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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggtggtttatattggtaggttatatcaacttctattattttttttttccttttcaaatccttatttcttatgtattgtcccttttgcattttctttttagGTACCAAGCTACAAAGGATGATCTTACTGTTTATGCAGCTTTGCCAACTGCTCCATCAGATGAATATGGAAATGTTTCCAGGTGGTACAAGCACATTGAT

Basic information

species Glycine max
transcript GLYMA06G17930.4
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G17930.4 (Glycine max), 3'ss of exon 2
lower sequence: Vv17s0000g01540.t01 (Vitis vinifera), 3'ss of exon 2
-------------ggtggtttatattggtaggttatatcaacttctattattttttttttccttttcaaatcct---------tatttcttatgtattgtcccttttgcattt------tctttttagGTACCAAGCTACAAAGGATGATCTTACTGTTTATGCAGCTTTGCCAACTGCTCCATCAGATGAATATGGAAATGTTTCCAGGTGGTACAAGCACATTGAT
               || ||| | |     || ||  |  |  |||   |  |   | ||    |  |||             |  ||  ||  |||| |   |||   |  |      | || | |||||||||||| ||||||||||| | |||||| |||||||| |  |||  |||||||||  |||||| |  ||||| || ||||||||||| ||||| || 
gtaagttttggtatctgatttctttacaatggatactttgatctctcagacatgggtattgaagtgaaaacatgaaaagataatgattaatacatattatgattttgttaaatcattaattttctcagGTACCAAGCTTCAAAGGATGATATCACTGTTCATGCAGCTCTTTCAAAGGCTCCATCATCTGAATACGTGAATGTCTCTAGGTGGTACAACCACATAGAG
















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|298175581|gb|HO018292.1|HO018292
EST:     GGGTTGAAGAAACTTGATGAGTACCTTCTCCCACGCAGTTACATCACCGG                         GTACCAAGCTACAAAGGATGATCTTACTGTTTATGCAGCTTTGCCAACTGC
genomic: GGGTTGAAGAAACTTGATGAGTACCTTCTCCCACGCAGTTACATCACCGGgtatgtcact ... ttctttttagGTACCAAGCTACAAAGGATGATCTTACTGTTTATGCAGCTTTGCCAACTGC
EST: gi|7588414|gb|AW704210.1|AW704210
EST:     GGGTTGAAGAAACTTGATGAGTACCTTCTCCCACGCAGTTACATCACCGG                         GTACCAAGCTACAAAGGATGATCTTACTGTTTATGCAGCTTTGCCAACTGC
genomic: GGGTTGAAGAAACTTGATGAGTACCTTCTCCCACGCAGTTACATCACCGGgtatgtcact ... ttctttttagGTACCAAGCTACAAAGGATGATCTTACTGTTTATGCAGCTTTGCCAACTGC
EST: gi|16106028|gb|BI893768.1|BI893768
EST:     GGGTTGAAGAAACTTGATGAGTACCTTCTCCCACGCAGTTACATCACCGG                         GTACCAAGCTACAAAGGATGATCTTACTGTTTATGCAGCTTTGTTTTTTGC
genomic: GGGTTGAAGAAACTTGATGAGTACCTTCTCCCACGCAGTTACATCACCGGgtatgtcact ... ttctttttagGTACCAAGCTACAAAGGATGATCTTACTGTTTATGCAGCTTTGCCAACTGC
EST: gi|213617811|gb|DB959395.1|DB959395
EST:     GGGTTGAAGAAACTTGATGAGTACCTTCTCCCACGCAGTTACATCACCGG                         GTACCAAGCTACAAAGGATGATCTTACTGTTTATGCAGCTTTGCCAACCGC
genomic: GGGTTGAAGAAACTTGATGAGTACCTTCTCCCACGCAGTTACATCACCGGgtatgtcact ... ttctttttagGTACCAAGCTACAAAGGATGATCTTACTGTTTATGCAGCTTTGCCAACTGC
EST: gi|192328314|gb|FK020025.1|FK020025
EST:     GGGTTGAAGAAACTTGATGAGTACCTTCTCCCACGCAGTTACATCACCGG                         GTACCAAGCTACAAAGGATGATCTTACTGTTTATGCAGCTTTGCCAACTGC
genomic: GGGTTGAAGAAACTTGATGAGTACCTTCTCCCACGCAGTTACATCACCGGgtatgtcact ... ttctttttagGTACCAAGCTACAAAGGATGATCTTACTGTTTATGCAGCTTTGCCAACTGC
EST: gi|9259946|gb|BE348093.1|BE348093
EST:     GGGTTGAAGAAACTTGATGAGTACCTTCTCCCACGCAGTTACATCACCGG                         GTACCAAGCTACAAAGGATGATCTTACTGTTTATGCAGCTTTGCCAACTGC
genomic: GGGTTGAAGAAACTTGATGAGTACCTTCTCCCACGCAGTTACATCACCGGgtatgtcact ... ttctttttagGTACCAAGCTACAAAGGATGATCTTACTGTTTATGCAGCTTTGCCAACTGC
EST: gi|298194444|gb|HO041092.1|HO041092
EST:     GGGTTGAAGAAACTTGATGAGTACCTTCTCCCACGCAGTTACATCACCGG                         GTACCAAGCTACAAAGGATGATCTTACTGTTTATGCAGCTTTGCCAACTGC
genomic: GGGTTGAAGAAACTTGATGAGTACCTTCTCCCACGCAGTTACATCACCGGgtatgtcact ... ttctttttagGTACCAAGCTACAAAGGATGATCTTACTGTTTATGCAGCTTTGCCAACTGC
EST: gi|18040877|gb|BM309171.1|BM309171
EST:     GGGTTGAAGAAACTTGATGAGTACCTTCTCCCACGCAGTTACATCACCGG                         GTACCAAGCTACAAAGGATGATCTTACTGTTTATGCAGCTTTGCCAACTGC
genomic: GGGTTGAAGAAACTTGATGAGTACCTTCTCCCACGCAGTTACATCACCGGgtatgtcact ... ttctttttagGTACCAAGCTACAAAGGATGATCTTACTGTTTATGCAGCTTTGCCAACTGC
EST: gi|13790786|gb|BG653377.1|BG653377
EST:     GGGTTGAAGAAACTTGATGAGTACCTTCTCCCACGCAGTTACATCACCGG                         GTACCAAGCTACAAAGGATGATCTTACTGTTTATGCAGCTTTGCCAACTGC
genomic: GGGTTGAAGAAACTTGATGAGTACCTTCTCCCACGCAGTTACATCACCGGgtatgtcact ... ttctttttagGTACCAAGCTACAAAGGATGATCTTACTGTTTATGCAGCTTTGCCAACTGC
EST: gi|7232756|gb|AW568109.1|AW568109
EST:     GGGTTGAAGAAACTTGATGAGTACCTTCTCCCACGCAGTTACATCACCGG                         GTACCAAGCTACAAAGGATGATCTTACTGTTTATGCAGCTTTGCCAACTGC
genomic: GGGTTGAAGAAACTTGATGAGTACCTTCTCCCACGCAGTTACATCACCGGgtatgtcact ... ttctttttagGTACCAAGCTACAAAGGATGATCTTACTGTTTATGCAGCTTTGCCAACTGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttccttttcaaatccttatttcttatgtattgtcccttttgcattttctttttagGTACCAAGCTACAAAGGATGATCTTACTGTTTATGCAGCTTTGCCAACTGCTCCATCAGATGAATATGGAAATGTTTCCAGGTGGTACAAGCACATTGAT
                             ttgtcccttttgcatt  CT-rich tract
               ttatttcttatgtatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggtggtttatattggtaggttatatcaacttctattattttttttttccttttcaaatccttatttcttatgtattgtcccttttgcattttctttttagGTACCAAGCTACAAAGGATGATCTTACTGTTTATGCAGCTTTGCCAACTGCTCCATCAGATGAATATGGAAATGTTTCCAGGTGGTACAAGCACATTGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
ggtggtt
- - - - - - - - - - - - -caacttc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtccct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tttgcat