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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CACACAATGTATCTGCTGTATGCTTTCATCCTGAACTACCTATAATCATTACTGGCTCTGAGGATGGCACAGTGCGCATTTGGCATTCAACAACTTATAGgtaattttatgttgttcacagattactgagttgagagctttattttttcttatctaatttggtgcattgctcttgcctttttgtctcaatgtcatcactc...

Basic information

species Glycine max
transcript GLYMA07G03890.1
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G03890.1 (Glycine max), 5'ss of exon 8
lower sequence: LOC_Os06g05180.2 (Oryza sativa), 5'ss of exon 8
CACACAATGTATCTGCTGTATGCTTTCATCCTGAACTACCTATAATCATTACTGGCTCTGAGGATGGCACAGTGCGCATTTGGCATTCAACAACTTATAGgtaattttat--gttgttcacagattactgagttgagagctttattttttcttatctaatttggtgcattgctcttgcctttttgtctcaatgtcatcactc
|||||||  | |||||||| || || |||||||| || ||||||||||||||||| ||||| ||||||||||| ||||| |||||||| |||||||| ||||   |||    |||   |     ||  ||  |   ||  |  | | |||| ||  |    | ||    |  ||  |   | |  |   || |  |  ||| 
CACACAACATTTCTGCTGTTTGTTTCCATCCTGAGCTTCCTATAATCATTACTGGATCTGAAGATGGCACAGTTCGCATATGGCATTCGACAACTTACAGgttgctttcacagtttcacttgtgtttttgcttgttgatgtggactgtttcctagttctcattgtttgctattcaagtgctctc-tacgaaagaaacaact-

upper sequence: GLYMA07G03890.1 (Glycine max), 5'ss of exon 8
lower sequence: LOC_Os02g11830.2 (Oryza sativa), 5'ss of exon 8
CACACAATGTATCTGCTGTATGCTTTCATCCTGAACTACCTATAATCATTACTGGCTCTGAGGATGGCACAGTGCGCATTTGGCATTCAACAACTTATAGgtaattttatgttgttcacagattactgagttgagagctttattttttctta--tctaatttggtg--cattgctcttgcctttttgtctcaatgtcatcactc
|||| ||||| |||||||| || || ||||| ||  ||||||||||  ||||||||||||||||||| ||||| ||| | ||||| || || || || ||||  | |     | | | |  || |   |  | | ||  |  ||  | | ||  |  ||||| | |   | | |   | |   ||  ||||   |   |     
CACATAATGTCTCTGCTGTTTGTTTCCATCCGGAGTTACCTATAATACTTACTGGCTCTGAGGATGGGACAGTTCGCTTGTGGCACTCTACTACCTACAGgttctctcgctctctccccctatgatacaactcataggatacttcatgcatagtttgaattttgagataaattcatgtactcgttactctcgtgggtgtg----

upper sequence: GLYMA07G03890.1 (Glycine max), 5'ss of exon 8
lower sequence: GRMZM2G095348_T02 (Zea mays), 5'ss of exon 7
CACACAATGTATCTGCTGTATGCTTTCATCCTGAACTACCTATAATCATTACTGGCTCTGAGGATGGCACAGTGCGCATTTGGCATTCAACAACTTATAGgtaat-tttatgttgttcacagattactgagttgagagctttattttttcttatctaatttggt--gcattgctcttgcctttttgtctcaatgtcatcactc-
|||| ||  | |||||||| || || |||||||| || ||||||||||||||||| || || ||||| ||||| || || ||||||||||||||||| ||||||  |   | || ||     ||  ||  |||       || ||| |     |  || |  ||  |  ||  || |  |  |||| |    | |||   ||| 
CACATAACATTTCTGCTGTTTGTTTCCATCCTGAGCTCCCTATAATCATTACTGGATCCGAAGATGGTACAGTTCGTATATGGCATTCAACAACTTACAGgtaacatgctttttttttgtttatctctatgtttg----cttgtttatgtaagtagaagtctgtcagttttcatcgttacaatttggccatttatcaattctct

upper sequence: GLYMA07G03890.1 (Glycine max), 5'ss of exon 8
lower sequence: GRMZM2G000645_T02 (Zea mays), 5'ss of exon 8
CACACAATGTATCTGCTGTATGCTTTCATCCTGAACTACCTATAATCATTACTGGCTCTGAGGATGGCACAGTGCGCATTTGGCATTCAACAACTTATAGgtaattttatgttgttcacagattactgagttgagagctttattttttcttatctaatttggtgcattgctcttgcctttttgtctcaatgtcatcactc--------
|||| ||| | |||||||| || || |||||||| || ||||||||||||||||| ||||| ||||| ||||| || || |||||||| |||||||| ||||||    ||||| || |   ||  ||  |||      ||||| |   |  |     |  | |  |||  ||||  |  |||| | || | |||   |||        
CACATAATATTTCTGCTGTTTGTTTCCATCCTGAGCTCCCTATAATCATTACTGGATCTGAAGATGGTACAGTTCGTATATGGCATTCGACAACTTACAGgtaac---atgtt-tttatttatctctatgtttgcttgtttatgtaagcaga---ggtccgttcaatttttctttacaatttggc-cattatcaattctccatcctga

upper sequence: GLYMA07G03890.1 (Glycine max), 5'ss of exon 8
lower sequence: GRMZM2G419984_T01 (Zea mays), 5'ss of exon 7
CACACAATGTATCTGCTGTATGCTTTCATCCTGAACTACCTATAATCATTACTGGCTCTGAGGATGGCACAGTGCGCATTTGGCATTCAACAACTTATAGgtaattttatgttgttcacagattactgagttgagagctttattttttcttatctaatttggtgcattgctcttgcctttttgtctcaatgtcatcactc--------
                                   || ||||||||||||||||| ||||| ||||| ||||| || || |||||||| |||||||| ||||||    ||||| || |   ||  ||  |||      ||||| |   |  |     | |  |  |||  ||||  |  |||| | || | |||   |||        
-----------------------------------CTCCCTATAATCATTACTGGATCTGAAGATGGTACAGTTCGTATATGGCATTCGACAACTTACAGgtaac---atgtt-tttatttatctctatgtttgcttgtttatgtaagcaga---ggtctattcaatttttctttacaatttggc-cattatcaattctccatcctga

upper sequence: GLYMA07G03890.1 (Glycine max), 5'ss of exon 8
lower sequence: GRMZM2G141587_T01 (Zea mays), 5'ss of exon 8
CACACAATGTATCTGCTGTATGCTTTCATCCTGAACTACCTATAATCATTACTGGCTCTGAGGATGGCACAGTGCGCATTTGGCATTCAACAACTTATAGgtaattttatgttgttcacagattactgagttgagagctttattttttcttatctaatttggtgcattgctcttgcctttttgtctcaatgtcatcactc--
|||| ||||| ||||||||||| || || || || ||||||||||| |||||||| || |||||||| ||||| || || |||||||| || || || ||||| |  ||      |     | |||    | |   || |     || ||||| ||  |  |   | ||  ||| | ||||     |||       |  |  
CACATAATGTTTCTGCTGTATGTTTCCACCCAGAGCTACCTATAATAATTACTGGTTCAGAGGATGGGACAGTTCGAATGTGGCATTCTACTACCTACAGgtattgctacacatctattttagtacccc-tggcatgcatgtcgcttgcttatatatgtatgca-agtgtgctttcattttaaggccaaatctggtagccac

upper sequence: GLYMA07G03890.1 (Glycine max), 5'ss of exon 8
lower sequence: GRMZM2G124886_T04 (Zea mays), 5'ss of exon 8
CACACAATGTATCTGCTGTATGCTTTCATCCTGAACTACCTATAATCATTACTGGCTCTGAGGATGGCACAGTGCGCATTTGGCATTCAACAACTTATAGgtaattttatgttgttcacagattactgagttgagagctttattttttcttatctaatttggtgcattgctcttgcctttttgtctcaatgtcatcactc------
|||| ||||| || |||||||| || ||||| || ||||||||||| |||||||| || |||||||| ||||| || || |||||||| || || || ||||| |  ||| |  |  |   |   |  | |||     ||    |  | |   || |       || | |  |  |    | | | |||  || |  ||       
CACATAATGTGTCCGCTGTATGTTTCCATCCAGAGCTACCTATAATTATTACTGGTTCAGAGGATGGGACAGTTCGAATGTGGCATTCTACTACCTACAGgtattgctat-tcatctatttaggccccatttgg----ttgggctgctttgggctcaggctccacactacaataccagagtagccacaa-atcgtggcttatctgg

upper sequence: GLYMA07G03890.1 (Glycine max), 5'ss of exon 8
lower sequence: AT1G79990.1 (Arabidopsis thaliana), 5'ss of exon 12
CACACAATGTATCTGCTGTATGCTTTCATCCTGAACTACCTATAATCATTACTGGCTCTGAGGATGGCACAGTGCGCATTTGGCATTCAACAACTTATAGgtaattt-tatgttgttcacagattactgagttgagagctttattttttcttatctaatttggtgcattgctcttgcctttttgtctcaatg--tcatcactc----------------
|||||||||| ||||| ||||  |||||||| || ||||||||||| ||||| || || |||||||| || || ||||| |||||  | || ||||| |||||| |  |||| |||   |  |||   ||| ||  |  || ||||| ||||    || ||  | || |  |       | ||    |||    |  | |||                 
CACACAATGTTTCTGCAGTATCTTTTCATCCAGAGCTACCTATAATTATTACAGGATCCGAGGATGGAACTGTTCGCATATGGCACGCCACCACTTACAGgtaactcgtatgctgtctgc--attg--gagctgcta--ttgattttgtctttaaaaacttccttcaatttttcaaaaatcttcatccaacagttttttacttaatacttgacatctag

upper sequence: GLYMA07G03890.1 (Glycine max), 5'ss of exon 8
lower sequence: AT1G52360.1 (Arabidopsis thaliana), 5'ss of exon 8
CACACAATGTATCTGCTGTATGCTTTCATCCTGAACTACCTATAATCATTACTGGCTCTGAGGATGGCACAGTGCGCATTTGGCATTCAACAACTTATAGgtaattttatgttgttcacagattactgagttgagagctttatttt------ttcttatctaatttggtgcattgctcttgcctttttgtctcaatgtcat-cactc---------------------------------------------------------------------------
|||||||||||||||| ||||| || ||||| || || || || || || || || ||||| |||||||| || |||||||||||| |||| || || ||||| | | || ||   ||    ||  |  ||||      ||||  |      ||||| | |   ||||   |    |||  |  ||| |  ||| | |  | ||||                                                                            
CACACAATGTATCTGCAGTATGTTTCCATCCAGAGCTTCCAATTATAATCACAGGTTCTGAAGATGGCACCGTTCGCATTTGGCATGCAACCACATACAGgtattataatattaaaca-gtttttttttgttggacatattatagtaaacgcttcttgtatgccttggctaaaccatctc-cactttggcttcattcttgtgcactttttcaccattaccaatttcttttattgtccttccatttgtaatcccaatttcctaatgtctgttttttcttgcag

upper sequence: GLYMA07G03890.1 (Glycine max), 5'ss of exon 8
lower sequence: AT3G15980.2 (Arabidopsis thaliana), 5'ss of exon 8
CACACAATGTATCTGCTGTATGCTTTCATCCTGAACTACCTATAATCATTACTGGCTCTGAGGATGGCACAGTGCGCATTTGGCATTCAACAACTTATAGgtaattttatgttg---ttcacagattactgagttgagagc-tttattttttcttatctaatttggtgcattgctcttgcctttttgtctcaatgtcatcactc------------------------------------------------------------------------------
|||||||||| ||||| ||||| || ||||| || || || ||||| || || || |||||||||||||| || |||||||||||  | || || || ||||| |||||  |     ||  | |   |  ||  | | |    |||  |||| |    |  |||    | |||      | || ||  |     || ||  ||                                                                               
CACACAATGTTTCTGCCGTATGTTTCCATCCAGAGCTTCCAATAATAATCACAGGTTCTGAGGATGGCACTGTTCGCATTTGGCACGCCACTACCTACAGgtatttttacctaacgttttcctgtcaaaagacataacaatgcttacattttttggggttttttaacac-ttgaatacactttgttcacatgcggttatttcttgtattcattttcaccataggttcgctttctctattttgtcgtttgatttgttatcttcgattctctttctcttttcag

upper sequence: GLYMA07G03890.1 (Glycine max), 5'ss of exon 8
lower sequence: Vv09s0002g04810.t01 (Vitis vinifera), 5'ss of exon 8
CACACAATGTATCTGCTGTATGCTTTCATCCTGAACTACCTATAATCATTACTGGCTCTGAGGATGGCACAGTGCGCATTTGGCATTCAACAACTTATAGgtaa-ttttatgttgttcacagattactgagttgagagctttattttttcttatctaatttggtgcattgctcttgcctttttgtctcaatgtcatcactc--
|||||||||| ||||| || ||||| ||||||||||| || ||||| || || || ||||||||||| || || || || |||||| | || ||||||||||||  |  || |  |   ||  || || |  |||       || ||    ||   |  |||      |||| || | ||||| | |   | |   |  ||  
CACACAATGTTTCTGCAGTCTGCTTCCATCCTGAACTTCCCATAATAATAACAGGTTCTGAGGATGGGACTGTTCGAATATGGCATGCTACCACTTATAGgtaagctccatatcatatgcaattttctaatatgaagttcacatgttaaacta---accttgacatcctgctgtttcttttttatttatttttgggctttcaa

upper sequence: GLYMA07G03890.1 (Glycine max), 5'ss of exon 8
lower sequence: PP1S79_180V6.1 (Physcomitrella patens), 5'ss of exon 8
CACACAATGTATCTGCTGTATGCTTTCATCCTGAACTACCTATAATCATTACTGGCTCTGAGGATGGCACAGTGCGCATTTGGCATTCAACAACTTATAGgta---attttatgttgttcacagattac--tgagttgagagctttattttttcttatctaatttggtgcattgctcttgcctttttgtctcaatgtcatcactc
| |||||||||||||| |  || |||||||| || || ||||| ||| ||||||| || || ||||| ||||| || ||||||||| |||| || || |||||    |||  | ||  |  |    | |  |   ||  |   | | |    | |  | |  |||      |   | | |  | | ||| ||  |   ||     
CTCACAATGTATCTGCAGCGTGTTTTCATCCCGAGCTCCCTATCATCCTTACTGGTTCAGAAGATGGAACAGTTCGTATTTGGCATGCAACTACGTACAGgtatacgtttcctctttcttcctctcttccatagcttttggattgtgtggactttcgt-tgttttcagatttgaatatgggttctctgtatctttaaaatg----

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CACACAATGTATCTGCTGTATGCTTTCATCCTGAACTACCTATAATCATTACTGGCTCTGAGGATGGCACAGTGCGCATTTGGCATTCAACAACTTATAGgtaattttatgttgttcacagattactgagttgagagctttattttttcttatctaatttggtgcattgctcttgcctttttgtctcaatgtcatcactc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG