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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattgatatcttcttctcttaaaaactaaatagaaaaaaaaaattgatgctatcaattttgtttggtttgacatgatgtgagatctgaagtgtggtactgttttcacagGATGCTTGTGTATGAGTATGTAGACAATGGCAATCTAGAGCAATGGCTGCATGGGGACGTTGGAGCTGTAAGCCCTTTGACATGGAACATACGGATGAAC

Basic information

species Glycine max
transcript GLYMA09G39160.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G39160.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os03g03410.1 (Oryza sativa), 3'ss of exon 2
gtattgatatcttcttctcttaaaaactaaatagaaaaaaaaaattgatgc--tatcaattttgtttggtttgacatgatgtgagatctgaagtgtggtactgttttcacagGATGCTTGTGTATGAGTATGTAGACAATGGCAATCTAGAGCAATGGCTGCATGGGGACGTTGGAGCTGTAAGCCCTTTGACATGGAACATACGGATGAAC
                      | ||  ||||      |  || ||  |||  ||| | |     |  | || |   |||||   |     | ||  ||  || ||  |||||||||| |||||||| ||||||||||| |||||||| || |||||||| ||||| || || || |  || |||||  | || ||| |  |  ||||||||
--------------------gtacaatgaaatctcttcatcaattttgtgcattattattccctctctgattaatg-gatgttttactcacattgccgttttggttgaacagGATGCTCGTGTATGAATATGTAGACAACGGCAATCTTGATCAATGGCTTCATGGTGATGTAGGGGAAGTGAGCCCACTAACTTGGGAAGTCAGGATGAAC

upper sequence: GLYMA09G39160.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G014366_T03 (Zea mays), 3'ss of exon 2
gtattgatatcttcttctcttaaaaactaaatagaaaaaaaaaattgatgctatcaattttg--tttggtttgacatgatgtgagatctga-agtgtggtac-tgttttcacagGATGCTTGTGTATGAGTATGTAGACAATGGCAATCTAGAGCAATGGCTGCATGGGGACGTTGGAGCTGTAAGCCCTTTGACATGGAACATACGGATGAAC
|||| |||  | | ||    |     ||  ||           |    | || ||| ||| |  | |   |          |||   |||  | ||| ||   || ||  |||||||||||||||| |||||||| |||||||| ||||| || || ||||| ||||| || |||||||  ||||||||  | |||||| || |  ||||||||
gtat-gatggcatattgctatctcttcttcattcggtccggtgacacctactctcagtttggattctcaataatggaagcctgattcctgtcactgtcgtctatgcttgaacagGATGCTTGTGTACGAGTATGTGGACAATGGTAATCTTGACCAGTGGCTTCATGGTGATGTTGGAGAAGTAAGCCCACTAACATGGGACGTCAGGATGAAC

upper sequence: GLYMA09G39160.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G317938_T01 (Zea mays), 3'ss of exon 2
------------------gtattg--atatcttcttctctta----aaaactaaatagaaaaaaaaaattgatgctatcaattttgtttggtttgacatgatgtgagatctgaagtgtggtac-tgttttcacagGATGCTTGTGTATGAGTATGTAGACAATGGCAATCTAGAGCAATGGCTGCATGGGGACGTTGGAGCTGTAAGCCCTTTGACATGGAACATACGGATGAAC
                    ||||  || ||||||||  |      | | |||  |         || ||   | | |||||  ||    | |||      | |   |||   | | ||||   || ||  |||||||||| |||||||||||||| |||||||| ||||| || || ||||| ||||| || ||||| |  || |||||  |||||||| ||||  ||||||||
gtatgtgtgttggcaggcacattgcaatctcttcttcgttcggtggacacctagttgcttctctcaatttagggttctcaatgatgga-agcttgcttctgtat---atcactactatggtctatgcttgaacagGATGCTCGTGTATGAGTATGTGGACAATGGTAATCTTGACCAGTGGCTTCATGGTGATGTTGGCGAAGTGAGCCCACTGACATGGGACATCAGGATGAAC

upper sequence: GLYMA09G39160.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv15s0046g02030.t01 (Vitis vinifera), 3'ss of exon 2
gtattgatatct-tcttctcttaaaaactaaatagaaaaaaaaaattgatgctatcaattttgtttggtttgacatgatgtgagatctgaagtgtggtactgttttcacagGATGCTTGTGTATGAGTATGTAGACAATGGCAATCTAGAGCAATGGCTGCATGGGGACGTTGGAGCTGTAAGCCCTTTGACATGGAACATACGGATGAAC
|||||| || |  ||||||  ||||  || |              |||| | |   ||            | ||||  | | |  | | |  |||  |  | || ||  ||||||||||||||||||||||| |||||||| ||| | || || ||||| |||||||| || || |  || |||||| |||||||| | || ||||| |||
gtattgctacccatcttctgctaaatcctga--cactgggttttcttgaggatccaaa--------aaactaacattttttcatctttcatttgttttttttttgtc-tagGATGCTTGTGTATGAGTATGTGGACAATGGTAATTTGGACCAGTGGCTTCATGGGGATGTAGGGGAAGTCAGCCCTCTGACATGGGATATTCGGATTAAC

upper sequence: GLYMA09G39160.1 (Glycine max), 3'ss of exon 2
lower sequence: PP1S568_2V6.1 (Physcomitrella patens), 3'ss of exon 3
gtattgatatcttcttctcttaaaaactaaatagaaaaaaaaaattgatgctatcaattttgtttggtttgacatgatgtgagatctgaagtgtggtactgttttcacagGATGCTTGTGTATGAGTATGTAGACAATGGCAATCTAGAGCAATGGCTGCATGGGGACGTTGGAGCTGTAAGCCCTTTGACATGGAACATACGGATGAAC
    ||| | | | |  ||||   | ||            |   ||  || |  ||      ||   ||  || ||   ||  | ||   || |      | |||   |||||||||||||| ||||| || |||||||| ||||| ||||| ||||| |||||     |   |     || | |  |  ||||| |    || |||   
---gtga-agcatttattcttcccacctg----------gagtttttgtg-tgccagcacaattctcttacacgtgcaatgctaacttc-gtctctcgtggcttttgtagGATGCTTGTGTACGAGTACGTGGACAATGGGAATCTGGAGCAGTGGCTACATGGACCTCTGTCACAAACAAACACACTTCCATGGGAAGCTCGCATGCGG

upper sequence: GLYMA09G39160.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ27863 (Selaginella moellendorffii), 3'ss of exon 3
gtattgatatcttcttctcttaaaaactaaatagaaaaaaaaaattgatgctatcaattttgtttggtttgacatgatgtgagatctgaagtgtggtactgttttcacagGATGCTTGTGTATGAGTATGTAGACAATGGCAATCTAGAGCAATGGCTGCATGGGGACGTTGGAGCTGTAAGCCCTTTGACATGGAACATACGGATGAAC
                                                       |  |    ||    ||| |   | |   |  |    ||  | |||   |  |||||||||| || |||||||| ||||||||||| ||||| ||||| ||||| || ||    |       | | | | ||   |||||| |  |  ||||||| 
-----------------------------------------------------gtacgtcgaattctcatgaaagagtttttcactttggatgacgaact---tctacagGATGCTGGTATATGAGTACGTAGACAATGGTAATCTGGAGCAGTGGCTTCACGGCCCAGCCTCCATTCTCAACTCTCCAACATGGGAGGTTAGGATGAAA

upper sequence: GLYMA09G39160.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ36811 (Selaginella moellendorffii), 3'ss of exon 3
gtattgatatcttcttctcttaaaaactaaatagaaaaaaaaaattgatgctatcaattttgtttggtttgacatgatgtgagatctgaagtgtggtactgttttcacagGATGCTTGTGTATGAGTATGTAGACAATGGCAATCTAGAGCAATGGCTGCATGGGGACGTTGGAGCTGTAAGCCCTTTGACATGGAACATACGGATGAAC
                                                       |  |    ||    ||| |   | |   |  |    ||  | |||   |  |||||||||| || |||||||| ||||||||||| ||||| ||||| ||||| || ||    |       | | | | ||   |||||| |  | |||||||| 
-----------------------------------------------------gtacgtcgaattctcgtgaaagattttttcactttggatgacgaact---tctacagGATGCTGGTATATGAGTACGTAGACAATGGTAATCTGGAGCAGTGGCTTCACGGCCCAGCCTCCATTCTCAACTCTCCAACATGGGAAGTTCGGATGAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aattttgtttggtttgacatgatgtgagatctgaagtgtggtactgttttcacagGATGCTTGTGTATGAGTATGTAGACAATGGCAATCTAGAGCAATGGCTGCATGGGGACGTTGGAGCTGTAAGCCCTTTGACATGGAACATACGGATGAAC
           gtttgac  putative branch site (score: 4)
                                           ctgttttc  putative PPT
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattgatatcttcttctcttaaaaactaaatagaaaaaaaaaattgatgctatcaattttgtttggtttgacatgatgtgagatctgaagtgtggtactgttttcacagGATGCTTGTGTATGAGTATGTAGACAATGGCAATCTAGAGCAATGGCTGCATGGGGACGTTGGAGCTGTAAGCCCTTTGACATGGAACATACGGATGAAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA