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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...catgtgatctttgatgcatatatgtcatgaagttatcaacttgatactgtcctgatgcagtgtgggtttatgttttctgttgatcctcatattttactagGTAATAACGAAGTTCTGTTCAGAGCGAATTGCTAAATATGCATTCGAGTATGCTTACCTGAATAACAGAAAGAAGGTGACTGCCGTGCACAAAGCAAATA

Basic information

species Glycine max
transcript GLYMA16G22640.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G22640.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os02g38200.1 (Oryza sativa), 3'ss of exon 1
catgtgatctttgatgcatatatgtcatgaagttatcaacttgatactgtcctgatgcagtgtgggtttatgtt-ttctgttgatcctcatattttactagGTAATAACGAAGTTCTGTTCAGAGCGAATTGCTAAATATGCATTCGAGTATGCTTACCTGAATAACAGAAAGAAGGTGACTGCCGTGCACAAAGCAAATA
  | |||  |   | | || ||  |  |   || |         |  |   || | | | | |   | ||| |  | |||||  |      |||| ||||||| || || |||||||| || ||  | ||||| || ||||| || ||||| || ||||| || ||||||||||| |||||||||||||| |||||||| |
tttctgaaatagaacgtatgtaaatgtttttgtcacttttcatttcatcatctaaaggaatttttttctatatggtactgttactaaatggattt-actagGTGATCACAAAGTTCTGCTCTGAAAGGATTGCCAAGTATGCTTTTGAGTACGCGTACCTCAACAACAGAAAGAAAGTGACTGCCGTGCATAAAGCAAACA

upper sequence: GLYMA16G22640.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os04g40310.2 (Oryza sativa), 3'ss of exon 1
catgtgatctttgatgcatatatgtcatgaagttatcaacttgatactgtcctgatgcagtgtgggtttatgttttctgttgatcct------catattttactagGTAATAACGAAGTTCTGTTCAGAGCGAATTGCTAAATATGCATTCGAGTATGCTTACCTGAATAACAGAAAGAAGGTGACTGCCGTGCACAAAGCAAATA------------
             ||    | |||  ||||| |   || | |  |  | | |   | |  | || | || | ||   | ||  ||         |  ||||   |||| ||||| ||||| || || ||| | ||||| |||||||| || |||||||||||||| || ||| ||||||| || || || ||||| |||||||| |            
-------------attgcca-atggaatgaaatg--cacccttttttttttccagttc--tctgagcttcttttccatcttagtctcactgactaacttttgtcaggtgataacaaagTTTTGCTCTGAGAGGATTGCCAAATATGCTTTTGAGTATGCTTACCTTAACAACCGAAAGAAAGTCACAGCAGTGCATAAAGCAAACATCATGAAGCTTG

upper sequence: GLYMA16G22640.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os04g40310.1 (Oryza sativa), 3'ss of exon 1
catgtgatctttgatgcatatatgtcatgaagttatcaacttgatactgtcctgatgcagtgtgggtttatgttttctgttgatcct------catattttactagGTAATAACGAAGTTCTGTTCAGAGCGAATTGCTAAATATGCATTCGAGTATGCTTACCTGAATAACAGAAAGAAGGTGACTGCCGTGCACAAAGCAAATA
  |||| |   ||||    | |||  ||||| |   || | |  |  | | |   | |  | || | || | ||   | ||  ||         |  ||||   |||| ||||| ||||| || || ||| | ||||| |||||||| || |||||||||||||| || ||| ||||||| || || || ||||| |||||||| |
-ttgtgttacatgattgcca-atggaatgaaatg--cacccttttttttttccagttc--tctgagcttcttttccatcttagtctcactgactaacttttgtcagGTGATAACAAAGTTTTGCTCTGAGAGGATTGCCAAATATGCTTTTGAGTATGCTTACCTTAACAACCGAAAGAAAGTCACAGCAGTGCATAAAGCAAACA

upper sequence: GLYMA16G22640.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G025366_T01 (Zea mays), 3'ss of exon 1
--catgtgatctttgatgcatatatgtcatgaagttatcaacttgatactgtcctga--tgcagtgtgggtttatgttttctgttgatcctcatattttactagGTAATAACGAAGTTCTGTTCAGAGCGAATTGCTAAATATGCATTCGAGTATGCTTACCTGAATAACAGAAAGAAGGTGACTGCCGTGCACAAAGCAAATA
      |||  |   || ||   || | |||   ||    |     ||| || || |  || |   |   |  ||  || || ||  |      ||||  |||||| || || ||||| || || ||| | ||||| |||||||||||||||||||||||||| || ||| ||||||| || ||||| ||||| |||||||| |
tgttgttgaaatagaatccactcatttaatg---tttgtgatcctttacagttcttatctgaacctttcttccattattactcttactgaatggatttc-ctagGTGATCACAAAGTTTTGCTCTGAGAGGATTGCCAAATATGCATTCGAGTATGCTTACCTTAACAACCGAAAGAAAGTCACTGCAGTGCATAAAGCAAACA

upper sequence: GLYMA16G22640.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G025366_T02 (Zea mays), 3'ss of exon 1
catgtgatctttgatgcatatatgtcatgaagttatcaacttgatactgtcctgat--gcagtgtgggtttatgttttctgttgatcctcatattttactagGTAATAACGAAGTTCTGTTCAGAGCGAATTGCTAAATATGCATTCGAGTATGCTTACCTGAATAACAGAAAGAAGGTGACTGCCGTGCACAAAGCAAATA------------
             || ||   || | |||   ||    |     ||| || || ||  | |   |   |  ||  || || ||  |      ||||  |||||| || || ||||| || || ||| | ||||| |||||||||||||||||||||||||| || ||| ||||||| || ||||| ||||| |||||||| |            
----------agaatccactcatttaatg---tttgtgatcctttacagttcttatctgaacctttcttccattattactcttactgaatggatttc-ctaggtgatcacaaagTTTTGCTCTGAGAGGATTGCCAAATATGCATTCGAGTATGCTTACCTTAACAACCGAAAGAAAGTCACTGCAGTGCATAAAGCAAACATTATGAAGCTTG

upper sequence: GLYMA16G22640.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv04s0210g00180.t01 (Vitis vinifera), 3'ss of exon 1
catgtgatctttgatgcatatatgtcatgaagtt-atcaacttgatactgtcctgatgcagtgtgggtt-tatgttttctgttgatcctcatattttactagGTAATAACGAAGTTCTGTTCAGAGCGAATTGCTAAATATGCATTCGAGTATGCTTACCTGAATAACAGAAAGAAGGTGACTGCCGTGCACAAAGCAAATA
 | || | |||       | | ||  |||   || || ||||||   ||       ||||  ||  ||  |||||||   | | ||  |  |  ||| |||||||||||| ||||||||||||||||| ||||| |||||||| || |||||||| ||||| || ||||||||||| ||||| || |||||||||||||| |
gaggttaccttc--ctattctttgctatgcttttcatgaacttgcatcttgggcattgcacagtctgtagtatgtttgtggctcatgatgctcatttgctagGTAATAACAAAGTTCTGTTCAGAGCGCATTGCAAAATATGCTTTTGAGTATGCATACCTAAACAACAGAAAGAAAGTGACAGCTGTGCACAAAGCAAACA

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|21889461|gb|BQ742674.1|BQ742674
EST:     ACTCTGGCCTCGAACACGAGGTCGTTCCCGGCGTTGTTGAAAGCCTTAAG                         GTAATAACGAAGTTCTGTTCAGAGCGAATTGCTAAATATGCATTCGAGTAT
genomic: ACTCTGGCCTCGAACACGAGGTCGTTCCCGGCGTTGTTGAAAGCCTTAAGgtgcgttctt ... attttactagGTAATAACGAAGTTCTGTTCAGAGCGAATTGCTAAATATGCATTCGAGTAT
EST: gi|6482120|gb|AW201391.1|AW201391
EST:     ACTCTGGCCTCGAACACGAGGTCGTTCCCGGCGTTGTTGAAAGCCTTAAG                         GTAATAACGAAGTTCTGTTCAGAGCGAATTGCTAAATATGCATTCGAGTAT
genomic: ACTCTGGCCTCGAACACGAGGTCGTTCCCGGCGTTGTTGAAAGCCTTAAGgtgcgttctt ... attttactagGTAATAACGAAGTTCTGTTCAGAGCGAATTGCTAAATATGCATTCGAGTAT
EST: gi|21889392|gb|BQ742605.1|BQ742605
EST:     ACTCTGGCCTCGAACACGAGGTCGTTCCCGGCGTTGTTGAAAGCCTTAAG                         GTAATAACGAAGTTCTGTTCAGAGCGAATTGCTAAATATGCATTCGAGTAT
genomic: ACTCTGGCCTCGAACACGAGGTCGTTCCCGGCGTTGTTGAAAGCCTTAAGgtgcgttctt ... attttactagGTAATAACGAAGTTCTGTTCAGAGCGAATTGCTAAATATGCATTCGAGTAT
EST: gi|4304368|gb|AI443609.1|AI443609
EST:     ACTCTGGCCTCGAACACGAGGTCGTTCCCGGCGTTGTTGAAAGCCTTAAG                         GTAATAACGAAGTTCTGTTCAGAGCGAATTGCTAAATATGCATTCGAGTAT
genomic: ACTCTGGCCTCGAACACGAGGTCGTTCCCGGCGTTGTTGAAAGCCTTAAGgtgcgttctt ... attttactagGTAATAACGAAGTTCTGTTCAGAGCGAATTGCTAAATATGCATTCGAGTAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actgtcctgatgcagtgtgggtttatgttttctgttgatcctcatattttactagGTAATAACGAAGTTCTGTTCAGAGCGAATTGCTAAATATGCATTCGAGTATGCTTACCTGAATAACAGAAAGAAGGTGACTGCCGTGCACAAAGCAAATA
                                              ttttact  CT-rich tract
                                           atattttacta  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
catgtgatctttgatgcatatatgtcatgaagttatcaacttgatactgtcctgatgcagtgtgggtttatgttttctgttgatcctcatattttactagGTAATAACGAAGTTCTGTTCAGAGCGAATTGCTAAATATGCATTCGAGTATGCTTACCTGAATAACAGAAAGAAGGTGACTGCCGTGCACAAAGCAAATA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
catgtga
- - - - - - - tgcatat
- - - - - - - - - - - tgtcatg
- - - - - - - - - - - - - - - - - - - - - - tactgtc
- - - - - - - - - - - - - - - - - - - - - - - - - -ctgatgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtgtggg