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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cgttactggcaattcttaatctatagaattatcctaatttgtgcacttatctataaattcataatggcttacactatctttttcttttcatttttctcagGTTGAGACTGTTTTCCATGAATTTGGTCATGCACTTCAACATATGCTTACTAAGCAAGATGAGGGTCTGGTTGCTGGTATTAGAGGGATAGAGTGGGATG

Basic information

species Glycine max
transcript GLYMA09G33490.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G33490.1 (Glycine max), 3'ss of exon 10
lower sequence: LOC_Os02g58340.1 (Oryza sativa), 3'ss of exon 10
cgttactggcaattcttaatctatagaattat-cctaatttgtgcacttatctataaattcataatggc--ttacactatctttttcttttcatttttctcagGTTGAGACTGTTTTCCATGAATTTGGTCATGCACTTCAACATATGCTTACTAAGCAAGATGAGGGTCTGGTTGCTGGTATTAGAGGGATAGAGTGGGATG
| || | | | | | | || | | || | | | | || ||| || | || || | | | |||| | | ||| ||||||| ||||| |||||||||||||||||||| || || || |||||||| || |||||||| || | ||| |||||||| | || |||| |||||||
--tcacctgaagattgtgacacacctgcttccatatcaattaagtagtgctatactgatt-atgagggtaatttcttttttttttggcatgtgtcttttgtagGTTGAAACTGTGTTCCATGAATTTGGTCATGCGCTGCAGCACATGCTTACCAAACAAGATGAAGGATTTGTTTCTGGTATTCGTGGAGTAGAATGGGATG

upper sequence: GLYMA09G33490.1 (Glycine max), 3'ss of exon 10
lower sequence: GRMZM2G133919_T01 (Zea mays), 3'ss of exon 10
-------------------------cgttactggcaattcttaatctatagaattatcctaatttgtgcacttatctataaattcataatggcttacactatcttttt-cttttcatttttctcagGTTGAGACTGTTTTCCATGAATTTGGTCATGCACTTCAACATATGCTTACTAAGCAAGATGAGGGTCTGGTTGCTGGTATTAGAGGGATAGAGTGGGATG
|| | | || | | || | || | | | ||||| ||| || | | | | ||||| | || | || ||||||| ||||| |||||||||||||| || || ||||| || ||||||||||| |||||||| || | |||||||| ||| | || | || |||||||
gtaagtaatacatctgtgacatgtatgtgaataaggatatatggagaa-agcagtagctctctgcctctccttat-tatggtactatgaagttgtgtaaattctttctgctgtatgttgcctgtagGTTGAAACTGTGTTCCATGAATTTGGGCACGCCCTTCAGCACATGCTTACTAAACAAGATGAAGGCTTTGTTGCTGGCATTCGTGGAGTTGAATGGGATG

upper sequence: GLYMA09G33490.1 (Glycine max), 3'ss of exon 10
lower sequence: AT5G65620.1 (Arabidopsis thaliana), 3'ss of exon 10
cgttactggcaattcttaatctatagaattatccta-atttgtgcacttatctataaattcataatggcttacactatctttttcttttcatttt---tctcagGTTGAGACTGTTTTCCATGAATTTGGTCATGCACTTCAACATATGCTTACTAAGCAAGATGAGGGTCTGGTTGCTGGTATTAGAGGGATAGAGTGGGATG
|| | || || | ||| || | | | | | || | || | | | || ||| || ||| | | | | ||| | | | ||||| ||||| || || ||||||||||| ||||| ||||| || |||||||| ||||| |||||||| || ||||||||||| || || |||||||| |
-gtaaatgaaaaaac---atccattgcacttgcacatatctaagcg-taacatgaaatctcaaaaatcctttcttgttgactataacatcactctgatttacagGTAGAGACAGTATTTCATGAATTTGGACATGCTCTTCAGCACATGCTTACGAAGCAGGATGAGGGGCTAGTTGCTGGTATCCGAAATATCGAGTGGGACG

upper sequence: GLYMA09G33490.1 (Glycine max), 3'ss of exon 10
lower sequence: AT5G10540.1 (Arabidopsis thaliana), 3'ss of exon 10
--cgttactggcaattcttaat-ctatagaattatcctaatttgtgcacttatctataaattcataatggcttacactatctttttcttttcatttttctcagGTTGAGACTGTTTTCCATGAATTTGGTCATGCACTTCAACATATGCTTACTAAGCAAGATGAGGGTCTGGTTGCTGGTATTAGAGGGATAGAGTGGGATG
| |||| | || | | | || | | | | || | || | | | || || | | | | || || | |||| ||||| |||||||| |||||||||||||| ||||| ||||| ||||||||||| || | |||||||| || || |||||||| | || ||||||||||
ttccatacttgaaactttaggtgcttttggagaactcttacatgcatggtcaatgactcatgatccttgttctttatgacaatattattctgattt---acagGTAGAGACTGTGTTCCATGAATTTGGCCATGCTCTTCAGCATATGCTTACCAAAGAGGATGAGGGGCTAGTGGCTGGTATCCGGAATATCGAGTGGGATG

upper sequence: GLYMA09G33490.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv00s0211g00060.t01 (Vitis vinifera), 3'ss of exon 13
--------cgttactggcaattcttaatctatagaattatcctaatttgtgcacttatctataaattcataatggcttacactatctttt-tcttttcatttttctcagGTTGAGACTGTTTTCCATGAATTTGGTCATGCACTTCAACATATGCTTACTAAGCAAGATGAGGGTCTGGTTGCTGGTATTAGAGGGATAGAGTGGGATG
| | ||| || ||| | ||||||| ||| | |||| || | | | || || ||| |||| | | | | | | | ||| ||| ||||||||||||||||||||||||||||||||||||||||| ||||||||||| ||||| ||||||||||||||| |||||||| | ||||||||||||||||
agtgggggtgatggtggttatgttta-tacatagaat-atcat--cttgttca---gtttgtgcatgcacaat--cttatattgttagatatatatgcatgttttgcagGTTGAGACTGTTTTCCATGAATTTGGTCATGCACTTCAGCATATGCTTACCAAGCAGGATGAGGGTCTGGTTTCTGGTATTCGGGGGATAGAGTGGGATG

upper sequence: GLYMA09G33490.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv00s0211g00060.t01 (Vitis vinifera), 3'ss of exon 10
--------cgttactggcaattcttaatctatagaattatcctaatttgtgcacttatctataaattcataatggcttacactatctttt-tcttttcatttttctcagGTTGAGACTGTTTTCCATGAATTTGGTCATGCACTTCAACATATGCTTACTAAGCAAGATGAGGGTCTGGTTGCTGGTATTAGAGGGATAGAGTGGGATG
| | ||| || ||| | ||||||| ||| | |||| || | | | || | ||| |||| | | | | | | | ||| ||| ||||||||||||||||||||||||||||||||||||||||| ||||||||||| ||||| ||||||||||||||| |||||||| | ||||||||||||||||
agtgggggtgatggtggttatgttta-tacatagaat-atcat--cttgttca---gtttgtgcatgcgcaat--cttatattgttagatatatatgcatgttttgcagGTTGAGACTGTTTTCCATGAATTTGGTCATGCACTTCAGCATATGCTTACCAAGCAGGATGAGGGTCTGGTTTCTGGTATTCGGGGGATAGAGTGGGATG

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|192298500|gb|FG988486.1|FG988486
EST:     ATCAAACTCCTCCAGTAGGAAACAAGCCAAGTCTAATGACATTCCGTGAG                         GTTGAGACTGTTTTCCATGAATTTGGTCATGCACTTCAACATATGCTTACT
genomic: ATCAAACTCCTCCAGTAGGAAACAAGCCAAGTCTAATGACATTCCGTGAGgtaacctcaa ... tttttctcagGTTGAGACTGTTTTCCATGAATTTGGTCATGCACTTCAACATATGCTTACT
EST: gi|151410408|gb|EV280223.1|EV280223
EST:     ATCAAACTCCTCCAGTAGGAAACAAGCCAAGTCTAATGACATTCCGTGAG                         GTTGAGACTGTTTTCCATGAATTTGGTCATGCACTTCAACATATGCTTACT
genomic: ATCAAACTCCTCCAGTAGGAAACAAGCCAAGTCTAATGACATTCCGTGAGgtaacctcaa ... tttttctcagGTTGAGACTGTTTTCCATGAATTTGGTCATGCACTTCAACATATGCTTACT
EST: gi|192308087|gb|FK000415.1|FK000415
EST:     ATCAAACTCCTCCAGTAGGAAACAAGCCAAGTCTAATGACATTCCGTGAG                         GTTGAGACTGTTTTCCATGAATTTGGTCATGCACTTCAACATATGCTTACT
genomic: ATCAAACTCCTCCAGTAGGAAACAAGCCAAGTCTAATGACATTCCGTGAGgtaacctcaa ... tttttctcagGTTGAGACTGTTTTCCATGAATTTGGTCATGCACTTCAACATATGCTTACT
EST: gi|19347050|gb|BM891938.1|BM891938
EST:     ATCAAACTCCTCCAGTAGGAAACAAGCCAAGTCTAATGACATTCCGTGAG                         GTTGAGACTGTTTTCCATGAATTTGGTCATGCTCTTCAACATATGCTTACT
genomic: ATCAAACTCCTCCAGTAGGAAACAAGCCAAGTCTAATGACATTCCGTGAGgtaacctcaa ... tttttctcagGTTGAGACTGTTTTCCATGAATTTGGTCATGCACTTCAACATATGCTTACT
EST: gi|254336791|gb|GR842970.1|GR842970
EST:     ATCAAACTCCTCCAGTAG-AAACAAGCCAAGTCTAATGACATTCCGTGAG                         GTTGAGACTGTTT-CCATGAATTTGGTCATGC
genomic: ATCAAACTCCTCCAGTAGGAAACAAGCCAAGTCTAATGACATTCCGTGAGgtaacctcaa ... tttttctcagGTTGAGACTGTTTTCCATGAATTTGGTCATGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttatctataaattcataatggcttacactatctttttcttttcatttttctcagGTTGAGACTGTTTTCCATGAATTTGGTCATGCACTTCAACATATGCTTACTAAGCAAGATGAGGGTCTGGTTGCTGGTATTAGAGGGATAGAGTGGGATG
                    ggcttac  putative branch site (score: 3)
 cttacactatcttttt  CT-rich tract
 tatctttttcttttca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cgttactggcaattcttaatctatagaattatcctaatttgtgcacttatctataaattcataatggcttacactatctttttcttttcatttttctcagGTTGAGACTGTTTTCCATGAATTTGGTCATGCACTTCAACATATGCTTACTAAGCAAGATGAGGGTCTGGTTGCTGGTATTAGAGGGATAGAGTGGGATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
-gttactg
- - - - - - - - - - - - - - - - - - - - -tgcactt