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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgcagtatttctgtttgctaatagcatgttatgtatttgcaacaggatttgtttgatatattttatttttgacttttatttgccatcatatgtaattagGTTGTGGAGAGCGGAGGCAAGAACATAGAAGTTGCTGTGATGACTAAGGAGCATGGTCTGCATCAACTGGAGGAAGCTGAAATTGATGCCATCGTTGCTG

Basic information

species Glycine max
transcript GLYMA02G05190.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G05190.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv03s0038g02300.t01 (Vitis vinifera), 3'ss of exon 2
ttgcagtatttctgtttgctaatagcatgttatgtatttgcaacaggatttgtttgatatattttatt--tttgacttttatttgcca-tcatatgt------aattagGTTGTGGAGAGCGGAGGCAAGAACATAGAAGTTGCTGTGATGACTAAGGAGCATGGTCTGCATCAACTGGAGGAAGCTGAAATTGATGCCATCGTTGCTG
         |  |||     || ||| |||| |   | |  |||          || |   || | ||  | |||||||   ||   | |||| | |      || |||||||| ||||| || || || ||||||||  |||| |||||||| || ||||||||  |||  ||||| || |||||||| ||||||||||| |||||||
--------atcatgtccaagaaaagcctgtt-taattctataacttatccctcatggttgcttcttttgatctgactttagcttttgagtcatgttttgcttcaaatagGTTGTTGAGAGTGGGGGAAAAAACATAGAGATTGCCGTGATGACGAAAGAGCATGGATTGCGGCAACTTGAAGAAGCTGAGATTGATGCCATTGTTGCTG

upper sequence: GLYMA02G05190.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv04s0023g03690.t01 (Vitis vinifera), 3'ss of exon 2
--ttgcagt-atttctgtttgctaatagcatgttatgtatttgcaacaggatttgtttgatatattttatttttgacttttatt-tgccatcatatgtaattagGTTGTGGAGAGCGGAGGCAAGAACATAGAAGTTGCTGTGATGACTAAGGAGCATGGTCTGCATCAACTGGAGGAAGCTGAAATTGATGCCATCGTTGCTG
    | ||  | ||  ||    |  ||  ||| | ||||  |         ||  ||| | |    | | ||||| | | | || |   || | |||||    ||| || ||||| ||||| |||||||||||| ||||||||||||| | ||||||||||||||  ||||| || || ||||||||||||||||| |||||||
tggggtagcgagttgagtgatttggtatgatggtttgtacatttgtatatcttgatttcagaagcataacttttggcatgtgttatcttattacatgta----gGTGGTTGAGAGTGGAGGAAAGAACATAGAAATTGCTGTGATGACGAGGGAGCATGGTCTGCGGCAACTTGATGAGGCTGAAATTGATGCCATTGTTGCTG

upper sequence: GLYMA02G05190.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ31080 (Selaginella moellendorffii), 3'ss of exon 2
ttgcagtatttctgtttgctaatagcatgttatgtatttgcaacaggatttgtttgatatattttatttttgacttttatttgccatcatatgtaattagGTTGTGGAGAGCGGAGGCAAGAACATAGAAGTTGCTGTGATGACTAAGGAGCATGGTCTGCATCAACTGGAGGAAGCTGAAATTGATGCCATCGTTGCTG---
                                    |  ||||   | ||||   |||     ||  | |  ||||||        || |  ||   ||||||||||||||||| ||||||||||| ||  | ||||||||||| |     || || ||  |    ||||||||  | || || || |  || |||   |   
-----------------------------------gtaagcaaagagttttg---gatcgcgctttctctaaacttttggaacttgtc-tgggtctatagGTTGTGGAGAGCGGTGGCAAGAACATCGAGATCGCTGTGATGACCAG---ACAAGGGCTCAAATTGCTGGAGGAGCCCGAGATCGAAGAGATTGTTAACGGGA

upper sequence: GLYMA02G05190.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ34636 (Selaginella moellendorffii), 3'ss of exon 2
ttgcagtatttctgtttgctaatagcatgttatgtatttgcaacaggatttgtttgatatattttatttttgacttttatttgccatcatatgtaattagGTTGTGGAGAGCGGAGGCAAGAACATAGAAGTTGCTGTGATGACTAAGGAGCATGGTCTGCATCAACTGGAGGAAGCTGAAATTGATGCCATCGTTGCTG---
                        | | |  | |  |||   |  |   || | |   || |      | | ||||||    |   || |  ||   ||||||||||||||||| ||||||||||| ||  | ||||||||||| |     || || ||| |    ||||||||  | || || || |  || |||   |   
------------------------gtaagcaaagagttttggattgcgcttctctcggatctg-----tctaacttttg---gaactcgtgggtctatagGTTGTGGAGAGCGGTGGCAAGAACATCGAGATCGCTGTGATGACCAG---ACAAGGACTGAAATTGCTGGAGGAGCCCGAGATCGAAGAGATTGTTAACGGGA

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|192313981|gb|FK007685.1|FK007685
EST:     ACACCTCTGGCCAGGAGACTGTCAAGTTGGCTATTCGCGCATTGCTTGAA                         GTTGTGGAGAGCGGAGGCAAGAACATAGAAGTTGCTGTGATGACTAAGGAG
genomic: ACACCTCTGGCCAGGAGACTGTCAAGTTGGCTATTCGCGCATTGCTTGAAgtgagtttcg ... atgtaattagGTTGTGGAGAGCGGAGGCAAGAACATAGAAGTTGCTGTGATGACTAAGGAG
EST: gi|207696035|gb|GD678776.1|GD678776
EST:     GGCCGGGAGACTGTCAAGTTGGCTATTCGCGCATTGCTTGAA                         GTTGTGGAGAGCGGAGGCAAGAACATAGAAGTTGCTGTGATGACTAAGGAG
genomic: GGCCAGGAGACTGTCAAGTTGGCTATTCGCGCATTGCTTGAAgtgagtttcg ... atgtaattagGTTGTGGAGAGCGGAGGCAAGAACATAGAAGTTGCTGTGATGACTAAGGAG
EST: gi|193358710|gb|FK326708.1|FK326708
EST:     GGCCGGGAGACTGTCAAGTTGGCTATTCGCGCATTGCTTGAA                         GTTGTGGAGAGCGGAGGCAAGAACATAGAAGTTGCTGTGATGACTAAGGAG
genomic: GGCCAGGAGACTGTCAAGTTGGCTATTCGCGCATTGCTTGAAgtgagtttcg ... atgtaattagGTTGTGGAGAGCGGAGGCAAGAACATAGAAGTTGCTGTGATGACTAAGGAG
EST: gi|208064806|gb|GD861616.1|GD861616
EST:     ACACCTCTGGCCAGGAGACTGTCAAGTTGGCTATTCGCGCATTGCTTGAA                         GTTGTGGAGAGCGGAGGCAAGAACATAGAAGTTGCTGTGATGACTAAGGAG
genomic: ACACCTCTGGCCAGGAGACTGTCAAGTTGGCTATTCGCGCATTGCTTGAAgtgagtttcg ... atgtaattagGTTGTGGAGAGCGGAGGCAAGAACATAGAAGTTGCTGTGATGACTAAGGAG
EST: gi|10255934|gb|BE823700.1|BE823700
EST:     ACACCTCTGGCCAGGAGACTGTCAAGTTGGCTATTCGCGCATTGCTTGAA                         GTTGTGGAGAGCGGAGGCAAGAACATAGAAGTTGCTGTGATGACTAAGGAG
genomic: ACACCTCTGGCCAGGAGACTGTCAAGTTGGCTATTCGCGCATTGCTTGAAgtgagtttcg ... atgtaattagGTTGTGGAGAGCGGAGGCAAGAACATAGAAGTTGCTGTGATGACTAAGGAG
EST: gi|193410459|gb|FK379820.1|FK379820
EST:     ACTGTTCAAGTTGGCTATTCGCGCATTGCTTGAA                         GTTGTGGAGAGCGGAGGCAAGAACATAGAAGTTGCTGTGATGACTAAGGAG
genomic: ACTG-TCAAGTTGGCTATTCGCGCATTGCTTGAAgtgagtttcg ... atgtaattagGTTGTGGAGAGCGGAGGCAAGAACATAGAAGTTGCTGTGATGACTAAGGAG
EST: gi|193320191|gb|FK284368.1|FK284368
EST:     CACCTCTGGCCAGGAGACTGTCAAGTTGGCTATTCGCGCATTGCTTGAA                         GTTGTGGAGAGCGGAGGCAAGAACATAGAAGTTGCTGTGATGACTAAGGAG
genomic: CACCTCTGGCCAGGAGACTGTCAAGTTGGCTATTCGCGCATTGCTTGAAgtgagtttcg ... atgtaattagGTTGTGGAGAGCGGAGGCAAGAACATAGAAGTTGCTGTGATGACTAAGGAG
EST: gi|193613819|gb|FK566341.1|FK566341
EST:     ACACCTCTGGCCAGGAGACTGTCAAGTTGGCTATTCGCGCATTGCTTGAA                         GTTGTGGAGAGCGGAGGCAAGAACATAGAAGTTGCTGTGATGACTAAGGAG
genomic: ACACCTCTGGCCAGGAGACTGTCAAGTTGGCTATTCGCGCATTGCTTGAAgtgagtttcg ... atgtaattagGTTGTGGAGAGCGGAGGCAAGAACATAGAAGTTGCTGTGATGACTAAGGAG
EST: gi|193419656|gb|FK384062.1|FK384062
EST:     GGCCGGGAGACTGTTCAAGTTGGCTATTCGCGCATTGCTTGAA                         GTTGTGGAGAGCGGAGGCAAGAACATAGAAGTTGCTGTGATGACTAAGGAG
genomic: GGCCAGGAGACTG-TCAAGTTGGCTATTCGCGCATTGCTTGAAgtgagtttcg ... atgtaattagGTTGTGGAGAGCGGAGGCAAGAACATAGAAGTTGCTGTGATGACTAAGGAG
EST: gi|192313982|gb|FK007686.1|FK007686
EST:     ACACCTCTGGCCAGGAGACTGTCAAGTTGGCTATTCGCGCATTGCTTGAA                         GTTGTGGAGAGCGGAGGCAAGAACATAGAAGTTGCTGTGATGACTAAGGAG
genomic: ACACCTCTGGCCAGGAGACTGTCAAGTTGGCTATTCGCGCATTGCTTGAAgtgagtttcg ... atgtaattagGTTGTGGAGAGCGGAGGCAAGAACATAGAAGTTGCTGTGATGACTAAGGAG
EST: gi|208218606|gb|GE019662.1|GE019662
EST:     AGACTGTCAAGTTGGCTATTCGCGCATTGCTTGAA                         GTTGTGGAGAGCGGAGGCAAGAACATAGAAGTTGCTGTGATGACTAAGGAG
genomic: AGACTGTCAAGTTGGCTATTCGCGCATTGCTTGAAgtgagtttcg ... atgtaattagGTTGTGGAGAGCGGAGGCAAGAACATAGAAGTTGCTGTGATGACTAAGGAG
EST: gi|193638678|gb|FK586836.1|FK586836
EST:     ACACCTCTGGCCAGGAGACTGTCAAGTTGGCTATTCGCGCATTGCTTGAA                         GTTGTGGAGAGCGGAGGCAAGAACATAGAAGTTGCTGTGATGACTAAGGAG
genomic: ACACCTCTGGCCAGGAGACTGTCAAGTTGGCTATTCGCGCATTGCTTGAAgtgagtttcg ... atgtaattagGTTGTGGAGAGCGGAGGCAAGAACATAGAAGTTGCTGTGATGACTAAGGAG
EST: gi|193417269|gb|FK382541.1|FK382541
EST:     GGCCGGGAGACTGTTCAAGTTGGCTATTCGCGCATTGCTTGAA                         GTTGTGGAGAGCGGAGGCAAGAACATAGAAGTTGCTGTGAATGACTAAGGA
genomic: GGCCAGGAGACTG-TCAAGTTGGCTATTCGCGCATTGCTTGAAgtgagtttcg ... atgtaattagGTTGTGGAGAGCGGAGGCAAGAACATAGAAGTTGCTGTG-ATGACTAAGGA
EST: gi|208128292|gb|GD921292.1|GD921292
EST:     ACACCTCTGGCCAGGAGACTGTCAAGTTGGCTATTCGCGCATTGCTTGAA                         GTTGTGGAGAGCGGAGGCAAGAACATAGAAGTTGCTGTGATGACTAAGGAG
genomic: ACACCTCTGGCCAGGAGACTGTCAAGTTGGCTATTCGCGCATTGCTTGAAgtgagtttcg ... atgtaattagGTTGTGGAGAGCGGAGGCAAGAACATAGAAGTTGCTGTGATGACTAAGGAG
EST: gi|193330420|gb|FK292734.1|FK292734
EST:     GGCCGGGAGACTGTCAAGTTGGCTATTCGCGCATTGCTTGAA                         GTTGTGGAGAGCGGAGGCAAGAACATAGAAGTTGCTGTGATGACTAAGGAG
genomic: GGCCAGGAGACTGTCAAGTTGGCTATTCGCGCATTGCTTGAAgtgagtttcg ... atgtaattagGTTGTGGAGAGCGGAGGCAAGAACATAGAAGTTGCTGTGATGACTAAGGAG
EST: gi|23064196|gb|BU578969.1|BU578969
EST:     ACACCTCTGGCCAGGAGACTGTCAAGTTGGCTATTCGCGCATTGCTTGAA                         GTTGTGGAGAGCGGAGGCAAGAACATAGAAGTTGCTGTGATGACTAAGGAG
genomic: ACACCTCTGGCCAGGAGACTGTCAAGTTGGCTATTCGCGCATTGCTTGAAgtgagtttcg ... atgtaattagGTTGTGGAGAGCGGAGGCAAGAACATAGAAGTTGCTGTGATGACTAAGGAG
EST: gi|193330961|gb|FK297237.1|FK297237
EST:     GGCCGGGAGACTGTCAAGTTGGCTATTCGCGCATTGCTTGAA                         GTTGTGGAGAGCGGAGGCAAGAACATAGAAGTTGCTGTGATGACTAAGGAG
genomic: GGCCAGGAGACTGTCAAGTTGGCTATTCGCGCATTGCTTGAAgtgagtttcg ... atgtaattagGTTGTGGAGAGCGGAGGCAAGAACATAGAAGTTGCTGTGATGACTAAGGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggatttgtttgatatattttatttttgacttttatttgccatcatatgtaattagGTTGTGGAGAGCGGAGGCAAGAACATAGAAGTTGCTGTGATGACTAAGGAGCATGGTCTGCATCAACTGGAGGAAGCTGAAATTGATGCCATCGTTGCTG
                      ttttgac  putative branch site (score: 3)
     tgtttgatatatttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgcagtatttctgtttgctaatagcatgttatgtatttgcaacaggatttgtttgatatattttatttttgacttttatttgccatcatatgtaattagGTTGTGGAGAGCGGAGGCAAGAACATAGAAGTTGCTGTGATGACTAAGGAGCATGGTCTGCATCAACTGGAGGAAGCTGAAATTGATGCCATCGTTGCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
-tgcagta
- - - - - - tgtttgc
- - - - - - - - - - - - gcatgtt
- - - - - - - - - - - - - - - - - - - tgcaaca
- - - - - - - - - - - - - - - - - - - - - - - - -ttgtttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgccatc