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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGAAGAAGGGGCCGTGGACGCCAGAGGAGGATCAGAAGCTGGTGGCATACATTCAGGAACATGGTCATGGAAGCTGGCGGGAGCTCCCTGAGAAAGCCGgtaagctgcgtcctgcttcgaaaagtgacgaattttttcttgcatgagaccattacattgcgttcttcgaccccaggttttggatggatttgcagttaga...

Basic information

species Physcomitrella patens
transcript PP1S106_216V6.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S106_216V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: LOC_Os02g36890.1 (Oryza sativa), 5'ss of exon 1
GTGAAGAAGGGGCCGTGGACGCCAGAGGAGGATCAGAAGCTGGTGGCATACATTCAGGAACATGGTCATGGAAGCTGGCGGGAGCTCCCTGAGAAAGCCGgtaagc-tgcgtcctgc----------ttcgaaaagtgacgaatt-ttttcttgcatgagaccattacattgcgttcttcgaccccaggttttggatggatttgcagttaga------------
 |||||||||||||||||||||| |||||||| ||||||||| | || |||||  || | || || || ||  |||||||   ||| ||    || ||||||| |   | | | |||          ||||     |||  | |   |   | || |||        |     | ||   |        ||||||  | ||  |    | ||            
CTGAAGAAGGGGCCGTGGACGCCGGAGGAGGACCAGAAGCTGCTCGCCTACATCGAGCAGCACGGCCACGGCTGCTGGCGCTCGCTGCCCACCAAGGCCGgtacgtgcgtgccatgcgatctcggttttcggcctctgataactagctaaatcgcctgatcgatccgccaattgctcactggtgtggttttttgggggaatgcgtgtgttgacgcataattcag

upper sequence: PP1S106_216V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: LOC_Os04g38740.1 (Oryza sativa), 5'ss of exon 1
GTGAAGAAGGGGCCGTGGACGCCAGAGGAGGATCAGAAGCTGGTGGCATACATTCAGGAACATGGTCATGGAAGCTGGCGGGAGCTCCCTGAGAAAGCCGgtaagctgcg----tcctgcttcgaaaagtgacgaattttt----tcttgcatgagaccattacattgcgttcttcgaccccaggttttggatgga-tttgcagttaga------------------------------------
 | ||||||||||| |||||||| |||||||| ||||||||| |||| |||||  || | || || || ||  |||||||   ||| ||    || ||||||||||  ||    ||  ||||  |    |    ||  | |    || |   ||  |   ||   | | |    |||| ||  |    ||| |    | || | |  ||                                    
CTCAAGAAGGGGCCATGGACGCCGGAGGAGGACCAGAAGCTGCTGGCCTACATCGAGCAGCACGGCCACGGCTGCTGGCGCTCGCTACCCTCCAAGGCCGgtaagcgccgcttatctagcttaaatttcttctcaacctctgcaatcctagctgcaat-gttcggtcgaggcgatcgatcctcgaggctggctactctctgaactctgatctgaggtgcatgcaaaccgtgacaatcgtgtgcag

upper sequence: PP1S106_216V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: LOC_Os07g37210.1 (Oryza sativa), 5'ss of exon 1
GTGAAGAAGGGGCCGTGGACGCCAGAGGAGGATCAGAAGCTGGTGGCATACATTCAGGAACATGGTCATGGAAGCTGGCGGGAGCTCCCTGAGAAAGCCGgtaagc-tgcgt-cctgcttcgaaaagtgacgaatttttt-cttgcatgagacca--ttacattgcgttcttcgaccccaggttttggatggattt-gcagttaga---------
 |||||||||||||||||||||| ||||||||  |||||||  | || |||||  |||| || || || || | ||||||   ||||||  |||| |||||| |||  |||   | |||| |    |   | | |  |   | ||||  |  | |  ||| |||   || |   |     |||    |||  ||   ||   |            
CTGAAGAAGGGGCCGTGGACGCCCGAGGAGGACGAGAAGCTCATCGCCTACATCAAGGAGCACGGCCAGGGCAACTGGCGCACGCTCCCCAAGAATGCCGgtgagcgcgcgcgtcagctttgctctgccgccattgatgagcatgcacaaagctagcttagattagcttatcttatgaatggtaactgatatatccagcttctttgtttgtgcag

upper sequence: PP1S106_216V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: LOC_Os02g42870.1 (Oryza sativa), 5'ss of exon 1
GTGAAGAAGGGGCCGTGGACGCCAGAGGAGGATCAGAAGCTGGTGGCATACATTCAGGAACATGGTCATGGAAGCTGGCGGGAGCTCCCTGAGAAAGCCGgta--agctgcgtcctgcttcgaaaagtgacgaattttttcttgcatgagaccattacattgcgttcttcgaccccaggttttggatggatttgcagttaga-
 | |||||||||||||||||||| ||||||||  ||   || || |  ||||| ||||   | || || || ||||||||    |||||  ||   || ||||   ||||  | ||   |      | | | |   ||| |||   | |     |    || ||     ||  | |  ||  || |  | |   |||      
CTCAAGAAGGGGCCGTGGACGCCGGAGGAGGACAAGCTCCTCGTCGACTACATCCAGGCCAACGGCCACGGCAGCTGGCGCCTCCTCCCCAAGCTCGCAGgtaccggctggcttctctgttcttgcgaggcaatgctttgcttctgtcacgttttcgtgtt-cgcgtgccg--cactagtgctgaactgctgatcagcacatt

upper sequence: PP1S106_216V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: GRMZM2G166337_T01 (Zea mays), 5'ss of exon 2
GTGAAGAAGGGGCCGTGGACGCCAGAGGAGGATCAGAAGCTGGTGGCATACATTCAGGAACATGGTCATGGAAGCTGGCGGGAGCTCCCTGAGAAAGCCGgtaagct-gcgtcctgct----tcgaaaagtgacgaattttttcttgcatgagaccattacattgcgttcttcgaccccaggttttggatggatttgcagttaga
 |||||||||||||||||||||||||||||||  ||||||| || || |||||  || | || || || |||| ||||||    |||||  |||| |||||| |||  ||| ||||||     |||     | |||   |   | |  ||     |||  |  |||   | |||| |     | |   |||   | ||||     
CTGAAGAAGGGGCCGTGGACGCCAGAGGAGGACGAGAAGCTCGTCGCCTACATCAAGAAGCACGGCCAGGGAAACTGGCGCACCCTCCCCAAGAATGCCGgtgagcgagcgacctgctggccccgatcgacgtcgatcatgcgcatatataca--catatccatgctcacctcgatcgtccttctc--atgtcatggcag-----

upper sequence: PP1S106_216V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: GRMZM2G032655_T01 (Zea mays), 5'ss of exon 1
GTGAAGAAGGGGCCGTGGACGCCAGAGGAGGATCAGAAGCTGGTGGCATACATTCAGGAACATGGTCATGGAAGCTGGCGGGAGCTCCCTGAGAAAGCCGgtaagctgcgtcctgc---ttcgaaaagtgacgaattttttcttgcatgagac------cattacattgcgttcttcgaccc---caggttttggatggatttgcagttaga---------------------
 | |||||||| ||||||||||| |||||||| ||||||||| | || |||||| || | || || || ||  |||||||   ||| || |  ||||||||| ||||   |   ||    | |   ||| || | ||  |         || |      ||||    | || | || |       | || |     | ||  ||||    ||                     
CTCAAGAAGGGCCCGTGGACGCCGGAGGAGGACCAGAAGCTGCTCGCCTACATTGAGCAGCACGGCCACGGCTGCTGGCGCTCGCTGCCCGCCAAAGCCGgtgagcttgctatagcgagctagtgtagttactagttagtaacaatcaaagtccagcagcattcggctacgctgtttggtttgcgctggctcctccttgacatgcatgcggatatggccgtgtggtgtggcag

upper sequence: PP1S106_216V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: GRMZM2G001223_T03 (Zea mays), 5'ss of exon 1
GTGAAGAAGGGGCCGTGGACGCCAGAGGAGGATCAGAAGCTGGTGGCATACATTCAGGAACATGGTCATGGAAGCTGGCGGGAGCTCCCTGAGAAAGCCGgtaagctgcgtcctgcttcgaaaagtgacgaattttttcttg----catgagaccattacattgcgttc-ttcgaccccaggt----tttggatggatttgcagttaga------------------------
 |||||||||||||||||||| | |||||||| ||||| ||| |||| | |||  || | || || || ||  |||||||   ||| || |  || |||||| ||     |||  |  || |    |||||  | |   | |    || |    | |  |||| | ||| ||  |    |  |    |   |  | || |   | |                           
CTGAAGAAGGGGCCGTGGACGTCCGAGGAGGACCAGAAACTGCTGGCCTTCATCGAGCAGCACGGACACGGCTGCTGGCGCTCGCTGCCGGCCAAGGCCGgtgagg---atccgacgacggagctcgacgatatatccatcgacctcacgttttcttcgcattccattcgttttattatatttgccatccagcagaatataatgctcatctatgcgtgtgcgtctctctgcag

upper sequence: PP1S106_216V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: GLYMA09G37040.1 (Glycine max), 5'ss of exon 2
GTGAAGAAGGGGCCGTGGACGCCAGAGGAGGATCAGAAGCTGGTGGCATACATTCAGGAACATGGTCATGGAAGCTGGCGGGAGCTCCCTGAGAAAGCCGgtaagctgcgtcctgcttcgaaaagtgacgaattttttcttgcatgagaccattacattgcgttcttcgaccccaggttttggatggatttgcagttaga---------------------------------------------------------------------------------------------------
 | |||||||| ||||||||||||||||| |||||||||||  |||| || ||| | |||||||| |||||||||||||| |   | || |  ||||| ||||| ||   |     |   |  | |||  ||| ||   |   |  |    | |    |  ||     |     |    ||        |  || ||                                                                                                      
TTAAAGAAGGGACCGTGGACGCCAGAGGAAGATCAGAAGCTCTTGGCTTATATTGAAGAACATGGCCATGGAAGCTGGCGTGCTTTGCCAGCAAAAGCTGgtaatctttttttatttattattattgataaatattagttattagaatgttaattttgttagtagagaggattgaacccttaacctttctctcatttttttctcttttaaccatccaaccgactttatatatatatattactatattactattaaaataaaatttatgaagtgaagctgctggctataattgtgttcag

upper sequence: PP1S106_216V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: GLYMA18G49630.1 (Glycine max), 5'ss of exon 1
GTGAAGAAGGGGCCGTGGACGCCAGAGGAGGATCAGAAGCTGGTGGCATACATTCAGGAACATGGTCATGGAAGCTGGCGGGAGCTCCCTGAGAAAGCCGgtaagctgcgtcctg----cttcgaaaagtgacgaattttttcttgcatgagaccattacattgcgttcttcgaccccaggttttggatggat-ttgcagttaga
 |||||||||| || |||||||||||||| |||||||||||  |||| || ||| | |||||||| |||||||||||||| |   | || |  ||||| |||||      |  |       | || |  | |  |  || |  ||  |  | | | || |  ||   | |  ||    |  |  | | ||| |  ||   | || 
TTGAAGAAGGGACCATGGACGCCAGAGGAAGATCAGAAGCTCTTGGCTTATATTGAAGAACATGGCCATGGAAGCTGGCGTGCTTTGCCAGCAAAAGCTGgtaaataatcttatatacatgttgatatataaatatcttgtaattaaagtaaaac-ttgccgtgtaatttgtgaagtgaattagttgctggctactgtgttcag-

upper sequence: PP1S106_216V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: GLYMA19G02890.1 (Glycine max), 5'ss of exon 2
GTGAAGAAGGGGCCGTGGACGCCAGAGGAGGATCAGAAGCTGGTGGCATACATTCAGGAACATGGTCATGGAAGCTGGCGGGAGCTCCCTGAGAAAGCCGgtaagctgcgtcctgcttcgaaaagtgacgaattttttcttgcatgagaccattacattgcgttcttcgaccccaggttttgg-atggatttgcagttaga-------
 | ||||| || || ||||| |||||||| |||||||||||  | || || ||| | |||||||| |||||||||||||| |   | || |  ||||| ||||  ||   |  |   |  | |  |      |||||| |||  | ||     |  ||   ||   |         ||  |    || |  | ||  || |       
TTAAAGAAAGGACCATGGACTCCAGAGGAAGATCAGAAGCTCTTAGCTTATATTGAAGAACATGGCCATGGAAGCTGGCGTGCTTTGCCAGCAAAAGCTGgta--ctatataatatatatacactt------ttttttgttgtgttagtttgatgtatattgtgtatatgttgtgagtaataatgtgtaagtacacatatatgaaatt

upper sequence: PP1S106_216V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: Vv18s0001g05670.t01 (Vitis vinifera), 5'ss of exon 1
GTGAAGAAGGGGCCGTGGACGCCAGAGGAGGATCAGAAGCTGGTGGCATACATTCAGGAACATGGTCATGGAAGCTGGCGGGAGCTCCCTGAGAAAGCCGgtaagctgcgtcctgcttcgaaaagtgacgaattttttcttgcatgagaccattacattgcgttcttcgaccccaggttttggatggatttgcagttaga
 ||||||| ||||| ||||| || || || ||||||||||||||    ||| ||||| ||||||| |||||||||||| | |  |||||| ||   || |||   ||  ||  |  ||       |  |      | |||  |||     || ||| |  |  | |    |  ||  |      |     |||||     
CTGAAGAAAGGGCCTTGGACTCCTGAAGAAGATCAGAAGCTGGTCAGCTACGTTCAGAAACATGGCCATGGAAGCTGGAGAGCTCTCCCTAAGCTTGCAGgt---ctatgt--taattaattggatccctctccctgtctctcattttttcagtacttcaccattt----catcatttcccttttactcctgcag-----

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGAAGAAGGGGCCGTGGACGCCAGAGGAGGATCAGAAGCTGGTGGCATACATTCAGGAACATGGTCATGGAAGCTGGCGGGAGCTCCCTGAGAAAGCCGgtaagctgcgtcctgcttcgaaaagtgacgaattttttcttgcatgagaccattacattgcgttcttcgaccccaggttttggatggatttgcagttaga

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT