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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactgaaaaattgtctctatttttaagttttagttcatataagagaaaatgggcacaattataaggaccaagtgaatagtttaacctactttcaattgaactttttcattctgtaaaatctatcagcaggatctaagtacttgacatgttaaatcttcagGTGGACTACCTTCTTGGGGACAACCCAAGAGCTACTAGTTACATGGTGGGCTATGGAAGCAACTTCCCACAAAGGGTTCATCACAGAGGTTCATCCATTG

Basic information

species Glycine max
transcript GLYMA08G02610.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G02610.1 (Glycine max), 3'ss of exon 6
lower sequence: AT4G11050.1 (Arabidopsis thaliana), 3'ss of exon 6
gtactgaaaaattgtctctatttttaagttttagttcatataagagaaaatgggcacaattataaggaccaagtgaatagtttaacctactttcaattgaactttttcattctgtaaaatctatcagcaggatctaagtacttgacatgttaaatcttcagGTGGACTACCTTCTTGGGGACAACCCAAGAGCTACTAGTTACATGGTGGGCTATGGAAGCAACTTCCCACAAAGGGTTCATCACAGAGGTTCATCCATTG
                                                 |   |  | ||||||    |  | | |||||   ||  ||   | || || |         | | |||| |  || |    |||| || || || | |      |   ||||||||| ||| ||||||| |||||||| ||||| || ||||||||||| || || |||   ||||  |||| |   ||||||||  | ||||| || ||||
-------------------------------------------------acatgttccattatatatccttaataaatagaa-aatgtatcgtgaaatggataac----ctgtctaaattggattatt--gatc-aattaattaaaact----actatcagGTGGATTACATTCTTGGAGACAACCCTAGAGCAACAAGTTACATGGTCGGATACGGAGAGAACTATCCACGACAAGTTCATCATCGTGGTTCGTCTATTG

upper sequence: GLYMA08G02610.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv02s0025g01380.t01 (Vitis vinifera), 3'ss of exon 8
gtactgaaaaattgtctctatttttaagttttagttcat-ataagagaaaatgggcacaattata-aggaccaagtgaatagtttaacctactttcaattgaactttttcattctgtaaaatctatcagcaggatctaagtact-tgacatgttaaatcttcagGTGGACTACCTTCTTGGGGACAACCCAAGAGCTACTAGTTACATGGTGGGCTATGGAAGCAACTTCCCACAAAGGGTTCATCACAGAGGTTCATCCATTG
                  || ||| |   |  | |  ||  ||  |    ||||     |||||| | ||   |  |  |  || ||  |||| |         | ||    |  | | || | |  |    | | ||| |    |||  ||| |||  | |||||||| ||  ||||||| |||||||||||||| || |||||||||||||| ||||||| |||||  || | |   || || ||| ||||||| || ||||
-----------------gtaatttgatcctggactggattgtagaatgttatggatgagattatatatgagtga--gggtgtttgaagatactctt--------tcttgtgattggaataaacaagtacagagttttaaatgggatgatttgt-aaacttgcagGTGGATTATATTCTTGGAGACAACCCAAGAGCCACGAGTTACATGGTGGGGTATGGAAACAACTATCCTCGACAAGTCCACCACCGAGGTTCCTCGATTG
















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|19937478|gb|BQ081304.1|BQ081304
EST:     GTTCAGGGAATGTCCCCCCTGCTGAGCTTCTCTCCCTTGCAAAGTCTCAG                         GTGGACTACCT
genomic: GTTCAGGGAATGTCCCCCCTGCTGAGCTTCTCTCCCTTGCAAAGTCTCAGgtactgaaaa ... aaatcttcagGTGGACTACCT
EST: gi|10233073|gb|BE802018.1|BE802018
EST:     GTTCAGGGAATGTCCCCCCTGCTGAGCTTCTCTCCCTTGCAAAGTCTCAG                         GTGGACTACCTTCTTGGGGACAACCCAAGAGCTACTAGTTACATGGTGGGC
genomic: GTTCAGGGAATGTCCCCCCTGCTGAGCTTCTCTCCCTTGCAAAGTCTCAGgtactgaaaa ... aaatcttcagGTGGACTACCTTCTTGGGGACAACCCAAGAGCTACTAGTTACATGGTGGGC
EST: gi|19937468|gb|BQ081301.1|BQ081301
EST:     GAGCTTCTCTCCCTTGCAAAGTCTCAG                         GTGGACTACCTTCTTGGGGACAACCCAAGAGCTACTAGTTACATGGTGGGC
genomic: GAGCTTCTCTCCCTTGCAAAGTCTCAGgtactgaaaa ... aaatcttcagGTGGACTACCTTCTTGGGGACAACCCAAGAGCTACTAGTTACATGGTGGGC
EST: gi|7795347|gb|AW780806.1|AW780806
EST:     GGGAATGTCCCCCCTGCTGAGCTTCTCTCCCTTGCAAAGTCTCAG                         GTGGACTACCTTCTTGGGGACAACCCAAGAGCTACTAGTTACATGGTGGGC
genomic: GGGAATGTCCCCCCTGCTGAGCTTCTCTCCCTTGCAAAGTCTCAGgtactgaaaa ... aaatcttcagGTGGACTACCTTCTTGGGGACAACCCAAGAGCTACTAGTTACATGGTGGGC
EST: gi|14011367|gb|BG726289.1|BG726289
EST:     GTTCAGGGAATGTCCCCCCTGCTGAGCTTCTCTCCCTTGCAAAGTCTCAG                         GTGGACTACCTTCTTGGGGACAACCCAAGAGCTACTAGTTACATGGTGGGC
genomic: GTTCAGGGAATGTCCCCCCTGCTGAGCTTCTCTCCCTTGCAAAGTCTCAGgtactgaaaa ... aaatcttcagGTGGACTACCTTCTTGGGGACAACCCAAGAGCTACTAGTTACATGGTGGGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcattctgtaaaatctatcagcaggatctaagtacttgacatgttaaatcttcagGTGGACTACCTTCTTGGGGACAACCCAAGAGCTACTAGTTACATGGTGGGCTATGGAAGCAACTTCCCACAAAGGGTTCATCACAGAGGTTCATCCATTG
                                 acttgac  putative branch site (score: 4)
                                                tcttc  putative PPT
        taaaatctat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtactgaaaaattgtctctatttttaagttttagttcatataagagaaaatgggcacaattataaggaccaagtgaatagtttaacctactttcaattgaactttttcattctgtaaaatctatcagcaggatctaagtacttgacatgttaaatcttcagGTGGACTACCTTCTTGGGGACAACCCAAGAGCTACTAGTTACATGGTGGGCTATGGAAGCAACTTCCCACAAAGGGTTCATCACAGAGGTTCATCCATTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA