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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttttgaacctaagaaagaagataaatcacattttcaatatttggtgaagttattagctgcttattgttgcattaatcactgagttatctttttcatgcagACTCCACCTCCATTAGATGTTCCTCTTAAATTGATAGGAAACGATCCAGTGGCAAAGGATATAAAGTGGGAAGATGATGGAGTGCTAGTTAGCTCGATTG

Basic information

species Glycine max
transcript GLYMA08G33520.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G33520.1 (Glycine max), 3'ss of exon 4
lower sequence: AT5G58140.2 (Arabidopsis thaliana), 3'ss of exon 22
ttttgaacctaagaaagaagataaatcacattttcaatatttggtgaagttattagctgcttattgttgcatta-atcactgagttatctttttcatgcagACTCCACCTCCATTAGATGTTCCTCTTAAATTGATAGGAAACGATCCAGTGGCAAAGGATATAAAGTGGGAAGATGATGGAGTGCTAGTTAGCTCGATTG
| | || | |||| ||| |||| | | | || || || |||||| | | || | |||| || | ||| |||| ||| || ||| | |||| || | | | || | ||| ||||| || || ||||||||||||||||||||||||||||| || | || | |
------------gtaggactaataatcgttatttttatatc-aatcagccttttccgtgtttgttgttggctgatataatagagtgat----tgcatacagAGTCCTCCACCACTGGATGCACCGTTGAGCATAATCGAAAAAGATCCGAATGCCAAAGATATAAAGTGGGAAGATGATGGAGTGCTTGTGAATTCTACGG

upper sequence: GLYMA08G33520.1 (Glycine max), 3'ss of exon 4
lower sequence: AT5G58140.3 (Arabidopsis thaliana), 3'ss of exon 21
ttttgaacctaagaaagaagataaatcacattttcaatatttggtgaagttattagctgcttattgttgcatta-atcactgagttatctttttcatgcagACTCCACCTCCATTAGATGTTCCTCTTAAATTGATAGGAAACGATCCAGTGGCAAAGGATATAAAGTGGGAAGATGATGGAGTGCTAGTTAGCTCGATTG
| | | || | |||| ||| |||| | | | || || || |||||| | | || | |||| || | ||| |||| ||| || ||| | |||| || | | | || | ||| ||||| || || ||||||||||||||||||||||||||||| || | || | |
-------gcatggtaggactaataatcgttatttttatatc-aatcagccttttccgtgtttgttgttggctgatataatagagtgat----tgcatacagAGTCCTCCACCACTGGATGCACCGTTGAGCATAATCGAAAAAGATCCGAATGCCAAAGATATAAAGTGGGAAGATGATGGAGTGCTTGTGAATTCTACGG
















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|208320879|gb|GE123818.1|GE123818
EST:     AACAGCATCC-TTTTTTCGTGGAATCAATTGGCCTCTTATCCGCAACATG                         ACTCCACCTCCATTAGATGTTCCTCTTAAATTGATAGGAAACGATCCAGTG
genomic: AACAGCATCCTTTTTTTCGTGGAATCAATTGGCCTCTTATCCGCAACATGgtaatattct ... tttcatgcagACTCCACCTCCATTAGATGTTCCTCTTAAATTGATAGGAAACGATCCAGTG
EST: gi|46492935|gb|CN472491.1|CN472491
EST:     AACAGCATCCNNNNNNNCGTGGAATCAATTGGCCTCTTATCCGCAACATG                         ACTCCACCTCCATTAGATGTTCCTCTTAAATTGATAGGAAACGATCCAGTG
genomic: AACAGCATCCTTTTTTTCGTGGAATCAATTGGCCTCTTATCCGCAACATGgtaatattct ... tttcatgcagACTCCACCTCCATTAGATGTTCCTCTTAAATTGATAGGAAACGATCCAGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaagttattagctgcttattgttgcattaatcactgagttatctttttcatgcagACTCCACCTCCATTAGATGTTCCTCTTAAATTGATAGGAAACGATCCAGTGGCAAAGGATATAAAGTGGGAAGATGATGGAGTGCTAGTTAGCTCGATTG
                        cattaat  putative branch site (score: 3)
 ttatctttttc  putative PPT
 ttatcttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttttgaacctaagaaagaagataaatcacattttcaatatttggtgaagttattagctgcttattgttgcattaatcactgagttatctttttcatgcagACTCCACCTCCATTAGATGTTCCTCTTAAATTGATAGGAAACGATCCAGTGGCAAAGGATATAAAGTGGGAAGATGATGGAGTGCTAGTTAGCTCGATTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - aagaaaga
- - - - - - - - - - - -aatcaca
- - - - - - - - - - - - - - - - - - - -tttggtg
- - - - - - - - - - - - - - - - - - - - - - - - - - -tagctgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcatta