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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatgtcatcattaacatatagtcagctttagttttatttatttaattctaaaaagatataatgtttatctctgttgataacattacatatacagGAACTTGGAGAGTTGGAGGTGTTCTTGCTGTTTCTCGTGCATTTGGTGATAGACTCCTGAAGCAGTATGTTGTTGCTGATCCAGAAATTCAG

Basic information

species Glycine max
transcript GLYMA04G06250.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G06250.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os02g05630.1 (Oryza sativa), 3'ss of exon 5
gtaatgtcatcattaacatatagtcagctttagttttatttatttaattctaaaaagatataatgtttatctctgttgataacattacatatacagGAACTTGGAGAGTTGGAGGTGTTCTTGCTGTTTCTCGTGCATTTGGTGATAGACTCCTGAAGCAGTATGTTGTTGCTGATCCAGAAATTCAG
||||| |||| |||    |  | | | ||    ||||  || | || || |||  |     | || || | |||   | |   |  || | | |||| || ||| | ||||| |||||||||||||||||||| |||||||||||||  ||  ||||||||||||| |||||||||||||| ||  ||
gtaatttcatgattcctttgaaattatct---attttgctt-tgtacttgtaatgat---cattggttctttctaacggttgaacgactt-tgcagGGACGTGGCGTGTTGGTGGTGTTCTTGCTGTTTCTCGAGCATTTGGTGATAAGCTATTGAAGCAGTATGTAGTTGCTGATCCAGAGATCAAG

upper sequence: GLYMA04G06250.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os02g05630.3 (Oryza sativa), 3'ss of exon 5
gtaatgtcatcattaacatatagtcagctttagttttatttatttaattctaaaaagatataatgtttatctctgttgataacattacatatacagGAACTTGGAGAGTTGGAGGTGTTCTTGCTGTTTCTCGTGCATTTGGTGATAGACTCCTGAAGCAGTATGTTGTTGCTGATCCAGAAATTCAG--------
||||| |||| |||    |  | | | ||    ||||  || | || || |||  |     | || || | |||   | |   |  || | | |||| || ||| | ||||| |||||||||||||||||||| |||||||||||||  ||  ||||||||||||| |||||||||||||| ||  ||        
gtaatttcatgattcctttgaaattatct---attttgctt-tgtacttgtaatgat---cattggttctttctaacggttgaacgactt-tgcagGGACGTGGCGTGTTGGTGGTGTTCTTGCTGTTTCTCGAGCATTTGGTGATAAGCTATTGAAGCAGTATGTAGTTGCTGATCCAGAGATCAAGGTTTGACT

upper sequence: GLYMA04G06250.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os06g48300.1 (Oryza sativa), 3'ss of exon 5
-----------------------gtaatgtcatcatta-acatatagtcagctttagttttatttatttaattctaaaaagatataa-tgtttat-ctctgttgataacattacatatacagGAACTTGGAGAGTTGGAGGTGTTCTTGCTGTTTCTCGTGCATTTGGTGATAGACTCCTGAAGCAGTATGTTGTTGCTGATCCAGAAATTCAG
                        |  ||       || |  ||   |    ||     ||    |   | | || ||   ||| || || | |   |||||||     | |   | |  |||||| ||| | || || |||||||||||||| ||||| ||||||||||| | |||||||||||| ||||| |||||||||||||| ||  ||
gtatttcaactcttgatctattcattgtgctgatgctacatttaccctttttttcgacattgaacaccaagtccttaatctataaaaatgctaaaattctgttggcggaaat---tttgtagGAACATGGCGCGTGGGTGGTGTTCTTGCTGTCTCTCGAGCATTTGGTGACAAACTCCTGAAGCAATATGTGGTTGCTGATCCAGAGATCAAG

upper sequence: GLYMA04G06250.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os04g56450.2 (Oryza sativa), 3'ss of exon 5
gtaatgtcatcattaacatatagtcagctttagttttatttatttaat-tctaaaaaga-tataatgtttatctctgttgataacattacatatac-agGAACTTGGAGAGTTGGAGGTGTTCTTGCTGTTTCTCGTGCATTTGGTGATAGACTCCTGAAGCAGTATGTTGTTGCTGATCCAGAAATTCAG
                    |  | |||  ||  ||   ||||||  | | | ||  || ||| ||   | |  ||  ||||   |||   |     |||||| ||| | ||||| ||||| |||||||||||||| || |||||||| | |||| | ||||||||||| ||||  ||||| || |||| |
-------------------gtgctaagcactacattatcttattttgtatatgaatggactatgat-cgtgttcctaatgatggtattttgttccttagGAACATGGCGTGTTGGTGGTGTGCTTGCTGTTTCTCGCGCTTTTGGTGACAAACTCTTAAAGCAGTATGTAGTTGTGGATCCTGAGATTCGG

upper sequence: GLYMA04G06250.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM5G829894_T02 (Zea mays), 3'ss of exon 3
gtaatgtcatcattaaca-tatagtcagctttagttttatttatttaattctaaaaagata-taatgtttatctctgttgataacattacatatacagGAACTTGGAGAGTTGGAGGTGTTCTTGCTGTTTCTCGTGCATTTGGTGATAGACTCCTGAAGCAGTATGTTGTTGCTGATCCAGAAATTCAG
||| ||    |  | |   |||    |     |   |   |||| | | | |       || |  || || |     |||||      | || |  ||| || ||| |||| || |||||||||||||| ||||| ||||||||||||| |||| |||||||||||||||| ||||| || |||||  ||
gtagtgattcctctgattctatctataaaaagaaactatcttatcttaatatgtgccattactgttgcttctactgcttgatttttcgaaatttgtagGGACATGGCGAGTGGGTGGTGTTCTTGCTGTCTCTCGCGCATTTGGTGATAAACTCTTGAAGCAGTATGTTGTCGCTGACCCTGAAATCAAG

upper sequence: GLYMA04G06250.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G166035_T02 (Zea mays), 3'ss of exon 5
gtaatgtcatcattaacatatagtcagctttagttttatttatttaattctaaaaagata-taatgtttatctctgttgataacattacatatacagGAACTTGGAGAGTTGGAGGTGTTCTTGCTGTTTCTCGTGCATTTGGTGATAGACTCCTGAAGCAGTATGTTGTTGCTGATCCAGAAATTCAG
||||||    |  | |  | |                || ||| | | |       | || |  | ||| |     ||||| |    | || |  ||| || |||||||| || || ||||| ||||| ||||| ||||||||||||| |||| |||||| ||||||||||||||| || |||||  ||
gtaatggttcctctgaatttttcaataaaaagaaaccatctatctcagtacgtgccgttactgttatttgtactgtttgattattcgaaatctgtagGGACATGGAGAGTGGGTGGCGTTCTCGCTGTCTCTCGAGCATTTGGTGATAAACTCTTGAAGCCGTATGTTGTTGCTGACCCTGAAATCAAG

upper sequence: GLYMA04G06250.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G056572_T02 (Zea mays), 3'ss of exon 5
gtaatgtcatcattaacatatagtcagctttagttttatttatttaatt--ctaaaaagatataatgtttatctctgttgataacattacata-tacagGAACTTGGAGAGTTGGAGGTGTTCTTGCTGTTTCTCGTGCATTTGGTGATAGACTCCTGAAGCAGTATGTTGTTGCTGATCCAGAAATTCAG
                  |||    | |  |  ||||  |||   | ||   |      |||| || | |   |||  ||   |   |   |  || |||||| ||| | ||||| ||||| ||||||||||| ||||| |||||||| | |||| | ||||| ||||| ||||  ||||| || || |  
-----------------gtatgccaatcacttttttttcttaaaaagtttcttggtggaatatgat-tatccttctaatgcccatgctttgttctatagGAACATGGCGCGTTGGTGGTGTACTTGCTGTTTCGCGTGCTTTTGGTGACAAACTCTTAAAGCAATATGTGGTTGTGGATCCGGAGATCCGA

upper sequence: GLYMA04G06250.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G056572_T05 (Zea mays), 3'ss of exon 5
gtaatgtcatcattaacatatagtcagctttagttttatttatttaattc--taaaaagatataatgtttatctctgttgataacattacata-tacagGAACTTGGAGAGTTGGAGGTGTTCTTGCTGTTTCTCGTGCATTTGGTGATAGACTCCTGAAGCAGTATGTTGTTGCTGATCCAGAAATTCAG--------
                  |||    | |  |  ||||  |||   | ||   |      |||| || | |   |||  ||   |   |   |  || |||||| ||| | ||||| ||||| ||||||||||| ||||| |||||||| | |||| | ||||| ||||| ||||  ||||| || || |          
-----------------gtatgccaatcacttttttttcttaaaaagtttcttggtggaatatgat-tatccttctaatgcccatgctttgttctatagGAACATGGCGCGTTGGTGGTGTACTTGCTGTTTCGCGTGCTTTTGGTGACAAACTCTTAAAGCAATATGTGGTTGTGGATCCGGAGATCCGAGTACGTAA

upper sequence: GLYMA04G06250.1 (Glycine max), 3'ss of exon 6
lower sequence: AT4G31750.1 (Arabidopsis thaliana), 3'ss of exon 6
gtaatgtcatcattaacatatagtcagctttagttttatttatttaattctaaaaagatataatgtttatctctgttgataacattacatatacagGAACTTGGAGAGTTGGAGGTGTTCTTGCTGTTTCTCGTGCATTTGGTGATAGACTCCTGAAGCAGTATGTTGTTGCTGATCCAGAAATTCAG
            | |  | | | | | ||  | |||   ||  ||| || |    | |||   || |||  |           |||| |   | |||||| |||||||||||||| |||||||||||||||||||||||||| |||||  |  ||||||||||||||||||||||||| || || |||
-----------gtaagaaaacatttaactgaaatttctctt-cttatttgtgcttatataatttgcttaatt--------ggaattatactaaaagGAACATGGAGAGTTGGAGGAGTTCTTGCTGTTTCTCGTGCATTTGGCGATAGGTTGTTGAAGCAGTATGTTGTTGCTGATCCGGAGATACAG

upper sequence: GLYMA04G06250.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv04s0008g07320.t01 (Vitis vinifera), 3'ss of exon 6
gtaatgtcatcattaacatatagtcagctttagttttatttatttaat----tctaaaaagatataatgtttatct-------ctgttgataacattacatatacagGAACTTGGAGAGTTGGAGGTGTTCTTGCTGTTTCTCGTGCATTTGGTGATAGACTCCTGAAGCAGTATGTTGTTGCTGATCCAGAAATTCAG
|||| | ||||| |  | |   ||       ||| ||| | ||  ||     | |  |  ||| |  |  ||   |       ||  ||||   | | | | ||||||||||||||| ||||| ||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||| |||
gtaaggacatcaat--cgttaggtttttccaagtattaatcatagaacaaagtttccagtgatttggtaattgcttgcatcttctaatgattgaaattcgtttacagGAACTTGGAGGGTTGGGGGTGTTCTTGCTGTTTCTCGTGCATTTGGTGATAGACTCTTGAAGCAGTATGTTGTTGCTGATCCAGAAATCCAG

upper sequence: GLYMA04G06250.1 (Glycine max), 3'ss of exon 6
lower sequence: PP1S225_37V6.2 (Physcomitrella patens), 3'ss of exon 5
gtaatgtcatcat-taacatatagtcagctttagttttatttatttaattc-taaaaagatataatgtttatc--tctgttgataacattacatatacagGAACTTGGAGAGTTGGAGGTGTTCTTGCTGTTTCTCGTGCATTTGGTGATAGACTCCTGAAGCAGTATGTTGTTGCTGATCCAGAAATTCAG
  | | ||||  | || | | |  |    |||  ||||||||||||| ||| |  |    | | | |   |      |  ||||||  |    ||| |||| |||||| | || || || ||||||||||| ||||| |||||||||||| | || |||||  | ||||||||||| || ||||||||||||
aaagtatcattctctatcgttttattttattttattttatttatttatttcatctatctgtttgaggagcactgtcttagtgataagttcgattatgcagGTACTTGGCGTGTAGGTGGCGTTCTTGCTGTGTCTCGGGCATTTGGTGATCGGCTGCTGAAAAAATATGTTGTTGCCGAACCAGAAATTCAG

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|192313213|gb|FK003333.1|FK003333
EST:     TGATGAGAGGCAAAGGATTGAAGAAGCAGGAGGCTTTGTTATGTGGGCAG                         GAACTTGGAGAGTTGGAGGTGTTCTTGCTGTTTCTCGTGCATTTGGTGATA
genomic: TGATGAGAGGCAAAGGATTGAAGAAGCAGGAGGCTTTGTTATGTGGGCAGgtaatgtcat ... acatatacagGAACTTGGAGAGTTGGAGGTGTTCTTGCTGTTTCTCGTGCATTTGGTGATA
EST: gi|254334939|gb|GR844724.1|GR844724
EST:     TGATGAGAGGCAAAGGATTGAAGAAGCAGGAGGCTTTGTTATGTGGGCAG                         GAACTTGGAGAGTTGGAGGTGTTCTTGCTGTTTCTCGTGCATTTGGTGATA
genomic: TGATGAGAGGCAAAGGATTGAAGAAGCAGGAGGCTTTGTTATGTGGGCAGgtaatgtcat ... acatatacagGAACTTGGAGAGTTGGAGGTGTTCTTGCTGTTTCTCGTGCATTTGGTGATA
EST: gi|209722646|gb|BW654653.1|BW654653
EST:     TGATGAGAGGCAAAGGATTGAAGAAGCAGGAGGCTTTGTTATGTGGGCAG                         GAACTTGGAGAGTTGGAGGTGTTCTTGCTGTTTCTCGTGCATTTGGTGATA
genomic: TGATGAGAGGCAAAGGATTGAAGAAGCAGGAGGCTTTGTTATGTGGGCAGgtaatgtcat ... acatatacagGAACTTGGAGAGTTGGAGGTGTTCTTGCTGTTTCTCGTGCATTTGGTGATA
EST: gi|11412749|gb|BF424760.1|BF424760
EST:     TGATGAGAGGCAAAGGATTGAAGAAGCAGGAGGCTTTGTTATGTGGGCAG                         GAACTTGGAGAGTTGGAGGTGTTCTTGCTGTTTCTCGTGCATTTGGTGATA
genomic: TGATGAGAGGCAAAGGATTGAAGAAGCAGGAGGCTTTGTTATGTGGGCAGgtaatgtcat ... acatatacagGAACTTGGAGAGTTGGAGGTGTTCTTGCTGTTTCTCGTGCATTTGGTGATA
EST: gi|192313214|gb|FK003334.1|FK003334
EST:     TGATGAGAGGCAAAGGATTGAAGAAGCAGGAGGCTTTGTTATGTGGGCAG                         GAACTTGGAGAGTTGGAGGTGTTCTTGCTGTTTCTCGTGCATTTGGTGATA
genomic: TGATGAGAGGCAAAGGATTGAAGAAGCAGGAGGCTTTGTTATGTGGGCAGgtaatgtcat ... acatatacagGAACTTGGAGAGTTGGAGGTGTTCTTGCTGTTTCTCGTGCATTTGGTGATA
EST: gi|11412737|gb|BF424748.1|BF424748
EST:     TGATGAGAGGCAAAGGATTGAAGAAGCAGGAGGCTTTGTTATGTGGGCAG                         GAACTTGGAGAGTTGGAGGTGTTCTTGCTGTTTCTCGTGCATTTGGTGATA
genomic: TGATGAGAGGCAAAGGATTGAAGAAGCAGGAGGCTTTGTTATGTGGGCAGgtaatgtcat ... acatatacagGAACTTGGAGAGTTGGAGGTGTTCTTGCTGTTTCTCGTGCATTTGGTGATA
EST: gi|209722645|gb|BW654652.1|BW654652
EST:     TGATGAGAGGCAAAGGATTGAAGAAGCAGGAGGCTTTGTTATGTGGGCAG                         GAACTTGGAGAGTTGGAGGTGTTCTTGCTGTTTCTCGTGCATTTGGTGATA
genomic: TGATGAGAGGCAAAGGATTGAAGAAGCAGGAGGCTTTGTTATGTGGGCAGgtaatgtcat ... acatatacagGAACTTGGAGAGTTGGAGGTGTTCTTGCTGTTTCTCGTGCATTTGGTGATA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttaattctaaaaagatataatgtttatctctgttgataacattacatatacagGAACTTGGAGAGTTGGAGGTGTTCTTGCTGTTTCTCGTGCATTTGGTGATAGACTCCTGAAGCAGTATGTTGTTGCTGATCCAGAAATTCAG
                                   tgataac  putative branch site (score: 2)
     attctaaaaagatata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatgtcatcattaacatatagtcagctttagttttatttatttaattctaaaaagatataatgtttatctctgttgataacattacatatacagGAACTTGGAGAGTTGGAGGTGTTCTTGCTGTTTCTCGTGCATTTGGTGATAGACTCCTGAAGCAGTATGTTGTTGCTGATCCAGAAATTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT