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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagtgcatatgacttcagtacttgagtttgcgtgcatgttcattgcttgactgttttgtactgcatgataagGTCCTACACAAGGTTGGGGCTGAAAGGGCAAGTGCTGCTGCGGTAACTCTAGATTCCCCTGGAGCAAATTATAGAACAGTTTGGGCTCTGAGCAAGCACT

Basic information

species Glycine max
transcript GLYMA07G08030.1
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G08030.1 (Glycine max), 3'ss of exon 16
lower sequence: LOC_Os04g58620.1 (Oryza sativa), 3'ss of exon 17
gtagtgcatatg-acttcagtacttgagtttgcgtgcatgttcattgcttgactgttttgtactg--catgataagGTCCTACACAAGGTTGGGGCTGAAAGGGCAAGTGCTGCTGCGGTAACTCTAGATTCCCCTGGAGCAAATTATAGAACAGTTTGGGCTCTGAGCAAGCACT
||||  ||  |  |  | |  | |  |   | |   | |||  |  | |   ||| | |  |  |    |    |||| || ||||| ||||||||||| |||||  | || |||||  | ||| ||||| ||||||| |||||||||||| | || |||||| |||||||  | |
gtagaacaagttcaactaaaaattctaccataca-acttgtcaaaaggt--gctgatctcaatcgatttttgccagGTACTGCACAAAGTTGGGGCTGAGAGGGCCTGCGCAGCTGCTATTACTTTAGATACCCCTGGTGCAAATTATAGAGCTGTCTGGGCTTTGAGCAAATATT

upper sequence: GLYMA07G08030.1 (Glycine max), 3'ss of exon 16
lower sequence: Vv15s0046g03390.t01 (Vitis vinifera), 3'ss of exon 15
gtagtgcatatgacttcagtacttga---gtttgcgtgcatgttcattgcttgac-tgtttt-----gtactgcatgataagGTCCTACACAAGGTTGGGGCTGAAAGGGCAAGTGCTGCTGCGGTAACTCTAGATTCCCCTGGAGCAAATTATAGAACAGTTTGGGCTCTGAGCAAGCACT
|||   | | |  |||||  |  |     | || |  |||  | ||||   | |  || |||      |||||  |||  |||| || ||||| ||||| |||||||| ||| ||||||||||  ||||||||||| | ||||| ||||| |||||||| |||||||| ||||||||| | |
gtaagacct-tatcttcaaaaaatagcatgcttaccagcagctccattttcttatatgcttttccatatactgagtgaacagGTTCTCCACAAAGTTGGTGCTGAAAGAGCATGTGCTGCTGCAATAACTCTAGATACTCCTGGTGCAAACTATAGAACTGTTTGGGCCCTGAGCAAGTATT
















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|16104878|gb|BI892618.1|BI892618
EST:     GGCGTTCCCTAGATCTCCCTGTGTACTTTGGAGATGCTGGTAGTCGAGAG                         GTCCTACACAAGGTTGGGGCTGAAAGGGCAAGTGCTGCTGCGGTAACTCTA
genomic: GGCGTTCCCTAGATCTCCCTGTGTACTTTGGAGATGCTGGTAGTCGAGAGgtagtgcata ... gcatgataagGTCCTACACAAGGTTGGGGCTGAAAGGGCAAGTGCTGCTGCGGTAACTCTA
EST: gi|10235459|gb|BE804347.1|BE804347
EST:     GGCGTTCCCTAGATCTCCCTGTGTACTTTGGAGATGCTGGTAGTCGAGAG                         GTCCTACACAAGGTTGGGGCTGAAAGGGCAAGTGCTGCTGCGGTAACTCTA
genomic: GGCGTTCCCTAGATCTCCCTGTGTACTTTGGAGATGCTGGTAGTCGAGAGgtagtgcata ... gcatgataagGTCCTACACAAGGTTGGGGCTGAAAGGGCAAGTGCTGCTGCGGTAACTCTA
EST: gi|13125620|gb|BG316190.1|BG316190
EST:     GGCGTTCCCTAGATCTCCCTGTGTACTTTGGAGATGCTGGTAGTCGAGAG                         GTCCTACACAAGGTTGGGGCTGAAAGGGCAAGTGCTGCTGCGGTAACTCTA
genomic: GGCGTTCCCTAGATCTCCCTGTGTACTTTGGAGATGCTGGTAGTCGAGAGgtagtgcata ... gcatgataagGTCCTACACAAGGTTGGGGCTGAAAGGGCAAGTGCTGCTGCGGTAACTCTA
EST: gi|20498319|gb|BQ273249.1|BQ273249
EST:     GGCGTTCCCTAGATCTCCCTGTGTACTTTGGAGATGCTGGTAGTCGAGAG                         GTCCTACACAAGGTTGGGGCT
genomic: GGCGTTCCCTAGATCTCCCTGTGTACTTTGGAGATGCTGGTAGTCGAGAGgtagtgcata ... gcatgataagGTCCTACACAAGGTTGGGGCT
EST: gi|13479391|gb|BG508734.1|BG508734
EST:     GGCGTTCCCTAGATCTCCCTGTGTACTTTGGAGATGCTGGTAGTCGAGAG                         GTCCTACACAAGGTTGGGGCTGAAAGGGCAAGTGCTGCTGCGGTAACTCTA
genomic: GGCGTTCCCTAGATCTCCCTGTGTACTTTGGAGATGCTGGTAGTCGAGAGgtagtgcata ... gcatgataagGTCCTACACAAGGTTGGGGCTGAAAGGGCAAGTGCTGCTGCGGTAACTCTA
EST: gi|8669480|gb|BE190587.1|BE190587
EST:     GGCGTTCCCTAGATCTCCCTGTGTACTTTGGAGATGCTGGTAGTCGAGAG                         GTCCTACACAAGGTTGGGGCTGAAAGGGCAAGTGCTGCTGCGGTAACTCTA
genomic: GGCGTTCCCTAGATCTCCCTGTGTACTTTGGAGATGCTGGTAGTCGAGAGgtagtgcata ... gcatgataagGTCCTACACAAGGTTGGGGCTGAAAGGGCAAGTGCTGCTGCGGTAACTCTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtacttgagtttgcgtgcatgttcattgcttgactgttttgtactgcatgataagGTCCTACACAAGGTTGGGGCTGAAAGGGCAAGTGCTGCTGCGGTAACTCTAGATTCCCCTGGAGCAAATTATAGAACAGTTTGGGCTCTGAGCAAGCACT
                           gcttgac  putative branch site (score: 4)
                                    ttttgta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagtgcatatgacttcagtacttgagtttgcgtgcatgttcattgcttgactgttttgtactgcatgataagGTCCTACACAAGGTTGGGGCTGAAAGGGCAAGTGCTGCTGCGGTAACTCTAGATTCCCCTGGAGCAAATTATAGAACAGTTTGGGCTCTGAGCAAGCACT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG