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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaggacccttttgaaaccttttacaaaaccaatttgattcaagtttaggagttattattggaacataatcaaggtgattttttttatgcgcagGCATTGCGGTTCTATGGGAGTTTTAATCCAACAGTTACAGGCATAACAATTCAAAATAGTCCACAATGCCATCTCAAGTTTGACAGCTGTAATGGGGTCA

Basic information

species Glycine max
transcript GLYMA08G39340.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G39340.2 (Glycine max), 3'ss of exon 3
lower sequence: Vv01s0127g00400.t01 (Vitis vinifera), 3'ss of exon 5
gtgaggacccttttgaaaccttttacaaaaccaatttgattcaagtttaggagttattattggaacataatcaaggtgattttttttatgcgcagGCATTGCGGTTCTATGGGAGTTTTAATCCAACAGTTACAGGCATAACAATTCAAAATAGTCCACAATGCCATCTCAAGTTTGACAGCTGTAATGGGGTCA
|| ||||||      ||||   |   |   ||||   || | ||  ||| ||      | || |    |||   | |  | |||||  ||| |||||| || |||||||||| || |||||    ||||| || ||||||||||||||||| ||||| |||||||| ||||||||||||| ||| |  || ||| 
gtaaggaccaccagaaaactgctggaattcccaa--agagtaaa--ttatgaccatgcaatgtatgtaaatt--gattgtatttttgttgcacagGCACTGAGGTTCTATGGAAGCTTTAACGTGACAGTCACGGGCATAACAATTCAAAACAGTCCCCAATGCCACCTCAAGTTTGACAACTGCATGGGAGTCT
















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|193420975|gb|FK390982.1|FK390982
EST:     TTCAAAGTGAGATGGGAGGAAAAATGCCATCCGTCAAGCCAACT                         GCATTGCGGTTCTAGGGGAGTTTTAATCCAACAGTTACAGGCATAACAATT
genomic: TTCAAAGTGAGATGGGAGGAAAAATGCCATCCGTCAAGCCAACTgtgaggaccc ... ttatgcgcagGCATTGCGGTTCTATGGGAGTTTTAATCCAACAGTTACAGGCATAACAATT
EST: gi|193609855|gb|FK565321.1|FK565321
EST:     AAAGTGAGATGGGNGGAAAAATGCCATCCGTCAAGCCAACT                         GCATTGCGGTTCTATGGGAGTTTTAATCCAACAGTTACAGGCATAACAATT
genomic: AAAGTGAGATGGGAGGAAAAATGCCATCCGTCAAGCCAACTgtgaggaccc ... ttatgcgcagGCATTGCGGTTCTATGGGAGTTTTAATCCAACAGTTACAGGCATAACAATT
EST: gi|193500009|gb|FK465136.1|FK465136
EST:     AAAGTGAGATGGGAGGAAAAATGCCATCCGTCAAGCCAACT                         GCATTGCGGTTCTATGGGAGTTTTAATCCAACAGTTACAGGCATAACAATT
genomic: AAAGTGAGATGGGAGGAAAAATGCCATCCGTCAAGCCAACTgtgaggaccc ... ttatgcgcagGCATTGCGGTTCTATGGGAGTTTTAATCCAACAGTTACAGGCATAACAATT
EST: gi|193435512|gb|FK401622.1|FK401622
EST:     CCGATTCAAAGTGAGATGGGAGGAAAAAATGCCATCCGTCAAGCCAACT                         GCATTGCGGTTCTATGGGAGTTTTAATCCAACAGTTACAGGCATAACAATT
genomic: CCGATTCAAAGTGAGATGGGAGG-AAAAATGCCATCCGTCAAGCCAACTgtgaggaccc ... ttatgcgcagGCATTGCGGTTCTATGGGAGTTTTAATCCAACAGTTACAGGCATAACAATT
EST: gi|207778769|gb|GD746770.1|GD746770
EST:     TTCAAAGTGAGATGGGAGGAAAAATAGCCATCCGTCAAGCCAACT                         GCATTGCGGTTCTATGGGAGTTTTAATCCAACAGTTACAGGCATAACAATT
genomic: TTCAAAGTGAGATGGGAGGAAAAAT-GCCATCCGTCAAGCCAACTgtgaggaccc ... ttatgcgcagGCATTGCGGTTCTATGGGAGTTTTAATCCAACAGTTACAGGCATAACAATT
EST: gi|193310602|gb|FK276766.1|FK276766
EST:     ATTCAAAGTGAGATGGGAGGAAAAATGCCATCCGTCAAGCCAACT                         GCATTGCGGTTCTATGGGAGTTTTAATCCAACTAGTTTACTAGGCATAACA
genomic: ATTCAAAGTGAGATGGGAGGAAAAATGCCATCCGTCAAGCCAACTgtgaggaccc ... ttatgcgcagGCATTGCGGTTCTATGGGAGTTTTAATCCAAC-AGTT-AC-AGGCATAACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcaagtttaggagttattattggaacataatcaaggtgattttttttatgcgcagGCATTGCGGTTCTATGGGAGTTTTAATCCAACAGTTACAGGCATAACAATTCAAAATAGTCCACAATGCCATCTCAAGTTTGACAGCTGTAATGGGGTCA
                                       ttttttttat  CT-rich tract
                                    tgattttttttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgaggacccttttgaaaccttttacaaaaccaatttgattcaagtttaggagttattattggaacataatcaaggtgattttttttatgcgcagGCATTGCGGTTCTATGGGAGTTTTAATCCAACAGTTACAGGCATAACAATTCAAAATAGTCCACAATGCCATCTCAAGTTTGACAGCTGTAATGGGGTCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG