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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gttgcagcgtaggtgccctaacatgttcatttgttccccaacatgcaagtttctattttgttaggtttacttccgtccttttccttaattcttgaatcagATAAATACCATGCTTGGGTTAATGCTGAATTCTTATTGGAAAAATGCTTTGTGGGTACCTTAGATGAAGGTCAGTGAAGATTTCATTCTAATAATGCATA

Basic information

species Glycine max
transcript GLYMA12G01150.2
intron # 5
splice site 3'
intron type U12 (go to U12 genes for details)

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G01150.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv13s0064g00450.t01 (Vitis vinifera), 3'ss of exon 5
gttgcag-cgtaggtgccctaacatgttcatttgttccccaacatgcaagt-ttctattttgttaggtttacttccgtccttttccttaattcttgaatcagATAAATACCATGCTTGGGTTAATGCTGAATTCTTATTGGAAAAATGCTTTGTGGGTACCTTAGATGAAGGTCAGTGAA----GATTTCATTCTAATAATGCATA
|||  || | ||| || |  |     |||||||    ||   | |     | ||| |   | | | |   ||     |   | ||||| |||||| | ||||| |||||||| |||||||| ||||||||||| ||| |||| |||||| |||||||||| ||||| ||  | ||||||        |   ||| | ||||     
gttataggcttagatggc--agtcccttcattttggtcctttcttttgcctcttcaaaaatttgatgcacacaggaattgctatccttgattcttcattcagACAAATACCACGCTTGGGTGAATGCTGAATTTTTACTGGAGAAATGCCTTGTGGGTACTTTAGACGATAGCCAGTGACCTGCAGCTATGTTCCAGTAATC----
















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|22929655|gb|BU546794.1|BU546794
EST:     TGTTGATATGTTGATGAAGGCGGTGGGAAAAGATTGCACATCTTTATTCA                         ATAAATACCATGCTTGGGTTAATGCTGAATTCTTATTGGAAAAATGCTTTG
genomic: TGTTGATATGTTGATGAAGGCGGTGGGAAAAGATTGCACATCTTTATTCAgtatcccttt ... cttgaatcagATAAATACCATGCTTGGGTTAATGCTGAATTCTTATTGGAAAAATGCTTTG
EST: gi|197661920|gb|FD480288.1|FD480288
EST:     TGTTGATATGTTGATGAAGGCGGTGGGAAAAGATTGCACATCTTTATTCA                         ATAAATACCATGCTTGGGTTAATGCTGAATTCTTATTGGAAAAATGCTTTG
genomic: TGTTGATATGTTGATGAAGGCGGTGGGAAAAGATTGCACATCTTTATTCAgtatcccttt ... cttgaatcagATAAATACCATGCTTGGGTTAATGCTGAATTCTTATTGGAAAAATGCTTTG
EST: gi|18732508|gb|BM527083.1|BM527083
EST:     TGTTGATATGTTGATGAAGGCGGTGGGAAAAGATTGCACATCTTTATTCA                         ATAAATACCATGCTTGGGTTAATGCTGAATTCTTATTGGAAAAATGCTTTG
genomic: TGTTGATATGTTGATGAAGGCGGTGGGAAAAGATTGCACATCTTTATTCAgtatcccttt ... cttgaatcagATAAATACCATGCTTGGGTTAATGCTGAATTCTTATTGGAAAAATGCTTTG
EST: gi|192299958|gb|FG992156.1|FG992156
EST:     TGTTGATATGTTGATGAAGGCGGTGGGAAAAGATTGCACATCTTTATTCA                         ATAAATACCATGCTTGGGTTAATGCTGAATTCTTATTGGAAAAATGCTTTG
genomic: TGTTGATATGTTGATGAAGGCGGTGGGAAAAGATTGCACATCTTTATTCAgtatcccttt ... cttgaatcagATAAATACCATGCTTGGGTTAATGCTGAATTCTTATTGGAAAAATGCTTTG
EST: gi|192317905|gb|FK010211.1|FK010211
EST:     TGTTGATATGTTGATGAAGGCGGTGGGAAAAGATTGCACATCTTTATTCA                         ATAAATACCATGCTTGGGTTAATGCTGAATTCTTATTGGAAAAATGCTTTG
genomic: TGTTGATATGTTGATGAAGGCGGTGGGAAAAGATTGCACATCTTTATTCAgtatcccttt ... cttgaatcagATAAATACCATGCTTGGGTTAATGCTGAATTCTTATTGGAAAAATGCTTTG
EST: gi|13479751|gb|BG509094.1|BG509094
EST:     TGTTGATATGTTGATGAAGGCGGTGGGAAAAGATTGCACATCTTTATTCA                         ATAAATACCATGCTTGGGTTAATGCTGAATTCTTATTGGAAAAATGCTTTG
genomic: TGTTGATATGTTGATGAAGGCGGTGGGAAAAGATTGCACATCTTTATTCAgtatcccttt ... cttgaatcagATAAATACCATGCTTGGGTTAATGCTGAATTCTTATTGGAAAAATGCTTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caagtttctattttgttaggtttacttccgtccttttccttaattcttgaatcagATAAATACCATGCTTGGGTTAATGCTGAATTCTTATTGGAAAAATGCTTTGTGGGTACCTTAGATGAAGGTCAGTGAAGATTTCATTCTAATAATGCATA
                                   ttccttaat  putative branch site 
                    tttacttccgtccttt  CT-rich tract
        tattttgtta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttgcagcgtaggtgccctaacatgttcatttgttccccaacatgcaagtttctattttgttaggtttacttccgtccttttccttaattcttgaatcagATAAATACCATGCTTGGGTTAATGCTGAATTCTTATTGGAAAAATGCTTTGTGGGTACCTTAGATGAAGGTCAGTGAAGATTTCATTCTAATAATGCATA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA