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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTACCTGATGGTCGTGAAGAATCTGTCATGAAGCGTACAACACTAGTGGCTAACACTTCAAACATGCCAGTGGCTGCTCGTGAAGCTTCAATTTATACAGgtgactttgtatctcttgaattctaggatatctctatttattgttgagaaataatatttactaactctttcctattgccaattgtaatttaattggcttg...

Basic information

species Glycine max
transcript GLYMA08G23990.1
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G23990.1 (Glycine max), 5'ss of exon 12
lower sequence: LOC_Os02g07870.1 (Oryza sativa), 5'ss of exon 11
TTACCTGATGGTCGTGAAGAATCTGTCATGAAGCGTACAACACTAGTGGCTAACACTTCAAACATGCCAGTGGCTGCTCGTGAAGCTTCAATTTATACAGgtgactttgtatctcttg-aattctaggatatctctatttattgttgagaaataatatttactaactctttcctattgccaattgtaatttaattggcttg--
  |   ||||| |||||||| ||||| |||||| | |||||||| ||||||||||| || |||||||| || ||||||||||||||||| |||||||||||| |   |||||  ||    |||    | ||  |  |   ||  | | |   | ||||  |   | | |  || | |     |  ||   || |||  |||  
ACAGAGGATGGACGTGAAGAGTCTGTGATGAAGAGAACAACACTGGTGGCTAACACATCCAACATGCCTGTCGCTGCTCGTGAAGCTTCCATTTATACAGgtaatggtgtattgctcctgattgattgctacattaagccataatagtgtc-tgatatccatatagtgtgccccacttt--gtcatatagtagttgttttgtt

upper sequence: GLYMA08G23990.1 (Glycine max), 5'ss of exon 12
lower sequence: LOC_Os06g45120.1 (Oryza sativa), 5'ss of exon 11
TTACCTGATGGTCGTGAAGAATCTGTCATGAAGCGTACAACACTAGTGGCTAACACTTCAAACATGCCAGTGGCTGCTCGTGAAGCTTCAATTTATACAGgtgactttgtatctcttgaattctaggatatctctattt----attgttgagaaataatatt-tactaactctttcctattgccaattgtaatttaattggcttg-
|| |||||||| |||||||| |||||||||||  | || ||||| || |||||||| || |||||||| || |||||||||||||| || |||||||||||| | |   ||| |  ||| | ||  ||| | | || ||    |||        ||| || |  |  ||    || | ||   |   || | || | ||    |  
TTGCCTGATGGACGTGAAGAGTCTGTCATGAAAAGAACTACACTTGTTGCTAACACATCCAACATGCCTGTTGCTGCTCGTGAAGCCTCCATTTATACAGgtaa-tacatatatactgattact--gatgtttttaatttcgcattccactagtatagtactacatgaatgtgtttcgatcttc---tgaagttcattttctctag

upper sequence: GLYMA08G23990.1 (Glycine max), 5'ss of exon 12
lower sequence: GRMZM2G421857_T02 (Zea mays), 5'ss of exon 11
TTACCTGATGGTCGTGAAGAATCTGTCATGAAGCGTACAACACTAGTGGCTAACACTTCAAACATGCCAGTGGCTGCTCGTGAAGCTTCAATTTATACAGgtgactttgtatctcttgaattctaggatatctctatttattgttgagaaataatattt---actaactctttcctattgccaattgtaatttaattggcttg
|| |||||||| ||||| || |||||||||||| | |||||||| ||||||||||| ||||||||||| || ||||||||||||||||| ||||| || ||| |     | |  | |  ||  |   |  |  | || ||      |||  |||    |   ||||   || |  ||  |   ||   ||| | |      | 
TTGCCTGATGGCCGTGAGGAGTCTGTCATGAAGAGAACAACACTGGTGGCTAACACATCAAACATGCCTGTCGCTGCTCGTGAAGCTTCCATTTACACTGgtaaaaccctgttaccttgatattc--acttggccatgtagccac-agatgtaagccctgaaactagtgctgtggtagggaacatatcaatattagaaatatt

upper sequence: GLYMA08G23990.1 (Glycine max), 5'ss of exon 12
lower sequence: GRMZM2G421857_T03 (Zea mays), 5'ss of exon 11
-------------------TTACCTGATGGTCGTGAAGAATCTGTCATGAAGCGTACAACACTAGTGGCTAACACTTCAAACATGCCAGTGGCTGCTCGTGAAGCTTCAATTTATACAGgtgactttgtatctcttgaattctaggatatctctatttattgttgagaaataatatttactaactctttcctattgccaattgtaatttaattggcttg
                   || |||||||| ||||| || |||||||||||| | |||||||| ||||||||||| ||||||||||| || ||||||||||||||||| ||||| || ||| |     | |  | |  ||  |   |  |  | || ||      |||  |||    |   ||     | || | |        |              
TCCCCAGTTGACGATGACATTGCCTGATGGCCGTGAGGAGTCTGTCATGAAGAGAACAACACTGGTGGCTAACACATCAAACATGCCTGTCGCTGCTCGTgaagcttccatttacactggtaaaaccctgttaccttgatattc--acttggccatgtagccac-agatgtaagccctg--aaactagtgctgtggtagggaaca--------------

upper sequence: GLYMA08G23990.1 (Glycine max), 5'ss of exon 12
lower sequence: GRMZM2G128877_T03 (Zea mays), 5'ss of exon 8
TTACCTGATGGTCGTGAAGAATCTGTCATGAAGCGTACAACACTAGTGGCTAACACTTCAAACATGCCAGTGGCTGCTCGTGAAGCTTCAATTTATACAGgtgactttgtatctcttgaattctaggatatctctatttat-tgttgagaaataatatttactaactctttcctattgccaattgtaatttaattggcttg--
|| |||||||| ||||| || || ||||||||| | |||||  | ||||||||||| ||||| ||||| || |||||||||||||| || |||||||||||| |   | | |  | |  ||  |     | || |  |  | |    | | |||  |  |   ||    ||  |  ||      | ||  ||      |    
TTGCCTGATGGCCGTGAGGAGTCAGTCATGAAGAGAACAACCTTGGTGGCTAACACATCAAATATGCCTGTTGCTGCTCGTGAAGCCTCCATTTATACAGgtaaaactctgttgccttgatattta---acctttggtcgtgtagccacagatatcaagtctgaaactcttagtgctgtggtaggaaacatatcaatatcaga

upper sequence: GLYMA08G23990.1 (Glycine max), 5'ss of exon 12
lower sequence: AT1G78900.2 (Arabidopsis thaliana), 5'ss of exon 12
TTACCTGATGGTCGTGAAGAATCTGTCATGAAGCGTACAACACTAGTGGCTAACACTTCAAACATGCCAGTGGCTGCTCGTGAAGCTTCAATTTATACAGgtgactttgtatctcttgaattctaggatatctctatttattgttgagaaataatatttactaactctttcctattgccaattgtaatttaattggcttg
|| |||||||| ||||| |||||||||||||| ||||| ||||| || |||||||| || |||||||| ||||||||||||||||| |||||||| |||||| |  ||    | |    |||  |         || |||||| |||     | |   || |     |||  | ||     || |||| | | |  |   
TTGCCTGATGGCCGTGAGGAATCTGTCATGAAACGTACCACACTTGTTGCTAACACCTCTAACATGCCTGTGGCTGCTCGTGAAGCCTCAATTTACACAGgtaatgttcaggcacacagatttaa---------tagttattgatgaatcccattgccta-tgctcattttttttttttttttttaatgtgaattccag-

upper sequence: GLYMA08G23990.1 (Glycine max), 5'ss of exon 12
lower sequence: Vv04s0008g02580.t01 (Vitis vinifera), 5'ss of exon 12
TTACCTGATGGTCGTGAAGAATCTGTCATGAAGCGTACAACACTAGTGGCTAACACTTCAAACATGCCAGTGGCTGCTCGTGAAGCTTCAATTTATACAGgtgactttgtatctcttgaattctaggatatctctatttattgttgagaaataatatttactaactctttcctattgccaattgtaatttaattggcttg---
 | ||||||||  | |||||||||||||||||| | || || || || ||||||||||| |||||||| ||||||||  | || |||||||||||||||||| |   | |   |||| | |  |  | |||   |    ||| ||  | |    || || |||   | ||| | ||    || |   |  | || | |||   
CTGCCTGATGGGAGAGAAGAATCTGTCATGAAGAGAACTACGCTCGTAGCTAACACTTCTAACATGCCTGTGGCTGCAAGGGAGGCTTCAATTTATACAGgtaatgctttga-tcttcattgttttgttatgaattgggattcttttgtatgtgtagtttcta--cccttcatttttttcatagggctaaactttgtttgagc

upper sequence: GLYMA08G23990.1 (Glycine max), 5'ss of exon 12
lower sequence: Vv09s0054g00890.t01 (Vitis vinifera), 5'ss of exon 12
TTACCTGATGGTCGTGAAGAATCTGTCATGAAGCGTACAACACTAGTGGCTAACACTTCAAACATGCCAGTGGCTGCTCGTGAAGCTTCAATTTATACAGgtgactttgtatctcttgaattctaggatatctctatttattgttgagaaataatatttactaactctttccta---ttgccaattgtaatttaattggcttg
 | |||||||| ||||||||||||||||||||||| || ||||| ||||| ||||||||||| ||||| |||||||||||||| |||||||||||||||||| | | | | |  |||  ||||     || | |     || | || |  | || ||||   || ||  |  ||   |   |  ||| ||||    ||  || 
CTGCCTGATGGCCGTGAAGAATCTGTCATGAAGCGAACTACACTTGTGGCCAACACTTCAAATATGCCTGTGGCTGCTCGTGAGGCTTCAATTTATACAGgtaaatatat-ttacttctattcattactagcacatgaaatggctgggtgaaaaaattt-tgaagtcaatattagcttcatcttttgcaattcttgtgtgtt-

upper sequence: GLYMA08G23990.1 (Glycine max), 5'ss of exon 12
lower sequence: PP1S44_102V6.1 (Physcomitrella patens), 5'ss of exon 12
TTACCTGATGGTCGTGAAGAATCTGTCATGAAGCGTACAACACTAGTGGCTAACACTTCAAACATGCCAGTGGCTGCTCGTGAAGCTTCAATTTATACAGgtgactttgtatctcttgaattctaggatatctctatttattgttgagaaat--------aatatttactaactctttcctattgccaa-ttgtaattta---attggcttg--------------------------------------------
||||| || ||||| || || || |||||||||||||| || || ||||| ||||| ||||||||||| ||||||||||||||||| || ||||||||||||  | |  | | | ||    ||||   | |   | || |||| || |  |          ||| || || |  | ||   || ||    ||| |||||    ||    |||                                            
TTACCCGACGGTCGGGAGGAGTCCGTCATGAAGCGTACTACGCTTGTGGCCAACACATCAAACATGCCTGTGGCTGCTCGTGAAGCATCTATTTATACAGgtttcctcctttttattct-ctctaaagtttaagtgttcattgctgcggcacctcatctagataatttctcaaacgttttcatcgcttccttggaattttcgcatataattgcgtcctttctacatttgctctgaagattctgttttctgttgcag

upper sequence: GLYMA08G23990.1 (Glycine max), 5'ss of exon 12
lower sequence: PP1S10_201V6.1 (Physcomitrella patens), 5'ss of exon 12
TTACCTGATGGTCGTGAAGAATCTGTCATGAAGCGTACAACACTAGTGGCTAACACTTCAAACATGCCAGTGGCTGCTCGTGAAGCTTCAATTTATACAGgtg---actttgtatc-tcttgaattctaggat---atctctatttattgttgagaaataatatttactaactctttcctattgccaattgtaatttaattggcttg-
|| ||||| || || || || ||||| |||||||| || || || ||||| || || ||||| ||||| |||||||||||||||||||| || |||||||||    |  |||  |  |  ||||   ||   |   ||| | || |    || |    | | || |   |    ||| |  |   ||  | |  || |  ||      
TTGCCTGACGGACGAGAGGAGTCTGTTATGAAGCGGACCACTCTCGTGGCCAATACATCAAATATGCCTGTGGCTGCTCGTGAAGCTTCCATCTATACAGgttcccatcttgagttattctgaagcttaacttttgatcgcaatgtgaccttaaagtttgaaatcttgaaggattttacgttcatcacattttgtt-atctgttgcag

upper sequence: GLYMA08G23990.1 (Glycine max), 5'ss of exon 12
lower sequence: PP1S8_312V6.1 (Physcomitrella patens), 5'ss of exon 12
TTACCTGATGGTCGTGAAGAATCTGTCATGAAGCGTACAACACTAGTGGCTAACACTTCAAACATGCCAGTGGCTGCTCGTGAAGCTTCAATTTATACAGgtgactttgtatc--tcttgaattctaggatatctctatttattgttgagaaataatatttactaactctttcctattgccaattgtaatttaattggcttg------------------------------------------
|||||||||||||||||||| ||||| ||||||||||| || || ||||| ||||| ||||||||||| ||||||||||||||||| || || || |||||| | ||| | |   |||   | ||||     | ||||  |  |||   ||||  || || |    ||||||     |   || ||  ||    |  | | |                                          
TTACCTGATGGTCGTGAAGAGTCTGTTATGAAGCGTACCACTCTCGTGGCCAACACCTCAAACATGCCTGTGGCTGCTCGTGAAGCATCTATCTACACAGgttattttcttttcttctgagactctac----tttctaggtgctgt-atgaaaccat-ttcatc--ctctttggatgtttgaaatgctatcctgtatgatcgcatacttccgcatcattatgcaaatgctgtttcctgttgcag

upper sequence: GLYMA08G23990.1 (Glycine max), 5'ss of exon 12
lower sequence: EFJ30330 (Selaginella moellendorffii), 5'ss of exon 12
TTACCTGATGGTCGTGAAGAATCTGTCATGAAGCGTACAACACTAGTGGCTAACACTTCAAACATGCCAGTGGCTGCTCGTGAAGCTTCAATTTATACAGgtgactttgtatctcttgaattctaggatatctctatttattgttgagaaataatatttactaactctttcctattgccaattgtaatttaattggcttg
 | |||||||| || ||||| |||||||||||||||||||| || || ||||| |||||||| ||||| ||||| || || |||||||||||||| || |||   |   |     |     || | | |   | |||  || |||                                                       
CTCCCTGATGGACGCGAAGAGTCTGTCATGAAGCGTACAACTCTCGTCGCTAATACTTCAAATATGCCTGTGGCGGCACGAGAAGCTTCAATTTACACGGgtatgtccttccaattcaggctcaacgctgattttatcgatggtttcag---------------------------------------------------

upper sequence: GLYMA08G23990.1 (Glycine max), 5'ss of exon 12
lower sequence: EFJ33015 (Selaginella moellendorffii), 5'ss of exon 11
TTACCTGATGGTCGTGAAGAATCTGTCATGAAGCGTACAACACTAGTGGCTAACACTTCAAACATGCCAGTGGCTGCTCGTGAAGCTTCAATTTATACAGgtgactttgtatctcttgaattctaggatatctctatttattgttgagaaataatatttactaactctttcctattgccaattgtaatttaattggcttg
 | |||||||| || ||||| |||||||||||||||||||| || || ||||| |||||||| ||||| ||||| || || |||||||||||||| || |||   |   |     |     ||   | |   | |||  || |||                                                       
CTTCCTGATGGACGCGAAGAGTCTGTCATGAAGCGTACAACTCTCGTCGCTAATACTTCAAATATGCCTGTGGCGGCACGAGAAGCTTCAATTTACACGGgtatgtccttccaattcaggctcagcgctgattttatcgatggtttcag---------------------------------------------------

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|16278104|gb|BI942728.1|BI942728
EST:     TAACACTTCAAACATGCCAGTGGCTGCTCGTGAAGCTTCAATTTATACAG                         GAATCACATTAGCTGAGTATTTCAGAGATATGGGTTATAATGTCAGTATGA
genomic: TAACACTTCAAACATGCCAGTGGCTGCTCGTGAAGCTTCAATTTATACAGgtgactttgt ... tcaattgcagGAATCACATTAGCTGAGTATTTCAGAGATATGGGTTATAATGTCAGTATGA
EST: gi|193692166|gb|FK631079.1|FK631079
EST:     TAACACTTCAAACATGCCAGTGGCTGCTCGTGAAGCTTCAATTTATACAG                         GAATCACATAAGCTGAGTATTTCAGAGATATGGGTTATAATGTCAGTATGA
genomic: TAACACTTCAAACATGCCAGTGGCTGCTCGTGAAGCTTCAATTTATACAGgtgactttgt ... tcaattgcagGAATCACATTAGCTGAGTATTTCAGAGATATGGGTTATAATGTCAGTATGA
EST: gi|151402942|gb|EV272755.1|EV272755
EST:     TAACACTTCAAACATGCCAGTGGCTGCTCGTGAAGCTTCAATTTATACAG                         GAATCACATTAGCTGAGTATTTCAGAGATATGGGTTATAATGTCAGTATGA
genomic: TAACACTTCAAACATGCCAGTGGCTGCTCGTGAAGCTTCAATTTATACAGgtgactttgt ... tcaattgcagGAATCACATTAGCTGAGTATTTCAGAGATATGGGTTATAATGTCAGTATGA
EST: gi|18692695|gb|BM521543.1|BM521543
EST:     TAACACTTCAAACATGCCAGTGGCTGCTCGTGAAGCTTCAATTTATACAG                         GAATCACATTAGCTGAGTATTTCAGAGATATGGGTTATAATGTCAGTATGA
genomic: TAACACTTCAAACATGCCAGTGGCTGCTCGTGAAGCTTCAATTTATACAGgtgactttgt ... tcaattgcagGAATCACATTAGCTGAGTATTTCAGAGATATGGGTTATAATGTCAGTATGA
EST: gi|193398769|gb|FK365181.1|FK365181
EST:     TTCAATTTATACAG                         GAATCACATTAGCTGAGTATTTCAGAGATATGGGTTATAATGTCAGTAATG
genomic: TTCAATTTATACAGgtgactttgt ... tcaattgcagGAATCACATTAGCTGAGTATTTCAGAGATATGGGTTATAATGTCAGT-ATG
EST: gi|33390421|gb|CA853616.1|CA853616
EST:     GTGAAGCTTCAATTTNTACAG                         GAATCACATTAGCTGAGTATTTCAGAGATATGGGTTATAATGTCAGTATGA
genomic: GTGAAGCTTCAATTTATACAGgtgactttgt ... tcaattgcagGAATCACATTAGCTGAGTATTTCAGAGATATGGGTTATAATGTCAGTATGA
EST: gi|207728603|gb|GD707731.1|GD707731
EST:     AAGCTTCAATTTATACAG                         GAATCACATTAGCTGAGTATTTCAGAGATATGGGTTATAATGTCAGTATGA
genomic: AAGCTTCAATTTATACAGgtgactttgt ... tcaattgcagGAATCACATTAGCTGAGTATTTCAGAGATATGGGTTATAATGTCAGTATGA
EST: gi|21889244|gb|BQ742457.1|BQ742457
EST:     TAACACTTCAAACATGCCAGTGGCTGCTCGTGAAGCTTCAATTTATACAG                         GAATCACATTAGCTGAGTATTTCAGAGATATGGGTTATAATGTCAGTATGA
genomic: TAACACTTCAAACATGCCAGTGGCTGCTCGTGAAGCTTCAATTTATACAGgtgactttgt ... tcaattgcagGAATCACATTAGCTGAGTATTTCAGAGATATGGGTTATAATGTCAGTATGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTACCTGATGGTCGTGAAGAATCTGTCATGAAGCGTACAACACTAGTGGCTAACACTTCAAACATGCCAGTGGCTGCTCGTGAAGCTTCAATTTATACAGgtgactttgtatctcttgaattctaggatatctctatttattgttgagaaataatatttactaactctttcctattgccaattgtaatttaattggcttg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctctttcc