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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...catgatgctttataacgtatgctttgttgcatattcctccttcctctattctaaaccctttatccatttgcattaatatctgtctctttgatggctgcagGTGTATCTGCAGCAATGAATGAGCTACGTCCATGTGCCCCAATAAGTCTAAAACATGTCCTTGCCCAAGAATTGATTAAGGGATTACAGGCTGTTTCTGA

Basic information

species Glycine max
transcript GLYMA02G04920.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G04920.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv04s0008g01350.t01 (Vitis vinifera), 3'ss of exon 10
------------catgatgctttataacgtatgctttgtt-gcatatt--cctccttcctctattctaaaccctttatccatttgcattaatatctgtctctttgatggctgcagGTGTATCTGCAGCAATGAATGAGCTACGTCCATGTGCCCCAATAAGTCTAAAACATGTCCTTGCCCAAGAATTGATTAAGGGATTACAGGCTGTTTCTGA
              |  ||   |  | | ||    | |   ||| |||    | |||| |   ||||   ||    |  |||     |   || |  |||||   |  | |  ||||||||||||||| |||||||||||||| || ||||| ||||||||  ||||||| || ||||| ||||||||||| || ||||| | |||||||||  |
gtaagttctatttctactgaagttcatcttagaactggcaagcaaattagttttcttcatacgttctcctcctagaactcatcgatttatctaccactctctgcaaatgttctagGTGTATCTGCAGCGATGAATGAGCTACGGCCCTGTGCTCCAATAAGCTTAAAACACGTGCTTGCGCAAGAATTGATCAACGGATTGCGGGCTGTTTCCAA
















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|58024825|gb|CX711566.1|CX711566
EST:     TCCGCCCTTTAATTTGATGGAGCATCCACCTCTTGCTGTTTTTATTAATG                         GTGTATCTGCAGCAATGAATGAGCTACGTCCATGTGCCCCAATAAGTCTAA
genomic: TCCGCCCTCTAATTTGATGGAGCATCCACCTCTTGCTGTTTTTATTAATGgtgagtctag ... atggctgcagGTGTATCTGCAGCAATGAATGAGCTACGTCCATGTGCCCCAATAAGTCTAA
EST: gi|254335102|gb|GR844887.1|GR844887
EST:     TCCGCCCTCTAATTTGATGGAGCATCCACCTCTTGCTGTTTTTATTAATG                         GTGTATCTGCAGCAATGAATGAGCTACGTCCATGTGCCCCAATAAGTCTAA
genomic: TCCGCCCTCTAATTTGATGGAGCATCCACCTCTTGCTGTTTTTATTAATGgtgagtctag ... atggctgcagGTGTATCTGCAGCAATGAATGAGCTACGTCCATGTGCCCCAATAAGTCTAA
EST: gi|208211795|gb|GE010420.1|GE010420
EST:     TCCGCCCTCTAATTTGATGGAGCATCCACCTCTTGCTGTTTTTATTAATG                         GTGTATCTGCAGCAATGA
genomic: TCCGCCCTCTAATTTGATGGAGCATCCACCTCTTGCTGTTTTTATTAATGgtgagtctag ... atggctgcagGTGTATCTGCAGCAATGA
EST: gi|151410266|gb|EV280081.1|EV280081
EST:     TCCGCCCTCTAATTTGATGGAGCATCCACCTCTTGCTGTTTTTATTAATG                         GTGTATCTGCAGCAATGAATGAGCTACGTCCATGTGCCCCA-TAAGTCTAA
genomic: TCCGCCCTCTAATTTGATGGAGCATCCACCTCTTGCTGTTTTTATTAATGgtgagtctag ... atggctgcagGTGTATCTGCAGCAATGAATGAGCTACGTCCATGTGCCCCAATAAGTCTAA
EST: gi|19347302|gb|BM892182.1|BM892182
EST:     TCCGCCCTCTAATTTGATGGAGCATCCACCTCTTGCTGTTTTTATTAATG                         GTGTATCTGCAGCAATGAATGAGCTACGTCCATGTGCCCCAATAAGTCTAA
genomic: TCCGCCCTCTAATTTGATGGAGCATCCACCTCTTGCTGTTTTTATTAATGgtgagtctag ... atggctgcagGTGTATCTGCAGCAATGAATGAGCTACGTCCATGTGCCCCAATAAGTCTAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctattctaaaccctttatccatttgcattaatatctgtctctttgatggctgcagGTGTATCTGCAGCAATGAATGAGCTACGTCCATGTGCCCCAATAAGTCTAAAACATGTCCTTGCCCAAGAATTGATTAAGGGATTACAGGCTGTTTCTGA
                    atttgcattaatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
catgatgctttataacgtatgctttgttgcatattcctccttcctctattctaaaccctttatccatttgcattaatatctgtctctttgatggctgcagGTGTATCTGCAGCAATGAATGAGCTACGTCCATGTGCCCCAATAAGTCTAAAACATGTCCTTGCCCAAGAATTGATTAAGGGATTACAGGCTGTTTCTGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT
- tgatgct
- - - - - - - - gtatgct
- - - - - - - - - - - - tgttgca
- - - - - - - - - - - - - - - - -ttcctcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgtctc