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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctgaatcttttaagcttcttatagttactgtcagaatgcaatatctatacattttttaatatagttccacgtataaactgatgatttttcattttttcagGATGCTAAGAAGGGTGTCCTGTTCATTGATTTCCCTCCTGTTCTTCAGCTTCAACTGAAAAGATTTGAATATGACTTTATGCGGGATACTATGGTCAAG

Basic information

species Glycine max
transcript GLYMA02G43930.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G43930.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os12g30540.1 (Oryza sativa), 3'ss of exon 8
ctgaatcttttaagcttcttatagttactgtcaga---atgcaatatctatacattttttaatatagttccacgtataaact-gatgatttttcattttttcagGATGCTAAGAAGGGTGTCCTGTTCATTGATTTCCCTCCTGTTCTTCAGCTTCAACTGAAAAGATTTGAATATGACTTTATGCGGGATACTATGGTCAAG
    || ||  ||| |  | |  |  | | |   |   |||| ||   ||||  ||| |||   |  | |  | |    ||| |||  | | | || |||||||||||| |||||||| || || ||| ||||||||||||||||| | || |||||||||||  | ||||||||||| |  ||||| ||||| |||||||||
---gattttccaagttaatgaatggcaatatagcatacatgccatgattatat-tttcttaccttgatactgcattggcacttgatattctgtaatcttttcagGATGCAAAGAAGGGAGTACTCTTCCTTGATTTCCCTCCTGTTTTGCAACTTCAACTGAAGCGTTTTGAATATGATTACATGCGAGATACAATGGTCAAG

upper sequence: GLYMA02G43930.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os11g36470.1 (Oryza sativa), 3'ss of exon 4
ctgaatcttttaagcttcttatagttactgtcagaatgcaatatctatacattttttaatatagttccacgtataaactgatgattttt---cattttttcagGATGCTAAGAAGGGTGTCCTGTTCATTGATTTCCCTCCTGTTCTTCAGCTTCAACTGAAAAGATTTGAATATGACTTTATGCGGGATACTATGGTCAAG
 |  |   |   |||||  |  |  ||   |    |    |   | ||   || ||   | | || |||  | |  ||| ||| |||||    ||| | ||||||||| || |||||||| |||||| |||||||||| || ||| | || |||||||||||  | ||||| || |||| |||| | ||||| ||||| |||
-tatactataacagcttgctccatctatattttataaatgaagcccattt-ttattggttttggtgccaattcttgact-atgtttttttgatattgtctcagGATGCGAAAAAGGGTGTTCTGTTCCTTGATTTCCCCCCAGTTTTGCAACTTCAACTGAAGCGTTTTGAGTACGACTATATGAGAGATACCATGGTTAAG

upper sequence: GLYMA02G43930.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G014805_T01 (Zea mays), 3'ss of exon 8
ctgaatcttttaagcttcttatagttactgtcagaatgcaatatctatacat-tttttaatatagttccacgtataaactgatgatttttcattttttcagGATGCTAAGAAGGGTGTCCTGTTCATTGATTTCCCTCCTGTTCTTCAGCTTCAACTGAAAAGATTTGAATATGACTTTATGCGGGATACTATGGTCAAG
 ||  |   |||   |   |   ||||   | |   |     | || |   | || ||| ||| |||   | |  |   | ||  | |||  | |||||||||||| | ||| ||||| || ||| ||||||||||||||||| | ||||||||||||||  | ||||||||||| |  ||||| ||||| ||||| |||
-tgtgtggattattatcagttcggttatgattatcttttctgacctttttttgttattactattgttgttccttaattttaatattattttttgttttcagGATGCAAGGAAAGGTGTGCTTTTCCTTGATTTCCCTCCTGTTTTGCAGCTTCAACTGAAGCGTTTTGAATATGATTACATGCGAGATACAATGGTTAAG

upper sequence: GLYMA02G43930.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv06s0009g00960.t01 (Vitis vinifera), 3'ss of exon 8
---ctgaatcttttaagcttcttatagttactgtcagaatgcaatatctatacatt--ttttaatatagttccacgtataaactgatgatttttcattttttcagGATGCTAAGAAGGGTGTCCTGTTCATTGATTTCCCTCCTGTTCTTCAGCTTCAACTGAAAAGATTTGAATATGACTTTATGCGGGATACTATGGTCAAG
    |  || |||   |  |       ||    | | ||    || |||||   |   |||  ||  |||  |   | | || |  || | |    || | ||||||||||| |||||||||| | |||||||| ||||||||||| ||||| ||||| |||||  ||||||||||||| ||||||||||| |||||||| |||
gggtttcatatttaccgtcttacccctttgtcatgaaaacctcat-tctatgtttcgctttccatcaagtgactgttttgaatt--tggtatgc--ttgtctcagGATGCTAGGAAGGGTGTCTTATTCATTGACTTCCCTCCTGTCCTTCAACTTCAGCTGAAGCGATTTGAATATGATTTTATGCGGGACACTATGGTAAAG

upper sequence: GLYMA02G43930.1 (Glycine max), 3'ss of exon 8
lower sequence: PP1S42_181V6.1 (Physcomitrella patens), 3'ss of exon 8
---ctgaatcttttaagcttcttata----gttactgtcagaa-tgcaatatctatacattttttaatat-agttccacgtataaact-------gatgattttt---cattt---tttcagGATGCTAAGAAGGGTGTCCTGTTCATTGATTTCCCTCCTGTTCTTCAGCTTCAACTGAAAAGATTTGAATATGACTTTATGCGGGATACTATGGTCAAG
   ||||||    |   | | ||  |     ||  ||   ||| |  | |     |    |  | | ||| | ||  |  | |||||         |  | |||    ||  |   || |||||||| || || || ||||| || || || ||||| |||||||||||||| ||||||||| | |||||||| ||||| ||||| || || ||||| |||
gtgctgaatgcgctgcaccttttgaatcaaattgatgcttgaactttactgatcttctgatcatgattatgaattgtatctgtaaaccctacttcaaccaatttggggcacgtacattgcagGATGCAAAAAAAGGAGTCCTATTTATAGACTTCCCCCCTGTTCTTCAGCTCCAACTGAAACGGTTTGAATACGACTTCATGCGAGACACAATGGTGAAG

upper sequence: GLYMA02G43930.1 (Glycine max), 3'ss of exon 8
lower sequence: EFJ19227 (Selaginella moellendorffii), 3'ss of exon 8
ctgaatcttttaagcttcttatagttactgtcagaatgcaatatctatacattttttaatatagttccacgtataaactgatgatttttcattttttcagGATGCTAAGAAGGGTGTCCTGTTCATTGATTTCCCTCCTGTTCTTCAGCTTCAACTGAAAAGATTTGAATATGACTTTATGCGGGATACTATGGTCAAG
                                               |    ||  || |   |||     |  |  ||||||   |||||  ||  |||||||||||||| || || || || || ||||| || |||||||| ||| | |||||||| |||||||||||||| || |  || || || |||||||||
----------------------------------------------gtgaccttcctattcacgtttagaatgcag-ctgatgggctttcaaattg-cagGATGCTAAGAAAGGAGTGCTCTTTATAGATTTTCCACCTGTTCTCCAGTTACAACTGAAGAGATTTGAATATGATTTCACTCGCGACACGATGGTCAAG

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|254342408|gb|GR858570.1|GR858570
EST:     AACGTCTTGAAGGGGATAACAAATATCATGCGGAACAATATGGTTTGCAG                         GATGCTAAGAAGGGTGTCCTGTTCATTGATTTCCCTCCTGTTCTTCAGCTT
genomic: AACGTCTTGAAGGGGATAACAAATATCATGCGGAACAATATGGTTTGCAGgttggttgca ... attttttcagGATGCTAAGAAGGGTGTCCTGTTCATTGATTTCCCTCCTGTTCTTCAGCTT
EST: gi|120496383|gb|EH224550.1|EH224550
EST:     AACGTCTTGAAGGGGATAACAAATATCATGCGGAACAATATGGTTTGCAG                         GATGCTAAGAAGGGTGTCCTGTTCATTGATTTCCCTCCTGTTCTTCAGCTT
genomic: AACGTCTTGAAGGGGATAACAAATATCATGCGGAACAATATGGTTTGCAGgttggttgca ... attttttcagGATGCTAAGAAGGGTGTCCTGTTCATTGATTTCCCTCCTGTTCTTCAGCTT
EST: gi|254342407|gb|GR858569.1|GR858569
EST:     AACGTCTTGAAGGGGATAACAAATATCATGCGGAACAATATGGTTTGCAG                         GATGCTAAGAAGGGTGTCCTGTTCATTGATTTCCCTCCTGTTCTTCAGCTT
genomic: AACGTCTTGAAGGGGATAACAAATATCATGCGGAACAATATGGTTTGCAGgttggttgca ... attttttcagGATGCTAAGAAGGGTGTCCTGTTCATTGATTTCCCTCCTGTTCTTCAGCTT
EST: gi|209717383|gb|BW659059.1|BW659059
EST:     AACGTCTTGAAGGGGATAACAAATATCATGCGGAACAATATGGTTTGCAG                         GATGCTAAGAAGGGTGTCCTGTTCATTGATTTCCCTCCTGTTCTTCAGCTT
genomic: AACGTCTTGAAGGGGATAACAAATATCATGCGGAACAATATGGTTTGCAGgttggttgca ... attttttcagGATGCTAAGAAGGGTGTCCTGTTCATTGATTTCCCTCCTGTTCTTCAGCTT
EST: gi|207734972|gb|GD710193.1|GD710193
EST:     AACGTCTTGAAGGGGATAACAAATATCATGCGGAACAATATGGTTTGCAG                         GGTGCTAAGAAGGGTGTCCTGTTCATTGATTTCCCTCCTGTTCTTCAGCTT
genomic: AACGTCTTGAAGGGGATAACAAATATCATGCGGAACAATATGGTTTGCAGgttggttgca ... attttttcagGATGCTAAGAAGGGTGTCCTGTTCATTGATTTCCCTCCTGTTCTTCAGCTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatacattttttaatatagttccacgtataaactgatgatttttcattttttcagGATGCTAAGAAGGGTGTCCTGTTCATTGATTTCCCTCCTGTTCTTCAGCTTCAACTGAAAAGATTTGAATATGACTTTATGCGGGATACTATGGTCAAG
                              aactgat  putative branch site (score: 3)
                                       tttttcattttttc  putative PPT
     attttttaatatagtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctgaatcttttaagcttcttatagttactgtcagaatgcaatatctatacattttttaatatagttccacgtataaactgatgatttttcattttttcagGATGCTAAGAAGGGTGTCCTGTTCATTGATTTCCCTCCTGTTCTTCAGCTTCAACTGAAAAGATTTGAATATGACTTTATGCGGGATACTATGGTCAAG

- - - - - - -gcttctt
- - - - - - - - - - - - -tactgtc
- - - - - - - - - - - - - - - - -gaatgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccacgta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - actgatg