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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttatttgccactatttttttttttttctcagtgtttgattattgtcaatttattatttttaactatagatattgacttttgctacctgtattgtttgtataataattagATGTATCCACAAGGACGGATGTCTCATCACTTTAGGGAGATACGTGAAGGTGATTACATGGCTGTGAAGGGACCAAAG

Basic information

species Glycine max
transcript GLYMA20G05640.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G05640.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv06s0009g01710.t01 (Vitis vinifera), 3'ss of exon 3
gttatttgccactatttttttttttttctcagtgtttgattattgtcaatttattatttttaactatagatattgacttttgctacctgtatt--gtttgtataataattagATGTATCCACAAGGACGGATGTCTCATCACTTTAGGGAGATACGTGAAGGTGATTACATGGCTGTGAAGGGACCAAAG
                || ||         | | ||  | | || |  ||  | | |  | |  |||   | ||         |   ||  ||   ||| | | |    |||||||||||||||||| ||||||| ||||| ||| |||||||  |||||||||||||| |||||||||||||||| |||
---------------gttcttaaacactcaaatattccaatgtt-ttgatacactgtcatcatttatttctctttttcccccttttttgattttaatttctcttaagggtagATGTATCCACAAGGAAGGATGTCCCATCATTTTCGGGAGATGTGTGAAGGTGATTACCTGGCTGTGAAGGGACCTAAG
















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|213597036|gb|DB966345.1|DB966345
EST:     CTCCTACAACATTGGATACTGATGTTGGATACTTTGAATTGGTTGTGAAG                         ATGTATCCACAAGGACGGATGTCTCATCACTTTAGGGAGATACGTGAAGGT
genomic: CTCCTACAACATTGGATACTGATGTTGGATACTTTGAATTGGTTGTGAAGgttatttgcc ... taataattagATGTATCCACAAGGACGGATGTCTCATCACTTTAGGGAGATACGTGAAGGT
EST: gi|193396351|gb|FK360985.1|FK360985
EST:     CTCCTACAACATTGGATACTGATGTTGGATACTTTGAATTGGTTGTGAAG                         ATGTATCCACAAGGACGGATGTCTCATCACT
genomic: CTCCTACAACATTGGATACTGATGTTGGATACTTTGAATTGGTTGTGAAGgttatttgcc ... taataattagATGTATCCACAAGGACGGATGTCTCATCACT
EST: gi|151395866|gb|EV265743.1|EV265743
EST:     CTCCTACAACATTGGATACTGATGTTGGATACTTTGAATTGGTTGTGAAG                         ATGTATCCACAAGGACGGATGTCTCATCACTTTAGGGAGATACGTGAAGGT
genomic: CTCCTACAACATTGGATACTGATGTTGGATACTTTGAATTGGTTGTGAAGgttatttgcc ... taataattagATGTATCCACAAGGACGGATGTCTCATCACTTTAGGGAGATACGTGAAGGT
EST: gi|254343624|gb|GR857380.1|GR857380
EST:     CTCCTACAACATTGGATACTGATGTTGGATACTTTGAATTGGTTGTGAAG                         ATGTATCCACAAGGACGGATGTCTCATCACTTTAGGGAGATACGTGAAGGT
genomic: CTCCTACAACATTGGATACTGATGTTGGATACTTTGAATTGGTTGTGAAGgttatttgcc ... taataattagATGTATCCACAAGGACGGATGTCTCATCACTTTAGGGAGATACGTGAAGGT
EST: gi|192309127|gb|FG999074.1|FG999074
EST:     CTCCTACAACATTGGATACTGATGTTGGATACTTTGAATTGGTTGTGAAG                         ATGTATCCACAAGGACGGATGTCTCATCACTTTAGGGAGATACGTGAAGGT
genomic: CTCCTACAACATTGGATACTGATGTTGGATACTTTGAATTGGTTGTGAAGgttatttgcc ... taataattagATGTATCCACAAGGACGGATGTCTCATCACTTTAGGGAGATACGTGAAGGT
EST: gi|151412854|gb|EV282666.1|EV282666
EST:     CTCCTACAACATTGGATACTGATGTTGGATACTTTGAATTGGTTGTGAAG                         ATGTATCCACAAGGACGGATGTCTCATCACTTTAGGGAGATACGTGAAGGT
genomic: CTCCTACAACATTGGATACTGATGTTGGATACTTTGAATTGGTTGTGAAGgttatttgcc ... taataattagATGTATCCACAAGGACGGATGTCTCATCACTTTAGGGAGATACGTGAAGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttttaactatagatattgacttttgctacctgtattgtttgtataataattagATGTATCCACAAGGACGGATGTCTCATCACTTTAGGGAGATACGTGAAGGTGATTACATGGCTGTGAAGGGACCAAAG
               tattgac  putative branch site (score: 2)
                                tgtattgtttgtataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttatttgccactatttttttttttttctcagtgtttgattattgtcaatttattatttttaactatagatattgacttttgctacctgtattgtttgtataataattagATGTATCCACAAGGACGGATGTCTCATCACTTTAGGGAGATACGTGAAGGTGATTACATGGCTGTGAAGGGACCAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT