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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtgtgatattctgctactttaagagagatgatgtctatggcatcaaactcttcctaatgttatcgtatcactatgaggtgtctgggctaatttttcttttctcttctgtgtgtttttgcagATTGATTACATCCTTGGAAATAACCCAAGGAAAATGAGTTATGTCGTAGGTTTTGGTAATCATTACCCAAAACACGTCCACCATAGAGGAGCATCTGTAC

Basic information

species Glycine max
transcript GLYMA09G02160.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G02160.1 (Glycine max), 3'ss of exon 5
lower sequence: AT5G49720.1 (Arabidopsis thaliana), 3'ss of exon 5
--------------------------------------gtgtgtgatattctgctactttaag---agagatgatgtct---------atggcatcaaactcttcctaatgttatcgtatcactatgaggtgtctgggctaatttttcttttctcttctgtgtgtttttgcagATTGATTACATCCTTGGAAATAACCCAAGGAAAATGAGTTATGTCGTAGGTTTTGGTAATCATTACCCAAAACACGTCCACCATAGAGGAGCATCTGTAC
                                       | |  |||||  |  |   | |     | | ||||    |         || | |  ||  ||||  |||  |     | | | | |||    |||    |   |||   |    |||   ||| |||| |||||||||||| || || || || |||||  ||||||||||||||||||| |||||||| |   | ||||||| ||| || || || |||||||| ||  |||
gtattgcttcttttcctttactctttacagaaatggtaatctcagatatagtaatggataagatccaaaaatgacacttttaaccaagattgtacgaagatctttttaaactccattttttattttga--catctaaattggatttaactcggccttgc-tgtattttggcagATTGATTATATACTGGGTAAAAACCCTCGGAAAATGAGTTATGTCGTTGGTTTTGGCACAAAATACCCAAGACATGTGCATCACAGAGGAGCTTCGATAC

upper sequence: GLYMA09G02160.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv12s0035g02180.t01 (Vitis vinifera), 3'ss of exon 5
gtgtgtgatattctgctactttaagagagatgatgtctatggcatcaaactcttcctaatgttatcg-tatcactatgaggtgtctgggctaatttttcttttctcttctgtgtgtttttg-cagATTGATTACATCCTTGGAAATAACCCAAGGAAAATGAGTTATGTCGTAGGTTTTGGTAATCATTACCCAAAACACGTCCACCATAGAGGAGCATCTGTAC
|| || ||||| ||| | | | ||   |  |  ||       ||| |  ||  || |   || ||   |||   |  ||     |  ||  | ||    |||||   ||| ||   || || ||||||||||||||||| || || || ||  | || ||||| ||| | | ||||||||| |||||||| |||| ||| |||||||||||||| |||||| | |
gtatgcgatat-ctgattcctcaattaaagttgtgaggg-aacatgagtctgctcatgtagtaataaatattgttg-gaaccaacaaggtcacttaaatttttcatatctctgaccttctggcagATTGATTACATCCTCGGCAAAAATCCTCGAAAGATGAGCTATATTGCAGGTTTTGGCAATCATTATCCAAGACATGTCCACCATAGAGGTGCATCTATCC
















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|6502056|gb|AW203429.1|AW203429
EST:     GACCTAATTTCTTTTCAACCGACGTGCTCCGTAGCTTTGCCAAGTCCCAG                         ATTGATTACATCCTTGGAAATAACCCAAGGAAAATGAGTTATGTCGTAGGT
genomic: GACCTAATTTCTTTTCAACCGACGTGCTCCGTAGCTTTGCCAAGTCCCAGgtgtgtgata ... gtttttgcagATTGATTACATCCTTGGAAATAACCCAAGGAAAATGAGTTATGTCGTAGGT
EST: gi|37994320|gb|CF806066.1|CF806066
EST:     GACCTAATTTCTTTTCAACCGACGTGCTCCGTAGCTTTGCCAAGTCCCAG                         ATTGATTACATCCTTGGAAATAACCCAAGGAAAATGAGTTATGTCGTAGGT
genomic: GACCTAATTTCTTTTCAACCGACGTGCTCCGTAGCTTTGCCAAGTCCCAGgtgtgtgata ... gtttttgcagATTGATTACATCCTTGGAAATAACCCAAGGAAAATGAGTTATGTCGTAGGT
EST: gi|16106049|gb|BI893789.1|BI893789
EST:     GACCTAATTTCTTTTCAACCGACGTGCTCCGTAGCTTTGCCAAGTCCCAG                         ATTGATTACATCCTTGGAAATAACCCA
genomic: GACCTAATTTCTTTTCAACCGACGTGCTCCGTAGCTTTGCCAAGTCCCAGgtgtgtgata ... gtttttgcagATTGATTACATCCTTGGAAATAACCCA
EST: gi|9258607|gb|BE346754.1|BE346754
EST:     GACCTAATTTCTTTTCAACCGACGTGCTCCGTAGCTTTGCCAAGTCCCAG                         ATTGATTACATCCTTGGAAATAACCCAAGGAAAATGAGTTATGTCGTAGGT
genomic: GACCTAATTTCTTTTCAACCGACGTGCTCCGTAGCTTTGCCAAGTCCCAGgtgtgtgata ... gtttttgcagATTGATTACATCCTTGGAAATAACCCAAGGAAAATGAGTTATGTCGTAGGT
EST: gi|26048689|gb|CA785142.1|CA785142
EST:     GACCTAATTTCTTTTCAACCGACGTGCTCCGGAGCTTTGCCAAGTCCCAG                         ATTGATTACATCCTTGGAAATAACCCAAGGAAAATGAGTTATGTCGTAAGT
genomic: GACCTAATTTCTTTTCAACCGACGTGCTCCGTAGCTTTGCCAAGTCCCAGgtgtgtgata ... gtttttgcagATTGATTACATCCTTGGAAATAACCCAAGGAAAATGAGTTATGTCGTAGGT
EST: gi|208252306|gb|GE048278.1|GE048278
EST:     GACCTAATTTCTTTTCAACCGACGTGCTCCGTAGCTTTGCCAAGTCCCAG                         ATTGATTACATCCTTGGAAATAACCCAAGGAAAATGAGTTATGTCGTAGGT
genomic: GACCTAATTTCTTTTCAACCGACGTGCTCCGTAGCTTTGCCAAGTCCCAGgtgtgtgata ... gtttttgcagATTGATTACATCCTTGGAAATAACCCAAGGAAAATGAGTTATGTCGTAGGT
EST: gi|5605872|gb|AI899970.1|AI899970
EST:     GACCTAATTTCTTTTCAACCGACGTGCTCCGTAGCTTTGCCAAGTCCCAG                         ATTGATTACATCCTTGGAAATAACCCAAGGAAAATGAGTTATGTCGTAGGT
genomic: GACCTAATTTCTTTTCAACCGACGTGCTCCGTAGCTTTGCCAAGTCCCAGgtgtgtgata ... gtttttgcagATTGATTACATCCTTGGAAATAACCCAAGGAAAATGAGTTATGTCGTAGGT
EST: gi|19934755|gb|BQ079785.1|BQ079785
EST:     GACCTAATTTCTTTTCAACCGACGTGCTCCGTAGCTTTGCCAAGTCCCAG                         ATTGATTACATCCTTGGAAATAACCCAAGGAAAATGAGTTATGTCGTAGGT
genomic: GACCTAATTTCTTTTCAACCGACGTGCTCCGTAGCTTTGCCAAGTCCCAGgtgtgtgata ... gtttttgcagATTGATTACATCCTTGGAAATAACCCAAGGAAAATGAGTTATGTCGTAGGT
EST: gi|58016974|gb|CX703716.1|CX703716
EST:     CGTAGCTTTGCCAAGTCCCAG                         ATTGATTACATCCTTGGAAATAACCCAAGGAAAATGAGTTATGTCGTAGGT
genomic: CGTAGCTTTGCCAAGTCCCAGgtgtgtgata ... gtttttgcagATTGATTACATCCTTGGAAATAACCCAAGGAAAATGAGTTATGTCGTAGGT
EST: gi|7588237|gb|AW704037.1|AW704037
EST:     GACCTAATTTCTTTTCAACCGACGTGCTCCGTAGCTGTGCCAAGTCCCAG                         ATTGATTACATCCTTGGAAATAACCCAAAGAAAATGAGTTATGTCGTAGGT
genomic: GACCTAATTTCTTTTCAACCGACGTGCTCCGTAGCTTTGCCAAGTCCCAGgtgtgtgata ... gtttttgcagATTGATTACATCCTTGGAAATAACCCAAGGAAAATGAGTTATGTCGTAGGT
EST: gi|9440465|gb|BE440969.1|BE440969
EST:     GACCTAATTTCTTTTCAACCGACGTGCTCCGTAGCTTTGCCAAGTCCCAG                         ATTGATTACATCCTTGGAAATAACCCAAGGAAAATGAGTTATGTCGTAGGT
genomic: GACCTAATTTCTTTTCAACCGACGTGCTCCGTAGCTTTGCCAAGTCCCAGgtgtgtgata ... gtttttgcagATTGATTACATCCTTGGAAATAACCCAAGGAAAATGAGTTATGTCGTAGGT
EST: gi|209729806|gb|BW658611.1|BW658611
EST:     TAGC-TTGCCAAGTCCCAG                         ATTGATTACATCCTTGGAAATAACCCAAGGAAAATGAGTTATGTCGTAGGT
genomic: TAGCTTTGCCAAGTCCCAGgtgtgtgata ... gtttttgcagATTGATTACATCCTTGGAAATAACCCAAGGAAAATGAGTTATGTCGTAGGT
EST: gi|209719123|gb|BW659400.1|BW659400
EST:     TGCCAAGTCCCAG                         ATTGATTACATCCTTGGAAATAACCCAAGGAAAATGAGTTATGTCGTAGGT
genomic: TGCCAAGTCCCAGgtgtgtgata ... gtttttgcagATTGATTACATCCTTGGAAATAACCCAAGGAAAATGAGTTATGTCGTAGGT
EST: gi|6454405|gb|AW185088.1|AW185088
EST:     GACCTAATTTCTTTTCAACCGACGTGCTCCGTAGCTTTGCCAAGTCCCAG                         ATTGATTACATCCTTGGAAATAACCCAAGGAAAATGAGTTATGTCGTAGGT
genomic: GACCTAATTTCTTTTCAACCGACGTGCTCCGTAGCTTTGCCAAGTCCCAGgtgtgtgata ... gtttttgcagATTGATTACATCCTTGGAAATAACCCAAGGAAAATGAGTTATGTCGTAGGT
EST: gi|22525618|gb|BU084429.1|BU084429
EST:     GACCTAATTTCTTTTCAACCGACGTGCTCCGTAGCTTTGCCAAGTCCCAG                         ATTGATTACATCCTTGGAAATAACCCAAGGAAAATGAGTTATGTCGTAGGT
genomic: GACCTAATTTCTTTTCAACCGACGTGCTCCGTAGCTTTGCCAAGTCCCAGgtgtgtgata ... gtttttgcagATTGATTACATCCTTGGAAATAACCCAAGGAAAATGAGTTATGTCGTAGGT
EST: gi|58016657|gb|CX703399.1|CX703399
EST:     CGTAGCTTTGCCAAGTCCCAG                         ATTGATTACATCCTTGGAAATAACCCAAGGAAAATGAGTTATGTCGTAGGT
genomic: CGTAGCTTTGCCAAGTCCCAGgtgtgtgata ... gtttttgcagATTGATTACATCCTTGGAAATAACCCAAGGAAAATGAGTTATGTCGTAGGT
EST: gi|21637832|gb|BM107987.1|BM107987
EST:     GACCTAATTTCTTTTCAACCGACGTGCTCCGTAGCTTTGCCAAGTCCCAG                         ATTGATTACATCCTTGGAAATAACCCAAGGAAAATGAGTTATGTCGTAGGT
genomic: GACCTAATTTCTTTTCAACCGACGTGCTCCGTAGCTTTGCCAAGTCCCAGgtgtgtgata ... gtttttgcagATTGATTACATCCTTGGAAATAACCCAAGGAAAATGAGTTATGTCGTAGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcactatgaggtgtctgggctaatttttcttttctcttctgtgtgtttttgcagATTGATTACATCCTTGGAAATAACCCAAGGAAAATGAGTTATGTCGTAGGTTTTGGTAATCATTACCCAAAACACGTCCACCATAGAGGAGCATCTGTAC
                  ggctaat  putative branch site (score: 3)
                        tttttcttttctcttc  CT-rich tract
                     taatttttcttttct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgtgtgatattctgctactttaagagagatgatgtctatggcatcaaactcttcctaatgttatcgtatcactatgaggtgtctgggctaatttttcttttctcttctgtgtgtttttgcagATTGATTACATCCTTGGAAATAACCCAAGGAAAATGAGTTATGTCGTAGGTTTTGGTAATCATTACCCAAAACACGTCCACCATAGAGGAGCATCTGTAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA