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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctttttgcatgcattaactttttagtatttagtaaaccaaataaagtttagtatttttggtgaccttctcaaagtccctaatatattttcccgttttcagACACCAAGGCATGGGAAGTGGATACTCTGAGAGGACACATGAATAATGTTTCATGTGTTATGTTCCATGCCAAACAGGACATCATTGTGTCAAATTCTGA

Basic information

species Glycine max
transcript GLYMA12G04290.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G04290.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os03g50340.1 (Oryza sativa), 3'ss of exon 2
---------ctttttgcatgcattaactttttagtatttagtaaaccaaataaagtttagtatttttggtgaccttctcaaagtccctaatatattttcccgttttcagACACCAAGGCATGGGAAGTGGATACTCTGAGAGGACACATGAATAATGTTTCATGTGTTATGTTCCATGCCAAACAGGACATCATTGTGTCAAATTCTGA
         ||      |  ||  |   | |   |||  || |||||      | |   ||||||    | |  |  || || |   |  ||| ||||        ||||||| ||||| |||||||| |||||| || | ||||||||||||||||| ||||| || ||||||||||| || || |||||||||||||| || || ||
attgctagactggccaaacacaaaactatatgcatatgcagcaaaccgct---attgaggtatttgaattaatgtaatctaaatg--tgctatttttttgga----cagACACGAAGGCTTGGGAAGTTGATACTTTGCGGGGACACATGAATAATGTGTCATGCGTGATGTTCCATGCTAAGCAAGACATCATTGTGTCCAACTCAGA

upper sequence: GLYMA12G04290.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os09g04110.1 (Oryza sativa), 3'ss of exon 2
ctttttgcatgcattaactttttagtatttagtaaaccaaataaagtttagtatttttggtgaccttctcaaagtc-cctaatatat-tttcccgtttt----cagACACCAAGGCATGGGAAGTGGATACTCTGAGAGGACACATGAATAATGTTTCATGTGTTATGTTCCATGCCAAACAGGACATCATTGTGTCAAATTCTGA
    |    | |   |  ||  ||| | |    ||||   || |  |  | ||    |  |||  |  |  || |     ||| ||  | | |  ||||    ||||||||||||| |||||||| |||||| || | || |||||||||||||| || || || ||||||||||| || || |||||||||||||| || || ||
----tattctactgcacattggtag-actggccaaacgctattatatgca-taccactattgaggtatttgaaatgatgcaatctaagtgtgctatttttggacagACACCAAGGCTTGGGAAGTTGATACTTTGCGGGGGCACATGAATAATGTGTCCTGCGTGATGTTCCATGCAAAGCAAGACATCATTGTGTCCAACTCAGA

upper sequence: GLYMA12G04290.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os03g50350.1 (Oryza sativa), 3'ss of exon 2
ctttttgcatgcattaactttttagtatttagtaaaccaaataaagtt-tagtatttttggtgaccttct-caaagtccctaatatattttcccgtttt-cagACACCAAGGCATGGGAAGTGGATACTCTGAGAGGACACATGAATAATGTTTCATGTGTTATGTTCCATGCCAAACAGGACATCATTGTGTCAAATTCTGA
         |   |    | |  |  ||| | |    | |  |   ||  | |||||   | ||   |     | |      | || |  |    |||  ||||||||||||| |||||||| |||||| || | || ||||||||||| || || ||||| ||||||||||| || || |||||||| ||||| || || ||
---gcaaactttgtggggtgtggaacattcacttccactatcaccattgcattatttaaagggataataggtgatgcaatctaaatgtgctgttttttgacagACACCAAGGCTTGGGAAGTTGATACTTTGCGGGGGCACATGAATAACGTGTCCTGTGTGATGTTCCATGCAAAGCAAGACATCATAGTGTCCAACTCAGA

upper sequence: GLYMA12G04290.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G010054_T01 (Zea mays), 3'ss of exon 2
ctttttgcatgcattaactttttagtatttagtaaac--caaataaagtttagtatttttggtgaccttctcaaagtccc-taatatat-----tttcccgttttcagACACCAAGGCATGGGAAGTGGATACTCTGAGAGGACACATGAATAATGTTTCATGTGTTATGTTCCATGCCAAACAGGACATCATTGTGTCAAATTCTGA
  ||| |||   || ||    |||||| |||| | |    ||| | ||| ||   | |     ||  |  |  || | |  |||| |||     ||     |   |||| |||||||| |||||||| |||||| | || || |||||||||||||| || ||||| ||||||||||| || || |||||||| |||||||| || ||
--tttagcag--atcaa----ttagtacttagcatatgtgaaaaagagtatacattctacaaggaaatgtttgaaatgcaataatctatatgtgttctttatggacagATACCAAGGCTTGGGAAGTTGATACTTTAAGGGGCCACATGAATAATGTGTCTTGTGTGATGTTCCATGCGAAGCAAGACATCATCGTGTCAAACTCAGA

upper sequence: GLYMA12G04290.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G149406_T01 (Zea mays), 3'ss of exon 2
ctttttgcatgcattaactttttagtatttagtaaaccaaataaagtttagtatttttggtgaccttctcaaagtccctaatatattttcccgtttt-----cagACACCAAGGCATGGGAAGTGGATACTCTGAGAGGACACATGAATAATGTTTCATGTGTTATGTTCCATGCCAAACAGGACATCATTGTGTCAAATTCTGA
 |||     | || | | |   ||| || |   |||  | ||| |  ||     |    |  |   | |  ||  |  |||| ||| |   |  |||     |||| |||||||| |||||||| |||||| | || || ||| |||||||||| || ||||| ||||||||||| || || |||||||||||||| || || ||
-tttagctgttcaattagtacctagcatatgtgaaagaatatatacatt----ctacaaggaaatatttggaatgcaataatttatgtctgctctttatggacagATACCAAGGCTTGGGAAGTTGATACTTTAAGGGGTCACGTGAATAATGTGTCCTGTGTGATGTTCCATGCGAAGCAAGACATCATTGTGTCTAACTCAGA

upper sequence: GLYMA12G04290.1 (Glycine max), 3'ss of exon 2
lower sequence: AT1G62020.1 (Arabidopsis thaliana), 3'ss of exon 3
---------------------------------ctttttgcatgc-attaactttttagtatttagtaaaccaaataaagtttagtat---------ttttggtgaccttctcaa-----------agtccctaatatattttc--ccgt----tttcagACACCAAGGCATGGGAAGTGGATACTCTGAGAGGACACATGAATAATGTTTCATGTGTTATGTTCCATGCCAAACAGGACATCATTGTGTCAAATTCTGA
                                  |||||  |||| || ||   |  |  || |     |    | ||  ||  | ||          || | |||   ||  ||           |||   ||| || ||||   |  |    || |||| || || || ||||| ||||||||  || |||| || |||||||| ||||||| ||||||||||||||| ||||||||||| ||||| ||||| |||||
gtaattatttggtggtatacttttgtgcttacaatttttatatgctatcaatcgtcaatgatgttactgatatgaaaatattctgcatgccttaatccttagatgaatctcgaaattgcaaagacgagttggtaacatgtttttaacgatatcattgcagAAACTAAAGCTTGGGAGGTGGATACATTGCGAGGCCATATGAATAACGTTTCATCTGTTATGTTCCATGCAAAACAGGACATAATTGTATCAAACTCTGA

upper sequence: GLYMA12G04290.1 (Glycine max), 3'ss of exon 2
lower sequence: AT2G21390.1 (Arabidopsis thaliana), 3'ss of exon 3
ctttttgcatgcattaactttttagtatttagtaaaccaaataaagtttagtatttttggtgaccttctcaaagtccctaatatattttcccgtttt--cagACACCAAGGCATGGGAAGTGGATACTCTGAGAGGACACATGAATAATGTTTCATGTGTTATGTTCCATGCCAAACAGGACATCATTGTGTCAAATTCTGA
          | |||  ||| |   ||| |            | ||     || ||||    | | |     ||   || ||   |||     || |  |||| || || || ||||| ||||||||  || |||| || |||||||| |||||||  |||||||||||||| ||||||||||| || |||||||| |||||
----------gtattt-cttatggatatctgtcttcttcttcacagaaagttaattttatgaatcatt---gaggtactgatgcgtttcaattttgttgcagAAACTAAAGCTTGGGAGGTGGATACATTGCGAGGTCATATGAATAACGTTTCATCCGTTATGTTCCATGCAAAACAGGACATTATCGTGTCAAACTCTGA

upper sequence: GLYMA12G04290.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv18s0001g13430.t01 (Vitis vinifera), 3'ss of exon 3
ctttttgcatgcattaacttt-ttagtatttagtaaaccaaataaagtttagtatttttggtgaccttctcaaagtccctaatatat-tttcccgttttcagACACCAAGGCATGGGAAGTGGATACTCTGAGAGGACACATGAATAATGTTTCATGTGTTATGTTCCATGCCAAACAGGACATCATTGTGTCAAATTCTGA
 ||  | |||   ||||   | ||    ||| || |     ||| |  || |||   |||   ||   || |  ||    ||  ||  ||| |   |||||||||| ||||| |||||||| |||||| |||| || |||||||||||||||||||||||  | || ||||| |  |||||  | |||||||||||||| ||
tttcatccatttgttaatcgtattttctttttgttagggttatagaactttgtagaattga--actagctaatggtttgcaacttaccttttctactttcagACACAAAGGCTTGGGAAGTAGATACTTTGAGGGGGCACATGAATAATGTTTCATGTGTCTTCTTTCATGCAAGGCAGGATGTGATTGTGTCAAATTCAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttagtatttttggtgaccttctcaaagtccctaatatattttcccgttttcagACACCAAGGCATGGGAAGTGGATACTCTGAGAGGACACATGAATAATGTTTCATGTGTTATGTTCCATGCCAAACAGGACATCATTGTGTCAAATTCTGA
                              ccctaat  putative branch site (score: 3)
                                      tattttcccgttttc  CT-rich tract
                                 taatatatttt  TA-rich tract