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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTATTGCAAGTGCGAGATGCCTTATAACCCAGATGACCTCATGGTGCAGTGTGAGGGGTGCAAGGATTGgtaaaaccagtatattctgcttttttttgtttactgttattacatttgtgagtggtttttggttgtctggttctctaattttagcattagatgcgttgtt...

Basic information

species Glycine max
transcript GLYMA13G34740.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G34740.1 (Glycine max), 5'ss of exon 3
lower sequence: LOC_Os09g21770.1 (Oryza sativa), 5'ss of exon 3
GTATTGCAAGTGCGAGATGCCTTATAACCCAGATGACCTCATGGTGCAGTGTGAGGGGTGCAAGGATTGgtaaaaccagtatattctgcttttttttgtttactgttattacatttgtgagtggtttttggttgtc-tggttctctaattttagcattagatgcgttgtt
||| ||||||||||||||||| |||||||| ||||| || ||||||||||| ||||| |||||||| ||||||| |   |     |  | ||   ||   |||||    |   |    ||  ||| |||  |   | |  || |        || || | |  |   || 
GTACTGCAAGTGCGAGATGCCGTATAACCCGGATGATCTAATGGTGCAGTGCGAGGGATGCAAGGACTGgtaaatcacttggggacatccttacctttcatactgcatctggctgaccgaagggtatttcatgcccgtcatttttaggaggaagtatcatagactcagt-

upper sequence: GLYMA13G34740.1 (Glycine max), 5'ss of exon 3
lower sequence: LOC_Os08g32620.2 (Oryza sativa), 5'ss of exon 2
-------------------------------GTATTGCAAGTGCGAGATGCCTTATAACCCAGATGACCTCATGGTGCAGTGTGAGGGGTGCAAGGATTGgtaaaaccagta-tattctgcttttttt-tgtttactgttattacat-ttgtgagtggtttttggttgtctggttctctaattttagcattag-atgcgttgtt
                                || |||||||| |||||||| || ||||| ||||| |||||||||||||| || |  |||||||| ||||||  ||| || ||  | || | | || || |   | | | |  || | |||| ||     |||              |||  |   ||| | |  | |    
TGCTTGTGTTTTCTTTTTCGTTTTTCTGAAGATACTGCAAGTGTGAGATGCCATACAACCCGGATGATCTCATGGTGCAGTGCGATGACTGCAAGGACTGgtaattccattaataaaccgcctctgttatgatgcatttcagtctatatagtgaatgtacactggaaaatcatggtaacaataatgaaattggcacccat----

upper sequence: GLYMA13G34740.1 (Glycine max), 5'ss of exon 3
lower sequence: LOC_Os08g32620.1 (Oryza sativa), 5'ss of exon 3
GTATTGCAAGTGCGAGATGCCTTATAACCCAGATGACCTCATGGTGCAGTGTGAGGGGTGCAAGGATTGgtaaaaccagta-tattctgctttt-ttttgtttactgttattacat-ttgtgagtggtttttggttgtctggttctctaattttagcattag-atgcgttgtt
 || |||||||| |||||||| || ||||| ||||| |||||||||||||| || |  |||||||| ||||||  ||| || ||  | || | | || || |   | | | |  || | |||| ||     |||              |||  |   ||| | |  | |    
ATACTGCAAGTGTGAGATGCCATACAACCCGGATGATCTCATGGTGCAGTGCGATGACTGCAAGGACTGgtaattccattaataaaccgcctctgttatgatgcatttcagtctatatagtgaatgtacactggaaaatcatggtaacaataatgaaattggcacccat----

upper sequence: GLYMA13G34740.1 (Glycine max), 5'ss of exon 3
lower sequence: GRMZM2G091265_T03 (Zea mays), 5'ss of exon 2
-------------------------------GTATTGCAAGTGCGAGATGCCTTATAACCCAGATGACCTCATGGTGCAGTGTGAGGGGTGCAAGGATTGgtaaaa-ccagtatattctgcttttttttgtttactgttattacat-ttgtgagtggtttttggttgtctggttctctaattttagcattagatgcgttgtt-
                                ||||||||||| |||||||| || ||||| ||||||||||||||||||||||| || |||||||| |||||||| || ||  |  || |    |||| |   |  ||| | ||| || |||| ||  |||   |       || ||  |   |    |  |    |||   
TGATCTTATGTGACATTGTTTGTATGTGAAGATATTGCAAGTGTGAGATGCCGTACAACCCGGATGACCTCATGGTGCAGTGTGAAGGATGCAAGGACTGgtaaaatcctgtgaaaactccacacttttctc--ccattagtgcatgttttgagaggggtttatctagtaaaatcactg-tgaaatggctccacattttgccc

upper sequence: GLYMA13G34740.1 (Glycine max), 5'ss of exon 3
lower sequence: GRMZM2G091265_T05 (Zea mays), 5'ss of exon 3
GTATTGCAAGTGCGAGATGCCTTATAACCCAGATGACCTCATGGTGCAGTGTGAGGGGTGCAAGGATTGgtaaaa-ccagtatattctgcttttttttgtttactgttattacat-ttgtgagtggtttttggttgtctggttctctaattttagcattagatgcgttgtt-
 ||||||||||| |||||||| || ||||| ||||||||||||||||||||||| || |||||||| |||||||| || ||  |  || |    |||| |   |  ||| | ||| || |||| ||  |||   |       || ||  |   |    |  |    |||   
ATATTGCAAGTGTGAGATGCCGTACAACCCGGATGACCTCATGGTGCAGTGTGAAGGATGCAAGGACTGgtaaaatcctgtgaaaactccacacttttctc--ccattagtgcatgttttgagaggggtttatctagtaaaatcactg-tgaaatggctccacattttgccc

upper sequence: GLYMA13G34740.1 (Glycine max), 5'ss of exon 3
lower sequence: GRMZM2G091265_T01 (Zea mays), 5'ss of exon 3
GTATTGCAAGTGCGAGATGCCTTATAACCCAGATGACCTCATGGTGCAGTGTGAGGGGTGCAAGGATTGgtaaaa-ccagtatattctgcttttttttgtttactgttattacat-ttgtgagtggtttttggttgtctggttctctaattttagcattagatgcgttgtt-
          || |||||||| || ||||| ||||||||||||||||||||||| || |||||||| |||||||| || ||  |  || |    |||| |   |  ||| | ||| || |||| ||  |||   |       || ||  |   |    |  |    |||   
----------TGTGAGATGCCGTACAACCCGGATGACCTCATGGTGCAGTGTGAAGGATGCAAGGACTGgtaaaatcctgtgaaaactccacacttttctc--ccattagtgcatgttttgagaggggtttatctagtaaaatcactg-tgaaatggctccacattttgccc

upper sequence: GLYMA13G34740.1 (Glycine max), 5'ss of exon 3
lower sequence: GRMZM2G119357_T01 (Zea mays), 5'ss of exon 3
GTATTGCAAGTGCGAGATGCCTTATAACCCAGATGACCTCATGGTGCAGTGTGAGGGGTGCAAGGATTGgtaaa---accagtatattctgcttttttttgtttactgttattacatttgtgagtggtttttggttgtctggttctctaatttta--gcattagatgcgttgtt
||||||||| || |||||||| || ||||| |||||||||||||||||||| || |  |||||||| ||||| |     |   ||  | | |  |||    || |||| ||||     | ||    || |    || | || ||||  ||    |  || ||| ||   | |  
GTATTGCAAATGTGAGATGCCATACAACCCGGATGACCTCATGGTGCAGTGCGAAGCTTGCAAGGACTGgtacatttgtctcaatgattttcaatttacatttcactgatatt-tgcctttgttcagtct---attttatgcttctacaaagcaaatgctttaaatctctgga-

upper sequence: GLYMA13G34740.1 (Glycine max), 5'ss of exon 3
lower sequence: GRMZM5G871463_T02 (Zea mays), 5'ss of exon 3
GTATTGCAAGTGCGAGATGCCTTATAACCCAGATGACCTCATGGTGCAGTGTGAGGGGTGCAAGGATTGgtaaaaccagtatatt---ctgcttttttttgtttactgttatt-acatttgtgagtggtttttggttgtctggttctctaattttagcattagatgcgttgtt
||||||||| || |||||||| || ||||| |||||||||||||||||||| || |  |||||| | ||||| |     || | |    |||  |||    || |||| ||||  | |||||     || |    || | ||  | |  ||     |  ||| ||    ||  
GTATTGCAAATGTGAGATGCCGTACAACCCCGATGACCTCATGGTGCAGTGCGATGCTTGCAAGCACTGgtacatttgttacaatgatttgcaatttacatttcactgatatttgcctttgttccccgtct---attatgtgactgtacaaagcatgttttaaatctcctga-

upper sequence: GLYMA13G34740.1 (Glycine max), 5'ss of exon 3
lower sequence: GRMZM5G871463_T01 (Zea mays), 5'ss of exon 1
-------------------------------GTATTGCAAGTGCGAGATGCCTTATAACCCAGATGACCTCATGGTGCAGTGTGAGGGGTGCAAGGATTGgtaaaaccagtatat---tctgcttttttttgtttactgttatt-acatttgtgagtggtttttggttgtctggttctctaattttagcattagatgcgttgtt
                               ||||||||| || |||||||| || ||||| |||||||||||||||||||| || |  |||||| | ||||| |     || |    | |||  |||    || |||| ||||  | |||||     || |    || | ||  | |  ||     |  ||| ||    ||  
GTGATGATTGGGTTGTCTATTTTCTCTCAAGGTATTGCAAATGTGAGATGCCGTACAACCCCGATGACCTCATGGTGCAGTGCGATGCTTGCAAGCACTGgtacatttgttacaatgatttgcaatttacatttcactgatatttgcctttgttccccgtct---attatgtgactgtacaaagcatgttttaaatctcctga-

upper sequence: GLYMA13G34740.1 (Glycine max), 5'ss of exon 3
lower sequence: AT4G22140.2 (Arabidopsis thaliana), 5'ss of exon 3
GTATTGCAAGTGCGAGATGCCTTATAACCCAGATGACCTCATGGTGCAGTGTGAGGGGTGCAAGGATTGgtaaa-accagtatat-tctgctttttt---ttgtttactgttattacatttgtgagtggtttttggttgtctggttctctaattttagcattagatgc-----gttgtt----------------------------
||| ||||| || || |||||||| || ||||| || ||||||||||||||||| || ||||| || |||||||      ||| | |||  ||| ||   ||  |||||  | || ||   |  |   |  | |   |||||| || |  || ||  | |||   | |      || ||                            
GTACTGCAAATGTGAAATGCCTTACAATCCAGACGATCTCATGGTGCAGTGTGAAGGCTGCAAAGACTGgtaaatgttgatatttgtcttttttattaacttccttacttgtgtttcaacagaaaagagactata--tgtctg-tttttaaacttacgtattcttttccaggaattattgataataagcattaattcgctgttgtag

upper sequence: GLYMA13G34740.1 (Glycine max), 5'ss of exon 3
lower sequence: Vv10s0116g00160.t01 (Vitis vinifera), 5'ss of exon 3
GTATTGCAAGTGCGAGATGCCTTATAACCCAGATGACCTCATGGTGCAGTGTGAGGGGTGCAAGGATTGgtaaaaccagtatattctgcttttttttgtttactgttattacatttgtgagtggtttttggttgtctggttctctaattttagcattagatgcgttgtt--
||||||||| |||||||||||||||||||||||||| || ||||| ||||| |||||||||||||| ||||||      | | || | ||||| || | || | |   ||    |||||  | || |    |    |   | ||| |||||   |  | |||     |   
GTATTGCAAATGCGAGATGCCTTATAACCCAGATGATCTTATGGTCCAGTGCGAGGGGTGCAAGGACTGgtaacctgcttttgttattcttttgttgggtttccg--gttgttgttgtgttttgtgtcatttcagttttgtatctgattttgtaaaaacatggaaactcaa

upper sequence: GLYMA13G34740.1 (Glycine max), 5'ss of exon 3
lower sequence: PP1S298_65V6.1 (Physcomitrella patens), 5'ss of exon 3
GTATTGCAAGTGCGAGATGCCTTATAACCCAGATGACCTCATGGTGCAGTGTGAGGGGTGCAAGGATTGgtaaaaccagtatattctgcttttttttgtttactgttattacatttgtgagtggtttttggttgtctggttctctaattttagcattagatgcgttgtt--
 ||||||||||||||||||||||| || || |||||| | ||||| || |||||    ||||| || |||||   | |   |  |||| |    |  |   |     ||| | |||||   ||        ||  |  |    |   || | |  | ||  || |||    
TTATTGCAAGTGCGAGATGCCTTACAATCCTGATGACTTGATGGTTCAATGTGAAATCTGCAAAGACTGgtaggcctatgcttctctgttcaactgcgacaaagtgcatttc-tttgtatttgcccggatatttgcaagaggacggtttcttgagtgaggagc-ttgcacc

upper sequence: GLYMA13G34740.1 (Glycine max), 5'ss of exon 3
lower sequence: EFJ26805 (Selaginella moellendorffii), 5'ss of exon 3
GTATTGCAAGTGCGAGATGCCTTATAACCCAGATGACCTCATGGTGCAGTGTGAGGGGTGCAAGGATTGgtaa-aaccagtatattctgcttttttttgtttactgttattacatttgtgagtggtttttggttgtctggttctctaattttagcattagatgcgttgtt
||| |||||||||||||||||||| ||||| ||||| || |||||||||||||||| |||||| || |||||| || |||| | |      |      |  |   |      |   ||  |    |    |                                       
GTACTGCAAGTGCGAGATGCCTTACAACCCGGATGATCTTATGGTGCAGTGTGAGGAGTGCAAAGACTGgtaagaatcagtttctctcaaatccaaaagcct-tggcagcctccgatgaaaaaaatggcag---------------------------------------

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|193300267|gb|FK267210.1|FK267210
EST:     CCTTATAACCCAGATGACCTCATGGTGCAGTGTGAGGGGTGCAAGGATTG                         GTACCATCCTGCTTGCGTGGGCATGACTATTGAAGAAGCAAAGAAATTGGA
genomic: CCTTATAACCCAGATGACCTCATGGTGCAGTGTGAGGGGTGCAAGGATTGgtaaaaccag ... ttttttgtagGTACCATCCTGCTTGCGTGGGCATGACTATTGAAGAAGCAAAGAAATTGGA
EST: gi|193368742|gb|FK335710.1|FK335710
EST:     CCTTATAACCCAGATGACCTCATGGTGCAGTGTGAGGGGTGCAAGGATTG                         GTACCATCCTGCTTGCGTGGGCATGACTATTGAAGAAGCAAAGAA-TTGGA
genomic: CCTTATAACCCAGATGACCTCATGGTGCAGTGTGAGGGGTGCAAGGATTGgtaaaaccag ... ttttttgtagGTACCATCCTGCTTGCGTGGGCATGACTATTGAAGAAGCAAAGAAATTGGA
EST: gi|214008997|gb|DB984557.1|DB984557
EST:     CATGGTGCAGTGTGAGGGGTGCAAGGATTG                         GTACTATCCTGCTTGCGTCGGCATGACTATTGAAGAAGCAAAGAAATTGGA
genomic: CATGGTGCAGTGTGAGGGGTGCAAGGATTGgtaaaaccag ... ttttttgtagGTACCATCCTGCTTGCGTGGGCATGACTATTGAAGAAGCAAAGAAATTGGA
EST: gi|209709125|gb|BW658841.1|BW658841
EST:     CCTTATAACCCAGATGACCTCATGGTGCAGTGTGAGGGGTGCAAGGATTG                         GTACCATCCTGCTTGCGTGGGCATGACTATTGAAGAAGCAAAGAAATTGGA
genomic: CCTTATAACCCAGATGACCTCATGGTGCAGTGTGAGGGGTGCAAGGATTGgtaaaaccag ... ttttttgtagGTACCATCCTGCTTGCGTGGGCATGACTATTGAAGAAGCAAAGAAATTGGA
EST: gi|193375728|gb|FK339153.1|FK339153
EST:     CCTTATAACCCAGATGACCTCATGGTGCAGTGTGAGGGGTGCAAGGATTG                         GTACCATCCTGCTTGCGTGGGCATGACTATTGAAGAAGCAAAGAAATTGGA
genomic: CCTTATAACCCAGATGACCTCATGGTGCAGTGTGAGGGGTGCAAGGATTGgtaaaaccag ... ttttttgtagGTACCATCCTGCTTGCGTGGGCATGACTATTGAAGAAGCAAAGAAATTGGA
EST: gi|7029681|gb|AW459464.1|AW459464
EST:     CCTTATAACCCAGATGACCTCATGGTGCAGAGTGAGGGGTGCAAGGATTG                         GTACCATCCTGCTTGCGTGGGCATGACTATTGAAGAAGCAAAGAAATTGGA
genomic: CCTTATAACCCAGATGACCTCATGGTGCAGTGTGAGGGGTGCAAGGATTGgtaaaaccag ... ttttttgtagGTACCATCCTGCTTGCGTGGGCATGACTATTGAAGAAGCAAAGAAATTGGA
EST: gi|9258286|gb|BE346433.1|BE346433
EST:     CCTTATGACCCATATGACCTCATGGTGCAGTGTGAGGGGTGCAAGGATTG                         GTACCATCCTGCTTGCGTGGGCATGACTATTGAATAAGCAAAGAAATTGGA
genomic: CCTTATAACCCAGATGACCTCATGGTGCAGTGTGAGGGGTGCAAGGATTGgtaaaaccag ... ttttttgtagGTACCATCCTGCTTGCGTGGGCATGACTATTGAAGAAGCAAAGAAATTGGA
EST: gi|193379467|gb|FK343569.1|FK343569
EST:     CCTTATAACCCAGATGACCTCATGGTGCAGTGTGAGGGGTGCAAGGATTG                         GTACCATCCTGCTTGCGTGGGCATGACTATTGAAGAAGCAAAGAAATTGGA
genomic: CCTTATAACCCAGATGACCTCATGGTGCAGTGTGAGGGGTGCAAGGATTGgtaaaaccag ... ttttttgtagGTACCATCCTGCTTGCGTGGGCATGACTATTGAAGAAGCAAAGAAATTGGA
EST: gi|209701039|gb|BW652617.1|BW652617
EST:     CCTTATAACCCAGATGACCTCATGGTGCAGTGTGAGGGGTGCAAGGATTG                         GTACCATCCTGCTTGCGTGGGCATGACTATTGAAGAAGCAAAGAAATTGGA
genomic: CCTTATAACCCAGATGACCTCATGGTGCAGTGTGAGGGGTGCAAGGATTGgtaaaaccag ... ttttttgtagGTACCATCCTGCTTGCGTGGGCATGACTATTGAAGAAGCAAAGAAATTGGA
EST: gi|208024940|gb|GD822386.1|GD822386
EST:     CCTTATAACCCAGATGACCTCATGGTGCAGTGTGAGGGGTGCAAGGATTG                         GTACCATCCTGCTTGCGTGGGCATGA
genomic: CCTTATAACCCAGATGACCTCATGGTGCAGTGTGAGGGGTGCAAGGATTGgtaaaaccag ... ttttttgtagGTACCATCCTGCTTGCGTGGGCATGA
EST: gi|151394164|gb|EV264035.1|EV264035
EST:     CCTTATAACCCAGATGACCTCATGGTGCAGTGTGAGGGGTGCAAGGATTG                         GTACCATCCTGCTTGCGTGGGCATGACTATTGAAGAAGCAAAGAAATTGGA
genomic: CCTTATAACCCAGATGACCTCATGGTGCAGTGTGAGGGGTGCAAGGATTGgtaaaaccag ... ttttttgtagGTACCATCCTGCTTGCGTGGGCATGACTATTGAAGAAGCAAAGAAATTGGA
EST: gi|193370284|gb|FK338134.1|FK338134
EST:     CCTTATAACCCAGATGACCTCATGGTGCAGTGTGAGGGGTGCAAGGATTG                         GTACCATCCTGCTTAGCGTGGGCATGACTATTGAAGAAGCAAAGAAATTGG
genomic: CCTTATAACCCAGATGACCTCATGGTGCAGTGTGAGGGGTGCAAGGATTGgtaaaaccag ... ttttttgtagGTACCATCCTGCTT-GCGTGGGCATGACTATTGAAGAAGCAAAGAAATTGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTATTGCAAGTGCGAGATGCCTTATAACCCAGATGACCTCATGGTGCAGTGTGAGGGGTGCAAGGATTGgtaaaaccagtatattctgcttttttttgtttactgttattacatttgtgagtggtttttggttgtctggttctctaattttagcattagatgcgttgtt

- - - - - - - - - - - - - -  CAGATG