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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagaatacaatcctatgattagtatgcttttttcttttcaatttattgctgactactgactttttcttcttcctcccatggaaacagTGTAGAATAATTCGGACAACCGAGTTAGCTGCTGCTAAGGAGAAACTAAATGAGCTTGAGAAGCAGAAAGAAGACATGTTGAAATTGAATTCCGCAGCAT

Basic information

species Glycine max
transcript GLYMA19G37230.2
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G37230.2 (Glycine max), 3'ss of exon 5
lower sequence: Vv08s0007g04470.t01 (Vitis vinifera), 3'ss of exon 5
gtaagaatac-aatcctatgattagtatgcttttttcttttcaatttattgctgactactgactttttcttcttcctcccatggaaacagTGTAGAATAATTCGGACAACCGAGTTAGCTGCTGCTAAGGAGAAACTAAATGAGCTTGAGAAGCAGAAAGAAGACATGTTGAAATTGAATTCCGCAGCAT
||||| || || ||| | ||| || |||| | | || || || | || | | | | ||||| |||||| |||||||| |||||||| |||||||||||||| |||||||| ||||||| || |||| ||||||||||| || || || || | ||| | ||||
gtaaggatttgaaccctttttttactaagcttaaaatt----ggaatgctgttggttagacatttcctttctgtgttttcatggccacagTGCAGAATAATCCGGACAACAGAGTTAGCTGCTGCACAGGAGAAATTAAATGAACTGGAGAGACAGAAAGAAGAGATCTTAAAGTTCTACTCCCCTGCAT
















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|6454511|gb|AW185194.1|AW185194
EST:     AGGAAAATCTTCAAAAGGAACCTCGTATCATGGAACTTAGGAATCAA                         TGTAGAATAATTCGGACAACCGAGTTAGCTG
genomic: AGGAAAATCTTCAAAAGGAACCTCGTATCATGGAACTTAGGAATCAAgtaagaatac ... atggaaacagTGTAGAATAATTCGGACAACCGAGTTAGCTG
EST: gi|151403740|gb|EV273550.1|EV273550
EST:     AGGAAAATCTTCAAAAGGAACCTCGTATCATGGAACTTAGGAATCAA                         TGTAGAATAATTCGGACAACCGAGTTAGCTGCTGCTAAGGAGAAACTAAAT
genomic: AGGAAAATCTTCAAAAGGAACCTCGTATCATGGAACTTAGGAATCAAgtaagaatac ... atggaaacagTGTAGAATAATTCGGACAACCGAGTTAGCTGCTGCTAAGGAGAAACTAAAT
EST: gi|254332261|gb|GR843845.1|GR843845
EST:     TCAAAAGGAACCTCGTATCATGGAACTTAGGAATCAA                         TGTAGAATAATTCGGACAACCGAGTTAGCTGCTGCTAAGGAGAAACTAAAT
genomic: TCAAAAGGAACCTCGTATCATGGAACTTAGGAATCAAgtaagaatac ... atggaaacagTGTAGAATAATTCGGACAACCGAGTTAGCTGCTGCTAAGGAGAAACTAAAT
EST: gi|151404632|gb|EV274446.1|EV274446
EST:     AGGAAAATCTTCAAAAGGAACCTCGTATCATGGAACTTAGGAATCAA                         TGTAGAATAATTCGGACAACCGAGTTAGCTGCTGCTAAGGAGAAACTAAAT
genomic: AGGAAAATCTTCAAAAGGAACCTCGTATCATGGAACTTAGGAATCAAgtaagaatac ... atggaaacagTGTAGAATAATTCGGACAACCGAGTTAGCTGCTGCTAAGGAGAAACTAAAT
EST: gi|254332260|gb|GR843844.1|GR843844
EST:     AGGAAAATCTTCAAAAGGAACCTCGTATCATGGAACTTAGGAATCAA                         TGTAGAATAATTCGGACAACCGAGTTAGCTGCTGCTAAGGAGAAACTAAAT
genomic: AGGAAAATCTTCAAAAGGAACCTCGTATCATGGAACTTAGGAATCAAgtaagaatac ... atggaaacagTGTAGAATAATTCGGACAACCGAGTTAGCTGCTGCTAAGGAGAAACTAAAT
EST: gi|21888222|gb|BQ741444.1|BQ741444
EST:     AGGAAAATCTTCAAAAGGAACCTCGTATCATGGAACTTAGGAATCAA                         TGTAGAATAATTCGGACAACCGAGTTAGCTGCTGCTAAGGAGAAACTAAAT
genomic: AGGAAAATCTTCAAAAGGAACCTCGTATCATGGAACTTAGGAATCAAgtaagaatac ... atggaaacagTGTAGAATAATTCGGACAACCGAGTTAGCTGCTGCTAAGGAGAAACTAAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttttcaatttattgctgactactgactttttcttcttcctcccatggaaacagTGTAGAATAATTCGGACAACCGAGTTAGCTGCTGCTAAGGAGAAACTAAATGAGCTTGAGAAGCAGAAAGAAGACATGTTGAAATTGAATTCCGCAGCAT
                     tactgac  putative branch site (score: 1)
 ctactgactttttctt  CT-rich tract
 tcaatttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagaatacaatcctatgattagtatgcttttttcttttcaatttattgctgactactgactttttcttcttcctcccatggaaacagTGTAGAATAATTCGGACAACCGAGTTAGCTGCTGCTAAGGAGAAACTAAATGAGCTTGAGAAGCAGAAAGAAGACATGTTGAAATTGAATTCCGCAGCAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG