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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attgaaaatctaagtaatattaattggctaattcacgtcttattaggagtcttggcttagttttgtttttgttttttttttttttttgtggtgaacacagGTCATGGAAGAAACAGGTTTTGATGTTTCAAAACTTCTGAACAAGGATGAATACCTTGAAGTTATTTTTGGACAACAGAGAGTTAGGCTTTACATTATTG

Basic information

species Glycine max
transcript GLYMA02G08170.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G08170.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv13s0019g04310.t01 (Vitis vinifera), 3'ss of exon 4
---------attgaaaatctaagtaatattaattggctaattcacgtcttattaggagtcttggcttagttttgtttttgttttttttttttttttgtggtgaacacagGTCATGGAAGAAACAGGTTTTGATGTTTCAAAACTTCTGAACAAGGATGAATACCTTGAAGTTATTTTTGGACAACAGAGAGTTAGGCTTTACATTATTG
          ||  ||||  ||| |  | ||| |    || |   ||  | |    |   ||  | || ||||    |   | |||  |        ||||| |  |||||   ||| ||||||||||||||||| ||||||||||| ||| | ||||| ||| ||||||  || ||||||||||| || ||  |||||||||| || |
tttgcctttgtttgaaataaaaggagaactaaat--taaactgctgttctctctatacctttctcatacttttcacctaactatttgct-------atggtggatgcagGTACAGGAGGAAACAGGTTTTGATGTCTCAAAACTTCTTAACCAAGATGAGTACATTGAAGAGATATTTGGACAACAAAGGGTGCGGCTTTACATAATCG
















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|192322569|gb|FK014690.1|FK014690
EST:     GTGGAAAAAAGAGCAAAGACGAAGAAGATCATGCATGTGCCATTAGAGAA                         GTCATGGAAGAAACAGGTTTTGATGTTTCAAAACTTCTGAACAAAGATG
genomic: GTGGAAAAAAGAGCAAAGACGAAGAAGATCATGCATGTGCCATTAGAGAAgtaagcatgc ... gtgaacacagGTCATGGAAGAAACAGGTTTTGATGTTTCAAAACTTCTGAACAAGGATG
EST: gi|151403573|gb|EV273383.1|EV273383
EST:     GTGGAAAAAAGAGCAAAGACGAAGAAGATCATGCATGTGCCATTAGAGAA                         GTCATGGAAGAAACAGGTTTTGATGTTTCAAAACTTCTGAACAAGGATGA-
genomic: GTGGAAAAAAGAGCAAAGACGAAGAAGATCATGCATGTGCCATTAGAGAAgtaagcatgc ... gtgaacacagGTCATGGAAGAAACAGGTTTTGATGTTTCAAAACTTCTGAACAAGGATGAA
EST: gi|13789427|gb|BG652018.1|BG652018
EST:     GTGGAAAAAAGAGCAAAGACGAAGAAGATCATGCATGTGCCATTAGAGAA                         GTCATGGAAGAAACAGGTTTTGATGTTTCAAAACTTCTGAACAAGGATGAA
genomic: GTGGAAAAAAGAGCAAAGACGAAGAAGATCATGCATGTGCCATTAGAGAAgtaagcatgc ... gtgaacacagGTCATGGAAGAAACAGGTTTTGATGTTTCAAAACTTCTGAACAAGGATGAA
EST: gi|193427446|gb|FK394858.1|FK394858
EST:     GTGGAAAAAAGAGCAAAGACGAAGAAGATCATGCATGTTCCATTAGAGAA                         GTCATGGAAGAAACAGGTTTTGATGTTTCAAAACTTCTGAACAAGGATGAA
genomic: GTGGAAAAAAGAGCAAAGACGAAGAAGATCATGCATGTGCCATTAGAGAAgtaagcatgc ... gtgaacacagGTCATGGAAGAAACAGGTTTTGATGTTTCAAAACTTCTGAACAAGGATGAA
EST: gi|298176465|gb|HO026700.1|HO026700
EST:     GTGGAAAAAAGAGCAAAGACGAAGAAGATCATGCATGTGCCATTAGAGAA                         GTCATGGAAGAAACAGGTTTTGATGTTTCAAAACTTCTGAACAAGGATGAA
genomic: GTGGAAAAAAGAGCAAAGACGAAGAAGATCATGCATGTGCCATTAGAGAAgtaagcatgc ... gtgaacacagGTCATGGAAGAAACAGGTTTTGATGTTTCAAAACTTCTGAACAAGGATGAA
EST: gi|151407825|gb|EV277640.1|EV277640
EST:     GTGGAAAAAAGAGCAAAGACGAAGAAGATCATGCATGTGCCATTAGAGAA                         GTCATGGAAGAAACAGGTTTTGATGTTTCAAAACTTCTGAACAAGGATGAA
genomic: GTGGAAAAAAGAGCAAAGACGAAGAAGATCATGCATGTGCCATTAGAGAAgtaagcatgc ... gtgaacacagGTCATGGAAGAAACAGGTTTTGATGTTTCAAAACTTCTGAACAAGGATGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggagtcttggcttagttttgtttttgttttttttttttttttgtggtgaacacagGTCATGGAAGAAACAGGTTTTGATGTTTCAAAACTTCTGAACAAGGATGAATACCTTGAAGTTATTTTTGGACAACAGAGAGTTAGGCTTTACATTATTG
                    tttttgtttttttttt  CT-rich tract
           ttagttttgtttttgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attgaaaatctaagtaatattaattggctaattcacgtcttattaggagtcttggcttagttttgtttttgttttttttttttttttgtggtgaacacagGTCATGGAAGAAACAGGTTTTGATGTTTCAAAACTTCTGAACAAGGATGAATACCTTGAAGTTATTTTTGGACAACAGAGAGTTAGGCTTTACATTATTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- -gaaaatc
- - - - - - - - - - - - - - - attcacg