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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAGAGAGCATCCAAAATCCGTAAACTGTTCAACCTGTCCAAGGAGGATGATGTTAGGAAGTATGTCAACACCTACCGTCGTACATTTACGACAAAAGCTGgtaaaattccatgtgcttttatgttgagtttaattttgtaattgactgattgattaaagaatttgtctaaaaaagaccaaagggttttggtaaaacgtgt...

Basic information

species Glycine max
transcript GLYMA18G26190.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G26190.1 (Glycine max), 5'ss of exon 4
lower sequence: LOC_Os07g42950.1 (Oryza sativa), 5'ss of exon 5
AAGAGAGCATCCAAAATCCGTAAACTGTTCAACCTGTCCAAGGAGGATGATGTTAGGAAGTATGTCAACACCTACCGTCGTACATTTACGACAAAAGCTGgtaaaattccatg---tgcttttatgttgagtttaattttgtaattgactgattgattaaagaatttgtctaaaaaagaccaaagggttttggtaaaacgtgt
||||| || ||||| ||| | || || |||||||| |||||||| ||||||||  | || |||||||||||||||||  | ||||| || || ||   |||| |  || | ||   || ||     |  |  | | || |   ||   ||| |        | |||  ||| |  |       |   || |  |  |      
AAGAGGGCCTCCAAGATCAGGAAGCTCTTCAACCTTTCCAAGGATGATGATGTCCGCAAATATGTCAACACCTACCGCAGGACATTCACTACCAAGAATGgtgagctttcctgcaatgtttaataatctacctcatttctagtatgtcctgctcctgatctgcattgatcttagtactgttttaattttcttatggataa---

upper sequence: GLYMA18G26190.1 (Glycine max), 5'ss of exon 4
lower sequence: AT4G31700.1 (Arabidopsis thaliana), 5'ss of exon 5
AAGAGAGCATCCAAAATCCGTAAACTGTTCAACCTGTCCAAGGAGGATGATGTTAGGAAGTATGTCAACACCTACCGTCGTACATTTACGACAAAAGCTGgtaaaattccatgtgcttttatgttgagtttaattttgtaattgactgattgattaaagaatttgtctaaaaaagaccaaagggttttggtaaaacgtgt-----
|||||||| ||||| |||||||||||||| |||||    ||||| |||||||| ||||  ||||||||||| ||||| || |  || || |  ||    ||| | |  |  ||  |||    |   | |     ||| | | | ||   ||||  ||  |  || ||| ||    ||       || || |   |  | |     
AAGAGAGCCTCCAAGATCCGTAAACTGTTTAACCTCAAGAAGGAAGATGATGTCAGGACCTATGTCAACACTTACCGCCGCAAGTTCACAAACAAGAAGGgtgagacac--tgaactt----gagaaatagtggtttctgaatcac-acttgagaaataatgttttctgaa----acttgtttcttctgtttggatttttgacag

upper sequence: GLYMA18G26190.1 (Glycine max), 5'ss of exon 4
lower sequence: Vv03s0017g01350.t01 (Vitis vinifera), 5'ss of exon 5
AAGAGAGCATCCAAAATCCGTAAACTGTTCAACCTGTCCAAGGAGGATGATGTTAGGAAGTATGTCAACACCTACCGTCGTACATTTACGACAAAAGCTGgtaaaattcc--atgtgcttttatgttga-gtttaattttgtaa-ttgactgattgattaaagaatttgtctaaaaaagaccaaagggttttggtaaaacgtgt
|||||||| || || || || || || |||||||| || ||||||||||||||| |||||||||||||||| || ||||| || || || |||||| |||||| ||||||  || |  | |  | || |  |||| ||||  || || |    |  |   || || |||| |||   |    ||    ||     |   | |  
AAGAGAGCTTCTAAGATTCGAAAGCTCTTCAACCTCTCTAAGGAGGATGATGTTCGGAAGTATGTCAACACATATCGTCGAACCTTCACAACAAAATCTGgtacaattcctgatttcttatctttttaatatttacttttagaagtttataagtgaagggaacaaattgtataatttaatttaa----ttcctacattgctttc

upper sequence: GLYMA18G26190.1 (Glycine max), 5'ss of exon 4
lower sequence: Vv07s0191g00060.t01 (Vitis vinifera), 5'ss of exon 5
AAGAGAGCATCCAAAATCCGTAAACTGTTCAACCTGTCCAAGGAGGATGATGTTAGGAAGTATGTCAACACCTACCGTCGTACATTTACGACAAAAGCTGgtaaa-attccatgtgcttttatgttgag---tttaattttgtaattgac-tgattgattaaagaatttgtctaaaaaagaccaaagggttttggtaaaacgtgt
||||| || || || || || || || || ||||| || ||||||||||||||| |||||||||| ||||| || || || || ||||| || ||| |||||     ||| |  | ||||| || || |   | | || |  | | |||| | ||| | ||||||  |    |       | |   | |  | || |        
AAGAGGGCCTCAAAGATTCGAAAGCTTTTTAACCTCTCGAAGGAGGATGATGTTCGGAAGTATGTGAACACTTATCGCCGAACTTTTACTACTAAATCTGgttggtgttctaatttcttttttgatgggaaatatgatatgtttactgacattatttactaaagatgtatgattggtcttatctgtgtgcct-ggcag-------

upper sequence: GLYMA18G26190.1 (Glycine max), 5'ss of exon 4
lower sequence: Vv18s0001g06290.t01 (Vitis vinifera), 5'ss of exon 5
AAGAGAGCATCCAAAATCCGTAAACTGTTCAACCTGTCCAAGGAGGATGATGTTAGGAAGTATGTCAACACCTACCGTCGTACATTTACGACAAAAGCTGgtaaaattccatgtgcttttatgttgagtttaattttgtaattgactgattga--ttaaagaatttgtctaaaaaagaccaaagggttttggtaaaacgtgt
||||| ||||| || || || ||||| |||||||| || ||||| ||||||||  | |||||||||||||| |||||  |  |||| || || ||| ||||||   ||     |  | |    || | | |  ||  ||| |  | |     |  ||||| || | |  |   |      |||| || ||  | |    |  
AAGAGGGCATCAAAGATTCGCAAACTCTTCAACCTCTCAAAGGATGATGATGTCCGAAAGTATGTCAACACATACCGCAGATCATTCACAACCAAATCTGgtaggttttttaattttatgtctttcaatatgtttaagtactgaagtagcctacattaaaaaagtgggatgctattt-taaaagagtattcttgatgtttt-

upper sequence: GLYMA18G26190.1 (Glycine max), 5'ss of exon 4
lower sequence: PP1S3195_1V6.1 (Physcomitrella patens), 5'ss of exon 2
AAGAGAGCATCCAAAATCCGTAAACTGTTCAACCTGTCCAAGGAGGATGATGTTAGGAAGTATGTCAACACCTACCGTCGTACATTTACGACAAAAGCTGgtaaaattccatgtgcttttatgttga-gtttaattttgtaattgactgattgattaaagaatttgtctaaaaaagaccaaagggttttggtaaaacgtgt--------------------------
||||||||  ||||||| || || || ||||| ||  |||||||||||||||| ||||| || ||||||||||| ||||| |  |||    |     | |||| | |  ||||     | |||| |  ||   ||||||  ||       ||  |  |        | || |   |     |  |||  |   |  | | |                          
AAGAGAGCCACCAAAATTCGCAAGCTCTTCAATCTCACCAAGGAGGATGATGTGAGGAAATACGTCAACACCTATCGTCGCAGCTTTGTATCGGCCACAGgtacagt--catggctcctgatgtgggtgtcgtattttgccatgcttcctttcgtgcagtcgccgatgtagagcgggggccattgttgcgaggagccctctactgacgtctgcgtgcgtgctttcag

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|9899141|gb|BE608168.1|BE608168
EST:     TGTTAGGAAGTATGTCAACACCTACCGTCGTACATTTACGACAAAAGCTG                         GGAAAAAGGTGAGCAAAGCTCCTAAGATACAAAGACTGGTCACCCCTCTTA
genomic: TGTTAGGAAGTATGTCAACACCTACCGTCGTACATTTACGACAAAAGCTGgtaaaattcc ... ttgattacagGGAAAAAGGTGAGCAAAGCTCCTAAGATACAAAGACTGGTCACCCCTCTTA
EST: gi|209699698|gb|BW652083.1|BW652083
EST:     TGTTAGGAAGTATGTCAACACCTACCGTCGTACATTTACGACAAAAGCTG                         GGAAAAAGGTGAGCAAAGCTCCTAAGATACAAAGACTGGTCACCCCTCTTA
genomic: TGTTAGGAAGTATGTCAACACCTACCGTCGTACATTTACGACAAAAGCTGgtaaaattcc ... ttgattacagGGAAAAAGGTGAGCAAAGCTCCTAAGATACAAAGACTGGTCACCCCTCTTA
EST: gi|6482119|gb|AW201390.1|AW201390
EST:     TGTTAGGAAGTATGTCAACACCTACCGTCGTACATTTACGACAAAAGCTG                         GGAAAAAGGTGAGCAAAGCTNCTAAGATACAAAGACTGGTCACCCCTCTTA
genomic: TGTTAGGAAGTATGTCAACACCTACCGTCGTACATTTACGACAAAAGCTGgtaaaattcc ... ttgattacagGGAAAAAGGTGAGCAAAGCTCCTAAGATACAAAGACTGGTCACCCCTCTTA
EST: gi|10846028|gb|BF069017.1|BF069017
EST:     TGTTAGGAAGTATGTCAACACCTACCGTCGTACATTTACGACAAAAGCTG                         GGAAAAAGGTGAGCAAAGCTCCTAAGATACAAAGACTGGTCACCCCTCTTA
genomic: TGTTAGGAAGTATGTCAACACCTACCGTCGTACATTTACGACAAAAGCTGgtaaaattcc ... ttgattacagGGAAAAAGGTGAGCAAAGCTCCTAAGATACAAAGACTGGTCACCCCTCTTA
EST: gi|192321667|gb|FK014011.1|FK014011
EST:     TGTTAGGAAGTATGTCAACACCTACCGTCGTACATTTACGACAAAAGCTG                         GGAAAAAGGTGAGCAAAGCTCCCAAGATACAAAGACTGGTC
genomic: TGTTAGGAAGTATGTCAACACCTACCGTCGTACATTTACGACAAAAGCTGgtaaaattcc ... ttgattacagGGAAAAAGGTGAGCAAAGCTCCTAAGATACAAAGACTGGTC
EST: gi|19053288|gb|BM731955.1|BM731955
EST:     TGTTAGGAAGTATGTCAACACCTACCGTCGTACATTTACGACAAAAGCTG                         GGAAAAAGGTGAGCAAAGCTCCTAAGATACAAAGACTGGTCACCCCTCTTA
genomic: TGTTAGGAAGTATGTCAACACCTACCGTCGTACATTTACGACAAAAGCTGgtaaaattcc ... ttgattacagGGAAAAAGGTGAGCAAAGCTCCTAAGATACAAAGACTGGTCACCCCTCTTA
EST: gi|192296729|gb|FG991297.1|FG991297
EST:     TGTTAGGAAGTATGTCAACACCTACCGTCGTACATTTACGACAAAAGCTG                         GGAAAAAGGTGAGCAAAGCTCCTAAGATACAA-GACTGGTCA
genomic: TGTTAGGAAGTATGTCAACACCTACCGTCGTACATTTACGACAAAAGCTGgtaaaattcc ... ttgattacagGGAAAAAGGTGAGCAAAGCTCCTAAGATACAAAGACTGGTCA
EST: gi|298187174|gb|HO034323.1|HO034323
EST:     TGTTAGGAAGTATGTCAACACCTACCGTCGTACATTTACGACAAAAGCTG                         GGAAAAAGGTGAGCAAAGCTCCTAAGATACAAAGACTGGTCACCCCTCTTA
genomic: TGTTAGGAAGTATGTCAACACCTACCGTCGTACATTTACGACAAAAGCTGgtaaaattcc ... ttgattacagGGAAAAAGGTGAGCAAAGCTCCTAAGATACAAAGACTGGTCACCCCTCTTA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAGAGAGCATCCAAAATCCGTAAACTGTTCAACCTGTCCAAGGAGGATGATGTTAGGAAGTATGTCAACACCTACCGTCGTACATTTACGACAAAAGCTGgtaaaattccatgtgcttttatgttgagtttaattttgtaattgactgattgattaaagaatttgtctaaaaaagaccaaagggttttggtaaaacgtgt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaaaaga