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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGCATCTTGAAGGAGCATTTGATTTCTTTTACAGCCAACCCCAGCTTAAAACATTTACTGATTCTAGGCACTTGGAGGAGCTATACAATAGATATAAAGgttagcaataaaggtgaaaataaaattgagacactgatagcttttaaaatagtctgatccgcacaacaaccaattggtgtggaaacatgaaaaataaata...

Basic information

species Glycine max
transcript GLYMA08G17580.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G17580.1 (Glycine max), 5'ss of exon 3
lower sequence: AT3G12760.1 (Arabidopsis thaliana), 5'ss of exon 3
TGGCATCTTGAAGGAGCATTTGATTTCTTTTACAGCCAACCCCAGCTTAAAA-CATT--TACTGATTCTAGGCACTTGGAGGAGCTATACAATAGATATAAAGgttagcaataaaggtgaaaataaaattgagacactgatagcttttaaaatagtctgatccgcacaacaaccaattggtgtggaaacatgaaaaataaata
   || ||||||| ||| |||||| | ||||||||||| || || |  | || || |  | ||||    || | |||||||||||| |||||||||||||||||  |||  |    ||    |     |||||    ||||   || |    ||   ||  |   |  |    ||  |   ||     | || |         
---CACCTTGAAGCAGCGTTTGATGTGTTTTACAGCCAGCCTCAACCAAGAAGCAATGCTGCTGAAGTAAGACGCTTGGAGGAGCTCTACAATAGATATAAAGgcaagc--ttcttgttgttactcttttgag---ttgatcatttgtgtg-taccttgtgctttagtattgacatgttacgt-----cttgcag--------

upper sequence: GLYMA08G17580.1 (Glycine max), 5'ss of exon 3
lower sequence: Vv19s0085g00630.t01 (Vitis vinifera), 5'ss of exon 3
TGGCATCTTGAAGGAGCATTTGATTTCTTTTACAGCCAACCCCAGCTTAAAACATTTACTGATTCTAGGCACTTGGAGGAGCTATACAATAGATATAAAGgttagcaataaaggtgaaaataaaat--tgagacactgatagcttttaaaata-gtctgatccgcacaacaaccaattggtgtggaaacatgaaaaataaata
|||||||||||||||||||||||| | |||||||| || |||||| ||||| |||||||||||||||| || ||||||||||| |||| ||||||||||||  ||   |     |   | |    |  | |   |||   | ||  | ||||  ||      | ||       || ||  | |       ||    ||||   
TGGCATCTTGAAGGAGCATTTGATGTATTTTACAGTCAGCCCCAGATTAAAGCATTTACTGATTCTAGACATTTGGAGGAGCTTTACAGTAGATATAAAGgcaagtttttcttttcccattgtgttcctaaatgactaccacctcctcaaatgtgtgcatgacacatgctgcacacttattttccttttttgtc--ataagc-
















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|120532941|gb|EH261074.1|EH261074
EST:     AACATTTACTGATTCTAGGCACTTGGAGGAGCTATACAATAGATATAAAG                         ATGCATATGTTGATATGATTTTGGCAGATGGTATCACTCTCCTTTGCAATG
genomic: AACATTTACTGATTCTAGGCACTTGGAGGAGCTATACAATAGATATAAAGgttagcaata ... ttctatacagATGCATATGTTGATATGATTTTGGCAGATGGTATCACTCTCCTTTGCAATG
EST: gi|23726204|gb|BU761086.1|BU761086
EST:     AACATTTACTGATTCTAGGCACTTGGAGGAGCTATACAATAGATATAAAG                         ATGCATATGTTGATATGATTTTGGCAGATGGTATCACTCTCCTTTGCAATG
genomic: AACATTTACTGATTCTAGGCACTTGGAGGAGCTATACAATAGATATAAAGgttagcaata ... ttctatacagATGCATATGTTGATATGATTTTGGCAGATGGTATCACTCTCCTTTGCAATG
EST: gi|209708243|gb|BW678613.1|BW678613
EST:     AACATTTACTGATTCTAGGCACTTGGAGGAGCTATACAATAGATATAAAG                         ATGCATATGTTGATATGATTTTGGCAGATGGTATCACTCTCCTTTGCAATG
genomic: AACATTTACTGATTCTAGGCACTTGGAGGAGCTATACAATAGATATAAAGgttagcaata ... ttctatacagATGCATATGTTGATATGATTTTGGCAGATGGTATCACTCTCCTTTGCAATG
EST: gi|254330010|gb|GR839563.1|GR839563
EST:     AACATTTACTGATTCTAGGCACTTGGAGGAGCTATACAATAGATATAAAG                         ATGCATATGTTGATATGATTTTGGCAGATGGTATCACTCTCCTTTGCAATG
genomic: AACATTTACTGATTCTAGGCACTTGGAGGAGCTATACAATAGATATAAAGgttagcaata ... ttctatacagATGCATATGTTGATATGATTTTGGCAGATGGTATCACTCTCCTTTGCAATG
EST: gi|209723711|gb|BW682790.1|BW682790
EST:     AACATTTACTGATTCTAGGCACTTGGAGGAGCTATACAATAGATATAAAG                         ATGCATATGTTGATATGATTTTGGCAGATGGTATCACTCTCCTTTGCAATG
genomic: AACATTTACTGATTCTAGGCACTTGGAGGAGCTATACAATAGATATAAAGgttagcaata ... ttctatacagATGCATATGTTGATATGATTTTGGCAGATGGTATCACTCTCCTTTGCAATG
EST: gi|120532010|gb|EH260143.1|EH260143
EST:     AACATTTACTGATTCTAGGCACTTGGAGGAGCTATACAATAGATATAAAG                         ATGCATATGTTGATATGATTTTGGCAGATGGTATCACTCTCCTTTGCAATG
genomic: AACATTTACTGATTCTAGGCACTTGGAGGAGCTATACAATAGATATAAAGgttagcaata ... ttctatacagATGCATATGTTGATATGATTTTGGCAGATGGTATCACTCTCCTTTGCAATG
EST: gi|213616987|gb|DB959299.1|DB959299
EST:     AACATTTACTGATTCTAGGCACTTGGAGGAGCTATACAATAGATATAAAG                         ATGCATATGTTGATATGATTTTGGCAGATGGTATCACTCTCCTTTGCAATG
genomic: AACATTTACTGATTCTAGGCACTTGGAGGAGCTATACAATAGATATAAAGgttagcaata ... ttctatacagATGCATATGTTGATATGATTTTGGCAGATGGTATCACTCTCCTTTGCAATG
EST: gi|26047849|gb|CA784504.1|CA784504
EST:     AACATTTACTGATTCTAGGCACTTGGAGGAGCTATACAATAGATATAAAG                         ATGCATATGTTGATATGATTTTGGCAGATGGTATCACTCTCCTTTGCAATG
genomic: AACATTTACTGATTCTAGGCACTTGGAGGAGCTATACAATAGATATAAAGgttagcaata ... ttctatacagATGCATATGTTGATATGATTTTGGCAGATGGTATCACTCTCCTTTGCAATG
EST: gi|209703862|gb|BW656912.1|BW656912
EST:     AACATTTACTGATTCTAGGCACTTGGAGGAGCTATACAATAGATATAAAG                         ATGCATATGTTGATATGATTTTGGCAGATGGTATCACTCTCCTTTGCAATG
genomic: AACATTTACTGATTCTAGGCACTTGGAGGAGCTATACAATAGATATAAAGgttagcaata ... ttctatacagATGCATATGTTGATATGATTTTGGCAGATGGTATCACTCTCCTTTGCAATG
EST: gi|151394270|gb|EV264141.1|EV264141
EST:     AACATTTACTGATTCTAGGCACTTGGAGGAGCTATACAATAGATATAAAG                         ATGCATATGTTGATATGATTTTGGCAGATGGTATCACTCTCCTTTGCAATG
genomic: AACATTTACTGATTCTAGGCACTTGGAGGAGCTATACAATAGATATAAAGgttagcaata ... ttctatacagATGCATATGTTGATATGATTTTGGCAGATGGTATCACTCTCCTTTGCAATG
EST: gi|192329316|gb|FK020235.1|FK020235
EST:     AACATTTACTGATTCTAGGCACTTGGAGGAGCTATACAATAGATATAAAG                         ATGCATATGTTGATATGATTTTGGCAGATGGTATCACTCTCCTTTGCAATG
genomic: AACATTTACTGATTCTAGGCACTTGGAGGAGCTATACAATAGATATAAAGgttagcaata ... ttctatacagATGCATATGTTGATATGATTTTGGCAGATGGTATCACTCTCCTTTGCAATG
EST: gi|22524065|gb|BU082876.1|BU082876
EST:     AACATTTACTGATTCTAGGCACTTGGAGGAGCTATACAATAGATATAAAG                         ATGCATATGTTGATATGATTTTGGCAGATGGTATCACTCTCCTTTGCAATG
genomic: AACATTTACTGATTCTAGGCACTTGGAGGAGCTATACAATAGATATAAAGgttagcaata ... ttctatacagATGCATATGTTGATATGATTTTGGCAGATGGTATCACTCTCCTTTGCAATG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGGCATCTTGAAGGAGCATTTGATTTCTTTTACAGCCAACCCCAGCTTAAAACATTTACTGATTCTAGGCACTTGGAGGAGCTATACAATAGATATAAAGgttagcaataaaggtgaaaataaaattgagacactgatagcttttaaaatagtctgatccgcacaacaaccaattggtgtggaaacatgaaaaataaata

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaataaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggtgtgg