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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tagtgatgcatttgctataaaattgctctgtctctatttctccatatgttagctttgtagtttaaactcgtgtatcatttttttgttttccccttcccagTTACTGTCAGTGAGGTTGAAGCACTGTTTGAGCTTTTTAGGAGCATCAGCAGTTCTGTTGTCGATGACGGACTGATAAGCAAG

Basic information

species Glycine max
transcript GLYMA05G05580.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G05580.1 (Glycine max), 3'ss of exon 2
lower sequence: AT4G17615.1 (Arabidopsis thaliana), 3'ss of exon 2
-tagtgatgcatttgctataaaattgctctgtctctatttctccatatgttagctttgtagtttaaactcgt-gtatcatttttttgttttccccttcccagTTACTGTCAGTGAGGTTGAAGCACTGTTTGAGCTTTTTAGGAGCATCAGCAGTTCTGTTGTCGATGACGGACTGATAAGCAAG
 ||    || |||   ||     ||  | ||| | | | | |     || ||  | | |  ||| | ||||| || |   || ||| ||||| | || ||||||| ||| ||||||||||||||| | |||||||| || | |||||| |||||||| ||||| ||||| || ||||| | ||||
ctaaatgtgaatt-attagtctctttgtttgtttgtttgtttgttcctggtaattctttgttttgatctcgtagtgttgcttgttt-ttttctcttttccagTTAGTGTGAGTGAGGTTGAAGCATTATTTGAGCTATTCAAGAGCATAAGCAGTTCGGTTGTTGATGATGGTCTGATTAACAAG

upper sequence: GLYMA05G05580.1 (Glycine max), 3'ss of exon 2
lower sequence: AT4G17615.2 (Arabidopsis thaliana), 3'ss of exon 2
-tagtgatgcatttgctataaaattgctctgtctctatttctccatatgttagctttgtagtttaaactcgt-gtatcatttttttgttttccccttcccagTTACTGTCAGTGAGGTTGAAGCACTGTTTGAGCTTTTTAGGAGCATCAGCAGTTCTGTTGTCGATGACGGACTGATAAGCAAG-----------------
 ||    || |||   ||     ||  | ||| | | | | |     || ||  | | |  ||| | ||||| || |   || ||| ||||| | || ||||||| ||| ||||||||||||||| | |||||||| || | |||||| |||||||| ||||| ||||| || ||||| | ||||                 
ctaaatgtgaatt-attagtctctttgtttgtttgtttgtttgttcctggtaattctttgttttgatctcgtagtgttgcttgttt-ttttctcttttccagTTAGTGTGAGTGAGGTTGAAGCATTATTTGAGCTATTCAAGAGCATAAGCAGTTCGGTTGTTGATGATGGTCTGATTAACAAGGTACAAAGTTTGTTTCT

upper sequence: GLYMA05G05580.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv02s0236g00150.t01 (Vitis vinifera), 3'ss of exon 2
--------tagtgatgcatttgctataaaattgctctgtctctatttctccatatgttagctttgtagttta--aactcgtgtatcatttttttgttttccccttcccagTTACTGTCAGTGAGGTTGAAGCACTGTTTGAGCTTTTTAGGAGCATCAGCAGTTCTGTTGTCGATGACGGACTGATAAGCAAG
           || ||||||    | |  |||  | | | | | ||| |    ||||  | ||  ||||     ||||    |  ||||| ||  || | |       ||||| ||| ||||| ||||||||||| |||||||| || | |||||| || ||||||||  | ||||| ||  | |||| ||||
tattttttctatggtgcattc-taacagcatta-tatctttttgtttattttgatgtc-gattgatagtgagccaactgtcttgccatttcttgattcttc-------agTTAGTGTGAGTGAAGTTGAAGCACTATTTGAGCTATTCAAGAGCATTAGTAGTTCTGTAATTGATGATGGGTTAATAAACAAG

upper sequence: GLYMA05G05580.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv02s0236g00140.t01 (Vitis vinifera), 3'ss of exon 2
--------tagtgatgcatttgctataaaattgctctgtctctatttctccatatgttagctttgtagttta--aactcgtgtatcatttttttgttttccccttcccagTTACTGTCAGTGAGGTTGAAGCACTGTTTGAGCTTTTTAGGAGCATCAGCAGTTCTGTTGTCGATGACGGACTGATAAGCAAG
           || ||||||    | |  |||  | | | | | ||| |    ||||  | ||  ||||     ||||    |  ||||| ||  || | |       ||||| ||| ||||| ||||||||||| |||||||| || | |||||| |||||||||||  | ||||| ||  | |||| ||||
tattttttctatggtgcattc-taacagcatta-tatctttttgtttattttgatgtc-gattgatagtgagccaactgtcttgccatttcttgattcttc-------agTTAGTGTGAGTGAAGTTGAAGCACTATTTGAGCTATTCAAGAGCATTAGCAGTTCTGTAATTGATGATGGGTTAATAAACAAG

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|151409699|gb|EV279507.1|EV279507
EST:     GCAGTTTCCTGCACAGGAGAATACTGCTAATCTTGCGGCAGAGACAGCTT                         TTACTGTCAGTGAGGTTGAAGCACTGTTTGAGCTTTTTAGGAGCATCAGCA
genomic: GCAGTTTCCTGCACAGGAGAATACTGTTAATCTTGCGGCAGAGACAGCTTgtacgttgat ... cccttcccagTTACTGTCAGTGAGGTTGAAGCACTGTTTGAGCTTTTTAGGAGCATCAGCA
EST: gi|192316102|gb|FK007163.1|FK007163
EST:     GCAGTTTCCTGCACAGGAGAATACTGTTAATCTTGCGGCAGAGACAGCTT                         TTACTGTCAGTGAGGTTGAAGCACTGTTTGAGCTTTTTAGGAGCATCAGCA
genomic: GCAGTTTCCTGCACAGGAGAATACTGTTAATCTTGCGGCAGAGACAGCTTgtacgttgat ... cccttcccagTTACTGTCAGTGAGGTTGAAGCACTGTTTGAGCTTTTTAGGAGCATCAGCA
EST: gi|17023266|gb|BM094300.1|BM094300
EST:     GCAGTTTCCTGCACAGGAGAATACTGTTAATCTTGCGGCAGAGACAGCTT                         TTACTGTCAGTGAGGTTGAAGCACTGTTTGAGCTTTTTAGGAGCATCAGCA
genomic: GCAGTTTCCTGCACAGGAGAATACTGTTAATCTTGCGGCAGAGACAGCTTgtacgttgat ... cccttcccagTTACTGTCAGTGAGGTTGAAGCACTGTTTGAGCTTTTTAGGAGCATCAGCA
EST: gi|4396493|gb|AI495490.1|AI495490
EST:     GCAGTTTCCTGCACAGGAGAATACTGTTAATCTTGCGGCAGAGACAGCTT                         TTACTGGCAGTGAGGTTGAAGCACTGTTTGAGCTTTTTAGGAGCATCAGCA
genomic: GCAGTTTCCTGCACAGGAGAATACTGTTAATCTTGCGGCAGAGACAGCTTgtacgttgat ... cccttcccagTTACTGTCAGTGAGGTTGAAGCACTGTTTGAGCTTTTTAGGAGCATCAGCA
EST: gi|192304797|gb|FG998799.1|FG998799
EST:     GCAGTTTCCTGCACAGGAGAATACTGTTAATCTTGCGGCAGAGACAGCTT                         TTACTGTCAGTGAGGTTGAAGCACTGTTTGAGCTTTTTAGGAGCATCAGCA
genomic: GCAGTTTCCTGCACAGGAGAATACTGTTAATCTTGCGGCAGAGACAGCTTgtacgttgat ... cccttcccagTTACTGTCAGTGAGGTTGAAGCACTGTTTGAGCTTTTTAGGAGCATCAGCA
EST: gi|151410148|gb|EV279956.1|EV279956
EST:     GCAGTTTCCTGCACAGGAGAATACTGTTAATCTTGCGGCAGAGACAGCTT                         TTACTGTCAGTGAGGTTGAAGCACTGTTTGAGCTTTTTAGGAGCATCAGCA
genomic: GCAGTTTCCTGCACAGGAGAATACTGTTAATCTTGCGGCAGAGACAGCTTgtacgttgat ... cccttcccagTTACTGTCAGTGAGGTTGAAGCACTGTTTGAGCTTTTTAGGAGCATCAGCA
EST: gi|192307027|gb|FK000005.1|FK000005
EST:     GCAGTTTCCTGCACAGGAGAATACTGTTAATCTTGCGGCAGAGACAGCTT                         TTACTGTCAGTGAGGTTGAAGCACTGTTTGAGCTTTTTAGGAGCATCAGCA
genomic: GCAGTTTCCTGCACAGGAGAATACTGTTAATCTTGCGGCAGAGACAGCTTgtacgttgat ... cccttcccagTTACTGTCAGTGAGGTTGAAGCACTGTTTGAGCTTTTTAGGAGCATCAGCA
EST: gi|17023184|gb|BM094218.1|BM094218
EST:     GCAGTTTCCTGCACAGGAGAATACTGTTAATCTTGCGGCAGAGACAGCTT                         TTACTGTCAGTGAGGTTGAAGCACTGTTTGAGCTTTTTAGGAGCATCAGCA
genomic: GCAGTTTCCTGCACAGGAGAATACTGTTAATCTTGCGGCAGAGACAGCTTgtacgttgat ... cccttcccagTTACTGTCAGTGAGGTTGAAGCACTGTTTGAGCTTTTTAGGAGCATCAGCA
EST: gi|213599163|gb|DB962242.1|DB962242
EST:     GCAGTTTCCTGCACAGGAGAATACTGTTAATCTTGCGGCAGAGACAGCTT                         TTACTGTCAGTGAGGTTGAAGCACTGTTTGAGCTTTTTAGGAGCATCAGCA
genomic: GCAGTTTCCTGCACAGGAGAATACTGTTAATCTTGCGGCAGAGACAGCTTgtacgttgat ... cccttcccagTTACTGTCAGTGAGGTTGAAGCACTGTTTGAGCTTTTTAGGAGCATCAGCA
EST: gi|213620263|gb|DB961408.1|DB961408
EST:     GCAGTTTCCTGCACAGGAGAATACTGTTAATCTTGCGGCAGAGACAGCTT                         TTACTGTCAGTGAGGTTGAAGCACTGTTTGAGCTTTTTAGGAGCATCAGCA
genomic: GCAGTTTCCTGCACAGGAGAATACTGTTAATCTTGCGGCAGAGACAGCTTgtacgttgat ... cccttcccagTTACTGTCAGTGAGGTTGAAGCACTGTTTGAGCTTTTTAGGAGCATCAGCA
EST: gi|192303847|gb|FG998199.1|FG998199
EST:     GCAGTTTCCTGCACAGGAGAATACTGTTAATCTTGCGGCAGAGACAGCTT                         TTACTGTCAGTGAGGTTGAAGCACTGTTTGAGCTTTTTAGGAGCATCAGCA
genomic: GCAGTTTCCTGCACAGGAGAATACTGTTAATCTTGCGGCAGAGACAGCTTgtacgttgat ... cccttcccagTTACTGTCAGTGAGGTTGAAGCACTGTTTGAGCTTTTTAGGAGCATCAGCA
EST: gi|192316103|gb|FK007164.1|FK007164
EST:     GCAGTTTCCTGCACAGGAGAATACTGTTAATCTTGCGGCAGAGACAGCTT                         TTACTGTCAGTGAGGTTGAAGCACTGTTTGAGCTTTTTAGGAGCATCAGCA
genomic: GCAGTTTCCTGCACAGGAGAATACTGTTAATCTTGCGGCAGAGACAGCTTgtacgttgat ... cccttcccagTTACTGTCAGTGAGGTTGAAGCACTGTTTGAGCTTTTTAGGAGCATCAGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgttagctttgtagtttaaactcgtgtatcatttttttgttttccccttcccagTTACTGTCAGTGAGGTTGAAGCACTGTTTGAGCTTTTTAGGAGCATCAGCAGTTCTGTTGTCGATGACGGACTGATAAGCAAG
                         tgtatcatttttttgt  CT-rich tract
                           tatcatttttttgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tagtgatgcatttgctataaaattgctctgtctctatttctccatatgttagctttgtagtttaaactcgtgtatcatttttttgttttccccttcccagTTACTGTCAGTGAGGTTGAAGCACTGTTTGAGCTTTTTAGGAGCATCAGCAGTTCTGTTGTCGATGACGGACTGATAAGCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - tgcattt
- - - - - - - - - - - -tgctctg
- - - - - - - - - - - - - - - - - - -ttctcca