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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtgtgcttattagttattaaatgacatctatttttctatcttgaatgttattaatcaaatacttcatgatgactgactctttcaatgttttttgatagGTTTGCCTCCAAGGTATCGAGATTCTGTTAGGGCTATAACACCTGGGTTACCATTATTTCTTTATAACTATACTACTCATCAGCTGCATGGTATTTTTGA

Basic information

species Glycine max
transcript GLYMA16G06100.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G06100.1 (Glycine max), 3'ss of exon 2
lower sequence: AT3G27090.1 (Arabidopsis thaliana), 3'ss of exon 2
gtgtgtgcttattagttattaaatgacatctatttttctatcttgaatgttattaatcaaatacttcatgatgactgact--ctttcaatgttttttgatagGTTTGCCTCCAAGGTATCGAGATTCTGTTAGGGCTATAACACCTGGGTTACCATTATTTCTTTATAACTATACTACTCATCAGCTGCATGGTATTTTTGA
              || |||     | | |  ||| |     || | || |||| |  || | |      || |||   |  ||||||   || ||    |||||| |||||||| ||  |||| |||||| | |||||||||||||| || ||  | |||||||| ||||| || ||||| ||||| |||||||| |||||
--------------gtaatttcccaatacccttttctagtgttttactgatattca--aactgcaagtaaataactttttgactttcatcattgttc---agGTTTACCTCCAAGATACAGAGACTCTGTTCGAGCTATAACACCTGGATTGCCTCTGTTTCTTTACAACTACACCACTCACCAGCTTCATGGTATCTTTGA

upper sequence: GLYMA16G06100.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv14s0068g02040.t01 (Vitis vinifera), 3'ss of exon 2
---gtgtgtgcttattagttattaaatgacatctat--ttttctatcttgaatgttattaatcaaatacttc-atgatgactgactctttcaatgttttttgatagGTTTGCCTCCAAGGTATCGAGATTCTGTTAGGGCTATAACACCTGGGTTACCATTATTTCTTTATAACTATACTACTCATCAGCTGCATGGTATTTTTGA
        |   | |  | ||| |||| | ||  ||  | |  | | || | | |  || |  |||| |||   || ||| |  |    |||      |||| ||||| | |||||||| ||| |||| |||||| ||||||||||||| || ||||| || ||||| |||||||| |||||||| ||  ||||||||||||||||
ataacacatctgtttctgatatcaaattatatggataatgtgatgtatttattttccttcaataaatccttttgtgttgattatcgtgctca------tttgttagGTCTACCTCCAAGATATAGAGACTCTGTTCGGGCTATAACACCAGGCTTACCTTTGTTTCTCTATAACTACACTACTCACCAATTGCATGGTATTTTTGA
















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|208156515|gb|GD956825.1|GD956825
EST:     AAGACTTGAAACGTCAGCTATTTG                         GTTTGCCTCCAAGGTATCGAGATTCTGTTAGGGCTATAACACCTGGGTTAC
genomic: AAGACTTGAAACGTCAGCTATTTGgtgtgtgctt ... tttttgatagGTTTGCCTCCAAGGTATCGAGATTCTGTTAGGGCTATAACACCTGGGTTAC
EST: gi|298190302|gb|HO032423.1|HO032423
EST:     TGTCTGTAACAATGACACAATGCAGGAAGACTTGAAACGTCGGCTATTTG                         GTTTGCCTCCAAGGTATCGAGATTCTGTTAGGGCTATAACACCTGGGTTAC
genomic: TGTCTGTAACAATGACACAATGCAGGAAGACTTGAAACGTCAGCTATTTGgtgtgtgctt ... tttttgatagGTTTGCCTCCAAGGTATCGAGATTCTGTTAGGGCTATAACACCTGGGTTAC
EST: gi|14011483|gb|BG726405.1|BG726405
EST:     GAAGACTTGAAACGTCAGCTATTTG                         GTTTGCCTACAA-GTATCGAGATTCTGTTAGGGCTATAACACCTGGGTTAC
genomic: GAAGACTTGAAACGTCAGCTATTTGgtgtgtgctt ... tttttgatagGTTTGCCTCCAAGGTATCGAGATTCTGTTAGGGCTATAACACCTGGGTTAC
EST: gi|254341084|gb|GR854812.1|GR854812
EST:     GTCAGCTATTTG                         GTTTGCCTCCAAGGTATCGAGATTCTGTTAGGGCTATAACACCTGGGTTAC
genomic: GTCAGCTATTTGgtgtgtgctt ... tttttgatagGTTTGCCTCCAAGGTATCGAGATTCTGTTAGGGCTATAACACCTGGGTTAC
EST: gi|298170392|gb|HO019016.1|HO019016
EST:     TGTCTGTAACAATGACACAATGCATGAAGACTTGAAACGTCAGCTATTTG                         GTTTGCCTCCAAGGTATCGAGATTCTGTTAAGGCTATAACACCTGGGTTAC
genomic: TGTCTGTAACAATGACACAATGCAGGAAGACTTGAAACGTCAGCTATTTGgtgtgtgctt ... tttttgatagGTTTGCCTCCAAGGTATCGAGATTCTGTTAGGGCTATAACACCTGGGTTAC
EST: gi|4282613|gb|AI440553.1|AI440553
EST:     TTGAAACGTCAGCTATTTG                         GTTTGCCTCCAAGGTATCGAGATTCTGTTAGGGCTATAACACCTGGGTTAC
genomic: TTGAAACGTCAGCTATTTGgtgtgtgctt ... tttttgatagGTTTGCCTCCAAGGTATCGAGATTCTGTTAGGGCTATAACACCTGGGTTAC
EST: gi|254320127|gb|GR831043.1|GR831043
EST:     ATGCAGGAAGAC-TGAAACGTCAGCTATTTG                         GTTTGCCTCCAAGGTATCGAGATTCTGTTAGGGCTATAACA-CTGGGTTAC
genomic: ATGCAGGAAGACTTGAAACGTCAGCTATTTGgtgtgtgctt ... tttttgatagGTTTGCCTCCAAGGTATCGAGATTCTGTTAGGGCTATAACACCTGGGTTAC
EST: gi|13563366|gb|BG551595.1|BG551595
EST:     AGGAAGACTTGAAACGTCAGCTATTTG                         GTTTGCCTCCAA-GTATCGAGATTCTGTTAGGGCTATAACACCTGGGTTAC
genomic: AGGAAGACTTGAAACGTCAGCTATTTGgtgtgtgctt ... tttttgatagGTTTGCCTCCAAGGTATCGAGATTCTGTTAGGGCTATAACACCTGGGTTAC
EST: gi|15000111|gb|BI320925.1|BI320925
EST:     TGTCTGTAACAATGACACAATGCAGGAAGACTTGAAACGTCAGCTATTTG                         GTTTGCCTCCAAGGTATCGAGATTCTGTTAGGGCTATAACACCTGGGTTAC
genomic: TGTCTGTAACAATGACACAATGCAGGAAGACTTGAAACGTCAGCTATTTGgtgtgtgctt ... tttttgatagGTTTGCCTCCAAGGTATCGAGATTCTGTTAGGGCTATAACACCTGGGTTAC
EST: gi|208137092|gb|GD934536.1|GD934536
EST:     AAGACTTGAAACGTCAGCTATTTG                         GTTTGCCTCCAAGGTATCGAGATTCTGTTAGGGCTATAACACCTGGGTTAC
genomic: AAGACTTGAAACGTCAGCTATTTGgtgtgtgctt ... tttttgatagGTTTGCCTCCAAGGTATCGAGATTCTGTTAGGGCTATAACACCTGGGTTAC
EST: gi|192320601|gb|FK012011.1|FK012011
EST:     TCTGTAACAATGACACAATGCAGGAAGACTTGAAACGTCAGCTATTTG                         GTTTGCCTCCAAGGTATCGAGATTCTGTTAGGGCTATAACACCTGGGTTAC
genomic: TCTGTAACAATGACACAATGCAGGAAGACTTGAAACGTCAGCTATTTGgtgtgtgctt ... tttttgatagGTTTGCCTCCAAGGTATCGAGATTCTGTTAGGGCTATAACACCTGGGTTAC
EST: gi|254336107|gb|GR841432.1|GR841432
EST:     GTAACAATGACACAATGCAGGAAGACTTGAAACGTCAGCTATTTG                         GTTTGCCTCCAAGGTATCGAGATTCTGTTAGGGCTATAACACCTGGGTTAC
genomic: GTAACAATGACACAATGCAGGAAGACTTGAAACGTCAGCTATTTGgtgtgtgctt ... tttttgatagGTTTGCCTCCAAGGTATCGAGATTCTGTTAGGGCTATAACACCTGGGTTAC
EST: gi|192310236|gb|FK001934.1|FK001934
EST:     TGTCTGTAACAATGACACAATGCAGGAAGACTTGAAACGTCAGCTATTTG                         GTTTGCCTCCAAGGTATCGAGATTCTGTTAGGGCTATAACACCTGGGTTAC
genomic: TGTCTGTAACAATGACACAATGCAGGAAGACTTGAAACGTCAGCTATTTGgtgtgtgctt ... tttttgatagGTTTGCCTCCAAGGTATCGAGATTCTGTTAGGGCTATAACACCTGGGTTAC
EST: gi|192300399|gb|FG987886.1|FG987886
EST:     TGTCTGTAACAATGACACAATGCAGGAAGACTTGAAACGTCAGCTATTTG                         GTTTGCCTCCAAGGTATCGAGATTCTGTTAGGGCTATAACACCTGGGTTAC
genomic: TGTCTGTAACAATGACACAATGCAGGAAGACTTGAAACGTCAGCTATTTGgtgtgtgctt ... tttttgatagGTTTGCCTCCAAGGTATCGAGATTCTGTTAGGGCTATAACACCTGGGTTAC
EST: gi|7232661|gb|AW568015.1|AW568015
EST:     TGTCTGTAACAATGACACAATGCAGGAAGACTTGAAACGTCAGCTATTTG                         GTTTGCCTCCAAGGTATCGAGATTCTGTTAGGGCTATAACACCTGGGTTAC
genomic: TGTCTGTAACAATGACACAATGCAGGAAGACTTGAAACGTCAGCTATTTGgtgtgtgctt ... tttttgatagGTTTGCCTCCAAGGTATCGAGATTCTGTTAGGGCTATAACACCTGGGTTAC
EST: gi|7232641|gb|AW567995.1|AW567995
EST:     TGTCTGTAACAATGACACAATGCAGGAAGACTTGAAACGTCAGCTATTTG                         GTTTGCCTCCAAGGTATCGAGATTCTGTTAGGGCTATAACACCTGGGTTAC
genomic: TGTCTGTAACAATGACACAATGCAGGAAGACTTGAAACGTCAGCTATTTGgtgtgtgctt ... tttttgatagGTTTGCCTCCAAGGTATCGAGATTCTGTTAGGGCTATAACACCTGGGTTAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatgttattaatcaaatacttcatgatgactgactctttcaatgttttttgatagGTTTGCCTCCAAGGTATCGAGATTCTGTTAGGGCTATAACACCTGGGTTACCATTATTTCTTTATAACTATACTACTCATCAGCTGCATGGTATTTTTGA
                           gactgac  putative branch site (score: 2)
                                          tgtttttt  putative PPT
     tattaatcaaatactt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgtgtgcttattagttattaaatgacatctatttttctatcttgaatgttattaatcaaatacttcatgatgactgactctttcaatgttttttgatagGTTTGCCTCCAAGGTATCGAGATTCTGTTAGGGCTATAACACCTGGGTTACCATTATTTCTTTATAACTATACTACTCATCAGCTGCATGGTATTTTTGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC