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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taattttcttgcagtcagtaaattattcatcatgattgaataccatttgcatcagcagtgttttcattaagaccatgcatgcaattgttccatgctgcagGAACCTTCTTGGTGAAGACTTGGGCCCACTAAATACCAAAGATCTTGAGCAGCTTGAGCGGCAACTGGATTCATCTCTCAAGCAAGTGAGGTCCACAAAG

Basic information

species Glycine max
transcript GLYMA13G06730.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G06730.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv14s0083g01050.t01 (Vitis vinifera), 3'ss of exon 3
------------------------------------------taattttcttgcagtcagtaaat-tattcatc--atgattga-ataccatttgcatcagcagtgttttcattaagaccatgcatgcaattgttccatgctgcagGAACCTTCTTGGTGAAGACTTGGGCCCACTAAATACCAAAGATCTTGAGCAGCTTGAGCGGCAACTGGATTCATCTCTCAAGCAAGTGAGGTCCACAAAG
                                          | |  ||  ||   |   ||| | | |||||   || |  || ||| | | |||| || |  ||  || ||| |    ||   ||    ||    ||  |  || ||||||||||| ||||||||||| ||| | || || ||||| |||||||||||||| || ||||| ||  ||||  | |||||||| ||||| || |||
gtgattaagtaccttagttgtggcttttttgaattctgcttctgaaatttctgagttggataattgttttcattcaattacggagatatcttatgcaacaacc-tgactttattcatgaaatatttgaccctg---aatattctagAAACCTTCTTGGGGAAGACTTGGGTCCATTGAACACAAAAGAGCTTGAGCAGCTTGAACGTCAACTTGAGACATCCTTGAAGCAAGTCAGGTCTACTAAG
















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|208244876|gb|GE042067.1|GE042067
EST:     GAGTACTTGAAGCTGAAAGCAAGATTTGAATCTCTTCAAAGGACCCAAAG                         GAACCTTCTTGGTGAAGACTCGGGCCCACTAAATACCAAAGATCTCGAGCA
genomic: GAGTACTTGAAGCTGAAAGCAAGATTTGAATCTCTTCAAAGGACCCAAAGgtgaatttca ... catgctgcagGAACCTTCTTGGTGAAGACTTGGGCCCACTAAATACCAAAGATCTTGAGCA
EST: gi|298176561|gb|HO023148.1|HO023148
EST:     GAGTACTTGAAGCTGAAAGCAAGATTTGAATCTCTTCAAAGGACCCAAAG                         GAACCTTCTTGGTGAAGACTTGGGCCCACTAAATACCAAAGATCTTGAGCA
genomic: GAGTACTTGAAGCTGAAAGCAAGATTTGAATCTCTTCAAAGGACCCAAAGgtgaatttca ... catgctgcagGAACCTTCTTGGTGAAGACTTGGGCCCACTAAATACCAAAGATCTTGAGCA
EST: gi|193697032|gb|FK638874.1|FK638874
EST:     AAGGACCCAAAG                         GAACCTTCTTGGTGAAGACTTGGGCCCACTAAATACCAAAGATCTTGAGCA
genomic: AAGGACCCAAAGgtgaatttca ... catgctgcagGAACCTTCTTGGTGAAGACTTGGGCCCACTAAATACCAAAGATCTTGAGCA
EST: gi|207693353|gb|GD674970.1|GD674970
EST:     GAGTACTTGAAGCTGAAAGCAAGGTTTGAATCTCTTCAAAGGACCCAAAG                         GAACCTTCTTGGTGAAGACTTGGGCCCACTAAATACCAAAGATCTTGAGC
genomic: GAGTACTTGAAGCTGAAAGCAAGATTTGAATCTCTTCAAAGGACCCAAAGgtgaatttca ... catgctgcagGAACCTTCTTGGTGAAGACTTGGGCCCACTAAATACCAAAGATCTTGAGC
EST: gi|207770397|gb|GD744139.1|GD744139
EST:     AGTACTTGAAGCTGAAAGCAAGATTTTGAATCTCTTCAAAGGACCCAAAG                         GAACCTTCTTGGTGAAGACTTGGGCCCACTAAATACCAAAGATCTTGAGCA
genomic: AGTACTTGAAGCTGAAAGCAAGA-TTTGAATCTCTTCAAAGGACCCAAAGgtgaatttca ... catgctgcagGAACCTTCTTGGTGAAGACTTGGGCCCACTAAATACCAAAGATCTTGAGCA
EST: gi|193379920|gb|FK346338.1|FK346338
EST:     GAGTACTTGAAGCTGAAAGCAAGATTTGAATCTCTTCAAAGGACCCAAAG                         GAACCTTCTTGGTGAAGACTTGGGCCCACTAAATACCAAAGATCTTGAGCA
genomic: GAGTACTTGAAGCTGAAAGCAAGATTTGAATCTCTTCAAAGGACCCAAAGgtgaatttca ... catgctgcagGAACCTTCTTGGTGAAGACTTGGGCCCACTAAATACCAAAGATCTTGAGCA
EST: gi|193510569|gb|FK468075.1|FK468075
EST:     CTGAAAGCAAGATTTGAATCTCTTCAAAGGACCCAAAG                         GAACCTTCTTGGTGAAGACTTGGGCCCACTAAATACCAAAGATCTTGAGCA
genomic: CTGAAAGCAAGATTTGAATCTCTTCAAAGGACCCAAAGgtgaatttca ... catgctgcagGAACCTTCTTGGTGAAGACTTGGGCCCACTAAATACCAAAGATCTTGAGCA
EST: gi|193625995|gb|FK576947.1|FK576947
EST:     GAGTACTTGAAGCTGAAAGCAAGATTTGAATCTCTTCAAAGGACCCAAAG                         GAACCTTCTTGGTGAAGACTTGGGCCCACTAAATA
genomic: GAGTACTTGAAGCTGAAAGCAAGATTTGAATCTCTTCAAAGGACCCAAAGgtgaatttca ... catgctgcagGAACCTTCTTGGTGAAGACTTGGGCCCACTAAATA
EST: gi|17020647|gb|BM091681.1|BM091681
EST:     GAGTACTTGAAGCTGAAAGCAAGATTTGAATCTCTTCAAAGGACCCAAAG                         GAACCTTCTTGGTGAAGACTTGGGCCCACTAAATACCAAAGATCTTGAGCA
genomic: GAGTACTTGAAGCTGAAAGCAAGATTTGAATCTCTTCAAAGGACCCAAAGgtgaatttca ... catgctgcagGAACCTTCTTGGTGAAGACTTGGGCCCACTAAATACCAAAGATCTTGAGCA
EST: gi|208331677|gb|GE132390.1|GE132390
EST:     GAGTACTTGAAGCTGAAAGCAAGATTTGAATCTCTTCAAAGGACCCAAAG                         GAACCTTCTTGGTGAAGACTTGGGCCCACTAAATACCAAAGATCTTGAGCA
genomic: GAGTACTTGAAGCTGAAAGCAAGATTTGAATCTCTTCAAAGGACCCAAAGgtgaatttca ... catgctgcagGAACCTTCTTGGTGAAGACTTGGGCCCACTAAATACCAAAGATCTTGAGCA
EST: gi|8284985|gb|BE022544.1|BE022544
EST:     GAGTACTTGAAGCTGAAAGCAAGATTTGAATCTCTTCAAAGGACCCAAAG                         GAACCTTCTTGGTGAAGACTTGGGCCCACTAAATACCAAAGATCTTGAGCA
genomic: GAGTACTTGAAGCTGAAAGCAAGATTTGAATCTCTTCAAAGGACCCAAAGgtgaatttca ... catgctgcagGAACCTTCTTGGTGAAGACTTGGGCCCACTAAATACCAAAGATCTTGAGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgcatcagcagtgttttcattaagaccatgcatgcaattgttccatgctgcagGAACCTTCTTGGTGAAGACTTGGGCCCACTAAATACCAAAGATCTTGAGCAGCTTGAGCGGCAACTGGATTCATCTCTCAAGCAAGTGAGGTCCACAAAG
                                       ttgttcc  CT-rich tract
               ttttcattaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taattttcttgcagtcagtaaattattcatcatgattgaataccatttgcatcagcagtgttttcattaagaccatgcatgcaattgttccatgctgcagGAACCTTCTTGGTGAAGACTTGGGCCCACTAAATACCAAAGATCTTGAGCAGCTTGAGCGGCAACTGGATTCATCTCTCAAGCAAGTGAGGTCCACAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG