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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtagctgctgatgtatttatcatttacattatctagtttacaggactgcatctcattgtgctatcactgttatataaatgcagGTTTGTTGAGATTATGGCTCCAGTGTTCTCAAGAGATGCATGGCGCTGTGTGTGGCATATGATTCAG

Basic information

species Glycine max
transcript GLYMA18G01710.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G01710.1 (Glycine max), 3'ss of exon 10
lower sequence: GRMZM2G162881_T01 (Zea mays), 3'ss of exon 3
gtaagtagctgctgatgtatttatcatttacattatctagtttacaggactgcatctcattgtgctatcactgttatataa-atgcagGTTTGTTGAGATTATGGCTCCAGTGTTCTCAAGAGATGCATGGCGCTGTGTGTGGCATATGATTCAG
         |     || | | ||   ||| ||||| |  ||  |   | | |   |  |           ||| || | | ||||||||||||||| || |||||  | || |||||||| ||||||||||||||||| |||||||||||||||
--------gtaggagtgcaatcatttattagattattttcttatcgaaatttctgtttttcaca-------tgtaatctgatatgcagGTTTGTTGAAATAATGGCAACTGTATTCTCAAGGGATGCATGGCGCTGTGTATGGCATATGATTCAG

upper sequence: GLYMA18G01710.1 (Glycine max), 3'ss of exon 10
lower sequence: AT1G24570.1 (Arabidopsis thaliana), 3'ss of exon 9
gtaagtagctgctgatgtatttatca--tttacattatctagtttacaggactgcatctcattgtgctatcactgttatataaatgcagGTTTGTTGAGATTATGGCTCCAGTGTTCTCAAGAGATGCATGGCGCTGTGTGTGGCATATGATTCAG
||| ||  |     | || | |||||   | |  ||    |  |      ||      | | |  | |||  || | ||| |||  ||| || || ||||| |||||||| || ||||||||||||||||||||||| |||||||||||||| |||
gtatgtttcaaaaaacgtctctatcaaactcaagtttcagacatatttaaaccattagtaacttcgttatgtctttaataaaaaaacagATTCGTGGAGATAATGGCTCCTGTATTCTCAAGAGATGCATGGCGCTGCGTGTGGCATATGATCCAG

upper sequence: GLYMA18G01710.1 (Glycine max), 3'ss of exon 10
lower sequence: AT3G26440.4 (Arabidopsis thaliana), 3'ss of exon 10
gtaagtagctgctgatgtatttatcatttacattatctagtttacaggactgcatctcattgtgctat-cactgttatataaatgcagGTTTGTTGAGATTATGGCTCCAGTGTTCTCAAGAGATGCATGGCGCTGTGTGTGGCATATGATTCAG---------------------------------
||| | | ||  |  |||    | || | ||| ||  || || | |           ||||  | | | ||| |||   ||    ||||||| | ||||||||||||||||| ||||| ||||| |||||||| |||||||||||||||||||||                                 
gtatggatctcatt-tgtcaaaaccaat-acaataagta-ttcatactctcttgatccattaagttttgcacggttccttat---cagGTTTATAGAGATTATGGCTCCAGTTTTCTCTAGAGAGGCATGGCGTTGTGTGTGGCATATGATTCAGAATGACTTGGTTCACGGTTGGGGTCTTGACTTT

upper sequence: GLYMA18G01710.1 (Glycine max), 3'ss of exon 10
lower sequence: AT1G13000.2 (Arabidopsis thaliana), 3'ss of exon 10
gtaagtagctgctgatgtatttatcatttacattatctagtttacaggactgcatctcattgtgctatcactgttatataaatgcagGTTTGTTGAGATTATGGCTCCAGTGTTCTCAAGAGATGCATGGCGCTGTGTGTGGCATATGATTCAG---------------------------------
||| ||||   |  ||||     ||||| |||      |    | ||  ||  |    | | |    ||  ||| ||||   | ||||||| | ||||||||||||||||| |||||||||||||||||||| || ||||||||||||||||||                                 
gtacgtagtctcaaatgt-----tcatt-aca------aaaacatagatctatacagtactcttgattccatgtaatattcttacagGTTTATAGAGATTATGGCTCCAGTATTCTCAAGAGATGCATGGCGTTGCGTGTGGCATATGATTCAGAACGATTTGGTTCACGGTTGGGGTCTTGATTTC

upper sequence: GLYMA18G01710.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv00s0187g00030.t01 (Vitis vinifera), 3'ss of exon 5
gtaagtag--ctgctgatgtattta----tcatttacattatc---tagttt-aca--ggactgcatctcattgtgcta-tcactgttatataaatgcagGTTTGTTGAGATTATGGCTCCAGTGTTCTCAAGAGATGCATGGCGCTGTGTGTGGCATATGATTCAG
 | || ||  ||| || | | |||     |||||  || |      | || | |||  ||| |  |    |   |  || |     || |  |||||||||||||||||||| |||||||| || || || |||||||||||||| ||||||||||||||| |||||
ttgagcagtactgttgttattttttctgttcattcccactcctgcatggtctgacaatggattagaaacaaaattattagttttccttttccaaatgcagGTTTGTTGAGATCATGGCTCCTGTATTTTCTAGAGATGCATGGCGGTGTGTGTGGCATATGCTTCAG

upper sequence: GLYMA18G01710.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv13s0106g00570.t01 (Vitis vinifera), 3'ss of exon 1
------------gtaagtag--ctgctgatgtattta----tcatttacattatc---tagttt-aca--ggactgcatctcattgtgcta-tcactgttatataaatgcagGTTTGTTGAGATTATGGCTCCAGTGTTCTCAAGAGATGCATGGCGCTGTGTGTGGCATATGATTCAG
             | || |   ||  || | | |||     |||||  || |      | || | |||  ||| |  |    |   |  || |     || |  |||||||||||||||||||| |||||||| || || || |||||||||||||| ||||||||||||||| |||||
gtatgaaaagctttgagcaatactattgttattttttctgttcattcccactcctgcatggtctgacaatggattagaaacaaaattattagttttccttttccaaatgcagGTTTGTTGAGATCATGGCTCCTGTATTTTCTAGAGATGCATGGCGGTGTGTGTGGCATATGCTTCAG

upper sequence: GLYMA18G01710.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv01s0137g00770.t01 (Vitis vinifera), 3'ss of exon 10
------------gtaagtag--ctgctgatgtattta----tcatttacattatc---tagttt-aca--ggactgcatctcattgtgcta-tcactgttatataaatgcagGTTTGTTGAGATTATGGCTCCAGTGTTCTCAAGAGATGCATGGCGCTGTGTGTGGCATATGATTCAG
             | || ||  ||  || | | |||     |||||  || |      | || | |||  ||| |  |    |   |  || |   | || |  |||||||||||||||||||| |||||||| || || || |||||||||||||| ||||||||||||||| |||||
gtatgaaaagctttgagcagtactattgttattttttgtgttcattcccactcctgcatggtctgacaatggattagaaacaaaattattagtttttcttttccaaatgcagGTTTGTTGAGATCATGGCTCCTGTATTTTCTAGAGATGCATGGCGGTGTGTGTGGCATATGCTTCAG

upper sequence: GLYMA18G01710.1 (Glycine max), 3'ss of exon 10
lower sequence: EFJ04271 (Selaginella moellendorffii), 3'ss of exon 5
gtaagtagctgctgatgtatttatcatttacattatctagtttacaggactgcatctcattgtg-ctatcactgttatataaatgcagGTTTGTTGAGATTATGGCTCCAGTGTTCTCAAGAGATGCATGGCGCTGTGTGTGGCATATGATTCAG---------------------------------
                |||  | |  | |  | | |||| ||  |     ||| |||   | |  |||||    | |  |   | ||| ||||| ||||| ||||||||||| || ||  |  | || ||||||||||||||||||||||||||                                  
----------------gtaagttttgtgtttagtttctatttatcttccttgcttctagctatttctatcgac-tgagtttgctacagATTTGTGGAGATCATGGCTCCAGTTTTTTCGCGCAAGGCCTGGCGCTGTGTGTGGCATATGATTCAAAATGACTTGGTGCATGGCTGGGGACTAGACTTT

upper sequence: GLYMA18G01710.1 (Glycine max), 3'ss of exon 10
lower sequence: EFJ32148 (Selaginella moellendorffii), 3'ss of exon 6
gtaagtagctgctgatgtatttatcatttacattatctagtttacaggactgcatctcattgtg-ctatcactgttatataaatgcagGTTTGTTGAGATTATGGCTCCAGTGTTCTCAAGAGATGCATGGCGCTGTGTGTGGCATATGATTCAG---------------------------------
                |||  | |  | |  | | |||| ||  |   | ||| |||   | |  |||||    | |  |   | ||| ||||| ||||| ||||||||||| || ||  |  | || ||||||||||||||||||||||||||                                  
----------------gtaagttttgtgtttagtttctatttatcttcattgcttctagctatttctatcgac-tgagtttgctacagATTTGTGGAGATCATGGCTCCAGTTTTTTCGCGCAAGGCCTGGCGCTGTGTGTGGCATATGATTCAAAATGACTTGGTGCATGGCTGGGGACTAGACTTT

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|15661819|gb|BI699190.1|BI699190
EST:     GAGGAAAAACCAGGATGGTGTTCTGACCCTCATTTGCCTCCTTGTGCAGC                         GTTTGTTGAGATTATGGCTCCAGTGTTCTCAAGAGATGCATGGCGCTGTGT
genomic: GAGGAAAAACCAGGATGGTGTTCTGACCCTCATTTGCCTCCTTGTGCAGCgtaagtagct ... ataaatgcagGTTTGTTGAGATTATGGCTCCAGTGTTCTCAAGAGATGCATGGCGCTGTGT
EST: gi|192319061|gb|FK010625.1|FK010625
EST:     GAGGAAAAACCAGGATGGTGTTCTGACCCTCATTTGCCTCCTTGTGCAGC                         GTTTGTTGAGATTATGGCTCCAGTGTTCTCAAGAGATGCATGGCGCTGTGT
genomic: GAGGAAAAACCAGGATGGTGTTCTGACCCTCATTTGCCTCCTTGTGCAGCgtaagtagct ... ataaatgcagGTTTGTTGAGATTATGGCTCCAGTGTTCTCAAGAGATGCATGGCGCTGTGT
EST: gi|193670535|gb|FK609045.1|FK609045
EST:     GGAAAAAACCAAGGATGGTGTTCTGACCCTCATTTGCCTCCTTGTGCAGC                         GTTTGTTGAGATTATGGCTCCAGTGTTCTCAAGAGATGCATGGCGCTGTGT
genomic: GG-AAAAACC-AGGATGGTGTTCTGACCCTCATTTGCCTCCTTGTGCAGCgtaagtagct ... ataaatgcagGTTTGTTGAGATTATGGCTCCAGTGTTCTCAAGAGATGCATGGCGCTGTGT
EST: gi|192319062|gb|FK010626.1|FK010626
EST:     GAGGAAAAACCAGGATGGTGTTCTGACCCTCATTTGCCTCCTTGTGCAGC                         GTTTGTTGAGATTATGGCTCCAGTGTTCTCAAGAGATGCATGGCGCTGTGT
genomic: GAGGAAAAACCAGGATGGTGTTCTGACCCTCATTTGCCTCCTTGTGCAGCgtaagtagct ... ataaatgcagGTTTGTTGAGATTATGGCTCCAGTGTTCTCAAGAGATGCATGGCGCTGTGT
EST: gi|193622076|gb|FK568122.1|FK568122
EST:     GAGGAAAAACCAGGATGGTGTTCTGACCCTCATTTGCCTCCTTGTGCAGC                         GTTTGTTGAGATTATGGCTCCAGTGTTCTCAAGAGATGCATGGCGCTGTGT
genomic: GAGGAAAAACCAGGATGGTGTTCTGACCCTCATTTGCCTCCTTGTGCAGCgtaagtagct ... ataaatgcagGTTTGTTGAGATTATGGCTCCAGTGTTCTCAAGAGATGCATGGCGCTGTGT
EST: gi|254347136|gb|GR856806.1|GR856806
EST:     GAGGAAAAACCAGGATGGTGTTCTGACCCTCATTTGCCTCCTTGTGCAGC                         GTTTGTTGAGATTATGGCTCCAGTGTTCTCAAGAGATGCATGGCGCTGTGT
genomic: GAGGAAAAACCAGGATGGTGTTCTGACCCTCATTTGCCTCCTTGTGCAGCgtaagtagct ... ataaatgcagGTTTGTTGAGATTATGGCTCCAGTGTTCTCAAGAGATGCATGGCGCTGTGT
EST: gi|208265459|gb|GE062651.1|GE062651
EST:     GAGGAAAAACCAGGATGGTGTTCTGACCCTCATTTGCCTCCTTGTGCAGC                         GTTTGTTGAGATTATGGCTCCAGTGTTCTCAAGAGATGCATGGCGCTGTGT
genomic: GAGGAAAAACCAGGATGGTGTTCTGACCCTCATTTGCCTCCTTGTGCAGCgtaagtagct ... ataaatgcagGTTTGTTGAGATTATGGCTCCAGTGTTCTCAAGAGATGCATGGCGCTGTGT
EST: gi|192302164|gb|FG995816.1|FG995816
EST:     CCCTCATTTGCCTCCTTGTGCAGC                         GTTTGTTGAGATTATGGCTCCAGTGTTCTCAAGAGATGCATGGCGCTGTGT
genomic: CCCTCATTTGCCTCCTTGTGCAGCgtaagtagct ... ataaatgcagGTTTGTTGAGATTATGGCTCCAGTGTTCTCAAGAGATGCATGGCGCTGTGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttatctagtttacaggactgcatctcattgtgctatcactgttatataaatgcagGTTTGTTGAGATTATGGCTCCAGTGTTCTCAAGAGATGCATGGCGCTGTGTGTGGCATATGATTCAG
                                     actgttatataaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtagctgctgatgtatttatcatttacattatctagtttacaggactgcatctcattgtgctatcactgttatataaatgcagGTTTGTTGAGATTATGGCTCCAGTGTTCTCAAGAGATGCATGGCGCTGTGTGTGGCATATGATTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG