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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atagatgtggccaatcatctataaaacatctacttggttttttttttttaagaaattcatttaacctgcaccatattttgctttgctatgtatccataagATTCAGGAAACTGACGAAGCAAGAAGGAAGTTCTCAAATGCTAAATCTATTTCTTCATCTCAATTTTTTGGAGATCAGAACAAAGCTGCAGATGTGGATT

Basic information

species Glycine max
transcript GLYMA01G12340.2
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA01G12340.2 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os03g63710.2 (Oryza sativa), 3'ss of exon 4
atagatgtggccaat-catctataaaacatctacttggttttttttttttaagaaattcatttaacctgcaccatattttgctttgc-tatgtatccataagATTCAGGAAACTGACGAAGCAAGAAGGAAGTTCTCAAATGCTAAATCTATTTCTTCATCTCAATTTTTTGGAGATCAGAACAAAGCTGCAGATGTGGATT
 | | | | || |     |   ||  | ||| | | | |||    || |  |||  ||  ||        |     |    ||   | |   || |  | |||||||||| |||||||||||||| |  || ||||| ||||| ||  | ||||| |||||||| ||||||||  |||| | || ||  |   | |  | | 
gttgttattgctagcatgttcttattatatcaaatagttttccgcttgt--agatttttgttatgttaataagtactgacactggacgtgaatacctttcagATTCAGGAGACTGACGAAGCAAGGAAAAAATTCTCTAATGCAAAGGCAATTTCATCATCTCAGTTTTTTGGCAATCAAAGCAGAGAAGAGAAAGACGCTC

upper sequence: GLYMA01G12340.2 (Glycine max), 3'ss of exon 5
lower sequence: Vv02s0012g01330.t01 (Vitis vinifera), 3'ss of exon 4
atagat-gtggccaatcatctataaaacatctacttggttttttttttttaagaaattcatttaacctgcaccatattttgctttgctatg-tatccataagATTCAGGAAACTGACGAAGCAAGAAGGAAGTTCTCAAATGCTAAATCTATTTCTTCATCTCAATTTTTTGGAGATCAGAACAAAGCTGCAGATGTGGATT
  | ||  |  | | |    | ||     |   ||     |||   | | ||| |  |  ||   || | || || |  | |||   | |   |   || ||||| |||||| ||| ||||| || ||||||||||||||||| |||||||| || ||| | |||| ||| || |||| ||  |||||    ||  |||| |
--acatcattactatttcagtttattgtgttagctgtaaatttgcatgtgaagcatgttcttcctccagtacaatttcattcttacatctaacaattatcagATTGAGGAAAGTGATGAAGCTAGGAGGAAGTTCTCAAATGCAAAATCTATCTCATCAGCCCAATATTTCGGGGATCCGAGTAAAGCCAATGACATGGACT
















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|11411566|gb|BF423577.1|BF423577
EST:     TGGATGGTGGCTTTCCAAAGAAATCTGGGCCAAGTTCCTCCAAAGTGCAA                         ATTCAGGAAACTGACGAAGCAAGAAGGAAGTTCTCAAATGCTAAATCTATT
genomic: TGGATGGTGGCTTTCCAAAGAAATCTGGGCCAAGTTCCTCCAAAGTGCAAgtaagccata ... tatccataagATTCAGGAAACTGACGAAGCAAGAAGGAAGTTCTCAAATGCTAAATCTATT
EST: gi|27424144|gb|CA935664.1|CA935664
EST:     TGGATGGTGGCTTTCCAAAGAAATCTGGGCCAAGTTCCTCCAAAGTGCAA                         ATTCAGGAAACTGACGAAGCAAGAAGGAAGTTCTCAAATGCTAAATCTATT
genomic: TGGATGGTGGCTTTCCAAAGAAATCTGGGCCAAGTTCCTCCAAAGTGCAAgtaagccata ... tatccataagATTCAGGAAACTGACGAAGCAAGAAGGAAGTTCTCAAATGCTAAATCTATT
EST: gi|254330187|gb|GR839740.1|GR839740
EST:     TGGATGGTGGCTTTCCAAAGAAATCTGGGCCAAGTTCCTCCAAAGTGCAA                         ATTCAGGAAACTGACGAAGCAAGAAGGAAGTTCTCAAATGCTAAATCTATT
genomic: TGGATGGTGGCTTTCCAAAGAAATCTGGGCCAAGTTCCTCCAAAGTGCAAgtaagccata ... tatccataagATTCAGGAAACTGACGAAGCAAGAAGGAAGTTCTCAAATGCTAAATCTATT
EST: gi|31309088|gb|CD394291.1|CD394291
EST:     TGGATGGTGGCTTTCCCAAGAGATCTGGGCCAAGTTCCTCCAAAGTGCGA                         ATTCAGGAAACTGACGAAGCCAGAAGGAAGTTCTCAAATGCTAAATCTATT
genomic: TGGATGGTGGCTTTCCAAAGAAATCTGGGCCAAGTTCCTCCAAAGTGCAAgtaagccata ... tatccataagATTCAGGAAACTGACGAAGCAAGAAGGAAGTTCTCAAATGCTAAATCTATT
EST: gi|208228828|gb|GE024234.1|GE024234
EST:     TGGATGGTGGCTTTCCAAAGAAATCTGGGCCAAGTTCCTCCAAAGTGCAA                         ATTCAGGAAGCTGACGAAGCAAGAAGGAAGTTCTCAAATGCTAAATCTATT
genomic: TGGATGGTGGCTTTCCAAAGAAATCTGGGCCAAGTTCCTCCAAAGTGCAAgtaagccata ... tatccataagATTCAGGAAACTGACGAAGCAAGAAGGAAGTTCTCAAATGCTAAATCTATT
EST: gi|254314431|gb|GR832016.1|GR832016
EST:     TGGATGGTGGCTTTCCAAAGAAATCTGGGCCAAGTTCCTCCAAAGTGCAA                         ATTCAGGAAACTGACGAAGCAAGAAGGAAGTTCTCAAATGCTAAATCTATT
genomic: TGGATGGTGGCTTTCCAAAGAAATCTGGGCCAAGTTCCTCCAAAGTGCAAgtaagccata ... tatccataagATTCAGGAAACTGACGAAGCAAGAAGGAAGTTCTCAAATGCTAAATCTATT
EST: gi|9564183|gb|BE473692.1|BE473692
EST:     TGGATGGTGGCTTTCCAAAGAAATCTGGGCCAAGTTCCTCCAAAGTGCAA                         ATTCAGGAAACTGACGAAGCAAGAAGGAAGTTCTCAAATGCTAAATCTATT
genomic: TGGATGGTGGCTTTCCAAAGAAATCTGGGCCAAGTTCCTCCAAAGTGCAAgtaagccata ... tatccataagATTCAGGAAACTGACGAAGCAAGAAGGAAGTTCTCAAATGCTAAATCTATT
EST: gi|10255901|gb|BE823667.1|BE823667
EST:     TGGATGGTGGCTTTCCAAAGAAATNNGGGCCAAGTTCCTCCAAAGTGCAA                         ATTCAGGAAACTGACGAAGCAAGAAGGAAGTTCTCAAATGCTAAATCTATT
genomic: TGGATGGTGGCTTTCCAAAGAAATCTGGGCCAAGTTCCTCCAAAGTGCAAgtaagccata ... tatccataagATTCAGGAAACTGACGAAGCAAGAAGGAAGTTCTCAAATGCTAAATCTATT
EST: gi|7590561|gb|AW706311.1|AW706311
EST:     TGGATGGTGGCTTTCCAAAGAAATCTGGGCCAAGTTCCTCCAAAGTGCAA                         ATTCAGGAAACTGACGAAGCAAGAAGGAAGTTCTCAAATGCTAAATCTATT
genomic: TGGATGGTGGCTTTCCAAAGAAATCTGGGCCAAGTTCCTCCAAAGTGCAAgtaagccata ... tatccataagATTCAGGAAACTGACGAAGCAAGAAGGAAGTTCTCAAATGCTAAATCTATT
EST: gi|193630140|gb|FK585309.1|FK585309
EST:     AAATCTGGGCCAAGTTCCTCCAAAGTGCAA                         ATTCAGGAAACTGACGAAGCAAGAAGGAAGTTCTCAAATGCTAAATCTATT
genomic: AAATCTGGGCCAAGTTCCTCCAAAGTGCAAgtaagccata ... tatccataagATTCAGGAAACTGACGAAGCAAGAAGGAAGTTCTCAAATGCTAAATCTATT
EST: gi|8670479|gb|BE191586.1|BE191586
EST:     TGGATGGTGGCTTTCCAAAGAAATCTGGGCCAAGTTCCTCCAAAGTGCAA                         ATTCAGGAAACTGACGAAGCAAGAAGGAAGTTCTCAAATGCTAAATCTATT
genomic: TGGATGGTGGCTTTCCAAAGAAATCTGGGCCAAGTTCCTCCAAAGTGCAAgtaagccata ... tatccataagATTCAGGAAACTGACGAAGCAAGAAGGAAGTTCTCAAATGCTAAATCTATT
EST: gi|31466806|gb|CD408834.1|CD408834
EST:     AGTTCCTCCAAAGTGCAA                         ATTCAGGAAACTGACGAAGCAAGAAGGAAGTTCTCAAATGCTAAATCTATT
genomic: AGTTCCTCCAAAGTGCAAgtaagccata ... tatccataagATTCAGGAAACTGACGAAGCAAGAAGGAAGTTCTCAAATGCTAAATCTATT
EST: gi|7028815|gb|AW458598.1|AW458598
EST:     TGGATGGTGGCTTTCCAAAGAAATCTGGGCCAAGTTCCTCCAAAGTGCAA                         ATTCAGGANACTGACGAAGCAAGAAGGAAGTTCTCAAATGCTAGATCTATG
genomic: TGGATGGTGGCTTTCCAAAGAAATCTGGGCCAAGTTCCTCCAAAGTGCAAgtaagccata ... tatccataagATTCAGGAAACTGACGAAGCAAGAAGGAAGTTCTCAAATGCTAAATCTATT
EST: gi|22524240|gb|BU083051.1|BU083051
EST:     TGGATGGTGGCTTTCCAAAGAAATCTGGGCCAAGTTCCTCCAAAGTGCAA                         ATTCAGGAAACTGACGAAGCAAGAAGGAAGTTCTCAAATGCTAAATCTATT
genomic: TGGATGGTGGCTTTCCAAAGAAATCTGGGCCAAGTTCCTCCAAAGTGCAAgtaagccata ... tatccataagATTCAGGAAACTGACGAAGCAAGAAGGAAGTTCTCAAATGCTAAATCTATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttaagaaattcatttaacctgcaccatattttgctttgctatgtatccataagATTCAGGAAACTGACGAAGCAAGAAGGAAGTTCTCAAATGCTAAATCTATTTCTTCATCTCAATTTTTTGGAGATCAGAACAAAGCTGCAGATGTGGATT
             atttaac  putative branch site (score: 3)
     agaaattcatttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atagatgtggccaatcatctataaaacatctacttggttttttttttttaagaaattcatttaacctgcaccatattttgctttgctatgtatccataagATTCAGGAAACTGACGAAGCAAGAAGGAAGTTCTCAAATGCTAAATCTATTTCTTCATCTCAATTTTTTGGAGATCAGAACAAAGCTGCAGATGTGGATT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG