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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgttgtgtgaacattttctttcattcacataccctctagaatgcgggtttaaactaagtagaagatgcatgcaaattaatcgttttttaaaactttgcagAAGGAGTTTCTTGATAAGTACGAAAGTTTTGCCCAACTTGTGGCTAAGATTTATCCTACTGAGACAATCCCGTCTGTAGCGGAGATGAGAGACCTTTTAG

Basic information

species Glycine max
transcript GLYMA09G18840.1
intron # 24
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G18840.1 (Glycine max), 3'ss of exon 24
lower sequence: Vv18s0001g11700.t01 (Vitis vinifera), 3'ss of exon 24
--tgttgtgtgaacattttctttcattcac---ataccctctagaatgcgggtttaaactaagtagaagatgcatgcaaattaatcgttttttaaaactttg-cagAAGGAGTTTCTTGATAAGTACGAAAGTTTTGCCCAACTTGTGGCTAAGATTTATCCTACTGAGACAATCCCGTCTGTAGCGGAGATGAGAGACCTTTTAG
   ||||||| ||   |   |  ||| | |   | |  |||     || | ||    |||   ||  | |||| |   ||| ||   || | | ||| |||| |||||||||||||| || || || || || || || ||||| || || |||||||||||||| ||||| || || |||||||| || ||||||||  || | |
aaggttgtgtcaaatctccttcacatgctctgaaaaaactcctctttgtgtgtc---acttgttatcaaatgcct---aatgaaggcttgtctcaaattttgacagAAGGAGTTTCTGGACAAATATGATAGCTTCGCACAACTGGTTGCCAAGATTTATCCTACCGAGACCATTCCATCTGTAGCAGAAATGAGAGAAATTCTGG
















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|51344685|gb|CO985418.1|CO985418
EST:     AGAATTTGACTTCGGAGGAATTGTTACCCTCCTTATGGGACAAATGCAAG                         AAGGAGTTTCTTGATAAGTACGAAAGTTTTGCCCAACTTGTGGCTAAGATT
genomic: AGAATTTGACTTCGGAGGAATTGTTACCCTCCTTATGGGACAAATGCAAGgtaagctgta ... aactttgcagAAGGAGTTTCTTGATAAGTACGAAAGTTTTGCCCAACTTGTGGCTAAGATT
EST: gi|21602822|gb|BQ613153.1|BQ613153
EST:     AGAATTTGACTTCGGAGGAATTGTTACCCTCCTTATGGGACAAATGCAAG                         AAGGAGTTTCTTGATAAGTACGAAAGTTTTGCCCAACTTGTGGCTAAGATT
genomic: AGAATTTGACTTCGGAGGAATTGTTACCCTCCTTATGGGACAAATGCAAGgtaagctgta ... aactttgcagAAGGAGTTTCTTGATAAGTACGAAAGTTTTGCCCAACTTGTGGCTAAGATT
EST: gi|208321603|gb|GE120860.1|GE120860
EST:     AGAATTTGACTTCGGAGGAATTGTTACCCTCCTTATGGGACAAATGCAAG                         AAGGAGTTTCTTGATAAGTACGAAAGTTTTGCCCAACTTGTGGCTAAGATT
genomic: AGAATTTGACTTCGGAGGAATTGTTACCCTCCTTATGGGACAAATGCAAGgtaagctgta ... aactttgcagAAGGAGTTTCTTGATAAGTACGAAAGTTTTGCCCAACTTGTGGCTAAGATT
EST: gi|208062746|gb|GD860851.1|GD860851
EST:     AGAATTTGACTTCGGAGGAATTGTTACCCTCCTTATGGGACAAATGCAAG                         AAGGAGTTTCTTGATAAGTACGAAAGTTTTGCCCAACTTGTGGCTAAGATT
genomic: AGAATTTGACTTCGGAGGAATTGTTACCCTCCTTATGGGACAAATGCAAGgtaagctgta ... aactttgcagAAGGAGTTTCTTGATAAGTACGAAAGTTTTGCCCAACTTGTGGCTAAGATT
EST: gi|193460531|gb|FK427972.1|FK427972
EST:     AGAATTTGACTTCGGAGGAATTGTTACCCTCCTTATGGGACAAATGCAAG                         AAGGAGTTTCTTGATAAGTACGAAAGTTTTGCCCAACTTGTGGCTAAGATT
genomic: AGAATTTGACTTCGGAGGAATTGTTACCCTCCTTATGGGACAAATGCAAGgtaagctgta ... aactttgcagAAGGAGTTTCTTGATAAGTACGAAAGTTTTGCCCAACTTGTGGCTAAGATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggtttaaactaagtagaagatgcatgcaaattaatcgttttttaaaactttgcagAAGGAGTTTCTTGATAAGTACGAAAGTTTTGCCCAACTTGTGGCTAAGATTTATCCTACTGAGACAATCCCGTCTGTAGCGGAGATGAGAGACCTTTTAG
                            aattaat  putative branch site (score: 3)
                           aaattaatcgtttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgttgtgtgaacattttctttcattcacataccctctagaatgcgggtttaaactaagtagaagatgcatgcaaattaatcgttttttaaaactttgcagAAGGAGTTTCTTGATAAGTACGAAAGTTTTGCCCAACTTGTGGCTAAGATTTATCCTACTGAGACAATCCCGTCTGTAGCGGAGATGAGAGACCTTTTAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
- -tgtgtga
- - - - - - - - - - tcattca
- - - - - - - - - - - - - -cataccc
- - - - - - - - - - - - - - - - - - - gaatgcg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gcatgca