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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cctcttcaatcctcctctaccgggattgtgtatgatttatgaagttgaatatatttaagtattgcactagtgtgtaatttcaaatccttgtcttttgcagTATACGCCTGCAATTGATATTTGGAGCATTGGATGCATATTTGCAGAAATGCTCAGTGGGAAGCCATTGTTTCCTGGAAAAAATGTAGTGCACCAATTGG

Basic information

species Glycine max
transcript GLYMA09G30790.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G30790.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os01g45620.1 (Oryza sativa), 3'ss of exon 3
cctcttcaatcctcctctaccgggat-tgtgtatgatttatgaagttgaatatatttaagtattgcactagtgtg-taatttcaaatccttgtcttttgcagTATACGCCTGCAATTGATATTTGGAGCATTGGATGCATATTTGCAGAAATGCTCAGTGGGAAGCCATTGTTTCCTGGAAAAAATGTAGTGCACCAATTGG
   |     || |   ||| ||  |  | ||  |    ||  || ||| |||  || || |        |   |  |||  ||||||   ||| |||||||||| || ||||||||||||||||||||| | || || |||||||| |||||||| |  || |||||| | ||||||||||| ||||| || || |||||||
atgccatgctcttgaactatcgatacatatgcttagcataccaatttggataatttcaaatgcacttgcaccatactaaactcaaatg--tgttttttgcagTACACTCCTGCAATTGATATTTGGAGCGTCGGTTGTATATTTGCTGAAATGCTTATGGGAAAGCCACTTTTTCCTGGAAAGAATGTGGTACATCAATTGG

upper sequence: GLYMA09G30790.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os05g50120.1 (Oryza sativa), 3'ss of exon 4
-------------------------------------------cctcttcaatcctcctctaccgggattgtgtat---gatttatgaag----------ttgaatatat----ttaagtattgcactagtgtgtaat-------ttcaaatcct-----tgtcttttgcagTATACGCCTGCAATTGATATTTGGAGCATTGGATGCATATTTGCAGAAATGCTCAGTGGGAAGCCATTGTTTCCTGGAAAAAATGTAGTGCACCAATTGG
                                               | |||   |  | ||     ||  | | |   |||  ||| ||          ||||  || |    |||   ||||    | |  || ||       || | ||  |     || ||||||||||| || ||||||||||||||||||||  | ||||| |||||||||||  |||| |  || |||||| | ||||| || |||||||| ||||| |||||||
gtaagggaatttccatttaacatggtgatggctatattattttttcttccaacattgttatattactatgatatgtttggatcaatgtagcaacagtgttttgagaatgttctcttagacattgtcgcattaggtgatatcttgatttatattttgtcattggcttttgcagTACACCCCTGCAATTGATATTTGGAGTGTAGGATGTATATTTGCAGAGCTGCTTACAGGAAAGCCACTCTTTCCAGGGAAAAATGTTGTGCATCAATTGG

upper sequence: GLYMA09G30790.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G062761_T02 (Zea mays), 3'ss of exon 4
cctcttcaatcctcctctac-cgggattgtgtatgatttatgaagttgaatatatttaagtattgcactagtgtgtaatttcaaatcc----ttgtcttttgcagTATACGCCTGCAATTGATATTTGGAGCATTGGATGCATATTTGCAGAAATGCTCAGTGGGAAGCCATTGTTTCCTGGAAAAAATGTAGTGCACCAATTGG
  |  |  | |    | |||   |  | | || |||| ||| |  |||  |   |  || | ||  |  |        ||   ||||     ||  ||||||||||| || ||||| ||||||||||||||| | || || |||||||| ||| ||||||  ||||||||| | ||||| || || ||||| ||||| || ||||
--tacttgaacagtgtgtacatagtgtggagtttgatgtatcagcttgttt---tacaaattttatagaatcacaaggttctgaatctggcattaacttttgcagTACACTCCTGCCATTGATATTTGGAGCGTAGGGTGTATATTTGCTGAATTGCTCACAGGGAAGCCACTCTTTCCAGGGAAGAATGTTGTGCATCAGTTGG

upper sequence: GLYMA09G30790.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G375975_T01 (Zea mays), 3'ss of exon 3
-------------cctcttcaatcctcctctaccgg-----gattg-tgtatgatttatgaa-gtt---gaatatatttaagtattgcact-agtgtgtaatttcaaatccttgtcttttgcagTATACGCCTGCAATTGATATTTGGAGCATTGGATGCATATTTGCAGAAATGCTCAGTGGGAAGCCATTGTTTCCTGGAAAAAATGTAGTGCACCAATTGG
             |  |   |  |  | |||||  |      |||| | |||| ||| | |  |||   || || |       |||   || | | |  || ||  ||  |||   ||||||||||||| ||||| |||||||| |||||| | || || |||||||| |||||||| |  ||||||||  | |||||||| || ||||| || || ||| |||
gtcggatagttttcacccggacacaacttctactagctcttcattgctatatggttttttactgtttaagagtacaccacttcattttgctgaatttacaactt--aacacttaa-ttttgcagTATACTCCTGCGATTGATATCTGGAGCCTAGGTTGTATATTTGCTGAAATGCTTATAGGGAAGCCTCTCTTTCCTGGCAAGAATGTGGTACATCAACTGG

upper sequence: GLYMA09G30790.1 (Glycine max), 3'ss of exon 4
lower sequence: AT3G18040.2 (Arabidopsis thaliana), 3'ss of exon 3
---------cctcttcaatcctcctctaccgggattgtgtatgatttatgaagttgaatatatttaagtattgcactagtgtgtaatttcaaatccttgtcttttgcagTATACGCCTGCAATTGATATTTGGAGCATTGGATGCATATTTGCAGAAATGCTCAGTGGGAAGCCATTGTTTCCTGGAAAAAATGTAGTGCACCAATTGG
           |  || ||  || | |      |   ||| ||||| |   |  | |  | |    |   |     ||    | | | |     | || | |  |||||||||| ||||| |||||||| |||||||| ||||||||||||||||||||||||| ||||||||||||||||||||| || ||||| |||||||||||||
gtaaaatgcaattctctattttcttttttgcaaaagttgtctgattcacata--ttatgacaccacaacctgaggttaaaacggattattg---ctttctttgctgcagTATACTCCTGCCATTGATATATGGAGCATAGGATGCATATTTGCAGAAATGCTCACTGGGAAGCCATTGTTTCCTGGGAAGAATGTGGTGCACCAATTGG

upper sequence: GLYMA09G30790.1 (Glycine max), 3'ss of exon 4
lower sequence: AT1G73670.1 (Arabidopsis thaliana), 3'ss of exon 4
--cctcttcaatcctcctctaccgggattgtgtatgatttatgaagttgaatata-tttaagtattgcactagtgtgtaatttcaaatccttgtcttttgcagTATACGCCTGCAATTGATATTTGGAGCATTGGATGCATATTTGCAGAAATGCTCAGTGGGAAGCCATTGTTTCCTGGAAAAAATGTAGTGCACCAATTGG
   || ||  ||      || |     ||   |||     |    |  | |||   ||| | ||  |  ||  ||  ||| |  |     |||     | |||||||| ||||| ||||||||||||||| |||| ||||||||||| ||||||||    ||||||||  | |||||||| |||||||| || ||||||||||
ccacttttgtatgaaggcctgctctagttagctatctacaagtgtgcaggataaggtttgattacagatctgatgc-taactcta--cttttgcgaaatacagTATACCCCTGCGATTGATATTTGGAGCGTTGGTTGCATATTTGCTGAAATGCTATTAGGGAAGCCGCTATTTCCTGGCAAAAATGTGGTTCACCAATTGG

upper sequence: GLYMA09G30790.1 (Glycine max), 3'ss of exon 4
lower sequence: AT1G18150.3 (Arabidopsis thaliana), 3'ss of exon 5
-----------------------------cctcttcaatcctcctctaccgggattgtgt-----atgatttatgaagttgaatatatttaagtattgcactagtgt--------------gtaatttcaa---------atccttgtctt-ttgcagTATACGCCTGCAATTGATATTTGGAGCATTGGATGCATATTTGCAGAAATGCTCAGTGGGAAGCCATTGTTTCCTGGAAAAAATGTAGTGCACCAATTGG
                             |   | | ||    | ||||| |||   ||       |  | |||   || ||||||  ||  ||  | |  ||||||              |  || ||||         |  |||||  | || |||||||| ||||| |||||||| |||||  | || ||||| ||||| ||||||||    || ||||| |||||||| || ||||| || |||||||||||||
gtaagattctttttcaccaaacccaactactcttgctatttctccctaccaggaaaatgcttctagttttctattttgtagaatattgttgtgtggttctatagtgttgttgagaagaccagccatctcaagctaagtctactcttgttatatttcagTATACCCCTGCGATTGATATCTGGAGTGTCGGTTGCATTTTTGCGGAAATGCTTTTGGGTAAGCCTTTGTTTCCCGGGAAAAACGTTGTGCACCAATTGG

upper sequence: GLYMA09G30790.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv17s0000g02570.t01 (Vitis vinifera), 3'ss of exon 4
cctcttcaatcctcctctaccgggattgtgtatgatttatgaagttgaatatatttaagtattgcacta-gtgtgtaatttc--aaatccttgtc--ttttgcagTATACGCCTGCAATTGATATTTGGAGCATTGGATGCATATTTGCAGAAATGCTCAGTGGGAAGCCATTGTTTCCTGGAAAAAATGTAGTGCACCAATTGG
    ||  ||        |||    | || ||| |  | | |       ||| |||   ||||  ||||  | |  ||||||  ||| |||| ||  |||| ||||| || ||||| ||||||||||||||||| ||||||||||||||||||||||| |  || || ||  ||||||| || ||||||||||||||||| ||||
--cttttgatgaaatatgacctctttggtttataaaatttaagtggagttatgttt---tattaaactatatatcaaatttcttaaaaccttctccatttttcagTACACTCCTGCGATTGATATTTGGAGCATAGGATGCATATTTGCAGAAATGCTTACAGGAAAACCGCTGTTTCCGGGGAAAAATGTAGTGCACCAGTTGG

upper sequence: GLYMA09G30790.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ26549 (Selaginella moellendorffii), 3'ss of exon 4
cctcttcaatcctcctctaccgggattgtgtatgatttatgaagttgaatatatttaagtattgcactagtgtgtaatttcaaatccttgtcttttgcagTATACGCCTGCAATTGATATTTGGAGCATTGGATGCATATTTGCAGAAATGCTCAGTGGGAAGCCATTGTTTCCTGGAAAAAATGTAGTGCACCAATTGG
                                        | |   | ||||   |   | ||   ||   |   | |    |   ||||| |   ||||||||| || ||||| || || ||||||||||| ||||||||||| || |   ||| | |||||||| ||||||||||||| || ||    || ||  | |
----------------------------------------gtaagaggatattggttcatttttttctgacgccaagt---gatctcttgtat---gcagTATACTCCAGCAATCGACATATGGAGCATTGGTTGCATATTTGCTGAGACAATCACTCGGAAGCCACTGTTTCCTGGAAAGAACGTTACTCATCAGCTCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgaatatatttaagtattgcactagtgtgtaatttcaaatccttgtcttttgcagTATACGCCTGCAATTGATATTTGGAGCATTGGATGCATATTTGCAGAAATGCTCAGTGGGAAGCCATTGTTTCCTGGAAAAAATGTAGTGCACCAATTGG
                                       tccttgtcttttgc  CT-rich tract
     atatttaagtatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cctcttcaatcctcctctaccgggattgtgtatgatttatgaagttgaatatatttaagtattgcactagtgtgtaatttcaaatccttgtcttttgcagTATACGCCTGCAATTGATATTTGGAGCATTGGATGCATATTTGCAGAAATGCTCAGTGGGAAGCCATTGTTTCCTGGAAAAAATGTAGTGCACCAATTGG

cctcttc
- - - - - -ctcctct
- - - - - - - - - - -gggattg
- - - - - - - - - - - - - - tgtatga
- - - - - - - - - - - - - - - - - - -tatgaag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgcacta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtgtgta