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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagaactttttttctgaaacattcaaagatattattctactacattttctaatcaaaaattaacttgcacgctttgttaaatctagGTGCTTAATCAAGACGAGACACCTCTCTTGTACAGTCTTGTCTTTGGAGAAGGTGTAGTGAACGATGCCACATCGGTCGTGCTCTTCAATGCAATACAGA

Basic information

species Arabidopsis thaliana
transcript AT3G06370.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G06370.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os07g47100.2 (Oryza sativa), 3'ss of exon 5
---gtaagaactttttttctgaaacattcaaagatattattctactacattttctaatcaaaaattaacttgcacgctttgttaaatctagGTGCTTAATCAAGACGAGACACCTCTCTTGTACAGTCTTGTCTTTGGAGAAGGTGTAGTGAACGATGCCACATCGGTCGTGCTCTTCAATGCAATACAGA
       ||||   ||||   | || |  | ||| |    |  | |  |  | |||||    ||| | |||   | |       ||   |||| || ||||| || ||||||||  | ||||||||||| || || || |||||||| ||||||||||| |||||  | ||||| ||||| ||| ||||||
gttagttgaacaaattttgccatacctcgagagagacc--tggattcaacgtgctaat--gtaatgatcttaacccc-------aaaacagGTCCTCAATCAGGATGAGACACCCTTTTTGTACAGTCTGGTATTCGGTGAAGGTGTTGTGAACGATGCTACATCAATTGTGCTTTTCAACGCACTACAGA

upper sequence: AT3G06370.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G063492_T01 (Zea mays), 3'ss of exon 6
gtaagaactttttttctgaaacattcaaagatattattctactacattttctaatcaaaaattaacttgcacg---ctttgttaaatctagGTGCTTAATCAAGACGAGACACCTCTCTTGTACAGTCTTGTCTTTGGAGAAGGTGTAGTGAACGATGCCACATCGGTCGTGCTCTTCAATGCAATACAGA
        ||| ||  ||||  |||      | ||||  || || |  ||   ||   ||   || ||    |    ||  |||  |  |||||||||| || || || ||||| ||  | || ||||| || ||||| |||||||| || || ||||||||||| || |||||||||||||||||  | |
-------gtttgttgttgaacaatttgccatttttatctta-taaaaattgagataggaagccaatttaattggaaattcattacttgcagGTGCTTAACCAGGATGAAACACCCCTACTCTATAGTCTAGTTTTTGGTGAAGGTGTTGTTAATGATGCCACATCTGTTGTGCTCTTCAATGCAATTGAAA

upper sequence: AT3G06370.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G701776_T01 (Zea mays), 3'ss of exon 2
gtaagaactttttttctgaaacattcaaagatattattctactacattttctaatcaaaaattaacttgcacgc---tttgttaaatctagGTGCTTAATCAAGACGAGACACCTCTCTTGTACAGTCTTGTCTTTGGAGAAGGTGTAGTGAACGATGCCACATCGGTCGTGCTCTTCAATGCAATACAGA-
         ||| || |  |||| ||    || ||||  || || |  ||   ||   ||   || ||    |    ||  |||  |  ||||| |||| || || || ||||| ||  | || ||||| || ||||| |||||||| || || ||||||||||| || |||||||||||||||||  | | 
--------gtttgttgttgaacaatctgccattttatctta-taaaaattgagataggaagccaatttaattggaaattcattacttgcagGTG-TTAACCAGGATGAAACACCCCTACTCTATAGTCTAGTTTTTGGTGAAGGTGTTGTTAATGATGCCACATCTGTTGTGCTCTTCAATGCAATTGAAAA

upper sequence: AT3G06370.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G704237_T01 (Zea mays), 3'ss of exon 3
gtaagaactttttttctgaaacattcaaagatattattctactacattttctaatcaaaaattaacttgcacg---ctttgttaaatctagGTGCTTAATCAAGACGAGACACCTCTCTTGTACAGTCTTGTCTTTGGAGAAGGTGTAGTGAACGATGCCACATCGGTCGTGCTCTTCAATGCAATACAGA-
        ||| ||  ||||  ||       | ||||  || || |  ||   ||   ||   || ||    |    ||  |||  |  ||||| |||| || || || ||||| ||  | || ||||| || ||||| |||||||| || || ||||||||||| || |||||||| ||||||||  | | 
-------gtttgttgttgaagaatctgccatttttatctta-taaaaattgagataggaagccaatttaattggaaattcattacttgcagGTG-TTAACCAGGATGAAACACCCCTACTCTATAGTCTAGTTTTTGGTGAAGGTGTTGTTAATGATGCCACATCTGTTGTGCTCTTTAATGCAATTGAAAA

upper sequence: AT3G06370.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv05s0020g01960.t01 (Vitis vinifera), 3'ss of exon 6
gtaagaactttttttctgaaacatt-caaagatattattctactacattttctaatcaaaaattaacttgcacgctttgttaaatctagGTGCTTAATCAAGACGAGACACCTCTCTTGTACAGTCTTGTCTTTGGAGAAGGTGTAGTGAACGATGCCACATCGGTCGTGCTCTTCAATGCAATACAGA
|||   |     || || |    |      | || || |            |   || | || | | ||   |  |    |   |  ||||||||||||| || ||||||||  |  | |||||||| || |||||||||||||| ||||| ||||||||||| || ||||| ||||||||||| ||||
gtacagatggccttactaagctgtgatcctgttactagttctaagggacaacacttccacaacttatttatccaatccaattg-tgcagGTGCTTAATCAGGATGAGACACCCTTACTCTACAGTCTGGTTTTTGGAGAAGGTGTTGTGAATGATGCCACATCTGTGGTGCTTTTCAATGCAATCCAGA

upper sequence: AT3G06370.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: PP1S31_203V6.1 (Physcomitrella patens), 3'ss of exon 6
gtaagaactttttttctgaaacattcaaagatattattctactacattttc--taatcaaaaattaacttgcacgctttgttaa--------------atctagGTGCTTAATCAAGACGAGACACCTCTCTTGTACAGTCTTGTCTTTGGAGAAGGTGTAGTGAACGATGCCACATCGGTCGTGCTCTTCAATGCAATACAGA
    | | |   || | ||||  | |||| | | |||||| ||   || |   ||   |  |  |     ||  || ||||| |              ||  |||| ||||||||||||||  |||||||  |||| |||||||| || |||||||| || ||||||||||| || ||||| ||  | |||   ||  | ||||
---ggtattgcattgcagaaatttacaaata-agtattcttctgatttcttggtagctatgaggtgttgagctggccttgttgacgtcttattttttcatgcagGTTCTTAATCAAGACGATTCACCTCTGCTGTATAGTCTTGTGTTCGGAGAAGGAGTTGTGAACGATGCTACCTCGGTAGTCTTATTCCGGGCTGTGCAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttattctactacattttctaatcaaaaattaacttgcacgctttgttaaatctagGTGCTTAATCAAGACGAGACACCTCTCTTGTACAGTCTTGTCTTTGGAGAAGGTGTAGTGAACGATGCCACATCGGTCGTGCTCTTCAATGCAATACAGA
                          aattaac  putative branch site (score: 2)
                                        ctttgtt  putative PPT
         tacattttctaatcaa  TA-rich tract