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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattatctaatgtgtttttctagttttccttttcaaaaataccatgaagttccctttgtttttgtaaacttcatattatttcaatatgttctgatgagattttggtaatgtttccagGTGGTCCTTGGGAGCGATAATGTATGAAATGTTAGTGGGGTATCCGCCCTTTTATTCAGATGAACCAATGTTGACTTGTAGAAAG

Basic information

species Glycine max
transcript GLYMA10G32480.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G32480.1 (Glycine max), 3'ss of exon 6
lower sequence: AT3G23310.1 (Arabidopsis thaliana), 3'ss of exon 7
gtattatctaatgtgtttttctagttttccttttcaaaaataccatgaagttccctttgtttttgtaaacttcatattatttcaatatgttct-gatgagattttggtaatgtttcc----agGTGGTCCTTGGGAGCGATAATGTATGAAATGTTAGTGGGGTATCCGCCCTTTTATTCAGATGAACCAATGTTGACTTGTAGAAAG
                                | ||  ||  |  |   ||    ||   ||||||   |||||  | |    |   |||| | ||| |  |||| |   | | | |    ||||||||  | || ||||| |||||||||||| | ||||||| ||| || ||||||||||| || ||||||   ||||||||||||
---------------------------gtaggtgcagcaaatctgttgggtcttgttctgttttgttt-cttcaactcaaaatacattgttgtcgataattttttcgggttttcttcctatagGTGGTCACTTGGTGCGATCATGTATGAAATGCTTGTGGGGTTTCCACCATTTTATTCAGACGAGCCAATGACAACTTGTAGAAAG

upper sequence: GLYMA10G32480.1 (Glycine max), 3'ss of exon 6
lower sequence: AT4G14350.3 (Arabidopsis thaliana), 3'ss of exon 7
gtattatctaatgtgtttttctagttttccttttcaaaaataccatgaagttccctttgtttttgtaaacttcatattatttcaatatgt--tctgatgagattttggtaatgtttccagGTGGTCCTTGGGAGCGATAATGTATGAAATGTTAGTGGGGTATCCGCCCTTTTATTCAGATGAACCAATGTTGACTTGTAGAAAG
                                |     ||  | |   | | |  |||||  |  |  | ||| | |  | | ||||  |  | ||     ||  |  | |  |||  ||||||||  | || || || |||||||||||| | ||||||| ||||||||||||||||||||| ||||||   |||||||| |||
-------------------------------gtaggtgaagccaacctattcctatttgtggtctttgatttctt-tggtgtaaataaataatatgggtgaataatcttgagattt--agGTGGTCTCTTGGCGCCATTATGTATGAAATGCTTGTGGGGTTTCCGCCCTTTTATTCAGATGACCCAATGACAACTTGTAGGAAG

upper sequence: GLYMA10G32480.1 (Glycine max), 3'ss of exon 6
lower sequence: EFJ29515 (Selaginella moellendorffii), 3'ss of exon 6
gtattatctaatgtgtttttctagttttccttttcaaaaataccatgaagttccctttgtttttgtaaacttcatattatttc---aatatgttctgatgagattttggtaatgtttccagGTGGTCCTTGGGAGCGATAATGTATGAAATGTTAGTGGGGTATCCGCCCTTTTATTCAGATGAACCAATGTTGACTTGTAGAAAG
                                                                ||||    ||| |    |    ||||| | | |    ||||    ||  ||  | ||||||||  | ||||| |||||||| || ||| |||| |||||||||||||| ||||| || ||||| ||||  |||||  | |||
----------------------------------------------------------------gtaagaggcatttctgattgaaaatatctaccggcttgattgatttatggtgcctagGTGGTCTCTTGGAGCTATAATGTACGAGATGCTAGTCGGGTATCCGCCCTTCTATTCCGACGAACCGATGTCTACTTGCCGGAAG

upper sequence: GLYMA10G32480.1 (Glycine max), 3'ss of exon 6
lower sequence: EFJ28086 (Selaginella moellendorffii), 3'ss of exon 6
gtattatctaatgtgtttttctagttttccttttcaaaaataccatgaagttccctttgtttttgtaaacttcatattatttcaatatgttctgatgagattttggtaatgtttccagGTGGTCCTTGGGAGCGATAATGTATGAAATGTTAGTGGGGTATCCGCCCTTTTATTCAGATGAACCAATGTTGACTTGTAGAAAG
                                                            |       |||||  |||     ||||| | | |    ||||    ||  ||  | ||||||||  | ||||| |||||||| || ||| |||| |||||||||||||| ||||| || ||||| ||||  |||||  | |||
-----------------------------------------------------------gtaagaggcacttctgattgaa--aatatctaccggcttgattgatttatggtgcctagGTGGTCTCTTGGAGCTATAATGTACGAGATGCTAGTCGGGTATCCGCCCTTCTATTCCGACGAACCGATGTCTACTTGCCGGAAG

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|13563179|gb|BG551399.1|BG551399
EST:     ATTGCCCCCGAAGTTCTTCTGAAGAAAGGATATGGCATGGAATGTGATTG                         GTGGTCCTTGGGAGCGATAATGTATGAAATGTTAGTGGGGTATCCGCCCTT
genomic: ATTGCCCCCGAAGTTCTTCTGAAGAAAGGATATGGCATGGAATGTGATTGgtattatcta ... atgtttccagGTGGTCCTTGGGAGCGATAATGTATGAAATGTTAGTGGGGTATCCGCCCTT
EST: gi|298165885|gb|HO008856.1|HO008856
EST:     ATTGCCCCCGAAGTTCTTCTGAAGAAAGGATATGGCATGGAATGTGATTG                         GTGGTCCCTGGGAGCGATAATGTATGAAATGTTAGTGGGGTATCCGCCCTT
genomic: ATTGCCCCCGAAGTTCTTCTGAAGAAAGGATATGGCATGGAATGTGATTGgtattatcta ... atgtttccagGTGGTCCTTGGGAGCGATAATGTATGAAATGTTAGTGGGGTATCCGCCCTT
EST: gi|192294765|gb|FG986614.1|FG986614
EST:     ATTGCCCCCGAAGTTCTTCTGAAGAAAGGATATGGCATGG-A----A-T-                         GTGGTCCTTGGGAGCGATAATGTATGAAATGTTAGTGGGGTATCCGCCCTT
genomic: ATTGCCCCCGAAGTTCTTCTGAAGAAAGGATATGGCATGGAATGTGATTGgtattatcta ... atgtttccagGTGGTCCTTGGGAGCGATAATGTATGAAATGTTAGTGGGGTATCCGCCCTT
EST: gi|16346917|gb|BI972512.1|BI972512
EST:     ATTGCCCCCGAAGTTCTTCTGAAGAAAGGATATGGCATGGAATGTGATTG                         GTGGTCCTTGGGAGCGATAATGTATGAAATGTTAGTGGGGTATCCGCCCTT
genomic: ATTGCCCCCGAAGTTCTTCTGAAGAAAGGATATGGCATGGAATGTGATTGgtattatcta ... atgtttccagGTGGTCCTTGGGAGCGATAATGTATGAAATGTTAGTGGGGTATCCGCCCTT
EST: gi|15815537|gb|BI787812.1|BI787812
EST:     ATTGCCCCCGAAGTTCTTCTGAAGAAAGGATATGGCATGGAATGTGATTG                         GTGGTCCTTGGGAGCGATAATGTATGAAATGTTAGTGGGGTATCCGCCCTT
genomic: ATTGCCCCCGAAGTTCTTCTGAAGAAAGGATATGGCATGGAATGTGATTGgtattatcta ... atgtttccagGTGGTCCTTGGGAGCGATAATGTATGAAATGTTAGTGGGGTATCCGCCCTT
EST: gi|298165881|gb|HO008852.1|HO008852
EST:     ATTGCCCCCGAAGTTCTTCTGAAGAAAGGATATGGCATGGAATGTGATTG                         GTGGTCCCTGGGAGCGATAATGTATGAAATGTTAGTGGGGTATCCGCCCTT
genomic: ATTGCCCCCGAAGTTCTTCTGAAGAAAGGATATGGCATGGAATGTGATTGgtattatcta ... atgtttccagGTGGTCCTTGGGAGCGATAATGTATGAAATGTTAGTGGGGTATCCGCCCTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtaaacttcatattatttcaatatgttctgatgagattttggtaatgtttccagGTGGTCCTTGGGAGCGATAATGTATGAAATGTTAGTGGGGTATCCGCCCTTTTATTCAGATGAACCAATGTTGACTTGTAGAAAG
                          ttctgat  putative branch site (score: 3)
                                              tgtttcc  putative PPT
       ttcatattatttcaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattatctaatgtgtttttctagttttccttttcaaaaataccatgaagttccctttgtttttgtaaacttcatattatttcaatatgttctgatgagattttggtaatgtttccagGTGGTCCTTGGGAGCGATAATGTATGAAATGTTAGTGGGGTATCCGCCCTTTTATTCAGATGAACCAATGTTGACTTGTAGAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG