |  || | |||  | || |  ||  |||   |                                                
TCCCTTCTCCAAGAAGGATTGGTATGACGTGAAGGCTCCTGGTTCTTTCACGAACAGGAATGTTGGGAAGACTCTTGTTTCCAGGACTCAGGGTACCAAGgtaatgtcttatg--tctttctattactatactggagaaaggttagagctttct-------aggttttgagtcta--tagttatctcatggcataggtc-atttgctgaatg-----------------------------------------------

upper sequence: PP1S46_147V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: EDP08964 (Chlamydomonas reinhardtii), 5'ss of exon 2
TCCCTTCTCCAAGAAGGATTGGTATGACATCAAGGCACCCAATACTTTCACTCAAAAGAACTTGGGAAAGACTCTCGTGACCAGGACCGCGGGAACGAAGgtggggggttatgcttctctctctcgctctgtttgtgtgtatctctcgcctccgtcccgtggggatttgattgaagttggacatttatgagagagatggatacgcttttttcttttgtgaagttgtacacggaactgacgcgggtttggatgcgacag
 |||||| |||||||||| ||||||||||||||||| ||||  |  ||||||      ||| |||| ||||| || |||||||||||   ||| || |||||| | |     ||  | | |    || |  | |  |     | || ||    |   |     |||||  |  ||    |                                                                              
CCCCTTCGCCAAGAAGGACTGGTATGACATCAAGGCGCCCACCATGTTCACTGTCCGCAACGTGGGCAAGACCCTGGTGACCAGGACGCAGGGTACCAAGgtgagcgagggggcggcgccc----gcaccatctccgcaggccgct-gcagttgcttcaccatgatttcctgcaacgcag------------------------------------------------------------------------------

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|208356487|gb|DC914335.1|DC914335
EST:     CTCAAAAGAACTTGGGAAAGACTCTCGTGACCAGGACCGCGGGAACGAAG                         ATTGCCTCCGATGGGTTGAAGGGACGCGTGTTCGAGGTCTCGTTAGCCGAC
genomic: CTCAAAAGAACTTGGGAAAGACTCTCGTGACCAGGACCGCGGGAACGAAGgtggggggtt ... gatgcgacagATTGCCTCCGATGGGTTGAAGGGACGCGTGTTCGAGGTCTCGTTAGCCGAC
EST: gi|208387007|gb|DC941641.1|DC941641
EST:     CTCAAAAGAACTTGGGAAAGACTCTCGTGACCAGGACCGCGGGAACGAAG                         ATTGCCTCCGATGGGTTGAAGGGACGCGTGTTCGAGGTCTCGTTAGCCGAC
genomic: CTCAAAAGAACTTGGGAAAGACTCTCGTGACCAGGACCGCGGGAACGAAGgtggggggtt ... gatgcgacagATTGCCTCCGATGGGTTGAAGGGACGCGTGTTCGAGGTCTCGTTAGCCGAC
EST: gi|18328426|gb|BJ160431.1|BJ160431
EST:     CTCAAAAGAACTTGGGAAAGACTCTCGTGACCAGGACCGCGGGAACGAAG                         ATTGCCTCCGATGGGTTGAAGGGACGCGTGTTCGAGGTCTCGTTAGCCGAC
genomic: CTCAAAAGAACTTGGGAAAGACTCTCGTGACCAGGACCGCGGGAACGAAGgtggggggtt ... gatgcgacagATTGCCTCCGATGGGTTGAAGGGACGCGTGTTCGAGGTCTCGTTAGCCGAC
EST: gi|208359722|gb|DC930298.1|DC930298
EST:     CTCAAAAGAACTTGGGAAAGACTCTCGTGACCAGGACCGCGGGAACGAAG                         ATTGCCTCCGATGGGTTGAAGGGACGCGTGTTCGAGGTCTCGTTAGCCGAC
genomic: CTCAAAAGAACTTGGGAAAGACTCTCGTGACCAGGACCGCGGGAACGAAGgtggggggtt ... gatgcgacagATTGCCTCCGATGGGTTGAAGGGACGCGTGTTCGAGGTCTCGTTAGCCGAC
EST: gi|18367195|gb|BJ199276.1|BJ199276
EST:     CTCAAAAGAACTTGGGAAAGACTCTCGTGACCAGGACCGCGGGAACGAAG                         ATTGCCTCCGATGGGTTGAAGGGACGCGTGTTCGAGGTCTCGTTAGCCGAC
genomic: CTCAAAAGAACTTGGGAAAGACTCTCGTGACCAGGACCGCGGGAACGAAGgtggggggtt ... gatgcgacagATTGCCTCCGATGGGTTGAAGGGACGCGTGTTCGAGGTCTCGTTAGCCGAC
EST: gi|18351958|gb|BJ184010.1|BJ184010
EST:     CTCAAAAGAACTTGGGAAAGACTCTCGTGACCAGGACCGCGGGAACGAAG                         ATTGCCTCCGATGGGTTGAAGGGACGCGTGTTCGAGGTCTCGTTAGCCGAC
genomic: CTCAAAAGAACTTGGGAAAGACTCTCGTGACCAGGACCGCGGGAACGAAGgtggggggtt ... gatgcgacagATTGCCTCCGATGGGTTGAAGGGACGCGTGTTCGAGGTCTCGTTAGCCGAC
EST: gi|208376111|gb|DC910991.1|DC910991
EST:     CTCAAAAGAACTTGGGAAAGACTCTCGTGACCAGGACCGCGGGAACGAAG                         ATTGCCTCCGATGGGTTGAAGGGACGCGTGTTCGAGGTCTCGTTAGCCGAC
genomic: CTCAAAAGAACTTGGGAAAGACTCTCGTGACCAGGACCGCGGGAACGAAGgtggggggtt ... gatgcgacagATTGCCTCCGATGGGTTGAAGGGACGCGTGTTCGAGGTCTCGTTAGCCGAC
EST: gi|208363669|gb|DC954640.1|DC954640
EST:     CTCAAAAGAACTT-GGAAAGACTCTCGTGACCANGACCGCGGNAACGAAG                         ATTGCNTCCGATGGGTTGAAGGGACGCGTGTTCGAGGTCTCGTTAGCCGAC
genomic: CTCAAAAGAACTTGGGAAAGACTCTCGTGACCAGGACCGCGGGAACGAAGgtggggggtt ... gatgcgacagATTGCCTCCGATGGGTTGAAGGGACGCGTGTTCGAGGTCTCGTTAGCCGAC
EST: gi|208350321|gb|DC906023.1|DC906023
EST:     CTCAAAAGAACTTGGGAAAGACTCTCGTGACCAGGACCGCGGGAACGAAG                         ATTGCCTCCGATGGGTTGAAGGGACGCGTGTTCGAGGTCTCGTTAGCTGAC
genomic: CTCAAAAGAACTTGGGAAAGACTCTCGTGACCAGGACCGCGGGAACGAAGgtggggggtt ... gatgcgacagATTGCCTCCGATGGGTTGAAGGGACGCGTGTTCGAGGTCTCGTTAGCCGAC
EST: gi|18348096|gb|BJ180143.1|BJ180143
EST:     CTCAAAAGAACTTGGGAAAGACTCTCGTGACCAGGACCGCGGGAACGAAG                         ATTGCCTCCGATGGGTTGAAGGGACGCGTGTTCGAGGTCTCGTTAGCCGAC
genomic: CTCAAAAGAACTTGGGAAAGACTCTCGTGACCAGGACCGCGGGAACGAAGgtggggggtt ... gatgcgacagATTGCCTCCGATGGGTTGAAGGGACGCGTGTTCGAGGTCTCGTTAGCCGAC

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), 31 (downstream exon)
Score: 18

TCCCTTCTCCAAGAAGGATTGGTATGACATCAAGGCACCCAATACTTTCACTCAAAAGAACTTGGGAAAGACTCTCGTGACCAGGACCGCGGGAACGAAGgtggggggtt ... gatgcgacagATTGCCTCCGATGGGTTGAAGGGACGCGTGTTCGAGGTCTCGTTAGCCGACTTGCAGAATGATGAAGACCAGGCTTTCCGCAAAATCAAGCTAAGGGCGG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCCCTTCTCCAAGAAGGATTGGTATGACATCAAGGCACCCAATACTTTCACTCAAAAGAACTTGGGAAAGACTCTCGTGACCAGGACCGCGGGAACGAAGgtggggggttatgcttctctctctcgctctgtttgtgtgtatctctcgcctccgtcccgtggggatttgattgaagttggacatttatgagagagatggatacgcttttttcttttgtgaagttgtacacggaactgacgcgggtttggatgcgacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC