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

TGATGAGAGACTTCAAGAGGCTGCAACAAGACCCGCCTGCAGGGATCAGCGGTGCCCCCCAGGATAACAACATAATGCTGTGGAATGCTGTCATATTTGGgtgagttgaattcaaattcgatataggtccaatgttgttttaatttatagtcaattggtcactattttttaatttcttatgttgtttaattactgatggataagtgatttttggtttcttgactgctttggattgcag

Basic information

species Glycine max
transcript GLYMA04G34170.2
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G34170.2 (Glycine max), 5'ss of exon 2
lower sequence: LOC_Os05g08960.2 (Oryza sativa), 5'ss of exon 2
TGATGAGAGACTTCAAGAGGCTGCAACAAGACCCGCCTGCAGGGATCAGCGGTGCCCCCCAGGATAACAACATAATGCTGTGGAATGCTGTCATATTTGGgtgagttgaattcaaattcgatataggtccaatgttgttttaatttatagtcaattggtcactattttttaatttcttatgttgtttaattactgatggataagtgatttttggtttcttgactgctttggattgcag
||||||| || |||||  | |||   || || || || || || || || || ||||| ||||| ||||| |||||||| ||||||||||| || ||||||| || ||   | | | |  | | |  |    | ||  |||   || || |   ||| ||  |  |  ||| ||    ||  ||| |  ||  ||  |                                        
TGATGAGGGATTTCAAACGACTGATGCAGGATCCTCCAGCTGGCATAAGTGGGGCCCCACAGGACAACAATATAATGCTTTGGAATGCTGTAATTTTTGGgtaaggtg---ttagacttaagagatatgttttattcctttcggttttatt---ttgatccattatacttagttgtcaattatgtcttgtt-ttgcag----------------------------------------

upper sequence: GLYMA04G34170.2 (Glycine max), 5'ss of exon 2
lower sequence: GRMZM2G110983_T02 (Zea mays), 5'ss of exon 2
TGATGAGAGACTTCAAGAGGCTGCAACAAGACCCGCCTGCAGGGATCAGCGGTGCCCCCCAGGATAACAACATAATGCTGTGGAATGCTGTCATATTTGGgtgagttg---aattcaaattcgatataggtccaa--tgttgttttaatttatagtcaattggtcactattttttaat-ttcttatgttgtttaattactgatggataagtgatttttggtttcttgactgctttggattgcag
||||||| || |||||| || ||   || ||||| || || || || || || ||||| |||||||||||||||||||||||||||||||||||||||||||  | ||   ||| |     |    |    || |  | ||  ||| | || || |  ||| | ||   | |||  || | ||||| |  ||||                                                  
TGATGAGGGATTTCAAGCGGTTGATGCAGGACCCTCCGGCCGGCATAAGTGGCGCCCCGCAGGATAACAACATAATGCTGTGGAATGCTGTCATATTTGGgtatgatgcagaatccccccgcccccttttccccacttcttagtttgaattgtaat--atttgacatcgtctttggatatgcttatttcttttacag-----------------------------------------------

upper sequence: GLYMA04G34170.2 (Glycine max), 5'ss of exon 2
lower sequence: Vv17s0000g05820.t01 (Vitis vinifera), 5'ss of exon 2
TGATGAGAGACTTCAAGAGGCTGCAACAAGACCCGCCTGCAGGGATCAGCGGTGCCCCCCAGGATAACAACATAATGCTGTGGAATGCTGTCATATTTGGgtgagttgaattcaaattcgatataggtccaatgttgttttaatttatagtcaattggtca--ctattttttaatttcttatgttgtttaattactgatggataagtgatttttggtttcttgactgctttggattgcag
|||||||||| || |||||| ||||||| ||||| ||||| || ||||| || || ||||| || ||||| |||||||| ||||||||||| |||||||||| |   | |   ||||||   | |  |   ||  |||||   | | |  |   ||  |     |   ||||| ||||| |   ||||||| ||  | ||||||||  |||| |||||||||  ||| ||||||||||||
TGATGAGAGATTTTAAGAGGTTGCAACAGGACCCCCCTGCCGGCATCAGTGGAGCTCCCCAAGACAACAATATAATGCTTTGGAATGCTGTTATATTTGGgtaatgggcaacaaaattcatgaaaactgttattgtgtttgcttatgttatgtgtttatttatttgccttttactttctcagtatgtttaagtatggttggataagccatttctggtttcttttctgatttggattgcag

upper sequence: GLYMA04G34170.2 (Glycine max), 5'ss of exon 2
lower sequence: PP1S91_87V6.1 (Physcomitrella patens), 5'ss of exon 1
TGATGAGAGACTTCAAGAGGCTGCAACAAGACCCGCCTGCAGGGATCAGCGGTGCCCCCCAGGATAACAACATAATGCTGTGGAATGCTGTCATATTTGGgtgagttgaattcaaattcgatataggtccaatgttgttttaatttatagtcaattg-gtcactatt--ttttaatttcttatgttgtttaattactgatggataagtgatttttggtttcttgactgctttggattgcag
||||| | ||||||||| | ||||| || || || || || || |||||||| ||||| ||||| |||||||| ||| ||||||||||||||||||| ||||       |  |||| ||         || || ||  ||   |  ||  ||||||| |||  |||   |   || ||| |  |  |   |  |    ||||    ||   |||                           
TGATGCGCGACTTCAAGCGCCTGCAGCATGATCCTCCGGCCGGCATCAGCGGCGCCCCGCAGGACAACAACATCATGTTGTGGAATGCTGTCATATTCGGgt-------acccaaactcctc-----cccgattttcgttc--tgcatgctcaattgtgtcggtatgaatgcgaaattcgtggggcgcggagatttgcatggcggtgtcggttt---------------------------

upper sequence: GLYMA04G34170.2 (Glycine max), 5'ss of exon 2
lower sequence: PP1S219_106V6.1 (Physcomitrella patens), 5'ss of exon 1
TGATGAGAGACTTCAAGAGGCTGCAACAAGACCCGCCTGCAGGGATCAGCGGTGCCCCCCAGGATAACAACATAATGCTGTGGAATGCTGTCATATTTGGgtgagttgaattcaaattcgatataggtccaatgttgttttaatttatagtcaattggtcactattttttaatttcttatgttgtttaattactgatggataagtgatttttggtttcttgactgctttggattgcag
||||| | ||||||||| |  ||||||| || || || || || |||||||| || || ||||| ||||| || ||||||||||||||||| ||||| |||| |         || | |      |||    | || | || | || |   |  | |     |  |    ||||      |      |    |   | |    ||   ||||                          
TGATGCGTGACTTCAAGCGCTTGCAACATGATCCTCCGGCCGGCATCAGCGGCGCTCCGCAGGACAACAATATCATGCTGTGGAATGCTGTGATATTCGGgtaa-------cgaagtgcctccctggtttcgttttttgttcaattgtgtccggtcg-----tggtgcggaattcgccgggcgtgggaggcgcacgtcggagtgtcggtttt--------------------------

upper sequence: GLYMA04G34170.2 (Glycine max), 5'ss of exon 2
lower sequence: EFJ21576 (Selaginella moellendorffii), 5'ss of exon 1
TGATGAGAGACTTCAAGAGGCTGCAACAAGACCCGCCTGCAGGGATCAGCGGTGCCCCCCAGGATAACAACATAATGCTGTGGAATGCTGTCATATTTGGgtgagttgaattcaaattcgatatagg----tccaatgttg-ttttaatttatagtcaattggtcactattttttaatttcttatgttgtttaattactgatggataagtgatttttggtttcttgactgctttggattgcag
||||| |||| |||||| | || || || || || || ||||| |||||||| || || ||||| ||||| || ||| ||||||||||||| || || |||||||||      |||       ||||    |  ||||| | || |   ||| ||                                                                                        
TGATGCGAGATTTCAAGCGCCTACAGCATGATCCTCCGGCAGGCATCAGCGGCGCTCCACAGGACAACAATATCATGTTGTGGAATGCTGTGATCTTCGGgtgagttctcgcgaaacctttcttagggtttttgaatgtcggttctttcttacag----------------------------------------------------------------------------------------

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|298176667|gb|HO026788.1|HO026788
EST:     GGTGCCCCCCAGGATAACAACATAATGCTGTGGAATGCTGTCATATTTGG                         TCCTGATGATACTCCATGGGATGGAG
genomic: GGTGCCCCCCAGGATAACAACATAATGCTGTGGAATGCTGTCATATTTGGgtgagttgaa ... tggattgcagTCCTGATGATACTCCATGGGATGGAG
EST: gi|13311815|gb|BG405466.1|BG405466
EST:     GGTGCCCCCCAGGATAACAACATAATGCTGTGGAATGCTGTCATATTTGG                         TCCTGATGATACTCCATGGGATGGAG
genomic: GGTGCCCCCCAGGATAACAACATAATGCTGTGGAATGCTGTCATATTTGGgtgagttgaa ... tggattgcagTCCTGATGATACTCCATGGGATGGAG
EST: gi|21675821|gb|BQ628172.1|BQ628172
EST:     GGTGCCCCCCAGGATAACAACATAATGCTGTGGAATGCTGTCATATTTGG                         TCCTGATGATACTCCATGGGATGGAG
genomic: GGTGCCCCCCAGGATAACAACATAATGCTGTGGAATGCTGTCATATTTGGgtgagttgaa ... tggattgcagTCCTGATGATACTCCATGGGATGGAG
EST: gi|8826329|gb|BE210059.1|BE210059
EST:     GGTGCCCCCCAGGATAACAACATAATGCTGTGGAATGCTGTCATATTTGG                         TCCTGATGATACTCCATGGGATGGAG
genomic: GGTGCCCCCCAGGATAACAACATAATGCTGTGGAATGCTGTCATATTTGGgtgagttgaa ... tggattgcagTCCTGATGATACTCCATGGGATGGAG
EST: gi|10710248|gb|BF009972.1|BF009972
EST:     GGTGCCCCCCAGGATAACAACATAATGCTGTGGAATGCTGTCATATTTGG                         TCCTGATGATACTTCATGGGATGGAC
genomic: GGTGCCCCCCAGGATAACAACATAATGCTGTGGAATGCTGTCATATTTGGgtgagttgaa ... tggattgcagTCCTGATGATACTCCATGGGATGGAG
EST: gi|19937736|gb|BQ081401.1|BQ081401
EST:     GGTGCCCCCCAGGATAACAACATAATGCTGTGGAATGCTGTCATATTTGG                         TCCTGATGATACTCCATGGGATGGAG
genomic: GGTGCCCCCCAGGATAACAACATAATGCTGTGGAATGCTGTCATATTTGGgtgagttgaa ... tggattgcagTCCTGATGATACTCCATGGGATGGAG
EST: gi|9258746|gb|BE346893.1|BE346893
EST:     GGTGCCCCCCAGGATAACAACATAATGCTGTGGAATGCTGTCATATTTGG                         TCCTGATGATACTCCATGGGATGGAG
genomic: GGTGCCCCCCAGGATAACAACATAATGCTGTGGAATGCTGTCATATTTGGgtgagttgaa ... tggattgcagTCCTGATGATACTCCATGGGATGGAG
EST: gi|19937295|gb|BQ081233.1|BQ081233
EST:     GGTGCCCCCCAGGATAACAACATAATGCTGTGGAATGCTGTCATATTTGG                         TCCTGATGATACTCCATGGGATGGAG
genomic: GGTGCCCCCCAGGATAACAACATAATGCTGTGGAATGCTGTCATATTTGGgtgagttgaa ... tggattgcagTCCTGATGATACTCCATGGGATGGAG
EST: gi|10709694|gb|BF009418.1|BF009418
EST:     GGTGCCCCCCAGGATAACAACATAATGCTGTGGAATGCTGTCATATTTGG                         TCCTGATGATACTCCATGGGATGGAG
genomic: GGTGCCCCCCAGGATAACAACATAATGCTGTGGAATGCTGTCATATTTGGgtgagttgaa ... tggattgcagTCCTGATGATACTCCATGGGATGGAG
EST: gi|193335969|gb|FK300669.1|FK300669
EST:     GGTGCCCCCCAGGATAACAACATAATGCTGTGGAATGCTGTCATATTTGG                         TCCTGATGATACTCCATGGGATGGAG
genomic: GGTGCCCCCCAGGATAACAACATAATGCTGTGGAATGCTGTCATATTTGGgtgagttgaa ... tggattgcagTCCTGATGATACTCCATGGGATGGAG
EST: gi|4313968|gb|AI461087.1|AI461087
EST:     GGTGCCCCCCAGGATAACAACATAATGCTGTGGAATGCTGTCATATTTGG                         TCCTGATGATACTCCATGGGATGGAG
genomic: GGTGCCCCCCAGGATAACAACATAATGCTGTGGAATGCTGTCATATTTGGgtgagttgaa ... tggattgcagTCCTGATGATACTCCATGGGATGGAG
EST: gi|193336100|gb|FK301500.1|FK301500
EST:     GGTGCCCCCCAGGATAACAACATAATGCTGTGGAATGCTGTCATATTTGG                         TCCTGATGATACTCCATGGGATGGAG
genomic: GGTGCCCCCCAGGATAACAACATAATGCTGTGGAATGCTGTCATATTTGGgtgagttgaa ... tggattgcagTCCTGATGATACTCCATGGGATGGAG
EST: gi|151406462|gb|EV276277.1|EV276277
EST:     AACATAATGCTGTGGAATGCTGTCATATTTGG                         TCCTGATGATACCCCATGGGATGGAG
genomic: AACATAATGCTGTGGAATGCTGTCATATTTGGgtgagttgaa ... tggattgcagTCCTGATGATACTCCATGGGATGGAG
EST: gi|254315330|gb|GR825139.1|GR825139
EST:     GGTGCCCCCCAGGATAACAACATAATGCTGTGGAATGCTGTCATATTTGG                         TCCTGATGATACTCCATGGGATGGAG
genomic: GGTGCCCCCCAGGATAACAACATAATGCTGTGGAATGCTGTCATATTTGGgtgagttgaa ... tggattgcagTCCTGATGATACTCCATGGGATGGAG
EST: gi|15286715|gb|BI470606.1|BI470606
EST:     GGTGCCCCCCAGGATAACAACATAATGCTGTGGAATGCTGTCATATTTGG                         TCCTGATGATACTCCATGGGATGGAG
genomic: GGTGCCCCCCAGGATAACAACATAATGCTGTGGAATGCTGTCATATTTGGgtgagttgaa ... tggattgcagTCCTGATGATACTCCATGGGATGGAG
EST: gi|7284147|gb|AW596745.1|AW596745
EST:     GGTGCCCCCCAGGATAACAACATAATGCTGTGGAATGCTGTCATATTTGG                         TCCTGATGATACTCCATGGGATGGAG
genomic: GGTGCCCCCCAGGATAACAACATAATGCTGTGGAATGCTGTCATATTTGGgtgagttgaa ... tggattgcagTCCTGATGATACTCCATGGGATGGAG
EST: gi|27424249|gb|CA935769.1|CA935769
EST:     GGTGCCCCCCAGGATAACAACATAATGCTGTGGAATGCTGTCATATTTGG                         TCCTGATGATACTCCATGGGATGGAG
genomic: GGTGCCCCCCAGGATAACAACATAATGCTGTGGAATGCTGTCATATTTGGgtgagttgaa ... tggattgcagTCCTGATGATACTCCATGGGATGGAG
EST: gi|9566017|gb|BE475588.1|BE475588
EST:     GGTGCCCCCCAGGATAACAACATAATGCTGTGGAATGCTGTCATATTTGG                         TCCTGATGATACTCCATGGGATGGAG
genomic: GGTGCCCCCCAGGATAACAACATAATGCTGTGGAATGCTGTCATATTTGGgtgagttgaa ... tggattgcagTCCTGATGATACTCCATGGGATGGAG
EST: gi|254315329|gb|GR825138.1|GR825138
EST:     GGTGCCCCCCAGGATAACAACATAATGCTGTGGAATGCTGTCATATTTGG                         TCCTGATGATACTCCATGGGATGGAG
genomic: GGTGCCCCCCAGGATAACAACATAATGCTGTGGAATGCTGTCATATTTGGgtgagttgaa ... tggattgcagTCCTGATGATACTCCATGGGATGGAG
EST: gi|151409661|gb|EV279469.1|EV279469
EST:     GGTGCCCCCCAGGATAACAACATAATGCTGTGGAATGCTGTCATATTTGG                         TCCTGATGATACTCCATGGGATGGAG
genomic: GGTGCCCCCCAGGATAACAACATAATGCTGTGGAATGCTGTCATATTTGGgtgagttgaa ... tggattgcagTCCTGATGATACTCCATGGGATGGAG
EST: gi|193669561|gb|FK614065.1|FK614065
EST:     GGTGCCCCCCAGGATAACAACATAATGCTGTGGAATGCTGTCATATTTGG                         TCCTGATGATACTCCATGGGATGGAG
genomic: GGTGCCCCCCAGGATAACAACATAATGCTGTGGAATGCTGTCATATTTGGgtgagttgaa ... tggattgcagTCCTGATGATACTCCATGGGATGGAG
EST: gi|192297673|gb|FG989937.1|FG989937
EST:     GGTGCCCCCCGGGATAACAACATAATGCTGTGGAATGCTGTCATATTTGG                         TCCTGATGATACTCCATGGGATGGAG
genomic: GGTGCCCCCCAGGATAACAACATAATGCTGTGGAATGCTGTCATATTTGGgtgagttgaa ... tggattgcagTCCTGATGATACTCCATGGGATGGAG
EST: gi|14990785|gb|BI316458.1|BI316458
EST:     GGTGCCCCCCAGGATAACAACATAATGCTGTGGAATGCTGTCATATTTGG                         TCCTGATGATACTCCATGGGATGGAG
genomic: GGTGCCCCCCAGGATAACAACATAATGCTGTGGAATGCTGTCATATTTGGgtgagttgaa ... tggattgcagTCCTGATGATACTCCATGGGATGGAG
EST: gi|23733374|gb|BU764884.1|BU764884
EST:     GGTGCCCCCCAGGATAACAACATAATGCTGTGGAATGCTGTCATATTTGG                         TCCTGATGATACTCCATGGGATGGAG
genomic: GGTGCCCCCCAGGATAACAACATAATGCTGTGGAATGCTGTCATATTTGGgtgagttgaa ... tggattgcagTCCTGATGATACTCCATGGGATGGAG
EST: gi|213603132|gb|DB960423.1|DB960423
EST:     GGTGCCCCCCAGGATAACAACATAATGCTGTGGAATGCTGTCATATTTGG                         TCCTGATGATACTCCATGGGATGGAG
genomic: GGTGCCCCCCAGGATAACAACATAATGCTGTGGAATGCTGTCATATTTGGgtgagttgaa ... tggattgcagTCCTGATGATACTCCATGGGATGGAG
EST: gi|6847744|gb|AW350034.1|AW350034
EST:     GGTGCCCCCCAGGATNNNAACATAATGCTGTGGAATGCTGTCATATTTGG                         TCCTGATGATACTCCATGGGATGGAG
genomic: GGTGCCCCCCAGGATAACAACATAATGCTGTGGAATGCTGTCATATTTGGgtgagttgaa ... 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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGATGAGAGACTTCAAGAGGCTGCAACAAGACCCGCCTGCAGGGATCAGCGGTGCCCCCCAGGATAACAACATAATGCTGTGGAATGCTGTCATATTTGGgtgagttgaattcaaattcgatataggtccaatgttgttttaatttatagtcaattggtcactattttttaatttcttatgttgtttaattactgatggataagtgatttttggtttcttgactgctttggattgcag

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