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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taaatgtgattaattattttttttaattagtgtgtcatttttttttcttttcttagttatgctatatcgtattgaaaatttcttgctcacttcaatgcagGAAGCTGTGAATGTATCACTTGGGAACCTATTGACATATCGATTTGTGAGAGATGCAGTTGTGAAGAAAACTCTTGCCTTGAAAGGTGCACATTACAATT

Basic information

species Glycine max
transcript GLYMA08G39510.2
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G39510.2 (Glycine max), 3'ss of exon 8
lower sequence: Vv01s0127g00720.t01 (Vitis vinifera), 3'ss of exon 8
taaatgtgattaattattttttttaattagtgtgtcatttttttttcttt----tcttagttatgctat-atcgtattgaaaatttcttgctcacttcaatgcagGAAGCTGTGAATGTATCACTTGGGAACCTATTGACATATCGATTTGTGAGAGATGCAGTTGTGAAGAAAACTCTTGCCTTGAAAGGTGCACATTACAATT
 | || | |||   || ||   ||  |  |     ||   | ||  | |     ||   |    ||||| | |  ||     ||||     |   ||   ||||||| |||||||||||||| || || ||||| || || || | |||||| ||||| || || ||||||||||| || ||  |||| |||||||| ||| |||
-agatctaattt-ctacttgaatttgtctgaacaacacactcttagcatcaaactcacggacgggctatgaccagatctcctattttcatgtggttt---tgcagGAGGCTGTGAATGTATCCCTGGGAAACCTGTTAACCTACCCATTTGTCAGAGAAGCTGTGGTGAAGAAAACCCTAGCTCTGAAGGGTGCACACTACGATT
















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|192297727|gb|FG989962.1|FG989962
EST:     CAGAAGCAAACACATTAGAATTCTCTGAGCAATGTACCAGCTGCGAGAAG                         GAAGCTGTGAATGTATCACTTGGGAACCTATTGACATATCGATTTGTGAGA
genomic: CAGAAGCAAACACATTAGAATTCTCTGAGCAATGTACCAGCTGCGAGAAGgcaagtaaat ... ttcaatgcagGAAGCTGTGAATGTATCACTTGGGAACCTATTGACATATCGATTTGTGAGA
EST: gi|14009065|gb|BG725678.1|BG725678
EST:     CAGAAGCAAACACATTAGAATTCTCTGAGCAATGTACCAGCTGCGAGAAG                         GAAGCTGTGAATGTATCACTTGGGAACCTATTGACATATCGATTTGTGAGA
genomic: CAGAAGCAAACACATTAGAATTCTCTGAGCAATGTACCAGCTGCGAGAAGgcaagtaaat ... ttcaatgcagGAAGCTGTGAATGTATCACTTGGGAACCTATTGACATATCGATTTGTGAGA
EST: gi|31307029|gb|CD392232.1|CD392232
EST:     CAGAAGCAAACACATTAGAATTCTCTGAGCAATGTACCAGCTGCGAGAAG                         GAAGCTGTGAATGTATCACTTGGGAACCTATTGACATATCGATTTGTGAGA
genomic: CAGAAGCAAACACATTAGAATTCTCTGAGCAATGTACCAGCTGCGAGAAGgcaagtaaat ... ttcaatgcagGAAGCTGTGAATGTATCACTTGGGAACCTATTGACATATCGATTTGTGAGA
EST: gi|192309131|gb|FG999400.1|FG999400
EST:     CAGAAGCAAACACATTAGAATTCTCTGAGCAATGTACCAGCTGCGAGAAG                         GAAGCTGTGAATGTATCACTTGGGAACCTATTGACATATCGATTTGTGAGA
genomic: CAGAAGCAAACACATTAGAATTCTCTGAGCAATGTACCAGCTGCGAGAAGgcaagtaaat ... ttcaatgcagGAAGCTGTGAATGTATCACTTGGGAACCTATTGACATATCGATTTGTGAGA
EST: gi|192309132|gb|FG999401.1|FG999401
EST:     CAGAAGCAAACACATTAGAATTCTTTGAGCAATGTACCAGCTGCGAGAAG                         GAAGCTGTGAATGTATCACTTGGGAACCTATTGACATATCGATTTGTGAGA
genomic: CAGAAGCAAACACATTAGAATTCTCTGAGCAATGTACCAGCTGCGAGAAGgcaagtaaat ... ttcaatgcagGAAGCTGTGAATGTATCACTTGGGAACCTATTGACATATCGATTTGTGAGA
EST: gi|192305002|gb|FG997128.1|FG997128
EST:     CAGAAGCAAACACATTAGAATTCTCTGAGCAATGTACCAGCTGCGAGAAG                         -AAGCTGTGAATGTATCACTTGGGAACCTATTGACATATCGATTTGTGAGA
genomic: CAGAAGCAAACACATTAGAATTCTCTGAGCAATGTACCAGCTGCGAGAAGgcaagtaaat ... ttcaatgcagGAAGCTGTGAATGTATCACTTGGGAACCTATTGACATATCGATTTGTGAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttttcttagttatgctatatcgtattgaaaatttcttgctcacttcaatgcagGAAGCTGTGAATGTATCACTTGGGAACCTATTGACATATCGATTTGTGAGAGATGCAGTTGTGAAGAAAACTCTTGCCTTGAAAGGTGCACATTACAATT
                                      tgctcac  putative branch site (score: 2)
                                 tttcttgctcacttc  CT-rich tract
                        tattgaaaatttctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taaatgtgattaattattttttttaattagtgtgtcatttttttttcttttcttagttatgctatatcgtattgaaaatttcttgctcacttcaatgcagGAAGCTGTGAATGTATCACTTGGGAACCTATTGACATATCGATTTGTGAGAGATGCAGTTGTGAAGAAAACTCTTGCCTTGAAAGGTGCACATTACAATT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - -gtgtgtc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgctata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttcttgc