Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatattctcttggctctttagctgataaaaaaattgaaattttgttccaaccatttaaacaataacaagcttgtccaattgtgacacagGGGGAGAAGGATGATAAAATTATTGCAGTATGTGCTGATGATCCAGAATATAAGCACTATACTGACTTCAAAGAACTTCCACCTCATCGCCTCATGGAGA

Basic information

species Glycine max
transcript GLYMA07G05390.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G05390.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os04g59040.3 (Oryza sativa), 3'ss of exon 6
gtatattctct-----tggctctttagctgataaaaaaa---ttgaa-------attttgttccaaccatttaaacaataacaagcttgtccaattgtgaca-cagGGGGAGAAGGATGATAAAATTATTGCAGTATGTGCTGATGATCCAGAATATAAGCACTATACTGACTTCAAAGAACTTCCACCTCATCGCCTCATGGAGA
||||||| |||     |   | | ||||  |   |||||    || |       | | | ||       |||      ||   |   | |   ||| ||  | ||||| ||||||||||| || || || |||||||||||||||||||| |||||    || || | |||| |||  || ||  | ||||| ||||||   ||||
gtatattttctactgttctgtttgtagcaaagggaaaaagacctgcacgggttcactctttttgttttgttttttttttactgacgatattggattttgtgatcagGGTGAGAAGGATGACAAGATAATAGCAGTATGTGCTGATGATCCTGAATACCGTCATTACAATGACATCAGTGAGCTGTCTCCTCACCGCCTCCAAGAGA

upper sequence: GLYMA07G05390.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os04g59040.2 (Oryza sativa), 3'ss of exon 5
gtatattctcttggctctttagctgataaaaaaa---ttgaa-------attttgttccaaccatttaaacaataacaagcttgtccaattgtgaca-cagGGGGAGAAGGATGATAAAATTATTGCAGTATGTGCTGATGATCCAGAATATAAGCACTATACTGACTTCAAAGAACTTCCACCTCATCGCCTCATGGAGA
 | | | || ||   | | ||||  |   |||||    || |       | | | ||       |||      ||   |   | |   ||| ||  | ||||| ||||||||||| || || || |||||||||||||||||||| |||||    || || | |||| |||  || ||  | ||||| ||||||   ||||
-tttctactgttctgtttgtagcaaagggaaaaagacctgcacgggttcactctttttgttttgttttttttttactgacgatattggattttgtgatcagGGTGAGAAGGATGACAAGATAATAGCAGTATGTGCTGATGATCCTGAATACCGTCATTACAATGACATCAGTGAGCTGTCTCCTCACCGCCTCCAAGAGA

upper sequence: GLYMA07G05390.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G104918_T03 (Zea mays), 3'ss of exon 6
gtatattctcttg--gctctttagctgataaaaaaattgaaa---ttttgttccaacc-atttaaacaataacaagcttgtccaattgtgacacagGGGGAGAAGGATGATAAAATTATTGCAGTATGTGCTGATGATCCAGAATATAAGCACTATACTGACTTCAAAGAACTTCCACCTCATCGCCTCATGGAGA
|||| |  | ||   ||||| |   || || |   | |  ||    | || | | ||   |||  |   |   |    |||       || ||  ||| || |||||||| || || || |||||||||||||||||||| |||||    ||||| |  ||| |||  || ||  | ||||| |||||    ||||
gtatttcatgttacagctctatttgtggtagagggaatagaagagctctgcttcgacttgtttctaaccttggatttctgttgggcgttgtca--gGGTGAAAAGGATGACAAGATAATAGCAGTATGTGCTGATGATCCTGAATACCGTCACTACAACGACATCAGCGAGCTGTCTCCTCACCGCCTGCAAGAGA

upper sequence: GLYMA07G05390.1 (Glycine max), 3'ss of exon 6
lower sequence: AT1G01050.1 (Arabidopsis thaliana), 3'ss of exon 6
------------------------gtatattctcttggctctttagctgataaaaaaattgaaattttgttccaaccatttaaa----caataacaagcttgtccaattgtgacac-agGGGGAGAAGGATGATAAAATTATTGCAGTATGTGCTGATGATCCAGAATATAAGCACTATACTGACTTCAAAGAACTTCCACCTCATCGCCTCATGGAGA
                          | | ||| ||   | |||  || |    ||   |  |  |  |||  ||   | |       ||||       || |     ||| |    |||| || || ||||| || || |||||||| |||| ||||||||| |||||||||||||| |||||| ||||||||||||| ||||| || |||   || |
gtaaaacctaaacttgatcaatgaaaagactctgttttttttttctcttactctaatcctttaggtcagtttaaatggtcttgtactccaatcttgtatttttggcgctgtaattttagGGTGAAAAAGATGACAAGATCATTGCAGTGTGTGTTGATGATCCTGAATATAAGCACTACACTGACATCAAAGAACTTCCTCCTCACCGTCTCTCTGAAA

upper sequence: GLYMA07G05390.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv02s0025g02980.t01 (Vitis vinifera), 3'ss of exon 5
gtatattctcttggctctttagctgataaaaaaattgaaattttgttccaaccatttaaacaataacaagctt-gtccaattgtgacac-agGGGGAGAAGGATGATAAAATTATTGCAGTATGTGCTGATGATCCAGAATATAAGCACTATACTGACTTCAAAGAACTTCCACCTCATCGCCTCATGGAGA
   |  | || |  ||||  |||  || |   ||     | ||  |  ||   | || |   |||  ||  |  || |  |  | | || |||| ||||| || ||||| || ||||| ||||| ||||| ||||||||||||   ||||| |||||| ||||||| |||||||||||| | ||    ||||
--gtgatgtcatttctctcaagcaaatcatgcaaccattagttcttcacagtgagttgaggcatatgaaattcagttctttattcataccagGGAGAGAATGACGATAAGATCATTGCTGTATGCGCTGACGATCCAGAATATCGACACTACACTGACATCAAAGAGCTTCCACCTCATAGACTAGCTGAGA

upper sequence: GLYMA07G05390.1 (Glycine max), 3'ss of exon 6
lower sequence: EFJ27171 (Selaginella moellendorffii), 3'ss of exon 4
gtatattctcttggctctttagctgataaaaaaattgaaattttgttccaaccatttaaacaataacaagcttgtccaattgtgacacagGGGGAGAAGGATGATAAAATTATTGCAGTATGTGCTGATGATCCAGAATATAAGCACTATACTGACTTCAAAGAACTTCCACCTCATCGCCTCATGGAGA
                          ||  ||| |    |  || ||   | | |||   |  ||| |   |  || |  | |||  |||||||||||||| ||||| || || ||||| || |||||||||||||| || ||||| |  || ||| ||||  | || || |||||  | ||    ||||
-------------------------gtagcaaagtgtttacattcttttcagcgttt---ctctaagagtgtcatcta--tctgat-cagGGGGAGAAGGACGATAAGATCATAGCAGTGTGCGCTGATGATCCAGAGTACAAGCATTGCACGGACATCAAGCAGCTCCCGCCTCACAGGCTAGCAGAGA

upper sequence: GLYMA07G05390.1 (Glycine max), 3'ss of exon 6
lower sequence: EFJ33488 (Selaginella moellendorffii), 3'ss of exon 5
gtatattctcttggctctttagctgataaaaaaattgaaattttgttccaaccatttaaacaataacaagcttgtccaattgtgacacagGGGGAGAAGGATGATAAAATTATTGCAGTATGTGCTGATGATCCAGAATATAAGCACTATACTGACTTCAAAGAACTTCCACCTCATCGCCTCATGGAGA
                          ||  |||||    |  |  ||   | | |||    || |      |  || |  | |||  |||||||||||||| ||||| || || ||||| || |||||||||||||| || ||||| |  || ||| ||||  | || || |||||  | ||   |||||
-------------------------gtagcaaaatgtttacatccttttcagcgtttttctaagagtg---tcatcta--tctgat-cagGGGGAGAAGGACGATAAGATCATAGCAGTGTGCGCTGATGATCCAGAGTACAAGCATTGCACGGACATCAAGCAGCTCCCGCCTCACAGGCTAGCGGAGA

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|254315135|gb|GR830128.1|GR830128
EST:     GTTGTTTCCTGCGAGCCAGGGCCATTGGATTGATGCCTATGATTGACCAG                         GGGGAGAAGGATGATAAAATTATTGCAGTATGTGCTGATGATCCAGAATAT
genomic: GTTGTTTCCTGCGAGCCAGGGCCATTGGATTGATGCCTATGATTGACCAGgtatattctc ... tgtgacacagGGGGAGAAGGATGATAAAATTATTGCAGTATGTGCTGATGATCCAGAATAT
EST: gi|254344222|gb|GR851025.1|GR851025
EST:     GTTGTTTCCTGCGAGCCAGGGCCATTGGATTGATGCCTATGATTGACCAG                         GGGGAGAAGGATGATAAAATTATTGCAGTATGTGCTGATGATCCAGAATAT
genomic: GTTGTTTCCTGCGAGCCAGGGCCATTGGATTGATGCCTATGATTGACCAGgtatattctc ... tgtgacacagGGGGAGAAGGATGATAAAATTATTGCAGTATGTGCTGATGATCCAGAATAT
EST: gi|17400209|gb|BM176991.1|BM176991
EST:     GTTGTTTCCTGCGAGCCAGGGCCATTGGATTGATGCCTATGATTGACCAG                         GGGGAGAAGGATGATAAAATTATTGCAGTATGTGCTGATGATCCAGAATAT
genomic: GTTGTTTCCTGCGAGCCAGGGCCATTGGATTGATGCCTATGATTGACCAGgtatattctc ... tgtgacacagGGGGAGAAGGATGATAAAATTATTGCAGTATGTGCTGATGATCCAGAATAT
EST: gi|254315134|gb|GR830127.1|GR830127
EST:     GTTGTTTCCTGCGAGCCAGGGCCATTGGATTGATGCCTATGATTGACCAG                         GGGGAGAAGGATGATAAAATTATTGCAGTATGTGCTGATGATCCAGAATAT
genomic: GTTGTTTCCTGCGAGCCAGGGCCATTGGATTGATGCCTATGATTGACCAGgtatattctc ... tgtgacacagGGGGAGAAGGATGATAAAATTATTGCAGTATGTGCTGATGATCCAGAATAT
EST: gi|254344223|gb|GR851026.1|GR851026
EST:     GTTGTTTCCTGCGAGCCAGGGCCATTGGATTGATGCCTATGATTGACCAG                         GGGGAGAAGGATGATAAAATTATTGCAGTATGTGCTGATGATCCAGAATAT
genomic: GTTGTTTCCTGCGAGCCAGGGCCATTGGATTGATGCCTATGATTGACCAGgtatattctc ... tgtgacacagGGGGAGAAGGATGATAAAATTATTGCAGTATGTGCTGATGATCCAGAATAT
EST: gi|18040990|gb|BM309284.1|BM309284
EST:     GTTGTTTCCTGCGAGCCAGGGCCATTGGATTGATGCCTATGATTGACCAG                         GGGGAGAAGGATGATAAAATTATTGCAGTATGTGCTGATGATCCAGAATAT
genomic: GTTGTTTCCTGCGAGCCAGGGCCATTGGATTGATGCCTATGATTGACCAGgtatattctc ... tgtgacacagGGGGAGAAGGATGATAAAATTATTGCAGTATGTGCTGATGATCCAGAATAT
EST: gi|209698574|gb|BW652427.1|BW652427
EST:     GTTGTTTCCTGCGAGCCAGGGCCATTGGATTGATGCCTATGATTGACCAG                         GGGGAGAAGGATGATAAAATTATTGCAGTATGTGCTGATGATCCAGAATAT
genomic: GTTGTTTCCTGCGAGCCAGGGCCATTGGATTGATGCCTATGATTGACCAGgtatattctc ... tgtgacacagGGGGAGAAGGATGATAAAATTATTGCAGTATGTGCTGATGATCCAGAATAT
EST: gi|151399288|gb|EV269159.1|EV269159
EST:     GTTGTTTCCTGCGAGCCAGGGCCATTGGATTGATGCCTATGATTGACCAG                         GGGGAGAAGGATGATAAAATTATTGCAGTATGTGCTGATGATCCAGAATAT
genomic: GTTGTTTCCTGCGAGCCAGGGCCATTGGATTGATGCCTATGATTGACCAGgtatattctc ... tgtgacacagGGGGAGAAGGATGATAAAATTATTGCAGTATGTGCTGATGATCCAGAATAT
EST: gi|21995190|gb|BQ786718.1|BQ786718
EST:     GTTGTTTCCTGCGAGCCAGGGCCATTGGATTGATGCCTATGATTGACCAG                         GGGGAGAAGGATGATAAAATTATTGCAGTATGTGCTGATGATCCAGAATAT
genomic: GTTGTTTCCTGCGAGCCAGGGCCATTGGATTGATGCCTATGATTGACCAGgtatattctc ... tgtgacacagGGGGAGAAGGATGATAAAATTATTGCAGTATGTGCTGATGATCCAGAATAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgaaattttgttccaaccatttaaacaataacaagcttgtccaattgtgacacagGGGGAGAAGGATGATAAAATTATTGCAGTATGTGCTGATGATCCAGAATATAAGCACTATACTGACTTCAAAGAACTTCCACCTCATCGCCTCATGGAGA
                         caataac  putative branch site (score: 2)
                  atttaaacaataacaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatattctcttggctctttagctgataaaaaaattgaaattttgttccaaccatttaaacaataacaagcttgtccaattgtgacacagGGGGAGAAGGATGATAAAATTATTGCAGTATGTGCTGATGATCCAGAATATAAGCACTATACTGACTTCAAAGAACTTCCACCTCATCGCCTCATGGAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA