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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGGATGAGGGGTGCGATGTGATCGTGTTGGGCACGGGTCTCAAGGAGTGCATTCTCAGCGGTCTTCTCTCTGTCGATGGCCTCAAGgtactcatcagtttcctatttctttaattttcttttcaatagatccaattctcgcatgttaattcctatttgttgttcgattcag

Basic information

species Glycine max
transcript GLYMA07G24480.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G24480.1 (Glycine max), 5'ss of exon 1
lower sequence: LOC_Os05g23860.1 (Oryza sativa), 5'ss of exon 1
-------------ATGGATGAGGGGTGCGATGTGATCGTGTTGGGCACGGGTCTCAAGGAGTGCATTCTCAGCGGTCTTCTCTCTGTCGATGGCCTCAAGgtactcatcagtttcctatttctttaattttctttt-caatagatccaattctcgcatgttaattcctatttgttgttcgattcag---------------
             |||||||||| || ||| ||||||||| |||| ||||| |||||||||||||| |||||||| || ||||| ||||| |||||||||||||   ||   | || | | | |       ||       | |   |  | ||| |   |      | ||  || | |||   |                 
GCCGCTCGCCGCCATGGATGAGGAGTACGACGTGATCGTGCTGGGGACGGGCCTCAAGGAGTGCATCCTCAGCGGCCTCCTCTCCGTCGACGGCCTCAAGgtacctctctcctacccaatccatccgccgcctcccgtgctcggatcggtgctccc-catcgtcgtcgatccgtagatcgccccccacttcatctcatctg

upper sequence: GLYMA07G24480.1 (Glycine max), 5'ss of exon 1
lower sequence: LOC_Os05g34540.1 (Oryza sativa), 5'ss of exon 1
-------------ATGGATGAGGGGTGCGATGTGATCGTGTTGGGCACGGGTCTCAAGGAGTGCATTCTCAGCGGTCTTCTCTCTGTCGATGGCCTCAAGgtactcatc--agtttcctatttctttaattttcttttcaatagatccaattctcgcatgttaattcctatttgttgttcgattcag----------------
             |||||||||| || ||| ||||||||| | || ||||| |||||||||||||| |||||||| || ||||| ||||| |||||||||||||    |   |  ||   | ||| |   | ||| |        ||    |||| |  | |     |    |  |        |||                
ACGAGCAGGAGCCATGGATGAGGAGTACGACGTGATCGTGCTCGGGACGGGCCTCAAGGAGTGCATCCTCAGCGGCCTCCTCTCCGTCGACGGCCTCAAGgtacgtggctagggctctcgtctctctctctctctctctctc---tctctctctcacccgctcgccgccggctactagcttccgcagatgctcgccgtcgccg

upper sequence: GLYMA07G24480.1 (Glycine max), 5'ss of exon 1
lower sequence: LOC_Os07g16970.2 (Oryza sativa), 5'ss of exon 1
-------------ATGGATGAGGGGTGCGATGTGATCGTGTTGGGCACGGGTCTCAAGGAGTGCATTCTCAGCGGTCTTCTCTCTGTCGATGGCCTCAAGgtactcatcagtttcctatttctttaattttct-tttcaatagatccaattctcgcatgttaattcctatttgttgttcgattcag----------------
             ||||| | || || ||| ||||||||| | || ||||| |||||||||||||| |||||||| || ||||| |||||| ||||||||||  ||  |   | | | | ||| |   | ||| | ||  |   ||    |||| |    |   |||     |  | |||||  ||                
CCGCCCGCCCGCCATGGACGTGGAGTACGACGTGATCGTGCTCGGGACGGGGCTCAAGGAGTGCATCCTCAGCGGCCTCCTCTCCGTCGATCGCCTCAAGgtggtctccttctccatctctctctctctctctctctctctctctctctctctctctctctctctcccgcccg--gatcgatctagctagggcatcgcgtca

upper sequence: GLYMA07G24480.1 (Glycine max), 5'ss of exon 1
lower sequence: GRMZM2G435373_T02 (Zea mays), 5'ss of exon 1
ATGGATGAGGGGTGCGATGTGATCGTGTTGGGCACGGGTCTCAAGGAGTGCATTCTCAGCGGTCTTCTCTCTGTCGATGGCCTCAAGgtactcatcagtttcctatttctttaattttcttttcaatagatccaattctcgcatgttaattcctatttgttgttcgattcag-------------------
||||| |||| || ||| ||||||||  |||||||||| |||||||||||||| ||||||||||| ||||||||||| |||||||||||   || |     ||    ||        |     |||| |  ||    | |        | ||| || ||    ||    | |                   
ATGGACGAGGAGTACGACGTGATCGTTCTGGGCACGGGGCTCAAGGAGTGCATCCTCAGCGGTCTCCTCTCTGTCGACGGCCTCAAGgtgagcaccgaccacccgcctcccgg----taacggcaatcggacctcaccccagtccccgagtccgatctgccactctcccccgcacgtacccggacgccgca

upper sequence: GLYMA07G24480.1 (Glycine max), 5'ss of exon 1
lower sequence: GRMZM2G117507_T01 (Zea mays), 5'ss of exon 1
-------------ATGGATGAGGGGTGCGATGTGATCGTGTTGGGCACGGGTCTCAAGGAGTGCATTCTCAGCGGTCTTCTCTCTGTCGATGGCCTCAAGgta--ctcatcagtttcctatttctttaattttcttt-------tcaatagatccaattctcgcatgttaattcc---tatttgttgttcgattcag---
             |||||||||| || ||| ||||||||  | |||||||| |||||||||||||| ||||||||||| |||||||| || ||||||||||||  | |  | | |  ||    ||  |        |       || |||| | |  | |||| |  ||   |||   |||  ||     | ||||    
CCGGCAGCCAGCCATGGATGAGGAGTACGACGTGATCGTACTAGGCACGGGGCTCAAGGAGTGCATCCTCAGCGGTCTCCTCTCTGTAGACGGCCTCAAGgtaagcccgcccgctcgcttcccctacagccgcagctagtacgatccatagctgccgtgctcggaatttgggtccgcgtataagtccggtgcttcaaggt

upper sequence: GLYMA07G24480.1 (Glycine max), 5'ss of exon 1
lower sequence: GRMZM2G435373_T01 (Zea mays), 5'ss of exon 1
-------------ATGGATGAGGGGTGCGATGTGATCGTGTTGGGCACGGGTCTCAAGGAGTGCATTCTCAGCGGTCTTCTCTCTGTCGATGGCCTCAAGgta--ctcatcagtttcctatttctttaattttc-----ttttcaatagatcca--------attctcgcatgttaattcctatttgttgttcgattcag
             |||||||||| || ||| ||||||||| | |||||||| |||||||||||||| ||||| ||||| || || ||||| |||||||||||   | | ||  |  ||   |   ||    | |            |||||||          | |||| || ||   |||   |  | || || | |  
CAGCCAGCCAGCCATGGATGAGGAGTACGACGTGATCGTGCTTGGCACGGGGCTCAAGGAGTGCATCCTCAGTGGTCTCCTTTCCGTCGACGGCCTCAAGgtgagcccgtcgatcgcccgctctcttctcctgcagccgccgctcgtagatccgtggctgccgtgctcggattttgggtccgcgtaatagtccggtgctt

upper sequence: GLYMA07G24480.1 (Glycine max), 5'ss of exon 1
lower sequence: GRMZM2G047431_T01 (Zea mays), 5'ss of exon 1
-------------ATGGATGAGGGGTGCGATGTGATCGTGTTGGGCACGGGTCTCAAGGAGTGCATTCTCAGCGGTCTTCTCTCTGTCGATGGCCTCAAGgtactcatcagtttcctatttctttaatt--ttcttttcaatagatccaattctcgcatgttaattcctatttgttgttcgattcag--------------
             ||||||| || || ||| ||||||||| ||||||| || |||||||||||||| |||||||| || |||||||| ||  ||||||||||||    |  |         | |  ||   | |  | |  |   |||     |||   |  | |||  ||  | |   ||     |              
CCGCGCGCGCGCCATGGATGTGGAGTACGACGTGATCGTGCTGGGCACCGGGCTCAAGGAGTGCATCCTCAGCGGCCTCCTCTCTGTGGACCGCCTCAAGgtacgttacgctactacgacgcctccatcgatcccctcctctctctccctccgtcgtcggccacttctaataagat-cgcgccctggtggttatccatttt

upper sequence: GLYMA07G24480.1 (Glycine max), 5'ss of exon 1
lower sequence: EDP02072 (Chlamydomonas reinhardtii), 5'ss of exon 2
ATGGATGAGGGGTGCGATGTGATCGTGTTGGGCACGGGTCTCAAGGAGTGCATTCTCAGCGGTCTTCTCTCTGTCGATGGCCTCAAGgtactcatcagtttcctatttctttaattttcttttcaatagatccaattctcgcatgttaattcctatttgttgt---tcgattcag
    | |||| ||  || ||||||||| ||||||||||||| |||||||||||  |||| || || || || || ||       ||||| |    |     | |    |   |||  |     |       |   |  ||||  | |     ||     | |      | | |||
---AACGAGGAGTATGACGTGATCGTGCTGGGCACGGGTCTGAAGGAGTGCATCATCAGTGGCCTGCTGTCGGTGGACAAGAAGAAGgtgcgggacctagacatgcg-cgcgaatgctgcaaccgggcctgcttttcttcgcgcgctggccgctcaccatcgcaacctgttgcag

upper sequence: GLYMA07G24480.1 (Glycine max), 5'ss of exon 1
lower sequence: PP1S167_1V6.1 (Physcomitrella patens), 5'ss of exon 1
-------------ATGGATGAGGGGTGCGATGTGATCGTGTTGGGCACGGGTCTCAAGGAGTGCATTCTCAGCGGTCTTCTCTCTGTCGATGGCCTCAAGgtactcatcagtttcctatttctttaattttcttttcaatagatccaat-tctcgca--tgttaattc-ctatttgttgttcgattcag--------------
             |||||||| | || ||||||||| ||| ||||||| || || ||||||||||| ||||| || || ||||| || ||| | ||||||||        |  ||  |  || |   |  ||| |   |      |  | |  || |  ||     || ||   ||| |   |  |  |              
TGGAGCCGGCACCATGGATGAAGAGTACGATGTGATTGTGCTGGGCACCGGGCTGAAGGAGTGCATCCTCAGTGGGCTACTCTCCGTGGATCGTCTCAAGgtg---ggtgggatcgcagatcgtggttgatctgtgtgactcgggcggtgtggcgtagctgccggctctctgggtgtagcgtggatttgtggtcggcgaggga

upper sequence: GLYMA07G24480.1 (Glycine max), 5'ss of exon 1
lower sequence: EFJ11673 (Selaginella moellendorffii), 5'ss of exon 1
-------------ATGGATGAGGGGTGCGATGTGATCGTGTTGGGCACGGGTCTCAAGGAGTGCATTCTCAGCGGTCTTCTCTCTGTCGATGGCCTCAAGgtactcatcagtttcctatttctttaattttcttttcaatagatccaattctcgcatgttaattcctatttgttgttcgattcag
             |||||||||| || ||| || || ||| |||| |||||||||||||||||||| |||||||| || || || || ||| | ||||||||        ||||      |  |  ||     ||  || | |||    |||||||                             
GTTTTGGTGCGCCATGGATGAGGAGTACGACGTCATTGTGCTGGGGACGGGTCTCAAGGAGTGCATCCTCAGCGGGCTGCTGTCGGTGGATCGTCTCAAGgtg------ggttt------ttctcgatcggagttggaagacatct--ctctcgcag----------------------------

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATGGATGAGGGGTGCGATGTGATCGTGTTGGGCACGGGTCTCAAGGAGTGCATTCTCAGCGGTCTTCTCTCTGTCGATGGCCTCAAGgtactcatcagtttcctatttctttaattttcttttcaatagatccaattctcgcatgttaattcctatttgttgttcgattcag

- - - - - - - - - - - - - - - - - - - - - AAGGAG