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

CATAATAATGTTATCCCCAATGGGCACTTCCGGAAACACTGGCAAAACTATGTGAAGACTTGGTTTAATCAACCAGCCCGAAAGACCAGAAGACGGTTGGgtaatttaacctaatctcttgctcttttttaacattgtaatacttaattaatcagtctggcttaatacttgtaattcaagaaacaagaatcagcttgagttgtcaacaattgttgtgtgtatctttatattttgactcgtgggtaacactttttcag

Basic information

species Glycine max
transcript GLYMA16G17370.2
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G17370.2 (Glycine max), 5'ss of exon 1
lower sequence: LOC_Os03g37970.1 (Oryza sativa), 5'ss of exon 2
CATAATAATGTTATCCCCAATGGGCACTTCCGGAAACACTGGCAAAACTATGTGAAGACTTGGTTTAATCAACCAGCCCGAAAGACCAGAAGACGGTTGGgtaatttaacctaatctcttgctcttttttaacattgt-aatacttaattaatcagtctggcttaatacttgtaattcaagaaacaagaatcagcttgagttgtcaacaattgttgtgtgtatctttatattttgactcgtgggtaacactttttcag
|| || || |||||||||||||| ||||||  ||| |||||||| |||||||| ||||| ||||| || || || ||||| |||   ||  | ||  | ||| |  |  |||   |||    ||     | ||  ||| |  | ||     |  |||   || |  | |||| |||| | |||  ||  | | | |       ||                                                     
CACAACAACGTTATCCCCAATGGCCACTTCAAGAAGCACTGGCAGAACTATGTCAAGACATGGTTCAACCAGCCCGCCCGCAAGCAGAGGCGCCGCATTGgtgagctc-cctggcctccctatcgcgcatgactatgttagcaattgcc--actagtactgcatg-tgcttg-aatttatgaattaaata-cggttatctccttct----------------------------------------------------

upper sequence: GLYMA16G17370.2 (Glycine max), 5'ss of exon 1
lower sequence: LOC_Os06g02510.3 (Oryza sativa), 5'ss of exon 2
CATAATAATGTTATCCCCAATGGGCACTTCCGGAAACACTGGCAAAACTATGTGAAGACTTGGTTTAATCAACCAGCCCGAAAGACCAGAAGACGGTTGGgtaatttaacctaatctcttgctcttt-tttaacattgtaatacttaattaatcagtctggcttaatacttgtaattcaagaaacaagaatcagcttgagttgtcaacaattgttgtgtgtatctttatattttgactcgtgggtaacactttttcag
|| || || || ||||| ||||||||||||  ||| |||||||| |||||||| ||||| ||||| || || || ||||| |||   ||  | ||  | |||||  | |  | |||||||||  | | | |||   |    |   | | | | ||   | ||||  ||||||    | |             | | |  |                                                          
CACAACAACGTCATCCCGAATGGGCACTTCAAGAAGCACTGGCAGAACTATGTCAAGACATGGTTCAACCAGCCCGCCCGCAAGCAGAGGCGCCGCATCGgtaaagtgat-tgatctcttgcgatctatctaatgattatgtgaatgaatgagcatgttagcttcctacttgctcgtgagattgtgctgtgtaacatatgc---------------------------------------------------------

upper sequence: GLYMA16G17370.2 (Glycine max), 5'ss of exon 1
lower sequence: GRMZM2G409407_T01 (Zea mays), 5'ss of exon 2
CATAATAATGTTATCCCCAATGGGCACTTCCGGAAACACTGGCAAAACTATGTGAAGACTTGGTTTAATCAACCAGCCCGAAAGACCAGAAGACGGTTGGgtaatttaacctaatctcttgctcttttttaacattgtaatacttaattaatcagtctggcttaatacttgtaattcaagaaacaagaatcagcttgagttgtcaacaattgttgtgtgtatctttatattttgactcgtgggtaacactttttcag
|| || || ||||||||||| |||||||||  ||| |||||||| |||||||| ||||| ||||| || || || ||||| |||   ||  | ||  | ||| |  |   ||     ||| | || ||| | | ||  ||||     ||      |     | || ||||     |  | | | |    |   | ||   ||  ||                                                   
CACAACAACGTTATCCCCAACGGGCACTTCAAGAAGCACTGGCAGAACTATGTCAAGACATGGTTCAACCAGCCCGCCCGCAAGCAGAGGCGCCGCATCGgttagctcttctg--tgcttaccctctttcagccttccaatat---gttgcgtgcttgaattcaagacttagttgtttacagatagt--ttgccatgccctgcaaat--------------------------------------------------

upper sequence: GLYMA16G17370.2 (Glycine max), 5'ss of exon 1
lower sequence: Vv13s0047g01160.t01 (Vitis vinifera), 5'ss of exon 1
CATAATAATGTTATCCCCAATGGGCACTTCCGGAAACACTGGCAAAACTATGTGAAGACTTGGTTTAATCAACCAGCCCGAAAGACCAGAAGACGGTTGGgtaatttaacctaatctcttgctcttttttaacattgtaatacttaattaatcagtctggcttaatacttgtaattcaa--gaaacaagaatcagcttgagttgtcaacaattgttgtgtgtatctttatattttgactcgtgggtaacactttttcag
||||| |||||| | || ||||||||||||  ||| |||||||| |||||||| ||||||||||| || ||||| ||||| || ||| ||||| |  | ||||  |   | |  ||||||   ||   ||||| |    ||   |  | | | ||| |    ||  | |    |||  |  | |  | | || |  ||     ||                                                      
CATAACAATGTTGTGCCTAATGGGCACTTCAAGAAGCACTGGCAGAACTATGTCAAGACTTGGTTCAACCAACCTGCCCGCAAAACCCGAAGAAGAGTTGgta--tgggctttttctctt---ctaggttaacttgtccatttcttgtcattgagtttc-tataccattgtggatttgaatggagtaggcataaaatttgtgggtt-----------------------------------------------------

upper sequence: GLYMA16G17370.2 (Glycine max), 5'ss of exon 1
lower sequence: Vv14s0006g00820.t01 (Vitis vinifera), 5'ss of exon 2
CATAATAATGTTATCCCCAATGGGCACTTCCGGAAACACTGGCAAAACTATGTGAAGACTTGGTTTAATCAACCAGCCCGAAAGACCAGAAGACGGTTGGgtaatttaacctaatctcttgctcttttttaacattgtaatacttaattaatcagtctggcttaatacttgtaattcaagaaacaagaatcagcttgagttgtcaa---caattgttgtgtgtatctttatattttgactcgtgggtaacact-ttttcag
||||| |||||| | || ||||||||||||  |||||| ||||| || ||||| || ||||||||||| ||||| || || || || ||||||||  | ||||  |  || ||| |          |||||| || | |||  |   ||   | |||| ||| | || |||        |  | ||  ||    ||   || ||||      || || ||||  ||    | | |||||  ||  || | ||  | | |||
CATAACAATGTTGTGCCTAATGGGCACTTCAAGAAACATTGGCAGAATTATGTCAAAACTTGGTTTAACCAACCTGCTCGCAAAACAAGAAGACGTATAGgtagct--acttaacca---------ttttaaaatggaaatggt-gtttttcctgtcttgctaattagttg--------gtcataatgattctgtttcattatcaagcttgcttattctgtgc-tcgcattttcttgacatgtctgttataccatctccag

upper sequence: GLYMA16G17370.2 (Glycine max), 5'ss of exon 1
lower sequence: PP1S126_52V6.1 (Physcomitrella patens), 5'ss of exon 2
CATAATAATGTTATCCCCAATGGGCACTTCCGGAAACACTGGCAAAACTATGTGAAGACTTGGTTTAATCAACCAGCCCGAAAGACCAGAAGACGGTTGGgtaatttaacctaatctcttgctcttttttaacattgtaatacttaattaatcagtctggcttaatact-tgtaattcaagaaacaagaatcagcttgagttgtcaacaattgttgtgtgtatctttatattttgactcgtgggtaacactttttcag
||||| ||||||||||||||||| ||||||  |||  |||||||||||||||||| ||| |||||||| || || ||||| ||||  |||||| |   ||||    || | |   |    ||| | ||     |||    |||  ||    || ||     || | ||| | | ||    |  |||    | | | |  |      ||  ||| ||                                          
CATAACAATGTTATCCCCAATGGCCACTTCAAGAAGGACTGGCAAAACTATGTGAGGACCTGGTTTAACCAGCCCGCCCGCAAGAAAAGAAGAAGAACGGgt----tagcat--cccaccgctgtattggtgaatttggttac--aaactgtccgtt--atttgagactctatgatatgtgtgacagcggtaaccctagg------acctttggtg------------------------------------------

upper sequence: GLYMA16G17370.2 (Glycine max), 5'ss of exon 1
lower sequence: PP1S58_38V6.1 (Physcomitrella patens), 5'ss of exon 2
CATAATAATGTTATCCCCAATGGGCACTTCCGGAAACACTGGCAAAACTATGTGAAGACTTGGTTTAATCAACCAGCCCGAAAGACCAGAAGACGGTTGGgtaatttaacctaatctcttgctcttttttaac--attgtaatacttaattaatcagtctggcttaatacttgtaattcaagaaacaagaatcagcttgagttgtcaacaattgttgtgtgtatctttatattttgactcgtgggtaacactttttcag
||||||||||||||||||||||| ||||||  |||  ||||||| |||||||||| ||| ||||| || || || ||||| ||||  |||||| |   |||||| |  |  |  | |   | ||||  | ||    |||| |   ||   | || |     |  ||||  || |   |  |  | |   || |    ||| ||                                                        
CATAATAATGTTATCCCCAATGGTCACTTCAAGAAGGACTGGCAGAACTATGTGAGGACCTGGTTCAACCAGCCCGCCCGCAAGAAAAGAAGAAGAACGGgtaactatagtt--ttttcggatcttcctgaattggttgttagctttcccttattacggaagtgtaatttttttgtctggaacatctcaaaccc-tatgaatt--------------------------------------------------------

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|254339157|gb|GR847874.1|GR847874
EST:     TGTGAAGACTTGGTTTAATCAACCAGCCCGAAAGACCAGAAGACGGTTGG                         CTCGGCAGAAGAAGGCTGTCAAGATTTTCCCCAGGCCTACTGCTGGATCTC
genomic: TGTGAAGACTTGGTTTAATCAACCAGCCCGAAAGACCAGAAGACGGTTGGgtaatttaac ... actttttcagCTCGGCAGAAGAAGGCTGTCAAGATTTTCCCCAGGCCTACTGCTGGATCTC
EST: gi|209719490|gb|BW650995.1|BW650995
EST:     TGTGAAGACTTGGTTTAATCAACCAGCCCGAAAGACCAGAAGACGGTTGG                         CTCGGCAGAAGAAGGCTGTCAAGATTTTCCCCAGGCCTACTGCTGGATCTC
genomic: TGTGAAGACTTGGTTTAATCAACCAGCCCGAAAGACCAGAAGACGGTTGGgtaatttaac ... actttttcagCTCGGCAGAAGAAGGCTGTCAAGATTTTCCCCAGGCCTACTGCTGGATCTC
EST: gi|20207618|gb|BQ133707.1|BQ133707
EST:     TGTGAAGACTTGGTTTAATCAACCAGCCCGAAAGACCAGAAGACGGTTGG                         CTCGGCAGAAGAAGGCTGTCAAGATTTTCCCCAGGCCTACTGCTGGATCTC
genomic: TGTGAAGACTTGGTTTAATCAACCAGCCCGAAAGACCAGAAGACGGTTGGgtaatttaac ... actttttcagCTCGGCAGAAGAAGGCTGTCAAGATTTTCCCCAGGCCTACTGCTGGATCTC
EST: gi|16348456|gb|BI974051.1|BI974051
EST:     TGTGAAGACTTGGTTTAATCAACCAGCCCGAAAGACCAGAAGACGGTTGG                         CTCGGCAGAAGAAGGCTGTCAAGATTTTCCCCAGGCCTACTGCTGGATCTC
genomic: TGTGAAGACTTGGTTTAATCAACCAGCCCGAAAGACCAGAAGACGGTTGGgtaatttaac ... actttttcagCTCGGCAGAAGAAGGCTGTCAAGATTTTCCCCAGGCCTACTGCTGGATCTC
EST: gi|13787483|gb|BG650075.1|BG650075
EST:     TGTGAAGACTTGGTTTAATCAACCAGCCCGAAAGACCAGAAGACGGTTGG                         CTCGGCAGAAGAAGGCTGTCAAGATTTTCCCCAGGCCTACTGCTGGATCTC
genomic: TGTGAAGACTTGGTTTAATCAACCAGCCCGAAAGACCAGAAGACGGTTGGgtaatttaac ... actttttcagCTCGGCAGAAGAAGGCTGTCAAGATTTTCCCCAGGCCTACTGCTGGATCTC
EST: gi|14008646|gb|BG725250.1|BG725250
EST:     TGTGAAGACTTGGTTTAATCAACCAGCCCGAAAGACCAGAAGACGGTTGG                         CTCGGCAGAAGAAGGCTGTCAAGATTTTCCCCAGGCCTACTGCTGGATCGC
genomic: TGTGAAGACTTGGTTTAATCAACCAGCCCGAAAGACCAGAAGACGGTTGGgtaatttaac ... actttttcagCTCGGCAGAAGAAGGCTGTCAAGATTTTCCCCAGGCCTACTGCTGGATCTC
EST: gi|120529623|gb|EH257757.1|EH257757
EST:     TGTGAAGACTTGGTTTAATCAACCAGCCCGAAAGACCAGAAGACGGTTGG                         CTCGGCAGAAGAAGGCTGTCAAGATTTTCCCCAGGCCTACTGCTGGATCTC
genomic: TGTGAAGACTTGGTTTAATCAACCAGCCCGAAAGACCAGAAGACGGTTGGgtaatttaac ... actttttcagCTCGGCAGAAGAAGGCTGTCAAGATTTTCCCCAGGCCTACTGCTGGATCTC
EST: gi|23726992|gb|BU761509.1|BU761509
EST:     TGTGAAGACTTGGTTTAATCAACCAGCCCGAAAGACCAGAAGACGGTTGG                         CTCGGCAGAAGAAGGCTGTCAAGATTTTCCCCAGGCCTACTGCTGGATCTC
genomic: TGTGAAGACTTGGTTTAATCAACCAGCCCGAAAGACCAGAAGACGGTTGGgtaatttaac ... actttttcagCTCGGCAGAAGAAGGCTGTCAAGATTTTCCCCAGGCCTACTGCTGGATCTC
EST: gi|6915365|gb|AW396895.1|AW396895
EST:     TGTGAAGACTTGGTTTAATCAACCAGCCCGAAAGACCAGAAGACGGTTGG                         CTCGGCAGAAGAAGGCTGTCAAGATTTTCCCCAGGCCTACTGCTGGATCTC
genomic: TGTGAAGACTTGGTTTAATCAACCAGCCCGAAAGACCAGAAGACGGTTGGgtaatttaac ... actttttcagCTCGGCAGAAGAAGGCTGTCAAGATTTTCCCCAGGCCTACTGCTGGATCTC
EST: gi|14011613|gb|BG726535.1|BG726535
EST:     TGTGAAGACTTGGTTTAATCAACCAGCCCGAAAGACCAGAAGACGGTTGG                         CTCGGCAGAAGAAGGCTGTCAAGATTTTCCCCAGGCCTACTGCTGGATCTC
genomic: TGTGAAGACTTGGTTTAATCAACCAGCCCGAAAGACCAGAAGACGGTTGGgtaatttaac ... actttttcagCTCGGCAGAAGAAGGCTGTCAAGATTTTCCCCAGGCCTACTGCTGGATCTC
EST: gi|213594019|gb|DB961935.1|DB961935
EST:     TGTGAAGACTTGGTTTAATCAACCAGCCCGAAAGACCAGAAGACGGTTGG                         CTCGGCAGAAGAAGGCTGTCAAGATTTTCCCCAGGCCTACTGCTGGATCTC
genomic: TGTGAAGACTTGGTTTAATCAACCAGCCCGAAAGACCAGAAGACGGTTGGgtaatttaac ... actttttcagCTCGGCAGAAGAAGGCTGTCAAGATTTTCCCCAGGCCTACTGCTGGATCTC
EST: gi|9204549|gb|BE330773.1|BE330773
EST:     TGTGAAGACTTGGTTTAATCAACCAGCCCGAAAGACCAGAAGACGGTTGG                         CTCGGCAGAAGAAGGCTGTCAAGATTTTCCCCAGGCCTACTGCTGGATCTC
genomic: TGTGAAGACTTGGTTTAATCAACCAGCCCGAAAGACCAGAAGACGGTTGGgtaatttaac ... actttttcagCTCGGCAGAAGAAGGCTGTCAAGATTTTCCCCAGGCCTACTGCTGGATCTC
EST: gi|18040171|gb|BM308465.1|BM308465
EST:     TGTGAAGACTTGGTTTAATCAACCAGCCCGAAAGACCAGAAGACGGTTGG                         CTCGGCAGAAGAAGGCTGTCAAGATTTTCCCCAGGCCTACTGCTGGATCTC
genomic: TGTGAAGACTTGGTTTAATCAACCAGCCCGAAAGACCAGAAGACGGTTGGgtaatttaac ... actttttcagCTCGGCAGAAGAAGGCTGTCAAGATTTTCCCCAGGCCTACTGCTGGATCTC
EST: gi|12688119|gb|BG154455.1|BG154455
EST:     TGTGAAGACTTGGTTTAATCAACCAGCCCGAAAGACCAGAAGACGGTTGG                         CTCGGCAGAAGAAGGCTGTCAAGATTTTCCCCAGGCCTACTGCTGGATCTC
genomic: TGTGAAGACTTGGTTTAATCAACCAGCCCGAAAGACCAGAAGACGGTTGGgtaatttaac ... actttttcagCTCGGCAGAAGAAGGCTGTCAAGATTTTCCCCAGGCCTACTGCTGGATCTC
EST: gi|207797429|gb|GD771227.1|GD771227
EST:     TGTGAAGACTTGGTTTAATCAACCAGCCCGAAAGGCCAGAAGACGGTTGG                         CTCGGCAGAAGAAGGCTGTCAAGATTTTCCCCAGGCCTACTGCTGGATCTC
genomic: TGTGAAGACTTGGTTTAATCAACCAGCCCGAAAGACCAGAAGACGGTTGGgtaatttaac ... actttttcagCTCGGCAGAAGAAGGCTGTCAAGATTTTCCCCAGGCCTACTGCTGGATCTC
EST: gi|26047262|gb|CA784114.1|CA784114
EST:     TGTGAAGACTTGGTTTAATCAACCAGCCCGAAAGACCAGAAGACGGTTGG                         CTCGGCAGAAGAAGGCTGTCAAGATTTTCCCCAGGCCTACTGCTGGATCTC
genomic: TGTGAAGACTTGGTTTAATCAACCAGCCCGAAAGACCAGAAGACGGTTGGgtaatttaac ... actttttcagCTCGGCAGAAGAAGGCTGTCAAGATTTTCCCCAGGCCTACTGCTGGATCTC
EST: gi|151402405|gb|EV272218.1|EV272218
EST:     TGTGAAGACTTGGTTTAATCAACCAGCCCGAAAGACCAGAAGACGGTTGG                         CTCGGCAGAAGAAGGCTGTCAAGATTTTCCCCAGGCCTACTGCTGGATCTC
genomic: TGTGAAGACTTGGTTTAATCAACCAGCCCGAAAGACCAGAAGACGGTTGGgtaatttaac ... actttttcagCTCGGCAGAAGAAGGCTGTCAAGATTTTCCCCAGGCCTACTGCTGGATCTC
EST: gi|17400476|gb|BM177258.1|BM177258
EST:     TGTGAAGACTTGGTTTAATCAACCAGCCCGAAAGACCAGAAGACGGTTGG                         CTCGGCAGAAGAAGGCTGTCAAGATTTTCCCCAGGCCTACTGCTGGATCTC
genomic: TGTGAAGACTTGGTTTAATCAACCAGCCCGAAAGACCAGAAGACGGTTGGgtaatttaac ... actttttcagCTCGGCAGAAGAAGGCTGTCAAGATTTTCCCCAGGCCTACTGCTGGATCTC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CATAATAATGTTATCCCCAATGGGCACTTCCGGAAACACTGGCAAAACTATGTGAAGACTTGGTTTAATCAACCAGCCCGAAAGACCAGAAGACGGTTGGgtaatttaacctaatctcttgctcttttttaacattgtaatacttaattaatcagtctggcttaatacttgtaattcaagaaacaagaatcagcttgagttgtcaacaattgttgtgtgtatctttatattttgactcgtgggtaacactttttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA