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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gcatgtattagagattatggtttaagatgtgtttgatctgctgtgtaaaataacttgtcttttgtgtgaattcttttctttttcctttggttttgataattattgtgtttactactttggatgtttgctatggaaggggaatatctatttgtaaattttgatagagaatttgacttgatttcttcgattgattgtagAAAGTATTTTGGCGAGGGGTTGTTGAAGAGCTTCTTTGGTTTATCAGTGGCTCAACAAATGCCAAG

Basic information

species Glycine max
transcript GLYMA06G01280.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G01280.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os12g26060.1 (Oryza sativa), 3'ss of exon 3
gcatgtattagagattatggtttaagatgtgtttgatctgctgtgtaaaataacttgtcttttgtgtgaattcttttctttttcctttggttttgataattattgtgtttactactttggatgtttgctatggaaggggaatatctatttgtaaattttgatagagaatttgacttgatttcttcgattgattgtagAAAGTATTTTGGCGAGGGGTTGTTGAAGAGCTTCTTTGGTTTATCAGTGGCTCAACAAATGCCAAG
                                                                                   | | ||  |||  ||||  |         ||   |  || |||  |          | ||||  |     | |||||| |       |||  || | |||| |  |  |   |||  ||||||||||| || ||| ||||||||||  | ||||| || ||||||||||||||||| |||
---------------------------------------------------------------------------------cccttgtgtatttactaatcctcaaacagcataacatttatttttattt---------attatcc-tggactacttttgaaaag-----tgaaatgttctctttgcctt-taccagAGGGTATTTTGGCGTGGTGTTCTTGAAGAGCTATTGTGGTTCATTAGTGGCTCAACAAATGCAAAG

upper sequence: GLYMA06G01280.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G005990_T01 (Zea mays), 3'ss of exon 4
gcatgtattagagattatggtttaagatgtgtttgatctgctgtgtaaaataacttgtcttttgtgtgaattcttttctttttcctttggttttgataattattgtgtttactactttggatgtttgctatg-gaaggggaatatctatttgtaaatt-ttgatagagaatttgacttgatttcttcgattgattgtagAAAGTATTTTGGCGAGGGGTTGTTGAAGAGCTTCTTTGGTTTATCAGTGGCTCAACAAATGCCAAG
                                                                                               ||    | |         | |||| |    |  |||  |       |||| ||  |   |||| || ||  |       || ||   ||||  |        |||  ||||||||||| || ||||| ||||| || |||||||| |||||||||||||||||||| |||
--------------------------------------------------------------------------------------------ccaatccaaagtccaaaataaagtttgaagaactattatatgttaccatatatttagctaccaattctttattaatggaacaacatgtgctctttaac-------agAGGGTATTTTGGCGTGGTGTTGTCGAAGAACTCCTTTGGTTCATCAGTGGCTCAACAAATGCAAAG

upper sequence: GLYMA06G01280.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G139880_T01 (Zea mays), 3'ss of exon 3
gcatgtattagagattatggtttaagatgtgtttgatctgctgtgtaaaataacttgtcttttgtgtgaattcttttctttttcctttggttttgataattattgtgtttact-actttggatgtttgctatggaaggggaatatctattt--gtaaattttgatagagaatttgacttgatttc-ttcgattgattgtagAAAGTATTTTGGCGAGGGGTTGTTGAAGAGCTTCTTTGGTTTATCAGTGGCTCAACAAATGCCAAG
                                                                                                        ||    ||| |    | | |||||       | || |  || |||||  |||    ||  |    |||   |    ||  | |  | |   |   |||  || |||||||| || ||||| ||||| || |||||||| |||||||||||||||||||| |||
-----------------------------------------------------------------------------------------------------ggagtccaaactcaaaaagaaagtttgaagaattatggtaccatatatttaggtagcacttcttgactaatgcaatacaataacatgtgctctttaacagAGGGTGTTTTGGCGTGGTGTTGTCGAAGAACTCCTTTGGTTCATCAGTGGCTCAACAAATGCAAAG

upper sequence: GLYMA06G01280.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv03s0038g04500.t01 (Vitis vinifera), 3'ss of exon 5
gcatgtattagagattatggtttaagatgtgtttgatctgctgtgtaaaataacttgtcttttgtgtgaattcttttctttttcctttggttttgataattattgtgtttactactttggatgtttgctatggaaggggaatatctatttgtaaattttgatagagaatttgacttgatttcttcgattgatt--gtagAAAGTATTTTGGCGAGGGGTTGTTGAAGAGCTTCTTTGGTTTATCAGTGGCTCAACAAATGCCAAG
| || ||||     ||     | ||||| |  || | |   |   |  | ||  ||||  | |||| | |||   |||  ||||       |||| |  |||||   |  | ||     ||  ||     || ||  ||||||| | ||||| ||||   |||    | || ||    |||  | | ||| ||   |||||||||||||||||||||||||||||||| || || ||||| |||||||||||||||||||| |||
gtatatattt----ttcaaaatgaagatttccttta-caaataattgtattagtttgt--tctgtgggtatttccttccgtttctcagaagtttggtt-ttatttgatgcattatgagtgaaattcaa-gtgaaaaaggaatattt-tttgtcaattc--atatgttagtttacacatttttattgtttgctttgatagAAAGTATTTTGGCGAGGGGTTGTTGAAGAACTGCTGTGGTTCATCAGTGGCTCAACAAATGCTAAG

upper sequence: GLYMA06G01280.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv18s0001g12940.t01 (Vitis vinifera), 3'ss of exon 3
gcatgtattagagattatggtttaagatgtgtttgatctgctgtgtaaaataacttgtcttttgtgtgaattcttttctttttcctttggttttgataattattgtgtttactactttggatgtttgctatggaaggggaatatctatttgtaaattttgatagagaatttgacttgatttcttcgattgattgtagAAAGTATTTTGGCGAGGGGTTGTTGAAGAGCTTCTTTGGTTTATCAGTGGCTCAACAAATGCCAAG
                                                                                    || | | |     ||| ||  |  |   ||  ||  |  |||  |            | |  || | |   || |        |||     | || | ||  | |  ||| ||| |||||||||| |||| ||||||||||||||| | |||||||| ||||| ||||||||||| |||
------------------------------------------------------------------------------------ctctaggtcactaaatgatcttcatctatatattatacatttttttc----------ttttcatctatgctttctaggttgtcattaa---ttatctgtttaaatatttgcagAGAGTATTTTGGAGAGGTGTTGTTGAAGAGCTTTTGTGGTTTATTAGTGGTTCAACAAATGCAAAG

upper sequence: GLYMA06G01280.1 (Glycine max), 3'ss of exon 4
lower sequence: PP1S34_360V6.1 (Physcomitrella patens), 3'ss of exon 3
gcatgtattagagattatggtttaagatgtgtttgatctgctgtgtaaaataacttgtcttttgtgtgaattcttttctttttcctttggttttgataattattgtgtttactactttggatgtttgctatggaaggggaatatctatttgtaaattttgatagagaatttgacttgatttcttcgattgattgtagAAAGTATTTTGGCGAGGGGTTGTTGAAGAGCTTCTTTGGTTTATCAGTGGCTCAACAAATGCCAAG
                                                                                   |   |  |    |||  | |     || ||||     || ||                ||| ||  ||       ||  ||    ||    ||||  |    |  |  | | ||   ||||| ||||| || ||||| || ||||| ||||||||||| ||||| || ||||||||||||
-----------------------------------------------------------------------------------caactattcgatataggtgtgaaactttctaccaactatattctt----------aggtatttacctgcgtgacctggaagtactttgattttgaaat----gggtattggcagCGTGTATTCTGGCGTGGTGTTGTGGAGGAGCTCCTTTGGTTTATTAGTGGGTCTACAAATGCCAAG

upper sequence: GLYMA06G01280.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ36491 (Selaginella moellendorffii), 3'ss of exon 3
gcatgtattagagattatggtttaagatgtgtttgatctgctgtgtaaaataacttgtcttttgtgtgaattcttttctttttcctttggttttgataattattgtgtttactactttggatgtttgctatggaaggggaatatctatttgtaaattttgatagagaatttgacttgatttcttcgattgattgtagAAAGTATTTTGGCGAGGGGTTGTTGAAGAGCTTCTTTGGTTTATCAGTGGCTCAACAAATGCCAAG
                                                                                                                              |  |  ||   | ||  ||| ||   || | | ||     |||        | |||||       ||  ||   || |||||||| || ||||| |||||||| ||||||||||| ||||| || ||||| || |||
------------------------------------------------------------------------------------------------------------------------------gtgagtgagctgaaacttctcttcacaa-tgtcgaggccaaat--------aattcttt------tttcagCGGGTGTTTTGGCGGGGAGTTGTCGAAGAGCTACTTTGGTTTATAAGTGGATCCACAAACGCGAAG

upper sequence: GLYMA06G01280.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ18561 (Selaginella moellendorffii), 3'ss of exon 5
gcatgtattagagattatggtttaagatgtgtttgatctgctgtgtaaaataacttgtcttttgtgtgaattcttttctttttcctttggttttgataattattgtgtttactactttggatgtttgctatggaaggggaatatctatttgtaaattttgatagagaatttgacttgatttcttcgattgattgtagAAAGTATTTTGGCGAGGGGTTGTTGAAGAGCTTCTTTGGTTTATCAGTGGCTCAACAAATGCCAAG
                                                                                                                              |  |  ||   | ||  ||| ||   || | | ||     |||        | |||||       ||  ||   || |||||||| || ||||| |||||||| ||||||||||| ||||| || ||||| || |||
------------------------------------------------------------------------------------------------------------------------------gtgagcgagctgaaacttctcttcacaa-tgtcgaggccaaat--------aattcttt------tttcagCGGGTGTTTTGGCGGGGAGTTGTCGAAGAGCTACTTTGGTTTATAAGTGGATCCACAAACGCGAAG

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|298168442|gb|HO009372.1|HO009372
EST:     ATGAGGTTCAATCTGCGTGGAAACTTTCCTCTTCTAACAACTAAG                         AAAGTATTTTGGCGAGGGGTTGTTGAAGAGCTTCTTTGGTTTATC
genomic: ATGAGGTTCAATCTGCGTGGAAACTTTCCTCTTCTAACAACTAAGgcatgtatta ... ttgattgtagAAAGTATTTTGGCGAGGGGTTGTTGAAGAGCTTCTTTGGTTTATC
EST: gi|192311470|gb|FK005201.1|FK005201
EST:     TCTGCGTGGAAACTTTCCTCTTCTAACAACTAAG                         AAAGTATTTTGGCGAGGGGTTGTTGAAGAGCTTCTTTGGTTTATCAGTGGC
genomic: TCTGCGTGGAAACTTTCCTCTTCTAACAACTAAGgcatgtatta ... ttgattgtagAAAGTATTTTGGCGAGGGGTTGTTGAAGAGCTTCTTTGGTTTATCAGTGGC
EST: gi|192311469|gb|FK005200.1|FK005200
EST:     TCTGCGTGGAAACTTTCCTCTTCTAACAACTAAG                         AAAGTATTTTGGCGAGGGGTTGTTGAAGAGCTTCTTTGGTTTATCAGTGGC
genomic: TCTGCGTGGAAACTTTCCTCTTCTAACAACTAAGgcatgtatta ... ttgattgtagAAAGTATTTTGGCGAGGGGTTGTTGAAGAGCTTCTTTGGTTTATCAGTGGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atctatttgtaaattttgatagagaatttgacttgatttcttcgattgattgtagAAAGTATTTTGGCGAGGGGTTGTTGAAGAGCTTCTTTGGTTTATCAGTGGCTCAACAAATGCCAAG
                                           gattgat  putative branch site (score: 4)
     tttgtaaattttgata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcatgtattagagattatggtttaagatgtgtttgatctgctgtgtaaaataacttgtcttttgtgtgaattcttttctttttcctttggttttgataattattgtgtttactactttggatgtttgctatggaaggggaatatctatttgtaaattttgatagagaatttgacttgatttcttcgattgattgtagAAAGTATTTTGGCGAGGGGTTGTTGAAGAGCTTCTTTGGTTTATCAGTGGCTCAACAAATGCCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT