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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagagcccaccaagtgaataactcgaagcatgctaggtgattcagcgcttcagcaccatcatctaatgtctctctcattatgcagGACAAGTTCCACTCCTTCCACCCGGTGGCCACCATCCTTAGCTACCTCACCAAGGCACCACTG

Basic information

species Zea mays
transcript GRMZM2G392513_T02
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G392513_T02 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os03g09250.1 (Oryza sativa), 3'ss of exon 8
gtaagagccc------accaag--tgaataactcgaagcatgctaggtgatt--cagcgctt----cagcaccatcatctaa-----tgtctctctcattat-----gcagGACAAGTTCCACTCCTTCCACCCGGTGGCCACCATCCTTAGCTACCTCACCAAGGCACCACTG
|||||||  |      ||  ||    | | ||||   || ||||  |  |||  || |  ||    |||||  ||   |||      ||| || ||  ||||     |||||| |||||||| |||||||| || ||||| |||||||| |||||||||||||||||||| || 
gtaagagttctgatggactgagatcaattgactctctgc-tgctctgcaattgccaccctttttgccagcaaaattgactatgttgttgtttcacttgttatcctgtgcagGAGAAGTTCCATTCCTTCCATCCAGTGGCTACCATCCTGAGCTACCTCACCAAGGCACCCCTT

upper sequence: GRMZM2G392513_T02 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os03g09250.2 (Oryza sativa), 3'ss of exon 8
gtaagagccc------accaag--tgaataactcgaagcatgctaggtgatt-cagcgctt-----cagcaccatcatctaa-----tgtctctctcattat-----gcagGACAAGTTCCACTCCTTCCACCCGGTGGCCACCATCCTTAGCTACCTCACCAAGGCACCACTG--------------------
|||||||  |      ||  ||    | | ||||   || ||||  |  ||| |  | |||     |||||  ||   |||      ||| || ||  ||||     |||||| |||||||| |||||||| || ||||| |||||||| |||||||||||||||||||| ||                     
gtaagagttctgatggactgagatcaattgactctctgc-tgctctgcaattgccaccctttttgccagcaaaattgactatgttgttgtttcacttgttatcctgtgcagGAGAAGTTCCATTCCTTCCATCCAGTGGCTACCATCCTGAGCTACCTCACCAAGGCACCCCTTGTGAGTGCATACATGCATCT

upper sequence: GRMZM2G392513_T02 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA08G14670.1 (Glycine max), 3'ss of exon 8
----gtaagagcccaccaagtgaataactcgaagcatgctaggtgat--tcagcgcttcagcaccatcatctaatgtctctctcattatgcagGACAAGTTCCACTCCTTCCACCCGGTGGCCACCATCCTTAGCTACCTCACCAAGGCACCACTG-------------------------------------
    |  | |     |  |   | | | || || |    |   | ||  | ||   || |    | |||  | | || | |  | |||  ||||  ||||||||||| |||||||| || || |||||||| || ||||| |||||||| || |||                                     
gtttgccatatgttgcttaaccattcattccaacctctatttcttatctttagttttttaaagac-tcaaatga-gtttatggcttta-acagGGAAAGTTCCACTCATTCCACCCAGTTGCGACCATCCTCAGTTACCTGACCAAGGCCCCTCTGGTAAGTATAATGTATCTGATTCATAATTGTTCAGTGA

upper sequence: GRMZM2G392513_T02 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA08G14670.2 (Glycine max), 3'ss of exon 8
----gtaagagcccaccaagtgaataactcgaagcatgctaggtgat--tcagcgcttcagcaccatcatctaatgtctctctcattatgcagGACAAGTTCCACTCCTTCCACCCGGTGGCCACCATCCTTAGCTACCTCACCAAGGCACCACTG
    |  | |     |  |   | | | || || |    |   | ||  | ||   || |    | |||  | | || | |  | |||  ||||  ||||||||||| |||||||| || || |||||||| || ||||| |||||||| || |||
gtttgccatatgttgcttaaccattcattccaacctctatttcttatctttagttttttaaagac-tcaaatga-gtttatggcttta-acagGGAAAGTTCCACTCATTCCACCCAGTTGCGACCATCCTCAGTTACCTGACCAAGGCCCCTCTG

upper sequence: GRMZM2G392513_T02 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA05G31450.4 (Glycine max), 3'ss of exon 5
-------gta-agagcccaccaagtgaataactcgaagcatgctaggtgattcagcgcttcagcaccatcatctaatgtctctctcattatg-cagGACAAGTTCCACTCCTTCCACCCGGTGGCCACCATCCTTAGCTACCTCACCAAGGCACCACTG
        || | |     |  | | | | | || ||||    |   | |||    | ||    |  |   || ||||  | | |   |    ||||  || |||||||| |||||||| || || ||||||||||| ||||| |||||||| || |||
gtttgtcatatatatgttgcttaatcattcattccaagctctatctcttatttttagttttttaaagac--tcaaatgagtttatggcttcaacagGGAAAATTCCACTCATTCCACCCAGTTGCGACCATCCTTAGTTACCTGACCAAGGCCCCTCTG

upper sequence: GRMZM2G392513_T02 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA05G31450.3 (Glycine max), 3'ss of exon 8
-------gta-agagcccaccaagtgaataactcgaagcatgctaggtgattcagcgcttcagcaccatcatctaatgtctctctcattatg-cagGACAAGTTCCACTCCTTCCACCCGGTGGCCACCATCCTTAGCTACCTCACCAAGGCACCACTG----
        || | |     |  | | | | | || ||||    |   | |||    | ||    |  |   || ||||  | | |   |    ||||  || |||||||| |||||||| || || ||||||||||| ||||| |||||||| || |||    
gtttgtcatatatatgttgcttaatcattcattccaagctctatctcttatttttagttttttaaagac--tcaaatgagtttatggcttcaacagGGAAAATTCCACTCATTCCACCCAGTTGCGACCATCCTTAGTTACCTGACCAAGGCCCCTCTGGTAA

upper sequence: GRMZM2G392513_T02 (Zea mays), 3'ss of exon 6
lower sequence: AT4G39800.1 (Arabidopsis thaliana), 3'ss of exon 8
gtaagagcccaccaagtgaataactcgaagcatgctaggtgattcagcgcttcagcaccatcatct-aatgtct-----ctctcattatgcagGACAAGTTCCACTCCTTCCACCCGGTGGCCACCATCCTTAGCTACCTCACCAAGGCACCACTG-------------------------------------
      |  |  || ||  | |   |     ||  | |||  |         | | |||    | |  |||| |     |     ||  |||||  ||||| ||||| ||||| || ||||||||||| || |||||||||||||||||||||||                                      
------gttcgtca-gttcacagtacatgttattttgggttctctgttttcactgaaccgcggttttgatgttttgaaacatctttttggcagGGAAAGTTTCACTCTTTCCATCCTGTGGCCACCATACTCAGCTACCTCACCAAGGCACCACTTGTACCGCCGGGAACTCCGGTGATTAACGCACTGTCGA

upper sequence: GRMZM2G392513_T02 (Zea mays), 3'ss of exon 6
lower sequence: Vv07s0031g00920.t01 (Vitis vinifera), 3'ss of exon 8
gtaagagcccaccaagtgaataactcgaagca--tgctaggtgattcagcgcttcagcaccatcatctaatgtctctctcattatgcagGACAAGTTCCACTCCTTCCACCCGGTGGCCACCATCCTTAGCTACCTCACCAAGGCACCACTG
||  |    |  |       | |   ||  |   ||||  |   || | |    ||     || ||  |  |  | |   ||| ||||||||||||| || ||||||||||| || ||||||||||| || |||||||||||||| || |||
gtctgttttcttctgcatccttatgggaccctcttgctttggtttttaccatcaca-tggaatgattcataggatgttcaattttgcagGACAAGTTTCATTCCTTCCACCCAGTTGCCACCATCCTCAGTTACCTCACCAAGGCCCCTCTG

upper sequence: GRMZM2G392513_T02 (Zea mays), 3'ss of exon 6
lower sequence: PP1S55_204V6.1 (Physcomitrella patens), 3'ss of exon 7
-----------------------------------gtaagagcccaccaagtgaataactcgaagcatgctaggtgattcagcgcttcagcaccatcatctaat--gtctctctcattatgcagGACAAGTTCCACTCCTTCCACCCGGTGGCCACCATCCTTAGCTACCTCACCAAGGCACCACTG-------------------------------------
                                    |   |  | | |    | || |  |          |  |  |     | ||  | |     ||  |||  |   || ||||  ||||||| |||||||| || ||||||||||| |||    |||| ||||||||||||||||| ||  ||                                     
gtaatctacaatctccaaatctctcttatattattctgttaatcaatcgcaaggattaacctctttggttcacattttctttggtttttggaattaaattgaatcgggtactttcatgttgcagGAGAAGTTCCATTCTTTCCACCCGGTTGCCGTACTCCTGAGCTACCTCACCAAGGCTCCCTTGGTACCCCCAGGTACCCCAGTGGTTAACGCGTTGGCTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgctaggtgattcagcgcttcagcaccatcatctaatgtctctctcattatgcagGACAAGTTCCACTCCTTCCACCCGGTGGCCACCATCCTTAGCTACCTCACCAAGGCACCACTG
                              atctaat  putative branch site (score: 3)
                                      tctctctcatt  CT-rich tract
                              atctaat  TA-rich tract