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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattattattgatcattatggagattatgctattgacattcttgcatttttttccctctattgaaattattcagtcttatagttctatcaattgtgttccctcagaattttcaaatctttttgatccgatcaattatattctcagGTACTATTCAAGTTTGGAAGTTGCTTCTGAATACTTTAGGTCTGGGGCTGATAAGATTTCCATTGGAAGTGATGCAGTTTATGCTGCAGAAGAATATTTA

Basic information

species Glycine max
transcript GLYMA18G12920.1
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G12920.1 (Glycine max), 3'ss of exon 13
lower sequence: LOC_Os03g15120.1 (Oryza sativa), 3'ss of exon 10
gtattattattgatcattatggagattatgctattgacattcttgcatttttttccctctattgaaattattcagtcttatagttctatcaattgtgttccctcagaatttt-caaatctttttgatccgatcaattatattctcagGTACTATTCAAGTTTGGAAGTTGCTTCTGAATACTTTAGGTCTGGGGCTGATAAGATTTCCATTGGAAGTGATGCAGTTTATGCTGCAGAAGAATATTTA
                                                | |   || ||| ||  |  | ||   | || |   || ||      |  |      |||     || |     |   |  |     ||   || |||| ||||| |||||||||||||| || || || ||||| |||||||| ||||| |||||||| ||||| |||||||| |||| |||||| ||||  ||||| 
-----------------------------------------------ctctcccccatctttttgaggtgttatttgttgtttgtcaatagtcaatactgagaaggaaaaggacagacagagtaattatgtattcttcccttgtcagATACTACTCAAGTTTGGAAGTAGCGTCAGAGTACTTCAGGTCTGGTGCTGACAAGATTTCAATTGGTAGTGATGCCGTTTTTGCTGCTGAAGCCTATTTG

upper sequence: GLYMA18G12920.1 (Glycine max), 3'ss of exon 13
lower sequence: AT4G26900.1 (Arabidopsis thaliana), 3'ss of exon 12
gtattattattgatcattatggagattatgctattgacat-tct-tgcatttttttccctctattgaaattattcagtcttatagttctatcaattgtgttccct-cagaattttcaaatctttttgatccgatcaattatattctcagGTACTATTCAAGTTTGGAAGTTGCTTCTGAATACTTTAGGTCTGGGGCTGATAAGATTTCCATTGGAAGTGATGCAGTTTATGCTGCAGAAGAATATTTA
   |   | || ||| ||   |   |  | || |  |||| ||| ||||    ||    ||| ||   ||  |||||    |    | |   | || | |||||| ||  | ||| | |||   || ||  |            |||||||||||||| || |||||||||||| |||| || || || || || ||||||||||| ||||| |||||||| || |||| ||||||||| || |   ||
--gtacatgttaatcttttcagcc-tgtttctgtgaacatgtctgtgcaggcattatgttctttt---atatttcagc--aaggactttgcaatttttattccctacaacaatttaacatcaagttaatttgg-----------ctcagGTACTATTCTAGCTTGGAAGTTGCTGCTGAGTATTTCAGATCCGGTGCTGATAAGATCTCCATAGGAAGTGACGCTGTTTCTGCTGCAGAGGAGTTCATA

upper sequence: GLYMA18G12920.1 (Glycine max), 3'ss of exon 13
lower sequence: Vv19s0090g00810.t01 (Vitis vinifera), 3'ss of exon 11
------------gtattattatt--gatcattatggagattatgctattgacattcttgcatttttttccctctattgaa-attattcagtctt--atagttctatcaattgtgttccctcagaattttcaaatctttttgatccga-tcaattatattctcagGTACTATTCAAGTTTGGAAGTTGCTTCTGAATACTTTAGGTCTGGGGCTGATAAGATTTCCATTGGAAGTGATGCAGTTTATGCTGCAGAAGAATATTTA
            || || || |   ||| ||| | |   || |   ||| |  || |  | ||| |||   | |||| ||  ||| |    |||   |  || | |  |   ||       |  ||| |  |  | || |  |   |  ||||    | |||||||| ||||| ||||||||||||||||| ||||| || ||||| ||||| ||||| ||||| |||||||||||||||||||||||||| ||||||||| ||
gtacacacttgggtgttgttttctggatgattgtcgttcttttttaatttat-ttttatcttttatttttttttattaaatgttaattctccttcagtgattttcttgag-atgaaagtgaactattatggatacattatattttaaaccaatctcttcctcagGTATTATTCTAGTTTGGAAGTTGCTTCAGAATATTTCAGGTCAGGGGCAGATAAAATTTCTATTGGAAGTGATGCAGTTTATGCTGCTGAAGAATATATA

upper sequence: GLYMA18G12920.1 (Glycine max), 3'ss of exon 13
lower sequence: PP1S43_232V6.1 (Physcomitrella patens), 3'ss of exon 12
gtattattattgatcattatggagattatgctattgacattcttgcatttttttccctctattgaaattattcagtcttatagttctatcaattgtgttccctcagaattttcaaatctttttgatccgatcaattatattctcagGTACTATTCAAGTTTGGAAGTTGCTTCTGAATACTTTAGGTCTGGGGCTGATAAGATTTCCATTGGAAGTGATGCAGTTTATGCTGCAGAAGAATATTTA
                                       | ||  ||| ||   ||     ||   || | ||| || | || ||      | | |||||    ||| |     | |||  |  |     |||  |  || | ||| |  |||||| |  | ||||| ||||| || ||||| || ||||| ||||| ||||| || |||||||||||||| ||||||||||| || || ||| | 
--------------------------------------ttcctcacatgttaagccgaac-ttttcatcactcaatcctgtattt------aatctgttcaag-agattgaagtactctcatcaactttgtcatatccatccacagATTTTATTCATGCCTAGAAGTGGCTTCAGAGTACTTCAGATCTGGAGCTGACAAGATATCTATTGGAAGTGATGCTGTTTATGCTGCTGAGGAGTATCTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attgtgttccctcagaattttcaaatctttttgatccgatcaattatattctcagGTACTATTCAAGTTTGGAAGTTGCTTCTGAATACTTTAGGTCTGGGGCTGATAAGATTTCCATTGGAAGTGATGCAGTTTATGCTGCAGAAGAATATTTA
                            ttttgat  putative branch site (score: 4)
                                              tattctc  putative PPT
               aattttcaaatctttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattattattgatcattatggagattatgctattgacattcttgcatttttttccctctattgaaattattcagtcttatagttctatcaattgtgttccctcagaattttcaaatctttttgatccgatcaattatattctcagGTACTATTCAAGTTTGGAAGTTGCTTCTGAATACTTTAGGTCTGGGGCTGATAAGATTTCCATTGGAAGTGATGCAGTTTATGCTGCAGAAGAATATTTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG