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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAGTTCATTTTTCACTGAGCAACTGACAGCTTTTGAGGTCTGGCTGGATCATGGATCTGAGCATAAGAAGCCACCAGAGCAGTTACCTATTGTTCTTCAGgtgccacctgaaccctaaatttacccctcctgtgttttaaaagaaggcccctatcttatggtccatgagaaactattcatatctatttgtcattcatcga...

Basic information

species Arabidopsis thaliana
transcript AT5G01770.1
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G01770.1 (Arabidopsis thaliana), 5'ss of exon 10
lower sequence: LOC_Os12g01922.1 (Oryza sativa), 5'ss of exon 10
AAGTTCATTTTTCACTGAGCAACTGACAGCTTTTGAGGTCTGGCTGGATCATGGATCTGAGCATAAGAAGCCACCAGAGCAGTTACCTATTGTTCTTCAGgtgccacctgaaccctaaatttacccctcctgtgttttaaaagaaggcccctatcttatggtccatgagaaactattcatatctatttgtcattcatcga--
 ||| |||||||||| |||||| ||||||| ||||| || ||||| |||||||| |||||  | ||||| || ||||| ||| ||||||||||||||||||    || |     | |  |  | |  | |    |  ||            | |  | ||     | ||    ||  |   |||     | ||      |  
GAGTCCATTTTTCACGGAGCAATTGACAGCATTTGAAGTTTGGCTTGATCATGGCTCTGAAGACAAGAAACCCCCAGAACAGCTACCTATTGTTCTTCAGgcaagacattttttcca--tccagctattcaagatgctagtgttttttttttgttatttgagtggtaagttggtaaccgactctccaaatgatggcaaaata

upper sequence: AT5G01770.1 (Arabidopsis thaliana), 5'ss of exon 10
lower sequence: LOC_Os11g01872.1 (Oryza sativa), 5'ss of exon 9
AAGTTCATTTTTCACTGAGCAACTGACAGCTTTTGAGGTCTGGCTGGATCATGGATCTGAGCATAAGAAGCCACCAGAGCAGTTACCTATTGTTCTTCAGgtgccacctgaaccctaaatttacccctcctgtgttttaaaagaaggcccctatcttatggtccatgagaaacta-ttcatatctatttgtc--attcatcga---
 ||| |||||||||| |||||| ||||||| ||||| || ||||| |||||||| |||||  | ||||| || ||||| ||| ||||||||||||||||||    || |      |  ||  | |  | |    |  ||       |    | | || || |   ||||     | ||  || ||   | ||  | | || |    
GAGTCCATTTTTCACGGAGCAATTGACAGCATTTGAAGTTTGGCTTGATCATGGCTCTGAAGACAAGAAACCCCCAGAACAGCTACCTATTGTTCTTCAGgcaagacattt-ttttccatccagctattcaagatgctagt-----gttttttttttttgttatttgagtggtaagttggtaactgactctccaaatgatggcaaa

upper sequence: AT5G01770.1 (Arabidopsis thaliana), 5'ss of exon 10
lower sequence: GRMZM2G460090_T01 (Zea mays), 5'ss of exon 1
AAGTTCATTTTTCACTGAGCAACTGACAGCTTTTGAGGTCTGGCTGGATCATGGATCTGAGCATAAGAAGCCACCAGAGCAGTTACCTATTGTTCTTCAGgt--gccacctgaaccctaaatttaccc-ctcctgtgttttaaaagaaggcccctatcttatggtccatgagaaactattcatatctatttgtcattcatcga--
|||| | ||||| || || |||||||| |||||||| || ||||| |||||||| |||||| | ||||| || || || |||||||| || |||||||||||  | ||  |      || | ||||   |   |   | |||   | |    ||  | | |     | |   || || ||||  | | | |    | |   |   
AAGTCCTTTTTTTACGGAACAACTGACGGCTTTTGAAGTGTGGCTTGATCATGGCTCTGAGGACAAGAAACCTCCTGAACAGTTACCCATAGTTCTTCAGgtaaggcattttgcttatacacttacatacaagtcaatattatctgtaaaatccagtttaa-----ctttgtaacctcttcacctttctctaagctgctatggtt

upper sequence: AT5G01770.1 (Arabidopsis thaliana), 5'ss of exon 10
lower sequence: GLYMA18G44210.1 (Glycine max), 5'ss of exon 10
AAGTTCATTTTTCACTGAGCAACTGACAGCTTTTGAGGTCTGGCTGGATCATGGATCTGAGCATAAGAAGCCACCAGAGCAGTTACCTATTGTTCTTCAGgtgccacctgaaccctaaatttacccctcctgtgttttaaaa-gaaggccccta--tcttatggtccatgagaaactattcatatctatttgtcattcatcga
 ||| |||||||||| |||||  ||||||| |||||||| ||||| || ||||| ||||| |||||||| |||||||||||||| ||||| ||||||||||||| | |     | |    ||      | | ||    |    |  ||| | ||   ||  || |   ||  |   ||     || | | ||  ||       
TAGTACATTTTTCACCGAGCAGTTGACAGCATTTGAGGTATGGCTTGACCATGGTTCTGAACATAAGAAACCACCAGAGCAGTTGCCTATAGTTCTTCAGgtgcgatccttgtcttggtctttgttaccatttgagccattttgttggctcataatactcttgttaggtggtaggttacatg-atttttatgaaatcagct--

upper sequence: AT5G01770.1 (Arabidopsis thaliana), 5'ss of exon 10
lower sequence: GLYMA09G41510.1 (Glycine max), 5'ss of exon 10
AAGTTCATTTTTCACTGAGCAACTGACAGCTTTTGAGGTCTGGCTGGATCATGGATCTGAGCATAAGAAGCCACCAGAGCAGTTACCTATTGTTCTTCAGgtgccacctgaaccctaaatttacccctcctgtgttttaa-aagaaggcccctatcttatggtccatgagaaactattcatatctatttgtcattcatcga
 ||| ||||||||||||||||  ||||||| |||||||| ||||| || ||||| ||||| |||||||| |||||||| ||||| ||||| ||||||||||||| | |     | |   |||      | | ||    |  | |  ||| | ||  |   | |   |   |   |      || | | ||  ||     | 
TAGTACATTTTTCACTGAGCAGTTGACAGCATTTGAGGTATGGCTTGACCATGGTTCTGAACATAAGAAACCACCAGAACAGTTGCCTATAGTTCTTCAGgtgcgatccttgtcttggtttttgtaaccatttgagccattatgttggctcataattctcgttaggttgtaggtttcgtg-atttttgtgaaatcagctgt

upper sequence: AT5G01770.1 (Arabidopsis thaliana), 5'ss of exon 10
lower sequence: Vv08s0058g00890.t01 (Vitis vinifera), 5'ss of exon 10
AAGTTCATTTTTCACTGAGCAACTGACAGCTTTTGAGGTCTGGCTGGATCATGGATCTGAGCATAAGAAGCCACCAGAGCAGTTACCTATTGTTCTTCAGgtgccacctgaaccctaaatttacccctcctgtgttttaaaagaaggcccctatcttatggtccatgagaaactattcatatctatttgtcattcatcga
|||| | || ||||||||||| ||||| ||||||||||| ||||| ||||||||||| || || ||||| |||||||||||||| || ||||||||||||||   |  |   || | | |             |   |  |    || |  | | || |   || | | |   |  |  | | ||  | |  ||    | 
AAGTCCTTTCTTCACTGAGCAGCTGACTGCTTTTGAGGTATGGCTAGATCATGGATCAGAACACAAGAAACCACCAGAGCAGTTGCCAATTGTTCTTCAGgtaggatattttccttgattcctataaattccaggactgtagtttggtctttgttttttccccccttatattatggtggtttttaagtatatttttatgg

upper sequence: AT5G01770.1 (Arabidopsis thaliana), 5'ss of exon 10
lower sequence: PP1S26_271V6.1 (Physcomitrella patens), 5'ss of exon 10
AAGTTCATTTTTCACTGAGCAACTGACAGCTTTTGAGGTCTGGCTGGATCATGGATCTGAGCATAAGAAGCCACCAGAGCAGTTACCTATTGTTCTTCAGgtgccacct-gaaccctaaatt-tacccctcctgtgttttaaaagaaggcccctatcttatggtccatgagaaactattcatatctatttgtcattcatcga
 |||   ||||| || |||||| ||||||||||||| || ||| |||| ||||| |||||    || ||||||||||||||| | || |||||||| |||||      | | |   ||  |   | ||    |    |  | | |   |    |   | |  |  | ||   |  |  |  |    ||   |     ||   
TAGTCTTTTTTTTACGGAGCAATTGACAGCTTTTGAAGTTTGGTTGGAGCATGGCTCTGATAGGAAAAAGCCACCAGAGCAGCTTCCCATTGTTCTGCAGgtattgtgtcgcatagtacctggcaacctggataaaatccagatgtgtgtttgtgattgaatgctcgtggacagatgctgtttgtgatcgttgggatatt--

upper sequence: AT5G01770.1 (Arabidopsis thaliana), 5'ss of exon 10
lower sequence: PP1S124_156V6.1 (Physcomitrella patens), 5'ss of exon 10
AAGTTCATTTTTCACTGAGCAACTGACAGCTTTTGAGGTCTGGCTGGATCATGGATCTGAGCATAAGAAGCCACCAGAGCAGTTACCTATTGTTCTTCAGgtgccacctgaaccctaaatttacccctcctgtgttttaaaagaag-gcccctatcttatggtccatgagaaac-tattcatatctatttgtcattcatcga--
 ||| | |||||||| |||||| |||||||||| ||||| |||||||| ||||| |||||    ||||||||||| |||||  | ||||| |||||||| ||      ||| |    ||   | |      ||| |   |  | ||   |  |   |    |  ||||| |||| || | |      ||| | ||     |   
TAGTCCTTTTTTCACAGAGCAATTGACAGCTTTCGAGGTGTGGCTGGAGCATGGTTCTGAAAGGAAGAAGCCACCTGAGCAACTTCCTATCGTTCTTCAAgtatagtgtgatc----aagccatctaagtagtgctcagactggagtatctatggatgcatgctcatgaaaaacgtagttagcgacgtttctgatgttctgtat

upper sequence: AT5G01770.1 (Arabidopsis thaliana), 5'ss of exon 10
lower sequence: PP1S199_73V6.1 (Physcomitrella patens), 5'ss of exon 10
AAGTTCATTTTTCACTGAGCAACTGACAGCTTTTGAGGTCTGGCTGGATCATGGATCTGAGCATAAGAAGCCACCAGAGCAGTTACCTATTGTTCTTCAGgtgccacctgaaccctaaatttacccctcctgtgt-tttaaaagaaggcccctatcttatggtccatgagaaactattcatatctatttgtcattcatcga-
 ||| | |||||||| |||||| ||||||| ||||| || ||| |||| ||||| |||||||  |||||||||||||||||| | ||||| ||||| |||||      |||      | | | ||  |     ||  | | |   |||  ||||| |    ||   |  ||     || |  |    | ||     ||    
TAGTCCTTTTTTCACAGAGCAATTGACAGCCTTTGAAGTGTGGTTGGACCATGGTTCTGAGCGGAAGAAGCCACCAGAGCAGCTCCCTATCGTTCTGCAGgtatagtgtgatgtagtactgtgccaataagtagtactcagattcaggtacctatgtaggagttttttggagg--gtttagtttgcgtcgttgactatgttc

Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAGTTCATTTTTCACTGAGCAACTGACAGCTTTTGAGGTCTGGCTGGATCATGGATCTGAGCATAAGAAGCCACCAGAGCAGTTACCTATTGTTCTTCAGgtgccacctgaaccctaaatttacccctcctgtgttttaaaagaaggcccctatcttatggtccatgagaaactattcatatctatttgtcattcatcga

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tacccctc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaagaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cccctatc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -agaaacta