Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCCATTTTCCTTGCTGCCAAGTTCTTGAAAGTGAAGCTTCCATCAGATGGTGAGAAGGTTTGGTGGCAAGAGTTTGATGTCACCCCACGCCAATTAGAGGgtcggtgtcatcccctcaattcatttgcatgctaacaaaattgatctgtttgggtagccttttgtgttcccttggtttaatgcattatgatcatttctgc...

Basic information

species Glycine max
transcript GLYMA20G02880.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G02880.1 (Glycine max), 5'ss of exon 5
lower sequence: LOC_Os12g30020.2 (Oryza sativa), 5'ss of exon 6
GCCATTTTCCTTGCTGCCAAGTTCTTGAAAGTGAAGCTTCCATCAGATGGTGAGAAGGTTTGGTGGCAAGAGTTTGATGTCACCCCACGCCAATTAGAGGgtcggtgtcatcccctcaattcatttgcatgctaacaaaattgatctgtttgggtagccttttgtgttcccttg-gtttaatgcattatgatcatttctgc---
|| || ||  | ||||| || ||  | ||||||||||||||||| ||||||||||||||||||||||| ||||||||||| || ||| | ||  | || ||| |||| |          |   ||   || ||   |    || ||  | ||    |  |       || | || |||| |  |   ||  |  |||   |   
GCTATCTTTTTGGCTGCTAAATTTCTCAAAGTGAAGCTTCCATCTGATGGTGAGAAGGTTTGGTGGCAGGAGTTTGATGTGACTCCAAGACAGCTGGAAGgttggtgcctagataatgttgtgttc-tatacttctat--ctggtccatatga-cggtttacaacaatctcctgagttttaaaccgcatattttttttaacgag

upper sequence: GLYMA20G02880.1 (Glycine max), 5'ss of exon 5
lower sequence: GRMZM2G308570_T02 (Zea mays), 5'ss of exon 14
GCCATTTTCCTTGCTGCCAAGTTCTTGAAAGTGAAGCTTCCATCAGATGGTGAGAAGGTTTGGTGGCAAGAGTTTGATGTCACCCCACGCCAATTAGAGGgtcggtgtcatcccctcaattcatttgcatgctaacaaaattgatctgtttgggtagccttttgtgttccct--tggtttaatgcattatgatcatttctgc
|| || ||||| ||||| |||||  | ||||| ||||||||||||||||| |||||||| |||||||||||||||||||| || || || || || || ||| ||| ||        || ||| | |  ||| |||  || ||  ||  |     |      |||  |   |  | ||||  | | | || | |  |   | 
GCAATCTTCCTGGCTGCGAAGTTTCTTAAAGTCAAGCTTCCATCAGATGGCGAGAAGGTCTGGTGGCAAGAGTTTGATGTAACTCCGCGGCAGTTGGAAGgttggtctctagatgcaaagtcactagtgtgc-aacttaactgcactactgtaaaaaaacaatgtcgtaagtgctagtttcctac-taattagctatctagt

upper sequence: GLYMA20G02880.1 (Glycine max), 5'ss of exon 5
lower sequence: AC233979.1_FGT009 (Zea mays), 5'ss of exon 5
GCCATTTTCCTTGCTGCCAAGTTCTTGAAAGTGAAGCTTCCATCAGATGGTGAGAAGGTTTGGTGGCAAGAGTTTGATGTCACCCCACGCCAATTAGAGGgtcggtgtcatcccctcaattcatttgcatgctaacaaaattgatctgtttgggtagccttttgtgttc-ccttggtttaatgcattatgatcatttctgc-
|| || ||||| ||||| |||||  | ||||| ||||||||||||||||| |||||||| |||||||||||||||||||| || ||  | ||  | || ||| ||| ||        || ||| | |  ||| | |  || ||  ||  |     |  | ||| |||      | ||||  | | | || | |  |   |  
GCAATCTTCCTCGCTGCGAAGTTTCTCAAAGTCAAGCTTCCATCAGATGGCGAGAAGGTCTGGTGGCAAGAGTTTGATGTAACTCCGTGGCAGCTGGAAGgttggtctctagatgcaaagtcactagtgtgc-accttaactgcactactgtaaaattcatttttgtaagtgctagtttcctac-taattagctatctagta

upper sequence: GLYMA20G02880.1 (Glycine max), 5'ss of exon 5
lower sequence: GRMZM2G115670_T01 (Zea mays), 5'ss of exon 5
GCCATTTTCCTTGCTGCCAAGTTCTTGAAAGTGAAGCTTCCATCAGATGGTGAGAAGGTTTGGTGGCAAGAGTTTGATGTCACCCCACGCCAATTAGAGGgtcggtgtcatcccctcaattcatttgcatgctaacaaaattgatctgtttgggtagccttttgtgttcccttggtttaatgcatta-tgatc--atttctgc-
|| || ||  | ||||| || ||  | ||||||||||||||||| |||||||| |||||||||||||| || ||||||||||| ||||| ||  | || ||| |||  | |     |||  | | || |||  ||  |  |   |||| ||   |     | | |||||          |||| ||| ||||   |||  |   
GCTATCTTTTTGGCTGCTAAATTTCTCAAAGTGAAGCTTCCATCTGATGGTGATAAGGTTTGGTGGCAGGATTTTGATGTCACACCACGGCAGCTTGAAGgttggt-ccttgtttgcaaagcctgtg-atg--aaacatttccttctgctttattttgtatatatgttctgcatacgacatgctttactgattgaattattatc

upper sequence: GLYMA20G02880.1 (Glycine max), 5'ss of exon 5
lower sequence: GRMZM2G377311_T01 (Zea mays), 5'ss of exon 6
GCCATTTTCCTTGCTGCCAAGTTCTTGAAAGTGAAGCTTCCATCAGATGGTGAGAAGGTTTGGTGGCAAGAGTTTGATGTCACCCCACGCCAATTAGAGGgtcggtgtcatcccctcaattcatttgcatgctaacaaaattgatctgtttgggtagccttttgtgttcccttggtttaatgcattatgatcatttctgc--
|| || |   | ||||| || ||  | |||||||| || ||||| |||||||| ||| |||||||||| || ||||||||||| ||||| ||| | || ||| |||           || | | |   |         | | | |||  || |      | || ||  |   || | | ||   |  ||||    |  ||  
GCTATCTATTTGGCTGCTAAATTTCTCAAAGTGAATCTCCCATCTGATGGTGATAAGATTTGGTGGCAGGATTTTGATGTCACGCCACGACAACTTGAAGgttggtccttatttgcgaagttagtgagaaatgtttccactcgctctactttgtctatttgttctg--catatgttgtgattgttattgattgaattggcac

upper sequence: GLYMA20G02880.1 (Glycine max), 5'ss of exon 5
lower sequence: AT5G45190.2 (Arabidopsis thaliana), 5'ss of exon 8
GCCATTTTCCTTGCTGCCAAGTTCTTGAAAGTGAAGCTTCCATCAGATGGTGAGAAGGTTTGGTGGCAAGAGTTTGATGTCACCCCACGCCAATTAGAGGgtcggtgtcatcccctcaattcatttgcatgctaacaaaattgatctgtttgggtagccttttgtgttccctt--ggtttaatgcattatgatcatttctgc-------
|| || || ||||| ||||||||| | ||||||||| | ||||||||||| |||||||||||||||||||| ||||||||||| ||  | ||| | ||||||  ||   ||    | |||| | |||    | |      ||    ||||||  |  | ||   | || | ||  | ||| | |  | ||  || ||| |         
GCAATATTTCTTGCGGCCAAGTTCCTTAAAGTGAAGTTACCATCAGATGGAGAGAAGGTTTGGTGGCAAGAATTTGATGTCACACCCAGACAACTGGAGGgtatgtacaata---tgaattgacttg---acaattcttgtttccttgtttgacttccattccctttttctttatgatttcaagagtaatcgtcttttgtatatctcag

upper sequence: GLYMA20G02880.1 (Glycine max), 5'ss of exon 5
lower sequence: AT4G19600.1 (Arabidopsis thaliana), 5'ss of exon 7
GCCATTTTCCTTGCTGCCAAGTTCTTGAAAGTGAAGCTTCCATCAGATGGTGAGAAGGTTTGGTGGCAAGAGTTTGATGTCACCCCACGCCAATTAGAGGgtcggtgtcatcccctcaattcatttgcatgctaacaaaattgat-ctgtttgggtagccttttgtgttcccttggtttaatgcattatgatcatttctgc-------------------
|| ||||| |||||||| |||||| | ||||||||  | ||||||||||| |||||||| ||||||||||| ||||||||||| || || ||| ||||||||  | |   |  | | |  |       |   | |  ||| || | |   ||     |  |    |||   | |  |||      | ||| | |   || |                   
GCAATTTTTCTTGCTGCGAAGTTCCTTAAAGTGAAATTACCATCAGATGGAGAGAAGGTCTGGTGGCAAGAATTTGATGTCACACCTCGACAACTAGAGGgtgagagaactatctttatctttgaattaattttatgaaactgtttccactttttctgtttgacttgtatgccttattttgcatctgatgctaagagctactcccttatgtatactgcag

upper sequence: GLYMA20G02880.1 (Glycine max), 5'ss of exon 5
lower sequence: Vv00s0125g00270.t01 (Vitis vinifera), 5'ss of exon 5
GCCATTTTCCTTGCTGCCAAGTTCTTGAAAGTGAAGCTTCCATCAGATGGTGAGAAGGTTTGGTGGCAAGAGTTTGATGTCACCCCACGCCAATTAGAGGgtcggtgtcatcccctcaattcatttgcatgctaacaaaattgatctgtttgggtagccttttgt--gttcccttggtttaatgcattatgatcattt-ctgc-
|||||||||||||||||||||||  | ||||||||||||||||| |||||||||  ||| ||||||||||| |||||||||||||||||||| || |||||| ||| || ||||||    |  || |  |   |     || ||     | ||  || |||      | ||  | |   |  |||   ||    ||   |||  
GCCATTTTCCTTGCTGCCAAGTTTCTCAAAGTGAAGCTTCCATCGGATGGTGAGGTGGTCTGGTGGCAAGAATTTGATGTCACCCCACGCCAGTTGGAGGgttggtttcctcccct----tttttggtgtaaaattggtatggactcaatgggacagtcttcaaacagctctgtggcactgttgctgcatatggatggactgac

upper sequence: GLYMA20G02880.1 (Glycine max), 5'ss of exon 5
lower sequence: EFJ27727 (Selaginella moellendorffii), 5'ss of exon 5
GCCATTTTCCTTGCTGCCAAGTTCTTGAAAGTGAAGCTTCCATCAGATGGTGAGAAGGTTTGGTGGCAAGAGTTTGATGTCACCCCACGCCAATTAGAGGgtcggtgtcatcccctcaattcatttgcatgctaacaaa-attgatctgtttgggtagccttttgtgttcccttggtttaa----tgcattatgatcatttctgc----
||||||||||| ||||| |||||  | || |||||||| ||    |||||||||  || |||||||||||||||||||||||| || || ||| | || |||      | | | ||  | |    |  |  |||      |||| ||| ||| | |    |||  || ||   | |   ||    ||||        |||| |      
GCCATTTTCCTGGCTGCAAAGTTTCTTAAGGTGAAGCTGCCGATCGATGGTGAGCGGGCTTGGTGGCAAGAGTTTGATGTCACGCCTCGGCAACTGGAAGgta-----cgttctctggactttgatagactctagtttccattgttcttttttgtttcattttcatggtcgtattgagaaagggatgcacgtctcctatttttttgcag

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|193551311|gb|FK506122.1|FK506122
EST:     GAGAAGGTTTTGGTGGCAAGAGTTTGATGTCACCCCACGCCAATTAGAGG                         AGGCTTGCAATCAAATGTTGGAACTCTATGAGCAGAGTAGACTTCCACCAG
genomic: GAGAAGGTTT-GGTGGCAAGAGTTTGATGTCACCCCACGCCAATTAGAGGgtcggtgtca ... tctcttgcagAGGTTTGCAATCAAATGTTGGAACTCTATGAGCAGAGTAGACTTCCACCAG




















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCCATTTTCCTTGCTGCCAAGTTCTTGAAAGTGAAGCTTCCATCAGATGGTGAGAAGGTTTGGTGGCAAGAGTTTGATGTCACCCCACGCCAATTAGAGGgtcggtgtcatcccctcaattcatttgcatgctaacaaaattgatctgtttgggtagccttttgtgttcccttggtttaatgcattatgatcatttctgc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - catcccc