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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgaacacaaaggggacaaagggaaacaaattactttaatgtactattctatattatctatatttgtttcttacaacttagtggacttaattcatgtgcagTTCCTCCAGCGTATTATGCACATTTGGCAGCTTTTCGAGCGCGGTTCTATATGGAGCCAGACCTGCAGCAGGAGAATGGCTCCTCAGGTGGTGGCTCCAA

Basic information

species Glycine max
transcript GLYMA02G00510.1
intron # 20
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G00510.1 (Glycine max), 3'ss of exon 20
lower sequence: LOC_Os06g39640.1 (Oryza sativa), 3'ss of exon 21
-----------tgaacacaaaggggacaaagggaaacaaattacttta-----atgtactattctatatta---------tctatatttgtttcttacaacttagtggacttaattcatgtgcagTTCCTCCAGCGTATTATGCACATTTGGCAGCTTTTCGAGCGCGGTTCTATATGGAGCCAGACCTGCAGCAGGAGAATGGCTCCTCAGGTGGTGGCTCCAA
           |||| |  |   | |||       |  | || ||||      ||||  |||| |   ||          |||  |  ||  |||| ||  |   |   | |  | ||    ||||||| || || || ||||| ||| |||| || ||||||||||||||||| |||||||||||  ||  | || |  |     | ||     |   | |   
gtacgttcttctgaa-atgatctgaacatttttccatcattttctttgtattcatgtgttattattagttggacacgaattctgaaggtgaatcttgcatttcttttttcctggtcca---acagTTCCACCTGCATACTATGCGCATCTGGCTGCGTTTCGAGCGCGGTTCTACATGGAGCCAGAGATGTCGGAGAACCAGACGACGTCGAAGAGCTCCACTGG

upper sequence: GLYMA02G00510.1 (Glycine max), 3'ss of exon 20
lower sequence: AT5G43810.2 (Arabidopsis thaliana), 3'ss of exon 20
tgaacacaaaggggacaaagggaaacaaattactt--taatgtactattctatattatctatatttgt---ttcttacaacttagtggacttaattcatgtgcagTTCCTCCAGCGTATTATGCACATTTGGCAGCTTTTCGAGCGCGGTTCTATATGGAGCCAGACCTGCAGCAGGAGAATGGCTCCTCAGGTGGTGGCTCCAA
          |   | ||    |       | |||  |  |||||      |||| |   | ||  |     || ||     |  |    |    |  ||| |||||||||||||||||||||| ||| | ||||| |||||||| || |||||  |||| || ||  |   ||| || || || ||  | |||        || 
----------gtaaataacaacatttcttcttcttcttcgtgtacccgcaaatatgacgaaaatcagcaaactcatatgttcttttattttctgatgttgtacagTTCCTCCAGCGTATTATGCTCATCTTGCAGCATTTCGAGCACGTTTCTACCTGGAACCGGAGATAATGCAAGACAACGGATCACCGGGTAAAAAGAACAC

upper sequence: GLYMA02G00510.1 (Glycine max), 3'ss of exon 20
lower sequence: Vv05s0020g04190.t01 (Vitis vinifera), 3'ss of exon 18
tgaacacaaaggggacaaagggaaacaaattactttaatgtactattctatattatctatatttgtttcttacaacttagtggacttaat---tcatgtgcagTTCCTCCAGCGTATTATGCACATTTGGCAGCTTTTCGAGCGCGGTTCTATATGGAGCCAGACCTGCAGCAGGAGAATGGCTCCTCAGGTGGTGGCTCCAA
    |    | |          |||       | || | |  ||     || || | | |||  | | |     |  |||   | |  ||   |||| ||||||||||||||| |||||||||||||| ||||| |||||||| || ||||| |||||||| ||| |||||   |||||||| ||    || ||||||     
--tcctttgaagttctttgttcaaattgtcctccttgaggagctccatcattttgt-tctatgagctgcaactgaaatagctaaatccatggctcatttgcagTTCCTCCAGCATATTATGCACATTTAGCAGCATTTCGAGCCCGATTCTACATGGAGCCTGACATGCAG---GAGAATGGTTCAAATGGAGGTGGCAGTG-

upper sequence: GLYMA02G00510.1 (Glycine max), 3'ss of exon 20
lower sequence: PP1S7_194V6.1 (Physcomitrella patens), 3'ss of exon 18
tgaacacaaaggggacaaagggaaacaaattactttaatgtactattctatattatctatatttgtttcttacaacttagtggacttaattcatg---tgcagTTCCTCCAGCGTATTATGCACATTTGGCAGCTTTTCGAGCGCGGTTCTATATGGAGCCAGACCTGCAGCAGGAGAATGGCTCCTCAGGTGGTGGCTCCAA---
    |  | |  |  ||||     | |   |   | | | |    ||   | | |  |    ||  ||  || ||      |  ||  | | |||    ||||||||||| || |||||||| |||||||| ||||| |||||||| ||||| ||||| |||||   ||  | | | | ||| ||   |  | ||||         
---ccggagaatgttcaaaattctagatgctttgtcatttttaatttaagtgtgagttcacattacttactagaatacgacgttctctaatgatgaatcgcagTTCCTCCGGCTTATTATGCGCATTTGGCTGCTTTCCGAGCGCGCTTCTACATGGATCCAGAA--GCTTCCG-ATACTGGATCTCTAACTAGTGGGATGGGAGG

upper sequence: GLYMA02G00510.1 (Glycine max), 3'ss of exon 20
lower sequence: PP1S28_182V6.1 (Physcomitrella patens), 3'ss of exon 19
-----------------------------------------------------------------------------------------------tgaacacaaaggggacaaagggaaacaaattactttaatgtactattctatattatctatatttgtttcttacaacttagtggacttaattcatgtgcagTTCCTCCAGCGTATTATGCACATTTGGCAGCTTTTCGAGCGCGGTTCTATATGGAGCCAGACCTGCAGCAGGAGAATGGCTCCTCAGGTGGTGGCTCCAA---
                                                                                               |    | |   ||||    | | | |  | ||  || || |  |  |  ||||    || | |       |  ||| |  || | | |  | || ||||||||||||||| |||||||||||| | || |||||||| ||  ||||||| ||||| |||||   ||  ||| | | ||| ||      | |||| |       
gtatgttcaaaaatcttctacgtcatataatggtttttgtctattcaacaaaatgtctcggctaagcgcattatttgaaatcttattcaacgttcttggtagacctgggattgggtgtatccgaatatcttgattt--tggttgatatcgcttagaatcaaaa--tgtaacgttttgtattga--tgatttgcagTTCCTCCAGCATATTATGCACATCTAGCTGCTTTTCGTGCCAGGTTCTACATGGATCCAGAA--GCTTCAG-ATACTGGTTCTGTTACTAGTGGGTTGGGAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctatattatctatatttgtttcttacaacttagtggacttaattcatgtgcagTTCCTCCAGCGTATTATGCACATTTGGCAGCTTTTCGAGCGCGGTTCTATATGGAGCCAGACCTGCAGCAGGAGAATGGCTCCTCAGGTGGTGGCTCCAA
     tattatctatatttgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgaacacaaaggggacaaagggaaacaaattactttaatgtactattctatattatctatatttgtttcttacaacttagtggacttaattcatgtgcagTTCCTCCAGCGTATTATGCACATTTGGCAGCTTTTCGAGCGCGGTTCTATATGGAGCCAGACCTGCAGCAGGAGAATGGCTCCTCAGGTGGTGGCTCCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- -acacaaa
- - - - - - - - - - - aaacaaa
- - - - - - - - - - - - - - - - - - aatgtac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cttagtg