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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctttttttctaagtgctgcaacgatcaatgcctgaagaattgaatgaagaaaaaaatgcttatgggtactgattgattcttcgttgtgtggtttgtgcagAAAGTTCAGAAGGCTCTTCTGCAATCCGATGTGCACTCAAAGTCAGACAAAAGTCCTGTCACAGTGGCTGATTATG

Basic information

species Glycine max
transcript GLYMA05G26250.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G26250.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G152757_T01 (Zea mays), 3'ss of exon 1
-----ctttttttctaagtgctgcaacgatcaatgcctgaagaattgaatgaagaaaaaaatgcttatgggtactgattgattcttcgttgtgtggtttgtgcagAAAGTTCAGAAGGCTCTTCTGCAATCCGATGTGCACTCAAAGTCAGACAAAAGTCCTGTCACAGTGGCTGATTATG
        |       |||| ||    |     |   |||    ||  |    | | |   |||   | || | | ||   || |  ||| |||    |   |||| ||||||  ||| | || |||| || |  || ||  | ||| |||||||||||||||||||||||||||||||||
aaaaagaatcacatatagtgatggggtggc--gtatttgattgtttagacc--ggataccgtgcagtttgg-atttatctcttttctgttttgtttcctccccagACAGTTCAACAGGATATTATGCATTCTGGCGTTCAGGCTAAGGCAGACAAAAGTCCTGTCACAGTGGCTGATTATG

upper sequence: GLYMA05G26250.1 (Glycine max), 3'ss of exon 1
lower sequence: AT5G63980.1 (Arabidopsis thaliana), 3'ss of exon 1
---ctttttttctaagtgctgcaacgatcaatgcctgaagaattgaatgaagaaaaaaatgcttatgggtactgattgattcttcgttgtgtggtttgtgcagAAAGTTCAGAAGGCTCTTCTGCAATCCGATGTGCACTCAAAGTCAGACAAAAGTCCTGTCACAGTGGCTGATTATG
     |   ||||| ||| |  |  |       |||  | |   |||    |   |||    | ||    |    ||   | |  ||| || | ||  | ||||||||||| |||||| |  ||||||| |||||||| ||||| || || |||||||| || || || ||||||||||
gggaatagattcta-gtgatatagtgtaatggtcctctacatacgaagctcgtgtaaatctttgatcaaaatc--ttatctttgtgttttgggtttgtttcagAAAGTTCAAAAGGCTTTGTTGCAATCAGATGTGCAATCAAAATCTGATAAAAGTCCAGTGACCGTTGCTGATTATG

upper sequence: GLYMA05G26250.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv04s0044g01480.t01 (Vitis vinifera), 3'ss of exon 1
------ctttttttctaagtgctgcaacgatcaatgcctgaagaattgaatgaagaaaaaaatgcttatgggtactgattgattcttcgttgtgtggtttgtgcagAAAGTTCAGAAGGCTCTTCTGCAATCCGATGTGCACTCAAAGTCAGACAAAAGTCCTGTCACAGTGGCTGATTATG
       |  |||| || |||         | | | | || |   || | ||   | | |  ||  |||  ||| | ||  ||   |  ||      |||   |||||||| || ||||| ||  ||||||| ||||| || || || ||||| ||||| ||||||||||||||||| ||||
tgaaatttgattttgtatgtgtgcgtgtcctgatttcatgtatggtttagtgtgtatatatgtggatatatgtatttatgtatgtattatt------ttttctcagAAAGTGCAAAAGGCGCTGTTGCAATCAGATGTCCAATCTAAATCAGATAAAAGCCCTGTCACAGTGGCTGACTATG

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|151398725|gb|EV268596.1|EV268596
EST:     AACTCGCCGCTGCAAAGAAAGCAGTCACTCTCGCTGCTCGTCTCTGCCAG                         AAAGTTCAGAAGGCTCTTCTGCAATCCGATGTGCACTCAAAGTCAGACAAA
genomic: AACTCGCCGCTGCAAAGAAAGCAGTCACTCTCGCTGCTCGTCTCTGCCAGgcaccccttc ... gtttgtgcagAAAGTTCAGAAGGCTCTTCTGCAATCCGATGTGCACTCAAAGTCAGACAAA
EST: gi|15813517|gb|BI785792.1|BI785792
EST:     AACTCGCCGCTGCAAAGAAAGCAGTCACTCTCGCTGCTCGTCTCTG-C--                         ------CAGAAGGCTCTTCTGCAATCCGATGTGCACTCAAAGTCAGACAAA
genomic: AACTCGCCGCTGCAAAGAAAGCAGTCACTCTCGCTGCTCGTCTCTGCCAGgcaccccttc ... gtttgtgcagAAAGTTCAGAAGGCTCTTCTGCAATCCGATGTGCACTCAAAGTCAGACAAA
EST: gi|192294187|gb|FG986276.1|FG986276
EST:     AACTCGCCGCTGCAAAGAAAGCAGTCACTCTCGCTGCTCGTCTCTGCCAG                         AAAGTTCGGAAGGCTCTTCTGCAATCCGATGTGCACTCAAAGTCAGACAAA
genomic: AACTCGCCGCTGCAAAGAAAGCAGTCACTCTCGCTGCTCGTCTCTGCCAGgcaccccttc ... gtttgtgcagAAAGTTCAGAAGGCTCTTCTGCAATCCGATGTGCACTCAAAGTCAGACAAA
EST: gi|192330285|gb|FK020570.1|FK020570
EST:     AACTCGCCGCTGCAAAGAAAGCAGTCACTCTCGCTGCTCGTCTCTGCCAG                         AAAGTTCAGAAGGCTCTTCTGCAATCCGATGTGCACTCAAAGTCAGACAAA
genomic: AACTCGCCGCTGCAAAGAAAGCAGTCACTCTCGCTGCTCGTCTCTGCCAGgcaccccttc ... gtttgtgcagAAAGTTCAGAAGGCTCTTCTGCAATCCGATGTGCACTCAAAGTCAGACAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaagaaaaaaatgcttatgggtactgattgattcttcgttgtgtggtttgtgcagAAAGTTCAGAAGGCTCTTCTGCAATCCGATGTGCACTCAAAGTCAGACAAAAGTCCTGTCACAGTGGCTGATTATG
     aaaaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctttttttctaagtgctgcaacgatcaatgcctgaagaattgaatgaagaaaaaaatgcttatgggtactgattgattcttcgttgtgtggtttgtgcagAAAGTTCAGAAGGCTCTTCTGCAATCCGATGTGCACTCAAAGTCAGACAAAAGTCCTGTCACAGTGGCTGATTATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - gtgctgc
- - - - - - - - - - - - -caatgcc
- - - - - - - - - - - - - - - - - - - - tgaatga
- - - - - - - - - - - - - - - - - - - - - - - - -aaaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcttatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctgattg