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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gttaagatggataaagcatgtatttgaattattgctaattaacatattttaaattttaataatttctacttatagagtgcttcattttcttcacttttagTTTATGATGTCACAAGGAGAGAAACCTTTACAAACTTATCAGAAGTGTGGTCTAAGGAAGTGGAACTCTACTCAACTAATCAGGATTGTGTGAAGATACT

Basic information

species Glycine max
transcript GLYMA19G37020.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G37020.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv08s0007g04740.t01 (Vitis vinifera), 3'ss of exon 3
----gttaagatggataaagcatgtatttgaattattgctaattaacatattttaaattttaataatttctacttatagagtgcttcattttcttcacttttagTTTATGATGTCACAAGGAGAGAAACCTTTACAAACTTATCAGAAGTGTGGTCTAAGGAAGTGGAACTCTACTCAACTAATCAGGATTGTGTGAAGATACT
     |||       |     |||  ||| ||  |||  | |||||    ||||   |  |   || |  ||  |   |  |   |  | || ||   ||||||| |||||||| ||| ||||||| | |||||||||||| || || |||||| |||| ||||| || || ||||| ||||||||||| ||||||||||| ||
attttttactgcatttttgcaatggttttaaaagatt--tgattaaggc-ttttctttggtgggaagtcttagctgatgcatatattttgttttttg-ttttagTATATGATGTGACACGGAGAGAGAGCTTTACAAACTTGTCCGATGTGTGGGCTAAAGAAGTAGAGCTTTACTCGACTAATCAGGACTGTGTGAAGATGCT
















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|192332578|gb|FK025683.1|FK025683
EST:     CAGGACTCTAAACAGTTCTTACTATAGAAAAGCACAAGGAATCATTCTCG                         TTTATGATGTCACAAGGAGAGAAACCTTTACAAACTTATCAGAAGTGTGGT
genomic: CAGGACTCTAAACAGTTCTTACTATAGAAAAGCACAAGGAATCATTCTCGgtatgctaac ... tcacttttagTTTATGATGTCACAAGGAGAGAAACCTTTACAAACTTATCAGAAGTGTGGT
EST: gi|192323686|gb|FK015992.1|FK015992
EST:     CAGGACTCTAAACAGTTCTTACTATAGAAAAGCACAAGGAATCATTCTCG                         TTTATGATGTCACAAGGAGAGAAACCTTTACAAACTTATCAGAAGTGTGGT
genomic: CAGGACTCTAAACAGTTCTTACTATAGAAAAGCACAAGGAATCATTCTCGgtatgctaac ... tcacttttagTTTATGATGTCACAAGGAGAGAAACCTTTACAAACTTATCAGAAGTGTGGT
EST: gi|192332579|gb|FK025684.1|FK025684
EST:     CAGGACTCTAAACAGTTCTTACTATAGAAAAGCACAAGGAATCATTCTCG                         TTTATGATGTCACAAGGAGAGAAACCTTTACAAACTTATCAGAAGTGTGGT
genomic: CAGGACTCTAAACAGTTCTTACTATAGAAAAGCACAAGGAATCATTCTCGgtatgctaac ... tcacttttagTTTATGATGTCACAAGGAGAGAAACCTTTACAAACTTATCAGAAGTGTGGT
EST: gi|16345184|gb|BI970779.1|BI970779
EST:     CAGGACTCTAAACAGTTCTTACTATAGAAAAGCACAAGGAATCATTCTCG                         TTTATGATGTCACAAGGAGAGAAACCTTTACAAACTTATCAGAAGTGTGGT
genomic: CAGGACTCTAAACAGTTCTTACTATAGAAAAGCACAAGGAATCATTCTCGgtatgctaac ... tcacttttagTTTATGATGTCACAAGGAGAGAAACCTTTACAAACTTATCAGAAGTGTGGT
EST: gi|192328600|gb|FK023576.1|FK023576
EST:     CAGGACTCTAAACAGTTCTTACTATAGAAAAGCACAAGGAATCATTCTCG                         TTTATGATGTCACAAGGAGAGAAACCTTTACAAACTTATCAGAAGTGTGGT
genomic: CAGGACTCTAAACAGTTCTTACTATAGAAAAGCACAAGGAATCATTCTCGgtatgctaac ... tcacttttagTTTATGATGTCACAAGGAGAGAAACCTTTACAAACTTATCAGAAGTGTGGT
EST: gi|8283505|gb|BE021064.1|BE021064
EST:     CAGGACTCTAAACAGTTCTTACTATAGAAAAGCACAAGGAATCATTCTCG                         TTTATGATGTCACAAGGAGAGAAACCTTTACAAACTTATCAAAAATGTGG
genomic: CAGGACTCTAAACAGTTCTTACTATAGAAAAGCACAAGGAATCATTCTCGgtatgctaac ... tcacttttagTTTATGATGTCACAAGGAGAGAAACCTTTACAAACTTATCAGAAGTGTGG
EST: gi|192328601|gb|FK023577.1|FK023577
EST:     CAGGACTCTAAACAGTTCTTACTATAGAAAAGCACAAGGAATCATTCTCG                         TTTATGATGTCACAAGGAGAGAAACCTTTACAAACTTATCAGAAGTGTGGT
genomic: CAGGACTCTAAACAGTTCTTACTATAGAAAAGCACAAGGAATCATTCTCGgtatgctaac ... tcacttttagTTTATGATGTCACAAGGAGAGAAACCTTTACAAACTTATCAGAAGTGTGGT
EST: gi|192329516|gb|FK022208.1|FK022208
EST:     CAGGACTCTAAACAGTTCTTACTATAGAAAAGCACAAGGAATCATTCTCG                         CTTATGATGTCACAAGGAGAGAAACCTTTACAAACTTATCAGAAGTGTGGT
genomic: CAGGACTCTAAACAGTTCTTACTATAGAAAAGCACAAGGAATCATTCTCGgtatgctaac ... tcacttttagTTTATGATGTCACAAGGAGAGAAACCTTTACAAACTTATCAGAAGTGTGGT
EST: gi|151393016|gb|EV262891.1|EV262891
EST:     CAGGACTCTAAACAGTTCTTACTATAGAAAAGCACAAGGAATCATTCTCG                         TTTATGATGTCACAAGGAGAGAAACCTTTACAAACTTATCAGAAGTGTGGT
genomic: CAGGACTCTAAACAGTTCTTACTATAGAAAAGCACAAGGAATCATTCTCGgtatgctaac ... tcacttttagTTTATGATGTCACAAGGAGAGAAACCTTTACAAACTTATCAGAAGTGTGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attttaaattttaataatttctacttatagagtgcttcattttcttcacttttagTTTATGATGTCACAAGGAGAGAAACCTTTACAAACTTATCAGAAGTGTGGTCTAAGGAAGTGGAACTCTACTCAACTAATCAGGATTGTGTGAAGATACT
        ttttaat  putative branch site (score: 3)
                                tgcttcattttcttca  putative PPT
     aaattttaataatttc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttaagatggataaagcatgtatttgaattattgctaattaacatattttaaattttaataatttctacttatagagtgcttcattttcttcacttttagTTTATGATGTCACAAGGAGAGAAACCTTTACAAACTTATCAGAAGTGTGGTCTAAGGAAGTGGAACTCTACTCAACTAATCAGGATTGTGTGAAGATACT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - -gcatgta