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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gaaatttttaatgggttgtaaagcatttattatctgtgcagtttttctgttgttgctttcatctctagaatgttataatatgttatgttctgcatggcagAAGCAGAAGTCCTTACAGCTCCTCCAAAGCTGGTATACAACAAACTGATTTTAAG

Basic information

species Glycine max
transcript GLYMA20G02940.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G02940.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os03g45400.1 (Oryza sativa), 3'ss of exon 3
gaaatttttaatgggttgtaaagcatttattatctgtgcagtttttctgttgttgctttcatctctagaatgttataatatgttatgttctgcatggcagAAGCAGAAGTCCTTACAGCTCCTCCAAAGCTGGTATACAACAAACTGATTTTAAG
 | ||| |     ||  | |     || |  |  |||     |  | | || ||| |    | | ||   ||  | || ||    |||  || |   ||||||||||||| ||| ||||||||||||||||||| ||||||||  |  | ||| |
tatattatgggacggagggagtatgttcacaacatgtctctgtagtatattcttgatgaattatttaatttgacacaagattcattgtcttgtaattcagAAGCAGAAGTTCTTTCAGCTCCTCCAAAGCTGGTGTACAACAACTTTGTGTTACG

upper sequence: GLYMA20G02940.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G134398_T03 (Zea mays), 3'ss of exon 4
gaaatttttaatgggtt--gtaaagcatttattatctgtgcagtttttctgttgttgctt--tcatctcta---gaatgttataatatgttatgttctgcatggcagAAGCAGAAGTCCTTACAGCTCCTCCAAAGCTGGTATACAACAAACTGATTTTAAG
       | |   |  |  ||| |   ||  || | |||  |  |||||  ||  || ||  ||||   |     ||   | | | ||||| |  | |      |||||||||| || ||| ||||||||||||| ||||| ||||||||  |  | ||| |
-------tcagctgactaagtatatatttctttttttgtaaatgttttccattagtgtttagtcattcttctgcaaagaatctgacatgtttttctttcatattcagAAGCAGATGTACTTTCAGCTCCTCCAAAACTGGTTTACAACAACTTTGTCTTACG

upper sequence: GLYMA20G02940.1 (Glycine max), 3'ss of exon 3
lower sequence: AT4G26370.1 (Arabidopsis thaliana), 3'ss of exon 3
-----------------------------------gaaatttttaatgggttgtaaagcatttattatctgtgcagtttttctgttgttgctttcatctc-tagaatgt----tataatatgttatgttctgcatggcagAAGCAGAAGTCCTTACAGCTCCTCCAAAGCTGGTATACAACAAACTGATTTTAAG
                                       ||  | ||   | | ||||    | || | ||    |  |    |   ||  |  |||||  ||  ||||    | |  | | || |  | | | || ||||||| ||||| ||| ||||||| ||||||||||| |||| ||||||  ||||| |
gtaggtctcttattcttaaaataagttttctcttctgctttactcatatatggcaaagagactcttgtttggatgggctcatgggaatt--tcccatcttgtaacatgtgaactgttgtttattctccttttcctg-cagAAGCCGAAGTGCTTTCAGCTCCCCCAAAGCTGGTGTACAGCAAACTTGTTTTACG

upper sequence: GLYMA20G02940.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv06s0004g00170.t01 (Vitis vinifera), 3'ss of exon 3
gaaatttttaatgggttgta-aagcatttattatctgtgcagtttttctgttgttgctttcatctctaga---atgttataatatgttatgttctgcatggcagAAGCAGAAGTCCTTACAGCTCCTCCAAAGCTGGTATACAACAAACTGATTTTAAG
     || |||||  ||  | |||   ||||| ||| ||  |   ||  |||  |  | | ||  || ||   |||    ||  | || |    ||  |  ||||||||||||| ||| |||||||||||||| |||| ||   |||||| |||||  |
----gttctaatgctttccataagtggttattttctttgttgccctttcgttactcttcttattactggaggcatgaaccaagtttttgttccttgtctttcagAAGCAGAAGTTCTTTCAGCTCCTCCAAAGTTGGTTTATGGCAAACTAATTTTGCG

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|208255999|gb|GE055638.1|GE055638
EST:     CGAAGAAGCAAATGAGCTACTGCGGCACATTGAAGAAGAGTCTGCCATTG                         AAGCAGAAGTCCTTACAGCTCCTCCAAAGCTGGTATACAACAAACTGATTT
genomic: CGAAGAAGCAAATGAGCTACTGCGGCACATTGAAGAAGAGTCTGCCATTGgtaacataac ... tgcatggcagAAGCAGAAGTCCTTACAGCTCCTCCAAAGCTGGTATACAACAAACTGATTT
EST: gi|192314699|gb|FK006625.1|FK006625
EST:     CGAAGAAGCAAATGAGCTACTGCGGCACATTGAAGAAGAGTCTGCCATTG                         AAGCAGAAGTCCTTACAGCTCCTCCAAAGCTGGTATACAACAAACTGATTT
genomic: CGAAGAAGCAAATGAGCTACTGCGGCACATTGAAGAAGAGTCTGCCATTGgtaacataac ... tgcatggcagAAGCAGAAGTCCTTACAGCTCCTCCAAAGCTGGTATACAACAAACTGATTT
EST: gi|9898905|gb|BE607873.1|BE607873
EST:     CGAAGAAGCAAATGAGCTACTGCGGCACATTGAAGAAGAGTCTGCCATTG                         AAGCAGAAGTCCTTACAGCTCCTCCAAAGCTGGTATACAACAAACTGATTT
genomic: CGAAGAAGCAAATGAGCTACTGCGGCACATTGAAGAAGAGTCTGCCATTGgtaacataac ... tgcatggcagAAGCAGAAGTCCTTACAGCTCCTCCAAAGCTGGTATACAACAAACTGATTT
EST: gi|58019927|gb|CX706669.1|CX706669
EST:     CGAAGAAGCAAATGAGCTACTGCGGCACATTGAAGAAGAGTCTGCCATTG                         AAGCAGAAGTCCTTACAGCTCCTCCAAAGCTGGTATACAACAAACTGATTT
genomic: CGAAGAAGCAAATGAGCTACTGCGGCACATTGAAGAAGAGTCTGCCATTGgtaacataac ... tgcatggcagAAGCAGAAGTCCTTACAGCTCCTCCAAAGCTGGTATACAACAAACTGATTT
EST: gi|192314700|gb|FK006626.1|FK006626
EST:     CGAAGAAGCAAATGAGCTACTGCGGCACATTGAAGAAGAGTCTGCCATTG                         AAGCAGAAGTCCTTACAGCTCCTCCAAAGCTGGTATACAACAAACTGATTT
genomic: CGAAGAAGCAAATGAGCTACTGCGGCACATTGAAGAAGAGTCTGCCATTGgtaacataac ... tgcatggcagAAGCAGAAGTCCTTACAGCTCCTCCAAAGCTGGTATACAACAAACTGATTT
EST: gi|209727508|gb|BW663744.1|BW663744
EST:     CGAAGAAGCAAATGAGCTACTGCGGCACATTGAAGAAGAGTCTGCCATTG                         AAGCAGAAGTCCTTACAGCTCCTCCAAAGCTGGTATACAACAAACTGATTT
genomic: CGAAGAAGCAAATGAGCTACTGCGGCACATTGAAGAAGAGTCTGCCATTGgtaacataac ... tgcatggcagAAGCAGAAGTCCTTACAGCTCCTCCAAAGCTGGTATACAACAAACTGATTT
EST: gi|51336196|gb|CO980062.1|CO980062
EST:     CGAAGAAGCAAATGAGCTACTGCGGCACATTGAAGAAGAGTCTGCCATTG                         AAGCAGAAGTCCTTACAGCTCCTCCAAAGCTGGTATACAACAAACTGATTT
genomic: CGAAGAAGCAAATGAGCTACTGCGGCACATTGAAGAAGAGTCTGCCATTGgtaacataac ... tgcatggcagAAGCAGAAGTCCTTACAGCTCCTCCAAAGCTGGTATACAACAAACTGATTT
EST: gi|9258967|gb|BE347114.1|BE347114
EST:     CGAAGAAGCACATGAGCTACTGCGGCACATTGAAGAAGAGTCTGCCATTG                         AAGCAGAAGTCCTTACAGCTCCTACAAAGCTGGTATACAACAGACTGGATT
genomic: CGAAGAAGCAAATGAGCTACTGCGGCACATTGAAGAAGAGTCTGCCATTGgtaacataac ... tgcatggcagAAGCAGAAGTCCTTACAGCTCCTCCAAAGCTGGTATACAACAAACTG-ATT
EST: gi|57574769|gb|CX547744.1|CX547744
EST:     CGAAGAAGCAAATGAGCTACTGCGGCACATTGAAGAAGAGTCTGCCATTG                         AAGCAGAAGTCCTTACAGCTCCTCCAAAGCTGGTATACAACAAACTGATTT
genomic: CGAAGAAGCAAATGAGCTACTGCGGCACATTGAAGAAGAGTCTGCCATTGgtaacataac ... tgcatggcagAAGCAGAAGTCCTTACAGCTCCTCCAAAGCTGGTATACAACAAACTGATTT
EST: gi|192294862|gb|FG987551.1|FG987551
EST:     CGAAGAAGCAAATGAGCTACTGCGGCACATTGAAGAAGAGTCTGCCATTG                         AAGCAGAAGTCCTTACAGCTCCTCCAAAGCTGGTATACAACAAACTGATTT
genomic: CGAAGAAGCAAATGAGCTACTGCGGCACATTGAAGAAGAGTCTGCCATTGgtaacataac ... tgcatggcagAAGCAGAAGTCCTTACAGCTCCTCCAAAGCTGGTATACAACAAACTGATTT
EST: gi|192316707|gb|FK006410.1|FK006410
EST:     CATTGAAGAAGAGTCTGCCATTG                         AAGCAGAAGTCCTTACAGCTCCTCCAAAGCTGGTATATAACAAACTGATTT
genomic: CATTGAAGAAGAGTCTGCCATTGgtaacataac ... tgcatggcagAAGCAGAAGTCCTTACAGCTCCTCCAAAGCTGGTATACAACAAACTGATTT
EST: gi|9899175|gb|BE608202.1|BE608202
EST:     CGAAGAAGCAAATGAGCTACTGCGGCACATTGAAGAAGAGTCTGCCATTG                         AAGCAGAAGTCCTTACAGCTCCTCCAAAGCTGGTATACAACAAACTGATTT
genomic: CGAAGAAGCAAATGAGCTACTGCGGCACATTGAAGAAGAGTCTGCCATTGgtaacataac ... tgcatggcagAAGCAGAAGTCCTTACAGCTCCTCCAAAGCTGGTATACAACAAACTGATTT
EST: gi|26058037|gb|CA800951.1|CA800951
EST:     CGAAGAAGCAAATGAGCTACTGCGGCACATTGAAGAAGAGTCTGCCATTG                         AAGCAGAAGTCCTTACAGCTCCTCCAAAGCTGGTATACAACAAACTGATTT
genomic: CGAAGAAGCAAATGAGCTACTGCGGCACATTGAAGAAGAGTCTGCCATTGgtaacataac ... tgcatggcagAAGCAGAAGTCCTTACAGCTCCTCCAAAGCTGGTATACAACAAACTGATTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctgttgttgctttcatctctagaatgttataatatgttatgttctgcatggcagAAGCAGAAGTCCTTACAGCTCCTCCAAAGCTGGTATACAACAAACTGATTTTAAG
                    tagaatgttataatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gaaatttttaatgggttgtaaagcatttattatctgtgcagtttttctgttgttgctttcatctctagaatgttataatatgttatgttctgcatggcagAAGCAGAAGTCCTTACAGCTCCTCCAAAGCTGGTATACAACAAACTGATTTTAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - -tgggttg
- - - - - - - - - - - - - - - - tctgtgc
- - - - - - - - - - - - - - - - - - - - - - -tctgttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgttatg