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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttgttacttaatcactgtctctatttgactaccttgtctttgcaaaagcaaattagaaagagagttaacatttttttctttctataaacaaatttacagGCCAGTGATCGATCAAAACTTCTACTACATGGGGCTGAAATATACGTCCCCAACGTTCTCATGCGCCATGAGTAACATGCTTCCGGCCATGACCTTTATC

Basic information

species Arabidopsis thaliana
transcript AT5G07050.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G07050.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os05g33900.1 (Oryza sativa), 3'ss of exon 1
gttgttacttaatcactgtctctatttgactaccttgtctttgcaaaagcaaattagaaaga-------gagttaacatttttttctttctataaacaaatttacagGCCAGTGATCGATCAAAACTTCTACTACATGGGGCTGAAATATACGTCCCCAACGTTCTCATGCGCCATGAGTAACATGCTTCCGGCCATGACCTTTATC
||   |||  |  ||     |  |  |   | |  ||  |||  |  |    ||| |    |       |   | ||       | | | | ||     |  |  ||||| ||||||||||| || |||||||||   ||||| || |  || || || || ||||| ||||||||||| |||||||| ||||||||||||||  ||
gtacgtacgcatacaaaaattggagatatatgctctgattttttagcacagtatttgctctattctcacgcactgaccggccaatgtgtatgtatgtccacgtgtagGCCGGTGATCGATCAGAATTTCTACTACGCCGGGCTCAAGTTCACCTCGCCGACCTTCTCCTGCGCCATGAGCAACATGCTCCCGGCCATGACCTTCGTC

upper sequence: AT5G07050.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os01g58910.1 (Oryza sativa), 3'ss of exon 2
gttgtta-cttaatcactgtctctatttg-actaccttgtctttgcaaaagcaaattagaaa-gagagttaacatttttttctttctataaacaaatttacagGCCAGTGATCGATCAAAACTTCTACTACATGGGGCTGAAATATACGTCCCCAACGTTCTCATGCGCCATGAGTAACATGCTTCCGGCCATGACCTTTATC
  ||    |||  |||       || | | |||||| |          | |||    ||||  |  ||||   |   |  |   |  ||   |    ||||||||| ||||||||||| ||||||||||||   || || || |  ||    ||||| ||| ||||||||||||| ||||| || || |||||||||||  | 
-ctgccggctttttcagaaatggtactggtactaccgtactagctagcatgcatgcaagaactgtcagtt--taacctcatgcatgcatgtccgtcattacagGCCTGTGATCGATCAGAACTTCTACTACGCCGGCCTCAAGTTCACCGGGCCAACCTTCGCATGCGCCATGAGCAACATCCTCCCCGCCATGACCTTCGTG

upper sequence: AT5G07050.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G136567_T02 (Zea mays), 3'ss of exon 1
-----------gttgttacttaatcactgtctc----tatttgactaccttgtctttgcaaaagcaaattagaaagagagttaacatttttttctttctataaacaaattt------acagGCCAGTGATCGATCAAAACTTCTACTACATGGGGCTGAAATATACGTCCCCAACGTTCTCATGCGCCATGAGTAACATGCTTCCGGCCATGACCTTTATC
           |  |   |||  |  ||||  |    ||||   ||      |  ||||      ||| |       || |     |   |     |||   ||    ||       ||||||| |||||||| || ||||||||||||  |||||| || |  || || || || ||||| ||||||||||| |||||||| || |||||||||||  ||
gtgcgtgcacagggggggcttggtt-ctgttccgagttattgcgctgttagtttcttgcttggcaaaactctgctctgactctgattgcatgcggctctgcgaatcgtttcgtgcgcacagGCCGGTGATCGACCAGAACTTCTACTACGCGGGGCTCAAGTTCACCTCGCCGACCTTCTCCTGCGCCATGAGCAACATGCTCCCCGCCATGACCTTCGTC

upper sequence: AT5G07050.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA06G46740.1 (Glycine max), 3'ss of exon 2
------------------------------------------------------------------------------------gttgttacttaatcactgtctctatttgactaccttgtctttg--caaaagcaa--------attagaaagagagttaacatttttttctttctataaacaa--atttacagGCCAGTGATCGATCAAAACTTCTACTACATGGGGCTGAAATATACGTCCCCAACGTTCTCATGCGCCATGAGTAACATGCTTCCGGCCATGACCTTTATC
                                                                                     |||||  | |||   | |    |   || ||   | |||| |  |||||  ||        ||| | ||  || | |     ||        | |  || |   |  ||||||||||||| |||||||||||||||||    ||| ||||||  || |||||||| |||||||| || ||||| ||| ||||||| |||||||| ||| | 
gttagttccataatttgatgcaccaatcgtatatatttagactatgtttgtttcatctaattaatttttttgaaaataatcaattttgtt-ttaaatttttcttgacaaaagaatattatttcttcgatcaaaaagaactaaatacattggcaaatgattaagttgcttacatcaagtgtttactattgtacacagGCCAGTGATTGATCAAAACTTCTACTATGCTGGGTTGAAATTAACCTCCCCAACTTTCTCATGTGCAATGAGCAACGTGCTTCCTGCCATGACTTTTGTT

upper sequence: AT5G07050.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA04G15590.1 (Glycine max), 3'ss of exon 2
---------------------------------------------------------gttgttacttaatcactgtctctatttgactaccttgtctttgcaaa------agcaaattagaaagagagttaacatttttttctttc--tataaacaaatttaca--gGCCAGTGATCGATCAAAACTTCTACTACATGGGGCTGAAATATACGTCCCCAACGTTCTCATGCGCCATGAGTAACATGCTTCCGGCCATGACCTTTATC
                                                           | ||    |||||  |  | ||||  |  |  || | | | ||||      |  | |||   ||  || | |     ||     |    | |  || | | ||||  |||| ||||| |||||||||||||||||    ||| ||||||  || |||||||| |||||||| || ||||| ||| ||||||| |||||||| ||| | 
gttagttccataatttgatgcactaaatatacatttggaccaagtttgtttcattaaaattttggaaaatcatcgatt-tattataaaattttatttcttcaaagaactaaatacattcataaatgaataagttgcttacatatcaagtgtttactattgtacacagGCCTGTGATTGATCAAAACTTCTACTATGCTGGGTTGAAATTAACCTCCCCAACCTTCTCATGTGCAATGAGCAACGTGCTTCCTGCCATGACTTTTGTT

upper sequence: AT5G07050.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA15G36200.1 (Glycine max), 3'ss of exon 2
----gttgtta--cttaat-cactgtc---tctatttgactaccttgtctttgcaaaagcaaattagaaagaga---gttaacat--ttttttctttctat--aaacaaatttacagGCCAGTGATCGATCAAAACTTCTACTACATGGGGCTGAAATATACGTCCCCAACGTTCTCATGCGCCATGAGTAACATGCTTCCGGCCATGACCTTTATC
    |||   |   ||||| ||||  |   ||||| |  |  |      |    | | | |   |  |||   |    |||| ||  || ||  ||| | |   |  ||    ||||||| ||||| |||||||| ||||||||    ||| ||||    || |||||||| |||||||| || ||||| ||||||||||| |||||||| ||| | 
gttagtttccaagtttaatgcactaacaattctatatagcaccgcaaggtgaatatatgaagtatgaaaatgcatatattaatatgattattaatttgtgttggattaataaaacagGCCTGTGATTGATCAAAATTTCTACTATGCTGGGTTGAAGCTCACATCCCCAACCTTCTCATGTGCAATGAGCAACATGCTTCCAGCCATGACTTTTGTG

upper sequence: AT5G07050.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv13s0084g00090.t01 (Vitis vinifera), 3'ss of exon 2
---------gttgttacttaatcactgtctctatttgactaccttgtctttgcaaaagcaaattagaaagagagtta---acatttttttctttctataaacaaattt----------acagGCCAGTGATCGATCAAAACTTCTACTACATGGGGCTGAAATATACGTCCCCAACGTTCTCATGCGCCATGAGTAACATGCTTCCGGCCATGACCTTTATC
          || ||  ||  ||  | ||| | |    |    |||    |    |  || || |   |     ||    | || ||     |  |  || ||| |||          | ||||| |||||||| || ||||| || ||    ||  ||||    || ||||| || ||||||||||| ||||| || ||||||||||||||||| ||  ||
gttagtctccttttttttttttccttttctttttcatgcattattgcaaatatgcagacacatcaatcaagctcttgtgtagatattcaatctgatcaaagcaagtttgtttggattgatagGCCTGTGATCGACCAGAACTTTTATTATGCTGGTTTGAAGCTGACTTCCCCGACCTTCTCATGCGCAATGAGCAATATGCTTCCGGCCATGACATTCGTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaagcaaattagaaagagagttaacatttttttctttctataaacaaatttacagGCCAGTGATCGATCAAAACTTCTACTACATGGGGCTGAAATATACGTCCCCAACGTTCTCATGCGCCATGAGTAACATGCTTCCGGCCATGACCTTTATC
                  agttaac  putative branch site (score: 3)
                  agttaacatttttttc  TA-rich tract