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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aatgcatctcgctgtgtgtgtgtgtttgtacatgggaaagaagataactgattgttggtttgagaatatgacacttcatgttatcaattgtctgttgcagAAAGTATTTGACCATGACACATTTTCTGCTGATGATATAATGGGAGAAGCAGACATTGATCTTCAGTCTCTGATAACATCTGCTATGGCATTTGGAGATG

Basic information

species Glycine max
transcript GLYMA09G02830.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G02830.1 (Glycine max), 3'ss of exon 8
lower sequence: AT4G05330.1 (Arabidopsis thaliana), 3'ss of exon 8
aatgcatctcgctgtgtgtgtgtgtttgtacatgggaaagaagataactgattgttggtttgagaatatgacacttcatgttatcaattgtctgttgcagAAAGTATTTGACCATGACACATTTTCTGCTGATGATATAATGGGAGAAGCAGACATTGATCTTCAGTCTCTGATAACATCTGCTATGGCATTTGGAGATG
             ||  | |    ||  |         |  |  | | | ||||           |||| | |  | | | | ||   |||  ||||||| |||| | |||  |||| ||||||||||||||||| ||||||||||||||||| |||||| | ||  || ||||||||||||| ||||| ||||| ||| 
-------------gtaagagcaaattcattttctattgacgatttcagtcattgccaaagcttatatat-atatcttacggtttcttatgtg-gttgcagCAAGTGTATGATTATGATACATTTTCTGCTGATGACATAATGGGAGAAGCAGATATTGATATACAACCTTTGATAACATCTGCAATGGCTTTTGGGGATC

upper sequence: GLYMA09G02830.1 (Glycine max), 3'ss of exon 8
lower sequence: AT4G21160.4 (Arabidopsis thaliana), 3'ss of exon 7
aatgcatctcgctgtgtgtgtgtgtttgtacatgggaaagaagataactgattgttggtttgagaatatgacacttcatgttatcaattgtctgtt---gcagAAAGTATTTGACCATGACACATTTTCTGCTGATGATATAATGGGAGAAGCAGACATTGATCTTCAGTCTCTGATAACATCTGCTATGGCATTTGGAGATG
             ||    |  || |   | ||    || |  |      | | ||| |     | ||    | ||  |    |  ||| | ||||   |||| |||| |||||| |||||||||||||||||||||| |||||||||||||| || |||||| | ||| ||||||| |||||||| ||||| ||||||||  
-------------gtaaaagcttggtctaatatttccaaaatcactttctactcttgatgaatcattacagaagtttttcccttacattttatgtttttgcagCAAGTGTTTGACTATGACACATTTTCTGCTGATGACATAATGGGAGAAGCTGAGATTGATATCCAGCCTCTGATTACATCTGCAATGGCTTTTGGAGACC

upper sequence: GLYMA09G02830.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv10s0003g04900.t01 (Vitis vinifera), 3'ss of exon 8
aatgcatctcgctgtgtgtgtgtgtttgtacatgggaaagaagataactgattgttggtttgagaat----atgacacttcatgttatcaat------tgtctgt-----tgcagAAAGTATTTGACCATGACACATTTTCTGCTGATGATATAATGGGAGAAGCAGACATTGATCTTCAGTCTCTGATAACATCTGCTATGGCATTTGGAGATG
                  |   |  || | |||   |||  | ||  |  ||  | | |   |   |    |||||| ||||| | ||  ||      ||||| |     |||||||||| |||||||||||||| || ||||||||||| |||||||||||||| || |||||  | ||  | ||||||||||| || |||||||||||| |||
---------------cctttcatcattattcataaaaaatcaaattccccatgctcgatcacaatgttttcatgacatttcatctaatatatgagtcctgtctctcacaatgcagAAAGTCTTTGACCATGACACGTTCTCTGCTGATGACATAATGGGAGAAGCCGAGATTGACATCCAACCCCTGATAACATCCGCCATGGCATTTGGAAATG

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|31306285|gb|CD391488.1|CD391488
EST:     ATGAGGAATACATGCTGTCTGTTCCTGAGCATTATGGACAGATAAAATTG                         AAAGTATTTGACCATGACACATTTTCTGCTGATGATATAATGGGAGAAGCA
genomic: ATGAGGAATACATGCTGTCTGTTCCTGAGCATTATGGACAGATAAAATTGgtatgattga ... tctgttgcagAAAGTATTTGACCATGACACATTTTCTGCTGATGATATAATGGGAGAAGCA
EST: gi|13252256|gb|BG363159.1|BG363159
EST:     ATGAGGAATACATGCTGTCTGTTCCTGAGCATTATGGACAGATAAAATTG                         AAAGTATTTGACCATGACACATTTTCTGCTGATGATATAATGGGAGAAGCA
genomic: ATGAGGAATACATGCTGTCTGTTCCTGAGCATTATGGACAGATAAAATTGgtatgattga ... tctgttgcagAAAGTATTTGACCATGACACATTTTCTGCTGATGATATAATGGGAGAAGCA
EST: gi|120495184|gb|EH223351.1|EH223351
EST:     ATGAGGAATACATGCTGTCTGTTCCTGAGCATTATGGACAGATAAAATTG                         AAAGTATTTGACCATGACACATTTTCTGCTGATGATATAATGGGAGAAGCA
genomic: ATGAGGAATACATGCTGTCTGTTCCTGAGCATTATGGACAGATAAAATTGgtatgattga ... tctgttgcagAAAGTATTTGACCATGACACATTTTCTGCTGATGATATAATGGGAGAAGCA
EST: gi|22928442|gb|BU545581.1|BU545581
EST:     ATGAGGAATACATGCTGTCTGTTCCTGAGCATTATGGACAGATAAAATTG                         AAAGTATTTGACCATGACACATTTTCTGCTGATGATATAATGGGAGAAGCA
genomic: ATGAGGAATACATGCTGTCTGTTCCTGAGCATTATGGACAGATAAAATTGgtatgattga ... tctgttgcagAAAGTATTTGACCATGACACATTTTCTGCTGATGATATAATGGGAGAAGCA
EST: gi|120495304|gb|EH223471.1|EH223471
EST:     ATGAGGAATACATGCTGTCTGTTCCTGAGCATTATGGACAGATAAAATTG                         AAAGTATTTGACCATGACACATTTTCTGCTGATGATATAATGGGAGAAGCA
genomic: ATGAGGAATACATGCTGTCTGTTCCTGAGCATTATGGACAGATAAAATTGgtatgattga ... tctgttgcagAAAGTATTTGACCATGACACATTTTCTGCTGATGATATAATGGGAGAAGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aactgattgttggtttgagaatatgacacttcatgttatcaattgtctgttgcagAAAGTATTTGACCATGACACATTTTCTGCTGATGATATAATGGGAGAAGCAGACATTGATCTTCAGTCTCTGATAACATCTGCTATGGCATTTGGAGATG
 aactgat  putative branch site (score: 3)
                                   ttatcaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aatgcatctcgctgtgtgtgtgtgtttgtacatgggaaagaagataactgattgttggtttgagaatatgacacttcatgttatcaattgtctgttgcagAAAGTATTTGACCATGACACATTTTCTGCTGATGATATAATGGGAGAAGCAGACATTGATCTTCAGTCTCTGATAACATCTGCTATGGCATTTGGAGATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
aatgcat
- - - - - gctgtgt
- - - - - - -gtgtgtg
- - - - - - - - - - - - - - -acatggg
- - - - - - - - - - - - - - - - - - - - - - - - - - -gttggtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgacact
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tcatgtt