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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctgtctgtcactttttgttattattatttcatctcatgtataaaacctagttcaatttcttaaaaagttgggaactttttgtgttttaatctgttgttgggtttttgtagAATGATACCACACAAGACAAAGCGTGGGGAAGCTGCTCTTGCTCGTTTGAAGGTTTATGAAGGAATCCCTCCTCCATATGACAAGACCAAGAGAATGGTT

Basic information

species Glycine max
transcript GLYMA15G13670.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G13670.1 (Glycine max), 3'ss of exon 1
lower sequence: AT3G07110.1 (Arabidopsis thaliana), 3'ss of exon 1
gtctgtctgtcactttttgttattattatt-tcatctcatgtataaaacctagttcaatttcttaaaaagttgggaactttttgtgttttaat-ctgttgttgggtttttg-tagAATGATACCACACAAGACAAAGCGTGGGGAAGCTGCTCTTGCTCGTTTGAAGGTTTATGAAGGAATCCCTCCTCCATATGACAAGACCAAGAGAATGGTT
               |||| | || || |  |  |   |||| ||     | |||   | | | | ||| |  |  |  |    ||||  | |  |||| |||  | | ||  || ||||| ||||||||||| |||||||| |    ||| ||||| || |||||||| | ||||||| | ||| ||||||||||||||| |||||| ||||| 
--------------ctttgatgtttttgtagttgtacaatgtgtagt-ttttgttttttgtttgagaaaatgtgccaaatccgatgttgaattgttgtttttgtttgtgtggcagTATGATTCCACACAAGACTAAGCGTGGAGCTAATGCACTTGCCCGCTTGAAGGTCTTTGAAGGAGTTCCTACTCCATATGACAAGATCAAGAGGATGGTC

upper sequence: GLYMA15G13670.1 (Glycine max), 3'ss of exon 1
lower sequence: AT4G13170.1 (Arabidopsis thaliana), 3'ss of exon 1
gtctgtctgtcactttttgttattattatttcatctcatgtataaaacctagttcaatttcttaaaaagttgggaactttttgtgttttaatctgttgttgggtttttgtagAATGATACCACACAAGACAAAGCGTGGGGAAGCTGCTCTTGCTCGTTTGAAGGTTTATGAAGGAATCCCTCCTCCATATGACAAGACCAAGAGAATGGTT
   | | ||| |   ||   |  | |    |  |   |   || ||  ||  |||  ||| ||  |   ||||  |  ||  |  ||||   || |||| |     ||| || ||||| ||||||||||| |||||||| |  ||||| |||||||| |||||||||| ||| |||||||| ||||| || |||||||  ||||||||||||
---tctttgtgaagattcagtgatgtagcgttttaataaagatgaagtct--ttctttttttttgagttttggtgaaatt--gaatttttggcttttgtgg-----ttgcagGATGATTCCACACAAGACCAAGCGTGGTGCTGCTGCACTTGCTCGCTTGAAGGTTTTTGAGGGAATCCCACCTCCTTACGACAAGATTAAGAGAATGGTT

upper sequence: GLYMA15G13670.1 (Glycine max), 3'ss of exon 1
lower sequence: AT5G48760.1 (Arabidopsis thaliana), 3'ss of exon 1
---------------------------------------------------------------------------------gtctgtctgtcactttttg-----ttattattatttcatctca-tgtataaaacctagttcaatttcttaaaaagttgggaactttttgtgttttaatctgttgttgggtttttgtagAATGATACCACACAAGACAAAGCGTGGGGAAGCTGCTCTTGCTCGTTTGAAGGTTTATGAAGGAATCCCTCCTCCATATGACAAGACCAAGAGAATGGTT
                                                                                  | ||| ||  |||| |       | |||  |  || || ||| |  |       |      ||   ||| | ||  | |   ||  |  ||| | || |||| |  | ||| || || ||||| ||||||||||| |||||||| |  |||||  | || ||| ||||||| ||||||||  | ||| ||||||||||||||| |||||| ||||| 
gttcgtatatcaatctctcttatctctccaattagatgaggtttcgagaaattgatggttcttgctctgtatggattaagtttgtgtttgatacttatgagtgaatcatttgtggttgatttcaattcaatgcttttgaaatgatgatttagatagcagagtgattcata-gttgttatgtgtttt--gatttgtgaagTATGATTCCACACAAGACGAAGCGTGGAGCTGCTGCATTAGCACGTCTGAAGGTATATGAAGGTGTTCCTACTCCATATGACAAGATCAAGAGGATGGTC

upper sequence: GLYMA15G13670.1 (Glycine max), 3'ss of exon 1
lower sequence: AT3G24830.1 (Arabidopsis thaliana), 3'ss of exon 1
gtctgtctgtcactttttgttattattatttcatctcatgtataaaacctagttcaatttcttaaaaagttgggaactttttgtgttttaatctgttgttgggtttttgtagAATGATACCACACAAGACAAAGCGTGGGGAAGCTGCTCTTGCTCGTTTGAAGGTTTATGAAGGAATCCCTCCTCCATATGACAAGACCAAGAGAATGGTT
        ||||  ||||| | ||  |           ||| | |     | ||  || | | | |  ||   | |   ||||   | | |||  ||||      |||  || ||||| ||||||||||| |||||||| |  ||||||||||| ||||||||||| | ||| ||| | || ||||| |||||||||  |||||||||||| 
-----atggtcagcttttgatctttgtgcaatgatgtctgtgttagg---aattgtatgtttgatagtgtgatggaggatttgaaatgtgatcatttgtca----tttacagGATGATTCCACACAAGACCAAGCGTGGTGCTGCTGCTCTTGCACGTTTGAAGGTGTTTGAGGGAGTACCACCTCCTTATGACAAGGTCAAGAGAATGGTC

upper sequence: GLYMA15G13670.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv07s0005g06490.t01 (Vitis vinifera), 3'ss of exon 1
gtctgtctgtcactttttgttattattatttcatctcatgtataaaacctagttcaatttcttaaaaagttgggaactttttgtgttttaatctgttgttgggtttttgtagAATGATACCACACAAGACAAAGCGTGGGGAAGCTGCTCTTGCTCGTTTGAAGGTTTATGAAGGAATCCCTCCTCCATATGACAAGACCAAGAGAATGGTT
   | |  ||  || |   ||    | | |||||   | |||  | ||  || | ||||||    ||   ||     ||||  ||  ||  | || | |||  || |||||| ||||| || |||||||| |||||||| | ||| || ||||| || ||||||| |||||| ||||||||||| |||||||| ||||  ||||| ||||| 
--attttggtgcctgtacctttccttcacttcatt--aggtaccatacagagcttaatttc----aacactg----tttttaatgaatttttttggttttgttttattgtagGATGATTCCGCACAAGACCAAGCGTGGAGCAGCAGCCCTTGCACGATTGAAGGCTTATGAGGGAATCCCTCCACCATATGATAAGATGAAGAGGATGGTC

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|9203983|gb|BE330207.1|BE330207
EST:     CCTATCCACTTCCGCGCCCCAGCCAAGATCTTCTGGCGCACCGTTCGTGG                         AATGATACCACACAAGACAAAGCGTGGGGAAGCTGCTCTTGCTCGTTTGAA
genomic: CCTATCCACTTCCGCGCCCCAGCCAAGATCTTCTGGCGCACCGTTCGTGGgtctgtctgt ... gtttttgtagAATGATACCACACAAGACAAAGCGTGGGGAAGCTGCTCTTGCTCGTTTGAA
EST: gi|193345625|gb|FK313736.1|FK313736
EST:     CCTATCCACTTCCGCGCCCCAGCCAAGATCTTCTGGCGCACCGTTCGTGG                         AATGATACCACACAAGACAAAGCGTGGGGAAGCTGCTCTTGCTCGTTTGAT
genomic: CCTATCCACTTCCGCGCCCCAGCCAAGATCTTCTGGCGCACCGTTCGTGGgtctgtctgt ... gtttttgtagAATGATACCACACAAGACAAAGCGTGGGGAAGCTGCTCTTGCTCGTTTGAA
EST: gi|193423956|gb|FK390295.1|FK390295
EST:     CCTATCCACTTCCGCGCCCCAGCCAAGATCTTCTGGCGCACCGTTCGTGG                         AATGATACCACACAAGACAAAGCGTGGGGAAGCTGCTCTTGCTCGTTTGAT
genomic: CCTATCCACTTCCGCGCCCCAGCCAAGATCTTCTGGCGCACCGTTCGTGGgtctgtctgt ... gtttttgtagAATGATACCACACAAGACAAAGCGTGGGGAAGCTGCTCTTGCTCGTTTGAA
EST: gi|254343697|gb|GR857453.1|GR857453
EST:     CCTATCCACTTCCGCGCCCCAGCCAAGATCTTCTGGCGCACCGTTCGTGG                         AATGATACCACACAAGACAAAGCGTGGGGAAGCTGCTCTTGCTCGTTTGAA
genomic: CCTATCCACTTCCGCGCCCCAGCCAAGATCTTCTGGCGCACCGTTCGTGGgtctgtctgt ... gtttttgtagAATGATACCACACAAGACAAAGCGTGGGGAAGCTGCTCTTGCTCGTTTGAA
EST: gi|27427510|gb|CA939030.1|CA939030
EST:     CCTATCCACTTCCGCGCCCCAGCCAAGATCTTCTGGCGCACCGTTCGTGG                         AATGATACCACACAAGACAAAGCGTGGGGAAGCTGCTCTTGCTCGTTTGAA
genomic: CCTATCCACTTCCGCGCCCCAGCCAAGATCTTCTGGCGCACCGTTCGTGGgtctgtctgt ... gtttttgtagAATGATACCACACAAGACAAAGCGTGGGGAAGCTGCTCTTGCTCGTTTGAA
EST: gi|298163268|gb|HO012001.1|HO012001
EST:     CCTATCCACTTCCGCGCCCCAGCCAAGATCTTCTGGCGCACCGTTCGTGG                         AATGATACCACACAAGACAAAGCGTGGGGAAGCTGCTCTTGCTCGTTTGAA
genomic: CCTATCCACTTCCGCGCCCCAGCCAAGATCTTCTGGCGCACCGTTCGTGGgtctgtctgt ... gtttttgtagAATGATACCACACAAGACAAAGCGTGGGGAAGCTGCTCTTGCTCGTTTGAA
EST: gi|16347249|gb|BI972844.1|BI972844
EST:     CCTATCCACTTCCGCGCCCCAGCCAAGATCTTCTGGCGCACCGTTCGTGG                         AATGATACCACACAAGACAAAGCGTGGGGAAGCTGCTCTTGCTCGTTTGAA
genomic: CCTATCCACTTCCGCGCCCCAGCCAAGATCTTCTGGCGCACCGTTCGTGGgtctgtctgt ... gtttttgtagAATGATACCACACAAGACAAAGCGTGGGGAAGCTGCTCTTGCTCGTTTGAA
EST: gi|298168387|gb|HO009317.1|HO009317
EST:     CCTATCCACTTCCGCGCCCCAGCCAAGATCTTCTGGCGCACCGTTCGTGG                         AATGATACCACACAAGACAAAGCGTGGGGAAGCTGCTCTTGCTCGTTTGAA
genomic: CCTATCCACTTCCGCGCCCCAGCCAAGATCTTCTGGCGCACCGTTCGTGGgtctgtctgt ... gtttttgtagAATGATACCACACAAGACAAAGCGTGGGGAAGCTGCTCTTGCTCGTTTGAA
EST: gi|298166806|gb|HO010245.1|HO010245
EST:     CCTATCCACTTCCGCGCCCCAGCCAAGATCTTCTGGCGCACCGTTCGTGG                         AATGATACCACACAAGACAAAGCGTGGGGAAGCTGCTCTTGCTCGTTTGAA
genomic: CCTATCCACTTCCGCGCCCCAGCCAAGATCTTCTGGCGCACCGTTCGTGGgtctgtctgt ... gtttttgtagAATGATACCACACAAGACAAAGCGTGGGGAAGCTGCTCTTGCTCGTTTGAA
EST: gi|298168781|gb|HO009711.1|HO009711
EST:     CCTATCCACTTCCGCGCCCCAGCCAAGATCTTCTGGCGCACCGTTCGTGG                         AATGATACCACACAAGACAAAGCGTGGGGAAGCTGCTCTTGCTCGTTTGAA
genomic: CCTATCCACTTCCGCGCCCCAGCCAAGATCTTCTGGCGCACCGTTCGTGGgtctgtctgt ... gtttttgtagAATGATACCACACAAGACAAAGCGTGGGGAAGCTGCTCTTGCTCGTTTGAA
EST: gi|9986840|gb|BE660948.1|BE660948
EST:     CCTATCCACTTCCGCGCCCCAGCCAAGATCTTCTGGCGCACCGTTCGTGG                         AATGATACCACACAAGACAAAGCGTGGGGAAGCTGCTCTTGCTCGTTTGAA
genomic: CCTATCCACTTCCGCGCCCCAGCCAAGATCTTCTGGCGCACCGTTCGTGGgtctgtctgt ... gtttttgtagAATGATACCACACAAGACAAAGCGTGGGGAAGCTGCTCTTGCTCGTTTGAA
EST: gi|24205749|gb|BU965002.1|BU965002
EST:     CCTATCCACTTCCGCGCCCCAGCCAAGATCTTCTGGCGCACCGTTCGTGG                         AATGATACCACACAAGACAAAGCGTGGGGAAGCTGCTCTTGCTCGTTTGAA
genomic: CCTATCCACTTCCGCGCCCCAGCCAAGATCTTCTGGCGCACCGTTCGTGGgtctgtctgt ... gtttttgtagAATGATACCACACAAGACAAAGCGTGGGGAAGCTGCTCTTGCTCGTTTGAA
EST: gi|193710761|gb|FK644672.1|FK644672
EST:     CCTATCCACTTCCGCGCCCCAGCCAAGATCTTCTGGCGCACCGTTCGTGG                         AATGATACCACACAAGACAAAGCGTGGGGAAGCTGCTCTTGCTCGTTTGAA
genomic: CCTATCCACTTCCGCGCCCCAGCCAAGATCTTCTGGCGCACCGTTCGTGGgtctgtctgt ... gtttttgtagAATGATACCACACAAGACAAAGCGTGGGGAAGCTGCTCTTGCTCGTTTGAA
EST: gi|16348184|gb|BI973779.1|BI973779
EST:     CCTATCCACTTCCGCGCCCCAGCCAAGATCTTCTGGCGCACCGTTCGTGG                         AATGATACCACACAAGACAAAGCGTGGGGAAGCTGCTCTTGCTCGTTTGAA
genomic: CCTATCCACTTCCGCGCCCCAGCCAAGATCTTCTGGCGCACCGTTCGTGGgtctgtctgt ... gtttttgtagAATGATACCACACAAGACAAAGCGTGGGGAAGCTGCTCTTGCTCGTTTGAA
EST: gi|254343696|gb|GR857452.1|GR857452
EST:     CCTATCCACTTCCGCGCCCCAGCCAAGATCTTCTGGCGCACCGTTCGTGG                         AATGATACCACACAAGACAAAGCGTGGGGAAGCTGCTCTTGCTCGTTTGAA
genomic: CCTATCCACTTCCGCGCCCCAGCCAAGATCTTCTGGCGCACCGTTCGTGGgtctgtctgt ... gtttttgtagAATGATACCACACAAGACAAAGCGTGGGGAAGCTGCTCTTGCTCGTTTGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttcttaaaaagttgggaactttttgtgttttaatctgttgttgggtttttgtagAATGATACCACACAAGACAAAGCGTGGGGAAGCTGCTCTTGCTCGTTTGAAGGTTTATGAAGGAATCCCTCCTCCATATGACAAGACCAAGAGAATGGTT
                            ttttaat  putative branch site (score: 3)
                                              tttttgt  putative PPT
                    tttttgtgttttaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtctgtctgtcactttttgttattattatttcatctcatgtataaaacctagttcaatttcttaaaaagttgggaactttttgtgttttaatctgttgttgggtttttgtagAATGATACCACACAAGACAAAGCGTGGGGAAGCTGCTCTTGCTCGTTTGAAGGTTTATGAAGGAATCCCTCCTCCATATGACAAGACCAAGAGAATGGTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA