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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgcatttggaagatgttattcctgatttatctgtcattgattcattaaacacatttgttttccactttcatctcataacggtttgattgtgtttgagcagGATGGAGTCTCAGGTGAAGCACGCACTTGTTGTCAAAGTAATGGGTCGTACTGGATCCAGAGGACAGGTGACCCAGGTTAGAGTGAAGTTTCTGGATGAT

Basic information

species Glycine max
transcript GLYMA03G36580.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G36580.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G455828_T01 (Zea mays), 3'ss of exon 1
tgcatttggaagatgttat-tcctgatttatctgtcattgattcattaaacaca-tttgttttccactttcatctcataacggtttgattgtgtttgagcagGATGGAGTCTCAGGTGAAGCACGCACTTGTTGTCAAAGTAATGGGTCGTACTGGATCCAGAGGACAGGTGACCCAGGTTAGAGTGAAGTTTCTGGATGAT
  || | | || |    || |     |  |  |   ||  | |   | | || |   | |  | ||| || ||  | | ||   |   || | ||   |||| |||||  | ||||||||||  ||  |||| || || || |||||  | || || ||||| || |||||||||||||| |||||||||||| ||||||| 
-ccagtagcaacaaaccatgtgacagtgcagttaaaatgaactatgtgatcaaagcatatggttcaccttgattac-tgacaaatgctttctattaatgcagCATGGACACCCAGGTGAAGCTTGCTGTTGTGGTGAAGGTGATGGGCAGGACCGGCTCCAGGGGTCAGGTGACCCAGGTCAGAGTGAAGTTTTTGGATGAC

upper sequence: GLYMA03G36580.1 (Glycine max), 3'ss of exon 1
lower sequence: AT3G10090.1 (Arabidopsis thaliana), 3'ss of exon 1
tgcatttggaagatgttattcctgatttatctgtcattgattcattaaacacatttgttttccactttcatctcataacggtttgattgtgtttgagcagGATGGAGTCTCAGGTGAAGCACGCACTTGTTGTCAAAGTAATGGGTCGTACTGGATCCAGAGGACAGGTGACCCAGGTTAGAGTGAAGTTT-CTGGATGAT
|  |       |||   | |    |    ||| |  ||       |   ||| | | || |  | |||  ||||  || | |||  || ||||  | ||| ||||| |||||| | ||||||||  |||| || ||||| |||||  | |||||||| || || || ||||| |||||||||||||||||  |||  |   
tatacagtcttgattcaaatgtgaacaattctctttttctaaggattttcacttcttttgtaaaatttggtctctgaatgtttttgttttgttgaatcagAATGGATTCTCAGATCAAGCACGCTGTTGTAGTGAAAGTGATGGGAAGGACTGGATCAAGGGGTCAAGTGACTCAGGTTAGAGTGAAGTTCACTGACTCG-

upper sequence: GLYMA03G36580.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv08s0007g07210.t01 (Vitis vinifera), 3'ss of exon 1
--tgcatttggaagatgttattcctgatttatctgtcattgattcattaaacacatttgttttccactttcatctcataac----ggtttgatt--gtgtttgagcagGATGGAGTCTCAGGTGAAGCACGCACTTGTTGTCAAAGTAATGGGTCGTACTGGATCCAGAGGACAGGTGACCCAGGTTAGAGTGAAGTTTCTGGATGAT
  ||  ||||     | |    | |||   |      |   ||| | | || |    || ||   | ||     | |||||      |||  ||  |     | ||   |||||  |   ||||||||| ||  | || || ||||| |||||||| |||||||| || || |||||||| ||||| |||||||||||| |||     
aatgagtttgcttt-tatagaacttgaa--aggaaaaaccaattaaatgaaaaatggtgcttagtatttatgaattataaccagcaattttctttggcagcagTGCGAAATGGATGCCGGGGTGAAGCATGCTGTGGTGGTGAAAGTTATGGGTCGAACTGGATCAAGGGGTCAGGTGACACAGGTGAGAGTGAAGTTTTTGG-----

upper sequence: GLYMA03G36580.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv08s0007g07210.t01 (Vitis vinifera), 3'ss of exon 4
----tgcatttggaagatgttattcctgatttatctgtcattg-attcattaaacacatttgttttccactttcatctcataacggtttgattgtgtttga-gcagGATGGAGTCTCAGGTGAAGCACGCACTTGTTGTCAAAGTAATGGGTCGTACTGGATCCAGAGGACAGGTGACCCAGGTTAGAGTGAAGTTTCTGGATGAT
       |||    | ||  | |   | | |     |  | |  | || || ||   ||     ||   | |  ||   | |    |||| |||| |     |||  ||||| |||  ||||||||| ||  | || || ||||| |||||||| ||||| || ||||| |||||||||||||| || ||||||||| |||     
tatacatattctttaaatagtctatgtaactagaaagaaaatacaatcttttaattgatgc-ccttatgcatctattataaatgattttgtttgtttgcagTGCAAAATGGAATCTGGGGTGAAGCATGCTGTGGTGGTGAAAGTTATGGGTCGAACTGGCTCAAGAGGTCAGGTGACCCAGGTGAGGGTGAAGTTTTTGG-----

upper sequence: GLYMA03G36580.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S41_71V6.2 (Physcomitrella patens), 3'ss of exon 1
tgcatttggaagatgttattcctgatttatctgtcattgattcattaaacacatttgttttccactttcatctcataacggtttgattgtgtttgagcagGATGGAGTCTCAGGTGAAGCACGCACTTGTTGTCAAAGTAATGGGTCGTACTGGATCCAGAGGACAGGTGACCCAGGTTAGAGTGAAGTTTCTGGATGAT-------------------
              |    |  |||| | ||||  | |  ||        |  ||  | |   | | |    |  || | | |  ||    ||||  ||||||    |||   |||||||  ||  ||||  | || || || ||||| ||||| ||| |||| ||||||||||| ||| | || |||||||||||||||                   
-----------tgcgacggttttgatct-tctg--actcttttgacggctagtttcttatgtaaatgtatatttgtatctgctatatca-atttgttcaggat----tctgccgtgaagCTGGCTATTGTAATGAAGGTGATTGGTCGCACTGGGTCCCGAGGTCAGGTGACCCAAGTTCGTGTTAAGTTTCTGGATGATCAAAATCGACTCATTATGC

upper sequence: GLYMA03G36580.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S41_71V6.1 (Physcomitrella patens), 3'ss of exon 1
tgcatttggaagatgttattcctgatttatctgtcattgattcattaaacacatttgttttccactttcatctcataacggt-ttgattgtgtttgagcagGATGGAGTCTCAGGTGAAGCACGCACTTGTTGTCAAAGTAATGGGTCGTACTGGATCCAGAGGACAGGTGACCCAGGTTAGAGTGAAGTTTCTGGATGAT----
    ||      || ||    | | |||     ||  ||| || ||  ||    | ||||   |  |  || | |||   || |    | | |           ||| |||   |||||||  ||  ||||  | || || || ||||| ||||| ||| |||| ||||||||||| ||| | || |||||||||||||||    
-agtttccatgtattttgcgacggttttgatcttc--tgactcttttgacg-gctagtttcttatgtaaatgt-atatttgtatctgctatatcaatttgttcagGATTCTGCCGTGAAGCTGGCTATTGTAATGAAGGTGATTGGTCGCACTGGGTCCCGAGGTCAGGTGACCCAAGTTCGTGTTAAGTTTCTGGATGATCAAA

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|13790969|gb|BG653560.1|BG653560
EST:     CTTCGTTCGTCTTTTACATCAG                         GATGGAGTCTCAGGTGAAGCACGCACTTGTTGTCAAAGTAATGGGTCGTAC
genomic: CTTCGTTCGTCTTTTACATCAGgtctgaatat ... gtttgagcagGATGGAGTCTCAGGTGAAGCACGCACTTGTTGTCAAAGTAATGGGTCGTAC
EST: gi|31312102|gb|CD397305.1|CD397305
EST:     CGCGTTCTTCGTTCGTCTTTTACATCAG                         GATGGAGTCTCAGGTGAAGCACGCACTTGTTGTCAAAGTAATGGGTCGTAC
genomic: CGCGTTCTTCGTTCGTCTTTTACATCAGgtctgaatat ... gtttgagcagGATGGAGTCTCAGGTGAAGCACGCACTTGTTGTCAAAGTAATGGGTCGTAC
EST: gi|24135523|gb|BU926033.1|BU926033
EST:     GCGTTCTTCGTTCGTCTTTTACATCAG                         GATGGAGTCTCAGGTGAAGCACGCACTTGTTGTCAAAGTAATGGGTCGTAC
genomic: GCGTTCTTCGTTCGTCTTTTACATCAGgtctgaatat ... gtttgagcagGATGGAGTCTCAGGTGAAGCACGCACTTGTTGTCAAAGTAATGGGTCGTAC
EST: gi|254316306|gb|GR827843.1|GR827843
EST:     CGTCTTTTACATCAG                         GATGGAGTCTCAGGTGAAGCACGCACTTGTTGTCAAAGTAATGGGTCGTAC
genomic: CGTCTTTTACATCAGgtctgaatat ... gtttgagcagGATGGAGTCTCAGGTGAAGCACGCACTTGTTGTCAAAGTAATGGGTCGTAC
EST: gi|5342745|gb|AI795029.1|AI795029
EST:     GTTCTTCGTTCGTCTTTTACATCAG                         GATGGAGTCTCAGGTGAAGCACGCACTTGTTGTCAAAGTAATGGGTCGTAC
genomic: GTTCTTCGTTCGTCTTTTACATCAGgtctgaatat ... gtttgagcagGATGGAGTCTCAGGTGAAGCACGCACTTGTTGTCAAAGTAATGGGTCGTAC
EST: gi|22932373|gb|BU549512.1|BU549512
EST:     CTTCGTTCGTCTTTTACATCAG                         GATGGAGTCTCAGGTGAAGCACGCACTTGTTGTCAAAGTAATGGGTCGTAC
genomic: CTTCGTTCGTCTTTTACATCAGgtctgaatat ... gtttgagcagGATGGAGTCTCAGGTGAAGCACGCACTTGTTGTCAAAGTAATGGGTCGTAC
EST: gi|254340158|gb|GR858283.1|GR858283
EST:     CTTTTACATCAG                         GATGGAGTCTCAGGTGAAGCACGCACTTGTTGTCAAAGTAATGGGTCGTAC
genomic: CTTTTACATCAGgtctgaatat ... gtttgagcagGATGGAGTCTCAGGTGAAGCACGCACTTGTTGTCAAAGTAATGGGTCGTAC
EST: gi|6727167|gb|AW311521.1|AW311521
EST:     GTTCGTCTTTTACATCAG                         GATGGAGTCTCAGGTGAAGCACGCACTTGTTGTCAAAGTAATGGGTCGTAC
genomic: GTTCGTCTTTTACATCAGgtctgaatat ... gtttgagcagGATGGAGTCTCAGGTGAAGCACGCACTTGTTGTCAAAGTAATGGGTCGTAC
EST: gi|21594998|gb|BQ610335.1|BQ610335
EST:     GCGTTCTTCGTTCGTCTTTTACATCAG                         GATGGAGTCTCAGGTGAAGCACGCACTTGTTGTCAAAGTAATGGGTCGTAC
genomic: GCGTTCTTCGTTCGTCTTTTACATCAGgtctgaatat ... gtttgagcagGATGGAGTCTCAGGTGAAGCACGCACTTGTTGTCAAAGTAATGGGTCGTAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taaacacatttgttttccactttcatctcataacggtttgattgtgtttgagcagGATGGAGTCTCAGGTGAAGCACGCACTTGTTGTCAAAGTAATGGGTCGTACTGGATCCAGAGGACAGGTGACCCAGGTTAGAGTGAAGTTTCTGGATGAT
       atttgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgcatttggaagatgttattcctgatttatctgtcattgattcattaaacacatttgttttccactttcatctcataacggtttgattgtgtttgagcagGATGGAGTCTCAGGTGAAGCACGCACTTGTTGTCAAAGTAATGGGTCGTACTGGATCCAGAGGACAGGTGACCCAGGTTAGAGTGAAGTTTCTGGATGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
tgcattt
- - - - - - - - - - cctgatt
- - - - - - - - - - - - - - -tctgtca
- - - - - - - - - - - - - - - - - - - - - - - aaacaca