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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatttctttctctctcttacttttactgggaatgatcagattataccgcttcttatttatagaaattgatttttttttttttttttttttttttttttttttgcggatgctctcattagGTTCACTCAATCCGCGATGCTGCTGCTAACAATCTCAAGCGGCTTGCTGAGGAATTTGGTCCTGAATGGGCAATGCAACATATAGTTCCTCAG

Basic information

species Arabidopsis thaliana
transcript AT3G25800.2
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G25800.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: LOC_Os09g07510.1 (Oryza sativa), 3'ss of exon 9
gtatttctttctctctcttacttttactgggaatgatcagattataccgcttcttatttatagaaattgattttttttttttttttttttttttttt------ttttttgcggatgctctcatt--agGTTCACTCAATCCGCGATGCTGCTGCTAACAATCTCAAGCGGCTTGCTGAGGAATTTGGTCCTGAATGGGCAATGCAACATATAGTTCCTCAG
                           || |     |  |||||||  | || || || ||  | | ||      |  | ||| |    |  | |||      |||||  | |   || | |||  ||||   ||||||| | ||||||||||| |||||  | ||||| || |||||||| |||||||| |||||||| ||||| |||||| | ||||||
--------------------------ttgtgttcagt--gattatatagtttttttttaatgcagaatggacaagtggtatttataacctgctatttaagatgtttttaactggatctttaattttagGTCTTCTCAATCAGAGATGCTGCTGCAAACAACTTGAAGCGCCTAGCTGAGGAGTTTGGTCCAGAATGGGCGATGCAGCATATAATCCCTCAG

upper sequence: AT3G25800.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GRMZM2G102858_T01 (Zea mays), 3'ss of exon 9
------------------------gtatttctttctctctcttacttt---tactgggaatga----tcagattataccgcttcttatttatagaaattgatttttttttt--tttttttttttttttttttttttgcggatgc--------tctcattagGTTCACTCAATCCGCGATGCTGCTGCTAACAATCTCAAGCGGCTTGCTGAGGAATTTGGTCCTGAATGGGCAATGCAACATATAGTTCCTCAG
                         |||| |      ||  ||| |      ||   | ||      ||  || ||     || |  | |||| || |||| || ||  ||  || | | |  | |  |  |   |    || |        |  | | |||||  ||| ||| | ||||||| ||| || ||| | |||||  |  | ||||||||||| ||||| ||||| |||||||||||| ||||||||
gtgcataaataatttcaccaaccattattacacaagttccattaatgcagaaaccatgcatactatttctaatgatggtctttttagtctatataagttgaattcttgattgattctatgtaatgtaatagtgactcaaaataccaaacatttggcttcagGTTTTCTCGATCAGAGATGCTGGTGCCAATAATTTAAAGCGTTTGACAGAGGAATTTGGCCCTGAGTGGGCGATGCAACATATAATTCCTCAG

upper sequence: AT3G25800.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GRMZM2G164352_T04 (Zea mays), 3'ss of exon 9
-----------------------gtatttctttctctctcttacttttactgggaatgatcagattataccgcttcttatttatagaaattgatttttttttttttttttttttttttttttttttgcggatgctctcatt--agGTTCACTCAATCCGCGATGCTGCTGCTAACAATCTCAAGCGGCTTGCTGAGGAATTTGGTCCTGAATGGGCAATGCAACATATAGTTCCTCAG
                         |    | ||||| |    || |  |  |   |  | |  ||||| |  |   |   ||| | | ||  |  | | ||   |    || |   |||   |   |  |   |   |||  ||||    |||||| | |||||||| ||||||||  | ||||| ||||| || || |||||||| || ||||||||||| |||||| | ||||||
gtttgtatcattagggttatgtcaaaacagtatctctttggagctgtctccagcg-tctttatcttatatccttgagtgcatattggactttgtaatgtattgactaaaattgtcagtttaacta-actaaaatttggatttcagGTCTTTTCAATCAGAGATGCTGCCGCTAACAACTTGAAGCGCCTTGCAGAAGAGTTTGGTCCAGAGTGGGCAATGCAGCATATAATCCCTCAG

upper sequence: AT3G25800.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA02G10790.1 (Glycine max), 3'ss of exon 9
gtatttctttctctctcttacttttactgggaatgatcagattataccgcttcttatttatagaaattgatttttttttttttttttttttttttttttttttgcggatgctctcattagGTTCACTCAATCCGCGATGCTGCTGCTAACAATCTCAAGCGGCTTGCTGAGGAATTTGGTCCTGAATGGGCAATGCAACATATAGTTCCTCAG
                      |||    ||| |   ||   ||    |   | |||||   ||||     |||| |   |   | || |  ||    |  |||       |     |||||||| || ||||| || || |||||||||||| | ||||| || ||||| |||||||||||||| ||||| |||||||| ||| |||| |||
---------------------gtttgt--ggactctacatgctagtttgag-catattttaggaaaccaccttttctacatgactattgtcgttaacctcattgt------ttgttgtagGTTCATTCGATCCGTGAGGCAGCTGCTAACAATTTGAAGCGCCTAGCTGAAGAATTTGGTCCTGAGTGGGCTATGCAACACATAATTCCACAG

upper sequence: AT3G25800.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA10G42250.1 (Glycine max), 3'ss of exon 9
gtatttctttctctctcttacttttactgggaatgatcagattataccgcttcttatttatagaaattgatttttttttttttttttttttttttttttttttgcggatgctctcattagGTTCACTCAATCCGCGATGCTGCTGCTAACAATCTCAAGCGGCTTGCTGAGGAATTTGGTCCTGAATGGGCAATGCAACATATAGTTCCTCAG
                     || | ||    |    |    ||    |  |   ||||   ||| |  || ||     |     ||||| ||       || |    ||       |||||||| ||||| || || || |||||||||||  | || || |||||||| |||||||||||||| ||||| ||||| || ||| ||||||||
-------------------gtttgtgctctacacttccttgctagtgtgggtgc-attttgggaactgcatattgcacatgacggtttttgttaaccaccttagttattg-------tagGTTCATTCAATTCGTGAAGCAGCTGCTAACAACTTGAAACGCCTTGCTGAAGAATTTGGTCCTGAGTGGGCTATGCAGCACATAATTCCTCAG

upper sequence: AT3G25800.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA20G24790.1 (Glycine max), 3'ss of exon 9
gtatttctttctctctcttacttttactgggaatgatcagattataccgcttcttatttatagaaattgatttt-----tttttttttttttttttttttttttttttgcggatgctctcat--tagGTTCACTCAATCCGCGATGCTGCTGCTAACAATCTCAAGCGGCTTGCTGAGGAATTTGGTCCTGAATGGGCAATGCAACATATAGTTCCTCAG
                                  | |     | | |   | |||  |  |     |  |||||      |   | ||     |   | ||||| ||  |        | ||  |||||||| ||||| ||||| || |||||||||||  | || || |||||||| |||||||| ||||| ||||| ||||| || ||| ||||||||
----------------------------------gtttgtgctctccacttccttgctagtgtgggtgcattttgggaactgcatattgcacatgactgtttttgttaacaaccttagttattgtagGTTCATTCAATTCGCGAAGCAGCTGCTAACAACTTGAAACGCCTTGCTGAAGAATTTGGACCTGAGTGGGCTATGCAGCACATAATTCCTCAG

upper sequence: AT3G25800.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: Vv01s0011g03280.t01 (Vitis vinifera), 3'ss of exon 8
gtatttctttctctctcttacttttactgggaatgatcagattataccgcttcttatttatagaaattgatttttttttttttttttttttttttttttttttgcggatgctctcat------tagGTTCACTCAATCCGCGATGCTGCTGCTAACAATCTCAAGCGGCTTGCTGAGGAATTTGGTCCTGAATGGGCAATGCAACATATAGTTCCTCAG
                      | |  |  ||  | |   || ||     |  |  |||       |||  | |  | | | | ||| | |  ||         |  ||  | ||||       ||||| |||| || || |||||||||||||||||  | ||||| ||||| || |||||||||||||| ||||||||||| ||  || |||| |||
----------------------tattttaagagggctttcatcatctttgtcatcgttttct----ttgtctgtcatctatgtatttatgtagttcaaaagggacaaatattatcatgttgtgcagGTTTACTCCATTCGTGATGCTGCTGCTAACAACTTAAAGCGCCTTGCAGAAGAATTTGGTCCTGACTGGGCAATGCAGCACTTAATTCCACAG

upper sequence: AT3G25800.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: PP1S214_34V6.1 (Physcomitrella patens), 3'ss of exon 8
----------------gtatttctttctctctcttacttttactgggaatgatca-----gattataccgcttcttatttatagaaattgatttttttttttttttttttttttttttttttttgcggatgctctcattagGTTCACTCAATCCGCGATGCTGCTGCTAACAATCTCAAGCGGCTTGCTGAGGAATTTGGTCCTGAATGGGCAATGCAACATATAGTTCCTCAG
                  |    | | ||  |  |  |||   | |  ||| ||       || | | | ||| | || | |     || |    |  ||   |  | |  |||  || |||||  ||||      | |||||  |||| ||||| || || ||||| |||||||||||||| ||||| || || ||||||||||| |||||| |||| || ||  |||| |||
gttcatatattcccatcaagcaatgtttcgatggtggtttgtgtcgagatggtcgtcctcaatcagatctcttttcatatttgcttctttagaactagttcagtaatataatttcattcttttt-tggat-----taatagGTGTACTCTATCCGAGAGGCAGCTGCCAACAATCTCAAGCGTCTTGCCGAAGAGTTTGGTCCTGAGTGGGCATTGCAGCACATCATTCCACAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attgatttttttttttttttttttttttttttttttttgcggatgctctcattagGTTCACTCAATCCGCGATGCTGCTGCTAACAATCTCAAGCGGCTTGCTGAGGAATTTGGTCCTGAATGGGCAATGCAACATATAGTTCCTCAG
 aattgat  putative branch site (score: 4)
       tttttttttttttttt  CT-rich tract
     tttttttttttttttt  TA-rich tract