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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttatgtcaaagtgttcttaatgccaactatgtctgactcgtttcatgttaatatctatagtttatcatctcattaccagttttcttctcctttgtgacagATGGACAGAGCTTCTATCCTTGGTGATGCAATTGAGTACTTGAAGGAGCTCCTGCAGAGGATTAACGATCTTCACAATGAACTTGAGTCTGCTCCTAGCT

Basic information

species Oryza sativa
transcript LOC_Os01g70310.2
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g70310.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G173534_T02 (Zea mays), 3'ss of exon 1
ttatgtcaaagtg-ttcttaatgccaac-tatgtctgactcgtttcatgttaatatctatagtttatcatctcattaccagttttcttctcctttgtgacagATGGACAGAGCTTCTATCCTTGGTGATGCAATTGAGTACTTGAAGGAGCTCCTGCAGAGGATTAACGATCTTCACAATGAACTTGAGTCTGCTCCTAGCT
  | |       | |||   |||  |    |||| ||       |||  ||  | |    | | |    |||||| | || || |||||| ||  |||||||||||| || |||||||||||||| || |||||||||||  |||||||||||||||||||||| | |||||||||||||||||||||||| ||||| ||||
acacgcttggacgcttcgccatgatagtacatgtttggtattaatcaacttgctttagtaaatgttgattctcatcagcatttctcttctgct--gtgacagATGGATAGGGCTTCTATCCTTGGCGACGCAATTGAGTATCTGAAGGAGCTCCTGCAGAGGATCAGCGATCTTCACAATGAACTTGAGTCAGCTCCGAGCT

upper sequence: LOC_Os01g70310.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA19G27480.1 (Glycine max), 3'ss of exon 1
ttatgtcaaagtgttcttaatgccaactatgtctgactcgtttcatgttaatatctatagtttatcatc--tcattaccagttttcttctcctttgtgacagATGGACAGAGCTTCTATCCTTGGTGATGCAATTGAGTACTTGAAGGAGCTCCTGCAGAGGATTAACGATCTTCACAATGAACTTGAGTCTGCTCCTAGCT-
|| |        ||   |  |    | || |  |||  |  ||| | |   |||    || |||  |    |   ||| | | |||||    ||  ||  ||||||| || ||||| || ||||| ||||||||||| |||||||||||| | |||||| ||||||| ||||||||  | || || |||||  |||| | || 
ttgttgttgccagtgactggttt--attaaggttgagacaattcctttatgtattaggagcttaggaatggtgcatactaatgttctttcatttgttggtagATGGATAGGGCTTCAATACTTGGGGATGCAATTGACTACTTGAAGGAGTTGCTGCAGCGGATTAATGATCTTCATCACGAGCTGGAGTCAACTCC-ACCTG

upper sequence: LOC_Os01g70310.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA05G38530.1 (Glycine max), 3'ss of exon 1
-------ttatgtcaaagtgttcttaatgccaactatgtctgactcgtttcatgttaatatct-atagtttatcatctcattaccagttttcttctcctttgtgacagATGGACAGAGCTTCTATCCTTGGTGATGCAATTGAGTACTTGAAGGAGCTCCTGCAGAGGATTAACGATCTTCACAATGAACTTGAGTCTGCTCCTAGCT-
        ||  ||||  | |   | ||   |  |   |   |  | ||   ||||| |||   ||  |||  |||| ||  |  |||||  ||        ||| |||||||||| ||||| |||||||| |||||||| ||||| |||||||| || ||||| ||||| |  || |||||||||||| | |||||  | || |||  
ttcactaataaatcaacatatatatcatataa--tggcttcaatgctttaattgttactattggattttttgacatc-caaaatgagtttgtttaaa----atga-agATGGACAGGGCTTCAATCCTTGGGGATGCAATCGAGTATTTGAAGGAACTTCTGCAAAGGATCAGTGAGCTTCACAATGAATTGGAGTCAACACC-AGCAG

upper sequence: LOC_Os01g70310.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA04G37750.1 (Glycine max), 3'ss of exon 4
---ttatgtcaaagtgttcttaatgccaactatgtctgactcgtttcatgttaatatctatagtttatcatctcattaccagttttcttctcctttgtgacagATGGACAGAGCTTCTATCCTTGGTGATGCAATTGAGTACTTGAAGGAGCTCCTGCAGAGGATTAACGATCTTCACAATGAACTTGAGTCTGCTCCTAGCT
     |    |     |  ||  ||     |  || ||    |     ||    | ||| | | || | ||  ||||    | |||  | |  ||||  | |||||||||| ||||| || ||||| ||||||||||||||  |||||||||| ||||| ||||| || ||||| || || ||| | |||||  | ||     
gttgcacactactagttaattggtgttggtttggtttggggtggaatctggatctgtctctgggttct-atgacattgtttggtttggtttggtttg--atagATGGACAGGGCTTCAATTCTTGGGGATGCAATTGAGTATCTGAAGGAGCTTCTGCAAAGGATCAATGATCTGCATAACGAATTGGAGTCGACGCCGGTGG

upper sequence: LOC_Os01g70310.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA16G05390.1 (Glycine max), 3'ss of exon 1
----ttatgtcaaagtgttcttaatgccaactatgtctgactcgtttcatgttaatatctatagtttatcatctcattaccagttttcttctcctttgtgacagATGGACAGAGCTTCTATCCTTGGTGATGCAATTGAGTACTTGAAGGAGCTCCTGCAGAGGATTAACGATCTTCACAATGAACTTGAGTCTGCTCCTAGCT-
    |  || ||  |  |  || ||     ||| | |     | ||   ||||   | ||  ||  |    | |  | |     |||| |||  ||      ||||||| || ||||| || ||||| ||||||||||| |||||||||||| | |||||| ||||||| |||||||| || || || |||||  |||| | || 
ttgttgttgccattgactggtttattaaggctaagacacttcctttatgtgttgggaacttaagaatggtgtatggtaatgtcctttcatctgttt----gtagATGGATAGGGCTTCAATACTTGGGGATGCAATTGACTACTTGAAGGAGTTGCTGCAGCGGATTAATGATCTTCATAACGAGCTAGAGTCAACTCC-ACCTG

upper sequence: LOC_Os01g70310.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA19G27480.2 (Glycine max), 3'ss of exon 1
ttatgtcaaagtgttcttaatgccaactatgtctgactcgtttcatgttaatatctatagtttatcatc--tcattaccagttttcttctcctttgtgacagATGGACAGAGCTTCTATCCTTGGTGATGCAATTGAGTACTTGAAGGAGCTCCTGCAGAGGATTAACGATCTTCACAATGAACTTGAGTCTGCTCCTAGCT-
                                 |||  |  ||| | |   |||    || |||  |    |   ||| | | |||||    ||  ||  ||||||| || ||||| || ||||| ||||||||||| |||||||||||| | |||||| ||||||| ||||||||  | || || |||||  |||| | || 
-------------------------------gttgagacaattcctttatgtattaggagcttaggaatggtgcatactaatgttctttcatttgttggtagATGGATAGGGCTTCAATACTTGGGGATGCAATTGACTACTTGAAGGAGTTGCTGCAGCGGATTAATGATCTTCATCACGAGCTGGAGTCAACTCC-ACCTG

upper sequence: LOC_Os01g70310.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA06G17330.1 (Glycine max), 3'ss of exon 3
ttatgtcaaagtgttcttaatgccaactatgtctgactcgtttcatgttaatatctatagtttatcatctcattaccagttttcttctcctttg---tgacagATGGACAGAGCTTCTATCCTTGGTGATGCAATTGAGTACTTGAAGGAGCTCCTGCAGAGGATTAACGATCTTCACAATGAACTTGAGTCTGCTCCTAGCT-
    || | | |    | |  |  || ||    ||  | | ||   | |   ||||  | | | ||     |||    |   |  | |  ||||   ||| |||||||||| ||||| || ||||| ||||||||||||||  |||||||||| ||||| ||||| || ||||| || || ||  | || ||  | || ||   
-ggggttagaat-caatcatagttaattagtgttggtttggtttgggctggaatctgga-tctgtctctggattctatgacattgtttggtttggtttgatagATGGACAGGGCTTCAATTCTTGGGGATGCAATTGAGTATCTGAAGGAGCTTCTGCAAAGGATCAATGATCTGCATAACGAGTTGGAATCGACACC-AGTGG

upper sequence: LOC_Os01g70310.1 (Oryza sativa), 3'ss of exon 2
lower sequence: AT3G26744.2 (Arabidopsis thaliana), 3'ss of exon 2
-------------------------------------------------------------------------------ttatgtcaaagtgttcttaatgccaa-ctatgtctg-actcgtttcatgttaatatctata--gtttatcatctcatt--accagttttcttctcctttgtgacagATGGACAGAGCTTCTATCCTTGGTGATGCAATTGAGTACTTGAAGGAGCTCCTGCAGAGGATTAACGATCTTCACAATGAACTTGAGTCTGCTCCTAGCT
                                                                                | |||       || ||  || ||| || ||  || | | | || |   |  |    |    | |  | ||    ||  |    |||||      ||||   |||||||| ||||| || || ||||| ||||||||||| ||  ||||||| || || || ||||| || |||||||||||||||||||||||  |||||    
gtaaacacttactttgtctcttttatctccttaagagcttgtttacttgttgctgttatagagaattgttgtgttgtagctttgtagggcctttgttgttgtcaaactttgcatgtagttgctttactcttttgaggaagaggctcgtgatagtgttttatggattttcgatgaatttg---cagATGGATAGAGCATCAATACTTGGAGATGCAATTGATTATCTGAAGGAACTTCTACAAAGGATCAATGATCTTCACAATGAACTTGAGTCAACTCCTCCTG

upper sequence: LOC_Os01g70310.1 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv17s0000g00330.t01 (Vitis vinifera), 3'ss of exon 1
ttatgtcaaagtgttcttaatgccaactatgtctgactcgtttcatgttaatatctatagtttatcat-----ctcattaccagttttcttctcctttgtgacagATGGACAGAGCTTCTATCCTTGGTGATGCAATTGAGTACTTGAAGGAGCTCCTGCAGAGGATTAACGATCTTCACAATGAACTTGAGTCTGCTCCTAGCT
   ||       |     | |   ||  |||| |     | || |   |  || |  |   |||| |      |  | ||  |||| | ||  | | | ||||||||||| || ||||| |||||||| ||||||||||||||||||||||| || ||||| ||||| ||| | || || |||||||| |||||  | |||    
---tgctgggtggaatccattaataag-atgtttttgaagcttgaaaattttagcagtgccttatgaaaatggcataatatgagttgtattggcttct-tgacagATGGATAGGGCTTCAATCCTTGGGGATGCAATTGAGTACTTGAAGGAACTTCTGCAAAGGATCAACAACCTCCATAATGAACTGGAGTCCACCCCTCCTG

upper sequence: LOC_Os01g70310.1 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv14s0068g01200.t01 (Vitis vinifera), 3'ss of exon 1
ttatgtcaaagtgttcttaatgccaactatgtctgactcgtttca-tgttaatatctatagtttatcatctc-attaccagttttcttctcctttgtgacagATGGACAGAGCTTCTATCCTTGGTGATGCAATTGAGTACTTGAAGGAGCTCCTGCAGAGGATTAACGATCTTCACAATGAACTTGAGTCTGCTCCTAGCT-
  ||     |    |  |  |  |  | ||| |  | | | ||   ||||  ||    |   |||   | || |||||  |   |  |   |    |  |||||||| ||||||||||||||||| ||||| ||||||||||||||||||||  |||| ||||| || ||||| || |||||||| || ||  | || | || 
--atcagggatcagttgtggtttcttcaatgacacaattgctttggtgtttttacgcgtttattaatgtgtctattacttgaactaatgctcaaatttgcagATGGATAGAGCTTCTATCCTTGGGGATGCCATTGAGTACTTGAAGGAGCTTTTGCAAAGGATCAATGATCTCCATAATGAACTGGAATCAAC-CCCATCTG

upper sequence: LOC_Os01g70310.1 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv01s0244g00130.t01 (Vitis vinifera), 3'ss of exon 1
ttatgtcaaagtgttcttaatgccaactatgtctgactc-gtttcatgttaatatc-tatagtttatcatctc--attaccagttttcttctcctttg--tgacagATGGACAGAGCTTCTATCCTTGGTGATGCAATTGAGTACTTGAAGGAGCTCCTGCAGAGGATTAACGATCTTCACAATGAACTTGAGTCTGCTCCTAGCT-
         |  | || ||   |  |  ||   |   || ||| |||  |   ||  | | |      || |   |||||| ||||   | | ||||   ||| ||||||| |||||||| ||||| |  ||||| |||||||||||||||||| | ||||||||||| ||||| || || |||||||| ||||||  ||  | || 
-----atggaccgatcatag-actgataatccattgttctgttgcataattggatggtttgggaagatatttaggattacctgtttaaatgttcttttgttgatagATGGATAGAGCTTCAATCCTGGCGGATGCTATTGAGTACTTGAAGGAGTTACTGCAGAGGATCAACGACCTCCAGAATGAACTGGAGTCTA-TCACACCTC

upper sequence: LOC_Os01g70310.1 (Oryza sativa), 3'ss of exon 2
lower sequence: PP1S30_360V6.1 (Physcomitrella patens), 3'ss of exon 5
------ttatgtcaaagtgttcttaatgccaactatgtctgactcgttt---catgttaatatctatagtttatcatctcattac--cagttttcttctcctttgtga-cagATGGACAGAGCTTCTATCCTTGGTGATGCAATTGAGTACTTGAAGGAGCTCCTGCAGAGGATTAACGATCTTCACAATGAACTTGAGTCTGCTCC-TAGCT
        || ||       ||   | |      |||  | | |  ||    ||   ||   | ||  | ||  |||    || |   |       |    || |||| ||||||||||| || || || || || |||||||| |||||| | ||||||||||||||| | || || ||  | ||||  || || ||  | ||     ||  
gtttgtgaatatccccacactcaacaagttttacatgcataaatacttcacacagaatacggtttaaggctttccatggagttgcagtaacacgtatgggtttggtgaacagATGGACAGGGCCTCCATACTCGGCGATGCAATCGAGTACCTTAAGGAGCTCCTGCAGCGTATAAATGACATCCACAGCGAGCTCGATGCAGCGAAACAGG-

upper sequence: LOC_Os01g70310.1 (Oryza sativa), 3'ss of exon 2
lower sequence: PP1S257_22V6.1 (Physcomitrella patens), 3'ss of exon 4
-------------tta-tgtcaaagtgttcttaatgcca-actatgtctg-actcgtttcatgttaatatctatagtttatcatctcattaccagttttcttct---cctttgtgacagATGGACAGAGCTTCTATCCTTGGTGATGCAATTGAGTACTTGAAGGAGCTCCTGCAGAGGATTAACGATCTTCACAATGAACTTGAGTCTGCTCCTAGCT--
             | | | || |  |  |||  ||||   |  |||  || || | ||  | ||||  || |    | ||   |  || |  ||  ||     |     |     ||||||||||||||| || || || ||||| |||||||||||| ||||||||||||| ||| | || |||||  ||||||| || || ||    ||    || |  
gttcaacgcaccttcactctcgatcttatctatatgctgtatgatggttgcacacattagaggttacgattttc--tataaggttccagtgacacattcaaagtgggtatggccaacagATGGACAGAGCCTCCATACTCGGTGACGCAATTGAGTACCTGAAGGAGCTCCTACAGCGCATCAACGACATTCACAACGAGCTGGAAGAAGCAA--AGTTGG

upper sequence: LOC_Os01g70310.1 (Oryza sativa), 3'ss of exon 2
lower sequence: PP1S212_62V6.1 (Physcomitrella patens), 3'ss of exon 2
ttatgtcaaagtgttcttaatgccaactatgtctg-actcgtttcatgttaatatctatagtttatcatctcattaccagttttcttctcctttgtg----acagATGGACAGAGCTTCTATCCTTGGTGATGCAATTGAGTACTTGAAGGAGCTCCTGCAGAGGATTAACGATCTTCACAATGAACTTGAGTCTGCTCCTAGCT--
                         |  |||  || || | ||  | ||||  || |    | ||   |  || |  || |||     |    | ||    ||||||||||||||| || || || ||||| |||||||||||| ||||||||||||| ||| | || |||||  ||||||| || || ||    ||    || |  
-----------------------gtatgatggttgcacacattagaggttacgattttc--tataaggttccagtgacactttcaaaattgggtatggccaacagATGGACAGAGCCTCCATACTCGGTGACGCAATTGAGTACCTGAAGGAGCTCCTACAGCGCATCAACGACATTCACAACGAGCTGGAAGAAGCAA--AGTTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttaatatctatagtttatcatctcattaccagttttcttctcctttgtgacagATGGACAGAGCTTCTATCCTTGGTGATGCAATTGAGTACTTGAAGGAGCTCCTGCAGAGGATTAACGATCTTCACAATGAACTTGAGTCTGCTCCTAGCT
 tgttaat  putative branch site (score: 3)
                           ttaccagttttcttct  putative PPT
     atatctatagtttat  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttatgtcaaagtgttcttaatgccaactatgtctgactcgtttcatgttaatatctatagtttatcatctcattaccagttttcttctcctttgtgacagATGGACAGAGCTTCTATCCTTGGTGATGCAATTGAGTACTTGAAGGAGCTCCTGCAGAGGATTAACGATCTTCACAATGAACTTGAGTCTGCTCCTAGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT