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

...tgtgtattggtgctcattgtccactgtatagttgtatttgttatgttatgcttctctgtatgcatgaagtagtctcactcctttgggctaatcttgcaggTATACTTGCTTGTCTAGATGGCTATATGAATATTGCAATGGAGCAGACAGAGGAGTACGTCAATGGACAACTGAAGAACAAGTATGGTGACGCTTTCATC

Basic information

species Glycine max
transcript GLYMA18G46370.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G46370.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os02g30624.1 (Oryza sativa), 3'ss of exon 1
---tgtgtattgg-tgctcattgtccactgtatagttgtatttgttatgttatgcttctctgtatgcatgaagt-agtctcactcctttgggctaatcttgcaggTATACTTGCTTGTCTAGATGGCTATATGAATATTGCAATGGAGCAGACAGAGGAGTACGTCAATGGACAACTGAAGAACAAGTATGGTGACGCTTTCATC
       ||||   ||   |       | ||  | || |  || ||   ||||||||   |  |    |||  | |       | | ||||  | | |   |||||||  | |||||||| ||||| || ||||| |||||||||||||| || || || || |||||||| || |||||||||||||| |||||||||||||| 
tcaaaaatattaactgacaacaaaatccagtgaaatt-tgattattccattatgcttacgtaaaaagctgatttcaaatgtctttcattggtatgaac---cagGTATTTTGGCTTGTCTTGATGGTTACATGAACATTGCAATGGAGCAAACGGAAGAATATGTCAATGGTCAGCTGAAGAACAAGTACGGTGACGCTTTCAT-

upper sequence: GLYMA18G46370.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os04g31950.1 (Oryza sativa), 3'ss of exon 1
---tgtgtattggtgctcattgtccactgtatagttgtatttgttatgttatgcttctctgtatgcatgaagtagtctcac--tcctttgggctaatcttgcaggTATACTTGCTTGTCTAGATGGCTATATGAATATTGCAATGGAGCAGACAGAGGAGTACGTCAATGGACAACTGAAGAACAAGTATGGTGACGCTTTCATC
    |||    || | | |  | | |     ||||| | ||||| | ||||||      | | | |      |  ||| ||  |  |||   || ||  | |||||||  | ||||| || ||||| |||||||| |||||||||||||| || || ||||| || ||||| ||||| ||||||||||||||||| || ||||| 
acaagtgatacggagtt-acggacaatgtcttagttctttttgtaa-gttatgtacgaatat-taccaattttcttctgaccattatttttcctgataat-cagGTATTTTGGCTTGCCTGGATGGGTATATGAACATTGCAATGGAGCAAACGGAAGAGTATGTGAATGGCCAACTCAAGAACAAGTATGGTGATGCCTTCAT-

upper sequence: GLYMA18G46370.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G159675_T02 (Zea mays), 3'ss of exon 1
-tgtgtattggtg-ctcattgtccactgtatagttgtatttgttatgttatgcttctctgtatgcatgaagtagtctcactcctttgggctaatcttg--caggTATACTTGCTTGTCTAGATGGCTATATGAATATTGCAATGGAGCAGACAGAGGAGTACGTCAATGGACAACTGAAGAACAAGTATGGTGACGCTTTCATC
  |   | | |   ||||| |  ||  |         |    ||  | | || |  |  || | ||| ||    |||     |      ||  |  ||  |||||||| | |||||||| ||||| |||||||| || |||||||||||||| ||||||||||| ||||| ||  |||||||||||||||| ||||| ||||| 
aggaaaaatagcatctcatgg--catggctctcgcagagaaattggggtttgatcgttagt-tccattaaactttcttttgtccgaactcttgtgatgaccagGTATATTGGCTTGTCTGGATGGTTATATGAACATCGCAATGGAGCAGACCGAGGAGTACGTGAATGGCCAGTTGAAGAACAAGTATGGCGACGCCTTCAT-

upper sequence: GLYMA18G46370.1 (Glycine max), 3'ss of exon 2
lower sequence: AT3G59810.1 (Arabidopsis thaliana), 3'ss of exon 2
tgtgtattggtgctcattgtccactgtat-agttgtatttgt-tatgttatgcttctctgtatgcatgaagtagt--ctcactcctttgggctaatcttgcaggTATACTTGCTTGTCTAGATGGCTATATGAATATTGCAATGGAGCAGACAGAGGAGTACGTCAATGGACAACTGAAGAACAAGTATGGTGACGCTTTCATC
    | |||       |  |    ||    |||    ||||| |||||| || |      ||    |||  |  |     | |  ||    ||  | |  |||| |  ||| ||||||| ||||| |||||||| || |||||||||||||| |||||||| || || || || || |||||||| ||||||||||| || || 
---ttgttgacttctttcctttcgtgcccgagtcagttttgtctatgttctgttcaagcttaatgttgagttcttgatcaagtttttattactcttttcacagGCACTCTTACTTGTCTTGATGGATATATGAACATAGCAATGGAGCAGACGGAGGAGTATGTAAACGGGCAGCTCAAGAACAAATATGGTGACGCCTTTAT-

upper sequence: GLYMA18G46370.1 (Glycine max), 3'ss of exon 2
lower sequence: AT2G43810.1 (Arabidopsis thaliana), 3'ss of exon 3
-----tgtgtattggtgctcattgtccactgtatagttgtatttgttatgttatgct-tctctgtatgcatgaagtagtctcactcctttgggctaatcttgcaggTATACTTGCTTGTCTAGATGGCTATATGAATATTGCAATGGAGCAGACAGAGGAGTACGTCAATGGACAACTGAAGAACAAGTATGGTGACGCTTTCATC
     | ||  ||       |  |||     |||  || | ||||  || | ||| | | ||  | | |||     | | |  |||  ||   ||  | ||||||| || ||| ||||||| ||||| |||||||| || ||||||||||| || || ||||| || ||||| || ||||||||||  ||||| ||||||||  | 
ctttctttggtttatctacaaaagtcagacttattctt-tctttggcatatcatgttgtatcaatctacatatgacactttgtctctctt---cttgt-ttgcagGCATTCTTACTTGTCTTGATGGATATATGAACATCGCAATGGAGCAAACCGAAGAGTATGTAAATGGCCAGCTGAAGAACACATATGGCGACGCTTTTGT-

upper sequence: GLYMA18G46370.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv05s0094g00940.t01 (Vitis vinifera), 3'ss of exon 2
----tgtgtattggtgctcattgtccactgtatagttgtatttgttatgttatgcttctctgta-tgcatgaagtagtctcactcctttgggctaatcttgcaggTATACTTGCTTGTCTAGATGGCTATATGAATATTGCAATGGAGCAGACAGAGGAGTACGTCAATGGACAACTGAAGAACAAGTATGGTGACGCTTTCATC
     |    || ||  |   | | |  || |       |    || | | ||  |  | | || |  |     ||  ||   | | ||   ||  |  | ||||||| || |||||||| || || |||||||| || ||||||||||| ||||| |||||||||||||| || || || ||||| ||||| || ||||| || 
gaaaagaaagttcgttgtagctttgctttg-acccacaaaacccttgtttcataatggtatataatatactggctaagctagtttcatt---cttcttatacagGTATTCTAGCTTGTCTTGACGGATATATGAACATAGCAATGGAGCAAACAGAAGAGTACGTCAATGGGCAGCTAAAAAACAAATATGGCGATGCTTTTAT-

upper sequence: GLYMA18G46370.1 (Glycine max), 3'ss of exon 2
lower sequence: EDP01446 (Chlamydomonas reinhardtii), 3'ss of exon 3
tgtgtattggtgctcattgtccactgtatagttgtatttgttatgttatgcttctctgtatgcatgaagtagtctcactcctttgggctaatcttgcaggTATACTTGCTT-GTCTAGATGGCTATATGAATATTG-CAATGGA-GCAGACAGAGGAGTACGTCAATGGACAACTGAAGAACAAGTATGGTGACGCTTTCATC-------------
                                          |||||    | ||||||  | | ||          || |||||||   ||   |      | |||| ||  | | |||       || |  | | |  |||| |       ||||||||||||| || ||||||||||||||||| || || ||||||||              
------------------------------------------atgttgctgtgctctgt-cggacga----------ctactttgggacgat--ggagatcctgcttgtttcatttggatttgctggtggacctgggctgtggatgtgtgtgcagGAGTACGTCAACGGGCAACTGAAGAACAAGTACGGAGATGCTTTCATTCGCGGGAATAACG

upper sequence: GLYMA18G46370.1 (Glycine max), 3'ss of exon 2
lower sequence: PP1S162_163V6.1 (Physcomitrella patens), 3'ss of exon 1
tgtgtattggtgctcattgtccactgtatagttgt-atttgttat-gttatgcttctctgtatgcatgaa-----gtagtctcactcctttgggctaatcttgcaggTATACTTGCTTGTCTAGATGGCTATATGAATATTGCAATGGAGCAGACAGAGGAGTACGTCAATGGACAACTGAAGAACAAGTATGGTGACGCTTTCATC
        | |  || |  ||||  || |||   | |     ||| | | ||   || ||   | |||||      || || |  |  |||||  |   |||  |||||| || |||||| | |||||||||||||| ||||| |||||||||||||||||||| || ||||| ||  ||||||||||||||||||| |||||||| 
------gagatcttcctcctccagcgtgtagagattacgcaatattgctgtggcactgtgatggaatgaatctggataatcgccttattttggtttgcacttttagGTATTCTGGCTTGTTTGGATGGCTATATGAACATTGCCATGGAGCAGACAGAGGAGTATGTAAATGGTCAGTTGAAGAACAAGTATGGTGATGCTTTCAT-

upper sequence: GLYMA18G46370.1 (Glycine max), 3'ss of exon 2
lower sequence: PP1S17_388V6.1 (Physcomitrella patens), 3'ss of exon 1
tgtgtattggtgctcattgtccactgtatagttgtatt-tgttatgttatgcttctctgtat----gcatgaagtagtctcactcctttgggctaatcttgcaggTATACTTGCTTGTCTAGATGGCTATATGAATATTGCAATGGAGCAGACAGAGGAGTACGTCAATGGACAACTGAAGAACAAGTATGGTGACGCTTTCATC
    || | || || ||||  || ||   | ||         |   | ||     |   ||     || |    ||    |    || |||   |   ||| |||| |  | |||||| | ||||| || ||||| || || |||||||||||||||||||| || ||||||||  ||||||||||||||||||| || ||||| 
-agatagtcgttct-attg--cattgagaaattacgcaacaatgcctgataaccttggataaaacagcttttgctaacagcttcactgtggttcacatttgtagGTGTTTTGGCTTGTTTGGATGGTTACATGAACATCGCCATGGAGCAGACAGAGGAGTATGTAAATGGACAGTTGAAGAACAAGTATGGTGATGCCTTCAT-

upper sequence: GLYMA18G46370.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ09640 (Selaginella moellendorffii), 3'ss of exon 1
tgtgtattggtgctcattgtccactgtatagttgtatttgttatgttatgcttct-ctgtatgcatgaagtagtctcactcctttgggctaatcttgcaggTATACTTGCTTGTCTAGATGGCTATATGAATATTGCAATGGAGCAGACAGAGGAGTACGTCAATGGACAACTGAAGAACAAGTATGGTGACGCTTTCATC
                                            || |||  ||   ||   || |  || | ||| | |     | ||    |  ||||| || || || || || ||||| || ||||| || || ||||||||||| ||||||||||||||||| || || |||||||||||||| ||||||||||| 
--------------------------------------------gtaatggatccattggcagcctagagaaatctaagtagacagtgcc---cgcgcagGGATTCTGGCGTGCCTGGATGGGTACATGAACATCGCCATGGAGCAGACCGAGGAGTACGTCAATGGGCAGCTCAAGAACAAGTATGGCGACGCTTTCAT-

upper sequence: GLYMA18G46370.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ18024 (Selaginella moellendorffii), 3'ss of exon 1
tgtgtattggtgctcattgtccactgtatagttgtatttgttatgttatgcttct-ctgtatgcatgaagtagtctcactcctttgggctaatcttgcaggTATACTTGCTTGTCTAGATGGCTATATGAATATTGCAATGGAGCAGACAGAGGAGTACGTCAATGGACAACTGAAGAACAAGTATGGTGACGCTTTCATC
                                            || |||  ||   ||   || |  || | ||| | |     | ||    |  ||||| || || || || || ||||| || ||||| || || ||||||||||| ||||||||||||||||| || || |||||||||||||| ||||||||||| 
--------------------------------------------gtaatggatccattggcagcctagagaaatctaagtggacggtgcc---cgcgcagGGATTCTGGCGTGCCTGGATGGGTACATGAACATCGCCATGGAGCAGACCGAGGAGTACGTCAATGGGCAGCTCAAGAACAAGTATGGCGACGCTTTCAT-

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|193684145|gb|FK622681.1|FK622681
EST:     CGTGGGAGGCCGGTTGTCGTCAAGCTCAATTCTGGTGTTGATTACAGAGG                         TATACTTGCTTGTCTAGATGGCTATATGAATATTGCAATGGAGCAGACAGA
genomic: CGTGGGAGGCCGGTTGTCGTCAAGCTCAATTCTGGTGTTGATTACAGAGGttcctctctt ... atcttgcaggTATACTTGCTTGTCTAGATGGCTATATGAATATTGCAATGGAGCAGACAGA
EST: gi|208306581|gb|GE110022.1|GE110022
EST:     CGTGGGAGGCCGGTTATCGTCAAGCTCAATTCTGGTGTTGATTACAGAGG                         TATACTTGCTTGTCTAGATGGCTATATGAATATTGCAACGGAGCAGACAGA
genomic: CGTGGGAGGCCGGTTGTCGTCAAGCTCAATTCTGGTGTTGATTACAGAGGttcctctctt ... atcttgcaggTATACTTGCTTGTCTAGATGGCTATATGAATATTGCAATGGAGCAGACAGA
EST: gi|192324452|gb|FK015803.1|FK015803
EST:     CGTGGGAGGCCGGTTGTCGCCAAGCTCAATTCTGGTGTTGATTACAGAGG                         TATACTTGCTTGTCTAGATGGCTATATGAATATTGCAATGGAGCAGACAGA
genomic: CGTGGGAGGCCGGTTGTCGTCAAGCTCAATTCTGGTGTTGATTACAGAGGttcctctctt ... atcttgcaggTATACTTGCTTGTCTAGATGGCTATATGAATATTGCAATGGAGCAGACAGA
EST: gi|208307692|gb|GE107174.1|GE107174
EST:     CGTGGGAGGCCGGTTGTCGTCAAGCTCAATTCTGGTGTTGATTACAGAGG                         TATACTTGCTTGTCTAGATGGCTATATGAATATTGCAATGGAGCAGACAGA
genomic: CGTGGGAGGCCGGTTGTCGTCAAGCTCAATTCTGGTGTTGATTACAGAGGttcctctctt ... atcttgcaggTATACTTGCTTGTCTAGATGGCTATATGAATATTGCAATGGAGCAGACAGA
EST: gi|151410204|gb|EV280019.1|EV280019
EST:     CGTGGGAGGCCGGTTGTCGTCAAGCTCAATTCTGGTGTTGATTACAGAGG                         TATACTTGCTTGTCTAGATGGCTATATGAATATTGCAATGGAGCAGACAGA
genomic: CGTGGGAGGCCGGTTGTCGTCAAGCTCAATTCTGGTGTTGATTACAGAGGttcctctctt ... atcttgcaggTATACTTGCTTGTCTAGATGGCTATATGAATATTGCAATGGAGCAGACAGA
EST: gi|19346736|gb|BM891616.1|BM891616
EST:     CGTGGGAGGCCGGTTGTCGTCAAGCTCAATTCTGGTGTTGATTACAGAGG                         TATACTTGCTTGTCTAGATGGCTATATGAATATTGCAATGGAGCAGACAGA
genomic: CGTGGGAGGCCGGTTGTCGTCAAGCTCAATTCTGGTGTTGATTACAGAGGttcctctctt ... atcttgcaggTATACTTGCTTGTCTAGATGGCTATATGAATATTGCAATGGAGCAGACAGA
EST: gi|151407789|gb|EV277604.1|EV277604
EST:     CGTGGGAGGCCGGTTGTCGTCAAGCTCAATTCTGGTGTTGATTACAGAGG                         TATACTTGCTTGTCTAGATGGCTATATGAATATTGCAATGGAGCAGACAGA
genomic: CGTGGGAGGCCGGTTGTCGTCAAGCTCAATTCTGGTGTTGATTACAGAGGttcctctctt ... atcttgcaggTATACTTGCTTGTCTAGATGGCTATATGAATATTGCAATGGAGCAGACAGA
EST: gi|193428401|gb|FK396681.1|FK396681
EST:     CGTGGGAGGCCGGTTGTCGTCAAGCTCAATTCTGGTGTTGATTACAGAGG                         TATACTTGCTTGTCTAGATGGCTATATGAATATTGCAATGGAGCAAGACAG
genomic: CGTGGGAGGCCGGTTGTCGTCAAGCTCAATTCTGGTGTTGATTACAGAGGttcctctctt ... atcttgcaggTATACTTGCTTGTCTAGATGGCTATATGAATATTGCAATGGAGCA-GACAG
EST: gi|9901469|gb|BE610437.1|BE610437
EST:     CGTGGGAGGCCGGTTGTCGTCAAGCTCAATTCTGGTGTTGATTACAGAGG                         TATACTTGCTTGTCTAGATGGCTATATGAATATTGCAATGGAGCAGACAGA
genomic: CGTGGGAGGCCGGTTGTCGTCAAGCTCAATTCTGGTGTTGATTACAGAGGttcctctctt ... atcttgcaggTATACTTGCTTGTCTAGATGGCTATATGAATATTGCAATGGAGCAGACAGA
EST: gi|207785641|gb|GD757390.1|GD757390
EST:     CGTGGGAGGCCGGTTGTCGTCAAGCTCAATTCTGGTGTTGATTACAGAGG                         TATACTTGCTTGTCTAGATGGCTATATGAATATTGCAATGGAGCAGACAGA
genomic: CGTGGGAGGCCGGTTGTCGTCAAGCTCAATTCTGGTGTTGATTACAGAGGttcctctctt ... atcttgcaggTATACTTGCTTGTCTAGATGGCTATATGAATATTGCAATGGAGCAGACAGA
EST: gi|193587878|gb|FK539147.1|FK539147
EST:     CGTGGGAGGCCGGTTGTCGTCAAGCTCAATTCTGGTGTTGATTACAGAGG                         TATACTTGCTTGTCTAGATGGCTATATGAATATTGCAATGGAGCAGACAGA
genomic: CGTGGGAGGCCGGTTGTCGTCAAGCTCAATTCTGGTGTTGATTACAGAGGttcctctctt ... atcttgcaggTATACTTGCTTGTCTAGATGGCTATATGAATATTGCAATGGAGCAGACAGA
EST: gi|4396101|gb|AI495098.1|AI495098
EST:     CGTGGGAGGCCGGTTGTCGTCAAGCTCAATTCTGGTGTTGATTACAGAGG                         TATACTTGCTTGTCTAGATGGCTATATGAATATTGCAATGGAGCAGACAGA
genomic: CGTGGGAGGCCGGTTGTCGTCAAGCTCAATTCTGGTGTTGATTACAGAGGttcctctctt ... atcttgcaggTATACTTGCTTGTCTAGATGGCTATATGAATATTGCAATGGAGCAGACAGA
EST: gi|192327084|gb|FK015476.1|FK015476
EST:     CGTGGGAGGCCGGTTGTCGTCAAGCTCAATTCTGGTGTTGATTACAGAGG                         TATACTTGCTTGTCTAGATGGCTATATGAATATTGCAATGGAGCAGACAGA
genomic: CGTGGGAGGCCGGTTGTCGTCAAGCTCAATTCTGGTGTTGATTACAGAGGttcctctctt ... atcttgcaggTATACTTGCTTGTCTAGATGGCTATATGAATATTGCAATGGAGCAGACAGA
EST: gi|208158322|gb|GD956885.1|GD956885
EST:     CGTGGGAGGCCGGTTGTCGTCAAGCTCAATTCTGGTGTTGATTACAGAGG                         TATACTTGCTTGTCTAGATGGCTATATGAATATTGCAATGGAGCAGACAGA
genomic: CGTGGGAGGCCGGTTGTCGTCAAGCTCAATTCTGGTGTTGATTACAGAGGttcctctctt ... atcttgcaggTATACTTGCTTGTCTAGATGGCTATATGAATATTGCAATGGAGCAGACAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttatgcttctctgtatgcatgaagtagtctcactcctttgggctaatcttgcaggTATACTTGCTTGTCTAGATGGCTATATGAATATTGCAATGGAGCAGACAGAGGAGTACGTCAATGGACAACTGAAGAACAAGTATGGTGACGCTTTCATC
                                        ggctaat  putative branch site (score: 3)
                                           taatctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgtgtattggtgctcattgtccactgtatagttgtatttgttatgttatgcttctctgtatgcatgaagtagtctcactcctttgggctaatcttgcaggTATACTTGCTTGTCTAGATGGCTATATGAATATTGCAATGGAGCAGACAGAGGAGTACGTCAATGGACAACTGAAGAACAAGTATGGTGACGCTTTCATC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
- - - -tggtgct
- - - - - - - - -tgtccac
- - - - - - - - - - - - - - - - - - - tgttatg
- - - - - - - - - - - - - - - - - - - - - - - - -gcttctc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcatgaa