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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCATGAGAGATTTCAAGAGGCTGCAACAAGACCCTCCTGCAGGAATCAGTGGCGCCCCTCAGGATAACAACATCATGCTGTGGAATGCTGTCATATTTGGgtgagctgaattgaaattggataaagataaaactgttctgcttacttgaataatatagttactttgttttttattttattttttttccacactttgtgtaagtatggatggataagcaatttctgctttcttgtctgctttggattgcag

Basic information

species Glycine max
transcript GLYMA17G10640.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G10640.1 (Glycine max), 5'ss of exon 2
lower sequence: GRMZM2G110983_T02 (Zea mays), 5'ss of exon 2
TCATGAGAGATTTCAAGAGGCTGCAACAAGACCCTCCTGCAGGAATCAGTGGCGCCCCTCAGGATAACAACATCATGCTGTGGAATGCTGTCATATTTGGgtgagctgaattgaaattggataaagataaaactgttctgctta-cttgaataatatagtt--actttgttttttattttattttttttccacactttgtgtaagtatggatggataagcaatttctgctttcttgtctgctttggattgcag
| ||||| ||||||||| || ||   || |||||||| || || || ||||||||||| |||||||||||||| ||||||||||||||||||||||||||||  | || |  |||                 |    || ||||  ||||||  ||   ||  || | || |||   | |  || |||     ||                                                          
TGATGAGGGATTTCAAGCGGTTGATGCAGGACCCTCCGGCCGGCATAAGTGGCGCCCCGCAGGATAACAACATAATGCTGTGGAATGCTGTCATATTTGGgtatgatgca--gaatccccccgcccccttttccccacttcttagtttgaattgtaatatttgacatcgtctttggatatgcttatttcttttacag--------------------------------------------------------

upper sequence: GLYMA17G10640.1 (Glycine max), 5'ss of exon 2
lower sequence: Vv17s0000g05820.t01 (Vitis vinifera), 5'ss of exon 2
TCATGAGAGATTTCAAGAGGCTGCAACAAGACCCTCCTGCAGGAATCAGTGGCGCCCCTCAGGATAACAACATCATGCTGTGGAATGCTGTCATATTTGGgtgagctgaattgaaattggataaagataaaactgttctgcttacttgaataatatagttactttgttttttattttattttttttccacactttgtgtaagtatggatggataagcaatttctgctttcttgtctgctttggattgcag
| ||||||||||| |||||| ||||||| ||||| ||||| || |||||||| || || || || ||||| || ||||| ||||||||||| |||||||||| |   | |   |||||    |||  |     | || || || |||   | || |  ||| ||   |||   ||||| ||| |     || | ||| ||||||||| ||||||||| ||||||| |||||| |||| ||||||||||||
TGATGAGAGATTTTAAGAGGTTGCAACAGGACCCCCCTGCCGGCATCAGTGGAGCTCCCCAAGACAACAATATAATGCTTTGGAATGCTGTTATATTTGGgtaatgggcaacaaaattcatgaaaactg---ttattgtgtttgcttatgttatgtgtttattt--atttgccttttactttct-----cagtatgtttaagtatggttggataagccatttctggtttcttttctgatttggattgcag

upper sequence: GLYMA17G10640.1 (Glycine max), 5'ss of exon 2
lower sequence: Vv17s0000g05820.t01 (Vitis vinifera), 5'ss of exon 2
TCATGAGAGATTTCAAGAGGCTGCAACAAGACCCTCCTGCAGGAATCAGTGGCGCCCCTCAGGATAACAACATCATGCTGTGGAATGCTGTCATATTTGGgtgagctgaattgaaattggataaagataaaactgttctgcttacttgaataatatagttactttgttttttattttattttttttccacactttgtgtaagtatggatggataagcaatttctgctttcttgtctgctttggattgcag
| ||||||||||| |||||| ||||||| ||||| ||||| || |||||||| || || || || ||||| || ||||| ||||||||||| |||||||||| |   | |   |||||    |||  |     | || || || |||   | || |  ||| ||   |||   ||||| ||| |     || | ||| ||||||||| ||||||||| ||||||| |||||| |||| ||||||||||||
TGATGAGAGATTTTAAGAGGTTGCAACAGGACCCCCCTGCCGGCATCAGTGGAGCTCCCCAAGACAACAATATAATGCTTTGGAATGCTGTTATATTTGGgtaatgggcaacaaaattcatgaaaactg---ttattgtgtttgcttatgttatgtgtttattt--atttgccttttactttct-----cagtatgtttaagtatggttggataagccatttctggtttcttttctgatttggattgcag

upper sequence: GLYMA17G10640.1 (Glycine max), 5'ss of exon 2
lower sequence: PP1S91_87V6.1 (Physcomitrella patens), 5'ss of exon 1
TCATGAGAGATTTCAAGAGGCTGCAACAAGACCCTCCTGCAGGAATCAGTGGCGCCCCTCAGGATAACAACATCATGCTGTGGAATGCTGTCATATTTGGgtgagctgaattgaaattggataaagataaaactgttctgcttacttgaataatatagttactttgttttttattttattttttttccacactttgtgtaagtatggatggataagcaatttctgctttcttgtctgctttggattgcag
| ||| | || |||||| | ||||| || || ||||| || || ||||| |||||||| ||||| |||||||||||| ||||||||||||||||||| |||| | |  || |       |||            ||||||| | ||          | ||   | | | |  ||   |  ||     |       | | |  | || ||||     |  | || | ||                      
TGATGCGCGACTTCAAGCGCCTGCAGCATGATCCTCCGGCCGGCATCAGCGGCGCCCCGCAGGACAACAACATCATGTTGTGGAATGCTGTCATATTCGGgt-acccaaactcctccccgattt--------tcgttctgcatgctc---------aattgtgtcggtatgaatgcgaaatt-----cgtggggcgcggagatttgcatgg-----cggtgtcggttt----------------------

upper sequence: GLYMA17G10640.1 (Glycine max), 5'ss of exon 2
lower sequence: PP1S219_106V6.1 (Physcomitrella patens), 5'ss of exon 1
TCATGAGAGATTTCAAGAGGCTGCAACAAGACCCTCCTGCAGGAATCAGTGGCGCCCCTCAGGATAACAACATCATGCTGTGGAATGCTGTCATATTTGGgtgagctgaattgaaattggataaagataaaactgttctgcttacttgaataatatagttactttgttttttattttattttttttccacactttgtgtaagtatggatggataagcaatttctgctttcttgtctgctttggattgcag
| ||| | || |||||| |  ||||||| || ||||| || || ||||| ||||| || ||||| ||||| |||||||||||||||||||| ||||| |||| |                   |||            ||| | | ||              || ||||||| ||  ||| | |     |    || | || |      |  |  |        |      |||| | |||         
TGATGCGTGACTTCAAGCGCTTGCAACATGATCCTCCGGCCGGCATCAGCGGCGCTCCGCAGGACAACAATATCATGCTGTGGAATGCTGTGATATTCGGgtaa-----------------cgaag------------tgcctccctgg------------tttcgttttttgttcaattgtgtccggtcgtggtgcggaattcgccgggcgtgggaggcgcacgtcggagtgtcggtttt---------

upper sequence: GLYMA17G10640.1 (Glycine max), 5'ss of exon 2
lower sequence: EFJ21576 (Selaginella moellendorffii), 5'ss of exon 1
TCATGAGAGATTTCAAGAGGCTGCAACAAGACCCTCCTGCAGGAATCAGTGGCGCCCCTCAGGATAACAACATCATGCTGTGGAATGCTGTCATATTTGGgtgagctgaattgaaa--ttggataaagataaaactgttctgcttacttgaataatatagttactttgttttttattttattttttttccacactttgtgtaagtatggatggataagcaatttctgctttcttgtctgctttggattgcag
| ||| ||||||||||| | || || || || ||||| ||||| ||||| ||||| || ||||| ||||| |||||| ||||||||||||| || || ||||||| |     ||||  ||   ||  | |        || | |   |   | |                                                                                                  
TGATGCGAGATTTCAAGCGCCTACAGCATGATCCTCCGGCAGGCATCAGCGGCGCTCCACAGGACAACAATATCATGTTGTGGAATGCTGTGATCTTCGGgtgagttctcgcgaaacctttcttagggtttttgaatgtcggttctttcttacag-------------------------------------------------------------------------------------------------

upper sequence: GLYMA17G10640.1 (Glycine max), 5'ss of exon 2
lower sequence: EFJ16328 (Selaginella moellendorffii), 5'ss of exon 1
TCATGAGAGATTTCAAGAGGCTGCAACAAGACCCTCCTGCAGGAATCAGTGGCGCCCCTCAGGATAACAACATCATGCTGTGGAATGCTGTCATATTTGGgtgagc-tgaattgaaattggataaagataaaactgttctgcttacttgaataatatagttactttgttttttattttattttttttccacactttgtgtaagtatggatggataagcaatttctgctttcttgtctgctttggattgcag
| ||| |||| |||||| | || ||||| || ||||| || |||||||| ||||| || ||||| |||||||||||||| ||||| || || || || ||||  |  || |        | |  | | ||    | |    |||  ||   |  |  ||                                                                                            
TGATGCGAGACTTCAAGCGCCTCCAACACGATCCTCCCGCGGGAATCAGCGGCGCGCCGCAGGACAACAACATCATGCTCTGGAACGCGGTGATCTTCGGgtaggaatgtagccgctcggcactagggtatcgatctaactcttggtttcgtgttgcag--------------------------------------------------------------------------------------------

upper sequence: GLYMA17G10640.1 (Glycine max), 5'ss of exon 2
lower sequence: EFJ17802 (Selaginella moellendorffii), 5'ss of exon 1
TCATGAGAGATTTCAAGAGGCTGCAACAAGACCCTCCTGCAGGAATCAGTGGCGCCCCTCAGGATAACAACATCATGCTGTGGAATGCTGTCATATTTGGgtgagc-tgaattgaaattggataaagataaaactgttctgcttacttgaataatatagttactttgttttttattttattttttttccacactttgtgtaagtatggatggataagcaatttctgctttcttgtctgctttggattgcag
| ||| |||| |||||| | || ||||| || ||||| || |||||||| ||||| || ||||| |||||||||||||| ||||| || || || || ||||  |  || |          |  | | ||    | |    |||  ||   |  |  ||                                                                                            
TGATGCGAGACTTCAAGCGCCTCCAACACGATCCTCCCGCGGGAATCAGCGGCGCGCCGCAGGACAACAACATCATGCTCTGGAACGCGGTGATCTTCGGgtaggaatgtagccgctcgacactagggtatcgatctaactcttggtttcgtgttgcag--------------------------------------------------------------------------------------------

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|16106211|gb|BI893951.1|BI893951
EST:     GGCGCCCCTCAGGATAACAACATCATGCTGTGGAATGCTGTCATATTTGG                         TCCTGATGATACTCCATGGGATGGAG
genomic: GGCGCCCCTCAGGATAACAACATCATGCTGTGGAATGCTGTCATATTTGGgtgagctgaa ... tggattgcagTCCTGATGATACTCCATGGGATGGAG
EST: gi|11689076|gb|BF596752.1|BF596752
EST:     GGCGCCCCTCAGGATAACAACATCATGCTGTGGAATGCTGTCATATTTGG                         TCCTGATGATACTCCATGGGATGGAG
genomic: GGCGCCCCTCAGGATAACAACATCATGCTGTGGAATGCTGTCATATTTGGgtgagctgaa ... tggattgcagTCCTGATGATACTCCATGGGATGGAG
EST: gi|192331367|gb|FK021035.1|FK021035
EST:     GGCGCCCCTCAGGATAACAACATCATGCTGTGGAATGCTGTCATATTTGG                         TCCTGATGATACTCCATGGGATGGAG
genomic: GGCGCCCCTCAGGATAACAACATCATGCTGTGGAATGCTGTCATATTTGGgtgagctgaa ... tggattgcagTCCTGATGATACTCCATGGGATGGAG
EST: gi|192331366|gb|FK021034.1|FK021034
EST:     GGCGCCCCTCAGGATAACAACATCATGCTGTGGAATGCTGTCATATTTGG                         TCCTGATGATACTCCATGGGATGGAG
genomic: GGCGCCCCTCAGGATAACAACATCATGCTGTGGAATGCTGTCATATTTGGgtgagctgaa ... tggattgcagTCCTGATGATACTCCATGGGATGGAG
EST: gi|21888252|gb|BQ741465.1|BQ741465
EST:     GGCGCCCCTCAGGATAACAACATCATGCTGTGGAATGCTGTCATATTTGG                         TCCTGATGATACTCCATGGGATGGAG
genomic: GGCGCCCCTCAGGATAACAACATCATGCTGTGGAATGCTGTCATATTTGGgtgagctgaa ... tggattgcagTCCTGATGATACTCCATGGGATGGAG
EST: gi|14259666|gb|BG882574.1|BG882574
EST:     GGCGCCCCTCAGGATAACAACATCATGCTGTGGAATGCTGTCATATTTGG                         TCCTGATGATACTCCATGGGATGGAG
genomic: GGCGCCCCTCAGGATAACAACATCATGCTGTGGAATGCTGTCATATTTGGgtgagctgaa ... tggattgcagTCCTGATGATACTCCATGGGATGGAG
EST: gi|192330437|gb|FK021196.1|FK021196
EST:     GGCGCCCCTCAGGATAACAACATCATGCTGTGGAATGCTGTCATATTTGG                         TCCTGATGATACTCCATGGGATGGAG
genomic: GGCGCCCCTCAGGATAACAACATCATGCTGTGGAATGCTGTCATATTTGGgtgagctgaa ... tggattgcagTCCTGATGATACTCCATGGGATGGAG
EST: gi|4294751|gb|AI442235.1|AI442235
EST:     GGCGCCCCTCAGGATAACAACATCATGCTGTGGAATGCTGTCATATTTGG                         TCCTGATGATACTCCATGGGATGGAG
genomic: GGCGCCCCTCAGGATAACAACATCATGCTGTGGAATGCTGTCATATTTGGgtgagctgaa ... tggattgcagTCCTGATGATACTCCATGGGATGGAG
EST: gi|254317221|gb|GR826166.1|GR826166
EST:     GGCGCCCCTCAGGATAACAACATCATGCTGTGGAATGCTGTCATATTTGG                         TCCTGATGATACTCCATGGGATGGAG
genomic: GGCGCCCCTCAGGATAACAACATCATGCTGTGGAATGCTGTCATATTTGGgtgagctgaa ... tggattgcagTCCTGATGATACTCCATGGGATGGAG
EST: gi|192330438|gb|FK021197.1|FK021197
EST:     GGCGCCCCTCAGGATAACAACATCATGCTGTGGAATGCTGTCATATTTGG                         TCCTGATGATACTCCATGGGATGGAG
genomic: GGCGCCCCTCAGGATAACAACATCATGCTGTGGAATGCTGTCATATTTGGgtgagctgaa ... tggattgcagTCCTGATGATACTCCATGGGATGGAG
EST: gi|254331190|gb|GR843309.1|GR843309
EST:     GGCGCCCCTCAGGATAACAACATCATGCTGTGGAATGCTGTCATATTTGG                         TCCTGATGATACTCCATGGGATGGAG
genomic: GGCGCCCCTCAGGATAACAACATCATGCTGTGGAATGCTGTCATATTTGGgtgagctgaa ... tggattgcagTCCTGATGATACTCCATGGGATGGAG
EST: gi|208058951|gb|GD858983.1|GD858983
EST:     GGCGCCCCTCAGGATAACAACATCATGCTGTGGAATGCTGTCATATTTGG                         TCCTGATGATACTCCATGGGATGGAG
genomic: GGCGCCCCTCAGGATAACAACATCATGCTGTGGAATGCTGTCATATTTGGgtgagctgaa ... tggattgcagTCCTGATGATACTCCATGGGATGGAG
EST: gi|254335069|gb|GR844854.1|GR844854
EST:     GGCGCCCCTCAGGATAACAACATCATGCTGTGGAATGCTGTCATATTTGG                         TCCTGATGATACTCCATGGGATGGAG
genomic: GGCGCCCCTCAGGATAACAACATCATGCTGTGGAATGCTGTCATATTTGGgtgagctgaa ... tggattgcagTCCTGATGATACTCCATGGGATGGAG
EST: gi|298177564|gb|HO027231.1|HO027231
EST:     GGCGCCCCTCAGGATAACAACATCATGCTGTGGAATGCTGTCATATTTGG                         TCCTGATGATACTCCATGGGATGGAG
genomic: GGCGCCCCTCAGGATAACAACATCATGCTGTGGAATGCTGTCATATTTGGgtgagctgaa ... tggattgcagTCCTGATGATACTCCATGGGATGGAG
EST: gi|254335070|gb|GR844855.1|GR844855
EST:     GGCGCCCCTCAGGATAACAACATCATGCTGTGGAATGCTGTCATATTTGG                         TCCTGATGATACTCCATGGGATGGAG
genomic: GGCGCCCCTCAGGATAACAACATCATGCTGTGGAATGCTGTCATATTTGGgtgagctgaa ... tggattgcagTCCTGATGATACTCCATGGGATGGAG
EST: gi|16996966|gb|BM086338.1|BM086338
EST:     GGCGCCCCTCAGGATAACAACATCATGCTGTGGAATGCTGTCATATTTGG                         TCCTGATGATACTCCATGGGATGGAG
genomic: GGCGCCCCTCAGGATAACAACATCATGCTGTGGAATGCTGTCATATTTGGgtgagctgaa ... tggattgcagTCCTGATGATACTCCATGGGATGGAG
EST: gi|151395570|gb|EV265447.1|EV265447
EST:     GGCGCCCCTCAGGATAACAACATCATGCTGTGGAATGCTGTCATATTTGG                         TCCTGATGATACTCCATGGGATGGAG
genomic: GGCGCCCCTCAGGATAACAACATCATGCTGTGGAATGCTGTCATATTTGGgtgagctgaa ... tggattgcagTCCTGATGATACTCCATGGGATGGAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCATGAGAGATTTCAAGAGGCTGCAACAAGACCCTCCTGCAGGAATCAGTGGCGCCCCTCAGGATAACAACATCATGCTGTGGAATGCTGTCATATTTGGgtgagctgaattgaaattggataaagataaaactgttctgcttacttgaataatatagttactttgttttttattttattttttttccacactttgtgtaagtatggatggataagcaatttctgctttcttgtctgctttggattgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG