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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ataattatgaaatttaatatccattgctaatgagtcaaatatgaccatagtatatatgataattttctaacgcttgcagtttcttttatttttgctacagGTACAGAAACTCGTTGAGATGGGATTTCCAGAAGCTCAAGTAAGGAGCATTTTGGAAGCTGTTGGTGGTGATGAAAACTTGGCTCTTGAAAGGTTGCTGT

Basic information

species Glycine max
transcript GLYMA04G37620.3
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G37620.3 (Glycine max), 3'ss of exon 5
lower sequence: Vv17s0000g00610.t01 (Vitis vinifera), 3'ss of exon 4
--------------------ataattatgaaatttaatatccattgctaatgagtcaaatatgaccatagtatatatgataattttctaacgcttgc--agtttcttttatttttgctacagGTACAGAAACTCGTTGAGATGGGATTTCCAGAAGCTCAAGTAAGGAGCATTTTGGAAGCTGTTGGTGGTGATGAAAACTTGGCTCTTGAAAGGTTGCTGT-
| ||||| ||| | ||| | | || | | || || ||| || | | | || | | |||| || || |||| |||||||||| ||||| || |||||||| || || |||||| ||||||||| | ||| |||| |||||||||||||||||||||||||||||| | | |||
gtattatcatcttggcttaaaaaattactgaatatggtataaac-attcatcgacctctcttcactattgta-attttttgaaaagtaaatgttcattaagttactgttggatttg-tacagGTACAAAAACTTGTGGAGATGGGCTTCCCTGAAGCTTCAGTAAGGAGTACCCTGGCAGCTTTTGGTGGTGATGAAAACTTGGCTCTTGAAAAGCT-CTGCT
















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|254321367|gb|GR824684.1|GR824684
EST:     ACTGGACAGAAAGTTTTGCCAAGGAATCGTCTCGCGGGATTGAAGACAAG                         GTACAGAAACTCGTTGAGATGGGATTTCCAGAAGCTCAAGTAAGGAGCATT
genomic: ACTGGACAGAAAGTTTTGCCAAGGAATCGTCTCGCGGGATTGAAGACAAGgtgctaagct ... tttgctacagGTACAGAAACTCGTTGAGATGGGATTTCCAGAAGCTCAAGTAAGGAGCATT
EST: gi|192329042|gb|FK019713.1|FK019713
EST:     ACTGGACAGAAAGTTTTGCCAAGGAATCGTCTCGCGGGATTGAAGACAAG                         GTACAGAAACTCGTTGAGATGGGATTTCCAGAAGCTCAAGTAAGGAGCATT
genomic: ACTGGACAGAAAGTTTTGCCAAGGAATCGTCTCGCGGGATTGAAGACAAGgtgctaagct ... tttgctacagGTACAGAAACTCGTTGAGATGGGATTTCCAGAAGCTCAAGTAAGGAGCATT
EST: gi|31466422|gb|CD408450.1|CD408450
EST:     ACTGGACAGAAAGTTTTGCCAAGGAATCGTCTCGCGGGATTGAAGACAAG                         GTACAGAAACTCGTTGAGATGGGATTTCCAGAAGCTCAAGTAAGGAGCATT
genomic: ACTGGACAGAAAGTTTTGCCAAGGAATCGTCTCGCGGGATTGAAGACAAGgtgctaagct ... tttgctacagGTACAGAAACTCGTTGAGATGGGATTTCCAGAAGCTCAAGTAAGGAGCATT
EST: gi|214006685|gb|DB987567.1|DB987567
EST:     ACTGGACAGAAAGTTTTGCCAAGGAATCGTCTCGCGGGATTGAAGACAAG                         GTACAGAAACTCGTTGAGATGGGATTTCCAGAAGCTCAAGTAAGGAGCATT
genomic: ACTGGACAGAAAGTTTTGCCAAGGAATCGTCTCGCGGGATTGAAGACAAGgtgctaagct ... tttgctacagGTACAGAAACTCGTTGAGATGGGATTTCCAGAAGCTCAAGTAAGGAGCATT
EST: gi|9440039|gb|BE440550.1|BE440550
EST:     ACTGGACAGAAAGTTTTGCCAAGGAATCGTCTCGCGGGATTGAAGACAAG                         GTACAGAAACTCGTTGAGATGGGATTTCCAGAAGCTCAAGTAAAGAGCATT
genomic: ACTGGACAGAAAGTTTTGCCAAGGAATCGTCTCGCGGGATTGAAGACAAGgtgctaagct ... tttgctacagGTACAGAAACTCGTTGAGATGGGATTTCCAGAAGCTCAAGTAAGGAGCATT
EST: gi|9205392|gb|BE331616.1|BE331616
EST:     ACTGGACAGACAGTTNTGCCAATGAATCGTCTCGCGGGATTGAAGACAAT                         GTACAGAAACTCGTTGAGATGGGATTT
genomic: ACTGGACAGAAAGTTTTGCCAAGGAATCGTCTCGCGGGATTGAAGACAAGgtgctaagct ... tttgctacagGTACAGAAACTCGTTGAGATGGGATTT
EST: gi|209715403|gb|BW682121.1|BW682121
EST:     ACTGGACAGAAAGTTTTGCCAAGGAATCGTCTCGCGGGATTGAAGACAAG                         GTACAGAAACTCGTTGAGATGGGATTTCCAGAAGCTCAAGTAAGGAGCATT
genomic: ACTGGACAGAAAGTTTTGCCAAGGAATCGTCTCGCGGGATTGAAGACAAGgtgctaagct ... tttgctacagGTACAGAAACTCGTTGAGATGGGATTTCCAGAAGCTCAAGTAAGGAGCATT
EST: gi|15204167|gb|BI426935.1|BI426935
EST:     ACTGGACAGAAAGTTTTGCCAAGGAATCGTCTCGCGGGATTGAAGACAAG                         GTACAGAAACTCGTTGAGATGGGATTTCCAGAAGCTCAAGTAAGGAGCATT
genomic: ACTGGACAGAAAGTTTTGCCAAGGAATCGTCTCGCGGGATTGAAGACAAGgtgctaagct ... tttgctacagGTACAGAAACTCGTTGAGATGGGATTTCCAGAAGCTCAAGTAAGGAGCATT
EST: gi|23727022|gb|BU761524.1|BU761524
EST:     ACTGGACAGAAAGTTTTGCCAAGGAATCGTCTCGCGGGATTGAAGACAAG                         GTACAGAAACTCGTTGAGATGGGATTTCCAGAAGCTCCAGTAAGGAGCATT
genomic: ACTGGACAGAAAGTTTTGCCAAGGAATCGTCTCGCGGGATTGAAGACAAGgtgctaagct ... tttgctacagGTACAGAAACTCGTTGAGATGGGATTTCCAGAAGCTCAAGTAAGGAGCATT
EST: gi|31467834|gb|CD409862.1|CD409862
EST:     ACTGGACAGAAAGTTTTGCCAAGGAATCGTCTCGCGGGATTGAAGACAAG                         GTACAGAAACTCGTTGAGATGGGATTTCCAGAAGCTCAAGTAAGGAGCCTT
genomic: ACTGGACAGAAAGTTTTGCCAAGGAATCGTCTCGCGGGATTGAAGACAAGgtgctaagct ... tttgctacagGTACAGAAACTCGTTGAGATGGGATTTCCAGAAGCTCAAGTAAGGAGCATT
EST: gi|298172946|gb|HO019930.1|HO019930
EST:     ACTGGACAGAAAGTTTTGCCAAGGAATCGTCTCGCGGGATTGAAGACAAG                         GTACAGAAACTCGTTGAGATGG
genomic: ACTGGACAGAAAGTTTTGCCAAGGAATCGTCTCGCGGGATTGAAGACAAGgtgctaagct ... tttgctacagGTACAGAAACTCGTTGAGATGG
EST: gi|10710312|gb|BF010036.1|BF010036
EST:     ACTGGACAGAAAGTTTTGCCAAGGAATCGTCTCGCGGGATTGAAGACAAG                         GTACAGAAACTCGTTGAGATGGGATTTCCAGAAGCTCAAGTAAGGAGCATT
genomic: ACTGGACAGAAAGTTTTGCCAAGGAATCGTCTCGCGGGATTGAAGACAAGgtgctaagct ... tttgctacagGTACAGAAACTCGTTGAGATGGGATTTCCAGAAGCTCAAGTAAGGAGCATT
EST: gi|26268069|gb|CA819132.1|CA819132
EST:     ACTGGACAGAAAGTTTTGCCAAGGAATCGTCTCGCGGGATTGAAGACAAG                         GTACAGAAACTCGTTGAGATGGGATTTCCAGAAGCTCAAGTAAGGAGCATT
genomic: ACTGGACAGAAAGTTTTGCCAAGGAATCGTCTCGCGGGATTGAAGACAAGgtgctaagct ... tttgctacagGTACAGAAACTCGTTGAGATGGGATTTCCAGAAGCTCAAGTAAGGAGCATT
EST: gi|10232663|gb|BE801551.1|BE801551
EST:     ACTGGACAGAGAGTGGTGCCAAGGAATCGTCTCGCGGGATTGAAGACAAG                         GTACAGAAACTCCTTGAGATG
genomic: ACTGGACAGAAAGTTTTGCCAAGGAATCGTCTCGCGGGATTGAAGACAAGgtgctaagct ... tttgctacagGTACAGAAACTCGTTGAGATG
EST: gi|151410843|gb|EV280658.1|EV280658
EST:     ACTGGACAGAAAGTTTTGCCAAGGAATCGTCTCGCGGGATTGAAGACAAG                         GTACAGAAACTCGTTGAGATGGGATTTCCAGAAGCTCAAGTAAGGAGCATT
genomic: ACTGGACAGAAAGTTTTGCCAAGGAATCGTCTCGCGGGATTGAAGACAAGgtgctaagct ... tttgctacagGTACAGAAACTCGTTGAGATGGGATTTCCAGAAGCTCAAGTAAGGAGCATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catagtatatatgataattttctaacgcttgcagtttcttttatttttgctacagGTACAGAAACTCGTTGAGATGGGATTTCCAGAAGCTCAAGTAAGGAGCATTTTGGAAGCTGTTGGTGGTGATGAAAACTTGGCTCTTGAAAGGTTGCTGT
                   ttctaac  putative branch site (score: 1)
 tttcttttatttttgc  putative PPT
 tatatatgataatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ataattatgaaatttaatatccattgctaatgagtcaaatatgaccatagtatatatgataattttctaacgcttgcagtttcttttatttttgctacagGTACAGAAACTCGTTGAGATGGGATTTCCAGAAGCTCAAGTAAGGAGCATTTTGGAAGCTGTTGGTGGTGATGAAAACTTGGCTCTTGAAAGGTTGCTGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - ccattgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcttgca