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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGGCTTGGCAAGATTACTTTGGAGACATACATTTCCCAGTTTCATATTTGGTTAAGgtgtgtatgcgtcgtgagccctccccgtgttatatgtctgaaatacattaagaggactccatgatgcatttgtacagtagtggctgtagtcagttattgt...

Basic information

species Glycine max
transcript GLYMA05G25780.1
intron # 14
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G25780.1 (Glycine max), 5'ss of exon 14
lower sequence: LOC_Os05g50510.1 (Oryza sativa), 5'ss of exon 13
GTGGCTTGGCAAGATTACTTTGGAGACATACATTTCCCAGTTTCATATTTGGTTAAGgtgtg-tatgcgtcgtgagccctccccgtgttata--tgtctgaaatacattaag-aggactccatgatgcatttgtacagtagtggctgtagtcagttattgt
 |||||||||||||| ||  | |||||||||||||||||| |||| |||||| | |||| || |||   |  |     |  |  ||||||    ||| | || ||| | | | | |||      |   |    |  |    || |      |||| ||   
CTGGCTTGGCAAGATCACACTAGAGACATACATTTCCCAGATTCACATTTGGCTCAGgtatggtatcaattttt--ttcagcatgtgttactgttgttttaattacttaatgcatgaccgttcaaaaaaaaaatttacgcatgacca-gtccagtaatca-

upper sequence: GLYMA05G25780.1 (Glycine max), 5'ss of exon 14
lower sequence: AT5G46340.1 (Arabidopsis thaliana), 5'ss of exon 14
GTGGCTTGGCAAGATTACTTTGGAGACATACATTTCCCAGTTTCATATTTGGTTAAGgtgtgtatgcgtcg--tgagccctccccgtgttatatgtctgaaatacattaagaggactccatgatgcatttgtacagtagtggctgtagtcagttattgt
||||||||||||||| ||||| ||||| |||||||||||||||||||| ||| |||||| ||| | |   |  | |  | |  ||  |     | | ||   || || ||   ||| |||   | ||                                
GTGGCTTGGCAAGATCACTTTAGAGACTTACATTTCCCAGTTTCATATATGGCTAAGgtttgttttctgtgacttaatcttttcctggaagcgtatttg--ttaaatcaaa--gacaccaattttcag-------------------------------

upper sequence: GLYMA05G25780.1 (Glycine max), 5'ss of exon 14
lower sequence: AT2G34410.3 (Arabidopsis thaliana), 5'ss of exon 13
GTGGCTTGGCAAGATTACTTTGGAGACATACATTTCCCAGTTTCATATTTGGTTAAGgtgtgtatgcgtc-gtgagccctccccgtgttatatgtctgaaatac-----attaagaggactccatgatgcatttgta-cagtagtggctgtagtcagttattgt
|||||| |||||||||||| |||| || || ||||| |||||||| || ||||||||||  |   |   | ||   |  || ||   |||| |     | | ||      |    ||||       ||| | || || | | |     |||  || |       
GTGGCTCGGCAAGATTACTCTGGAAACCTATATTTCTCAGTTTCACATCTGGTTAAGgtcagcgagaaactgtttcctttctcccaattatgtaggcaagagaccatttgtctgaaggatctaggaatgaaattttaactgcaaattatgtgttctgcag----

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|193704399|gb|FK644793.1|FK644793
EST:     GGCAAGATTACTTTGGAGACATACATTTCCCAGTTTCATATTTGGTTAAG                         GTCTAACATGCCAAACGGACAGCCCAAGTGGCTTCTTTCTCTTATCCCGGA
genomic: GGCAAGATTACTTTGGAGACATACATTTCCCAGTTTCATATTTGGTTAAGgtgtgtatgc ... ttgcatacagGTCTAACATGCCAAACGGACAGCCCAAGTGGCTTCTTTCTCTTATCCCGGA
EST: gi|254338250|gb|GR849775.1|GR849775
EST:     GGCAAGATTACTTTGGAGACATACATTTCCCAGTTTCATATTTGGTTAAG                         GTCTAACATGCCAAACGGACAGCCCAAGTGGCTTCTTTCTCTTATCCCGGA
genomic: GGCAAGATTACTTTGGAGACATACATTTCCCAGTTTCATATTTGGTTAAGgtgtgtatgc ... ttgcatacagGTCTAACATGCCAAACGGACAGCCCAAGTGGCTTCTTTCTCTTATCCCGGA
EST: gi|58014756|gb|CX701498.1|CX701498
EST:     GGCAAGATTACTTTGGAGACATACATTTCCCAGTTTCATATTTGGTTAAG                         GTCTAACATGCCAAACGGACAGCCCAAGTGGCTTCTTTCTCTTATCCCGGA
genomic: GGCAAGATTACTTTGGAGACATACATTTCCCAGTTTCATATTTGGTTAAGgtgtgtatgc ... ttgcatacagGTCTAACATGCCAAACGGACAGCCCAAGTGGCTTCTTTCTCTTATCCCGGA
EST: gi|207740974|gb|GD714352.1|GD714352
EST:     CAAGATTACTTTGGAGACATACATTTCCCAGTTTCATATTTTGGTTTAAG                         GTCTAACATGCCAAAACGGACAGCCCAAGTG
genomic: CAAGATTACTTTGGAGACATACATTTCCCAGTTTCATATTT-GGTT-AAGgtgtgtatgc ... ttgcatacagGTCTAACATGCCAAA-CGGACAGCCCAAGTG
EST: gi|208104675|gb|GD905044.1|GD905044
EST:     GGCAAGATTACTTTGGAGACATACATTTCCCAGTTTCATATTTGGTTAAG                         GTCTAACATGCCAAACGGACAGCCCAAGTGGCTTCTTTCTCTTATCCCGGA
genomic: GGCAAGATTACTTTGGAGACATACATTTCCCAGTTTCATATTTGGTTAAGgtgtgtatgc ... ttgcatacagGTCTAACATGCCAAACGGACAGCCCAAGTGGCTTCTTTCTCTTATCCCGGA
EST: gi|51337283|gb|CO981149.1|CO981149
EST:     ATACATTTCCCAGTTTCANATTTGGTTAAG                         GTCTAACATGCCAAACGGACAGCCCAAGTGGCTTCTTTCTCNNNTCCCGGA
genomic: ATACATTTCCCAGTTTCATATTTGGTTAAGgtgtgtatgc ... ttgcatacagGTCTAACATGCCAAACGGACAGCCCAAGTGGCTTCTTTCTCTTATCCCGGA
EST: gi|193464012|gb|FK427880.1|FK427880
EST:     GGCAAGATTACTTTGGAGACATACATTTCCCAGTTTCATATTTGGTTAAG                         GTCTAACATGCCAAACGGACAGCCCAAGTGGCTTCTTTCTCTTATCCC
genomic: GGCAAGATTACTTTGGAGACATACATTTCCCAGTTTCATATTTGGTTAAGgtgtgtatgc ... ttgcatacagGTCTAACATGCCAAACGGACAGCCCAAGTGGCTTCTTTCTCTTATCCC
EST: gi|208267765|gb|GE071182.1|GE071182
EST:     GGCAAGATTACTTTGGAGACATACATTTCCCAGTTTCATATTTGGTTGAG                         GCCTAACATGCCAAACGGACAGCCCAAGTGGCTTCTTTCTCTTATCCCGGA
genomic: GGCAAGATTACTTTGGAGACATACATTTCCCAGTTTCATATTTGGTTAAGgtgtgtatgc ... ttgcatacagGTCTAACATGCCAAACGGACAGCCCAAGTGGCTTCTTTCTCTTATCCCGGA
EST: gi|192300083|gb|FG991873.1|FG991873
EST:     AGCAAGATTACTTTGGAGACATACATTTCCCAGTTTCATATTTGGTTAAG                         GTCTAACATGCCAAACGGACAGCCCAAGTGGCTTCTTTCTCTTATCCCGGA
genomic: GGCAAGATTACTTTGGAGACATACATTTCCCAGTTTCATATTTGGTTAAGgtgtgtatgc ... ttgcatacagGTCTAACATGCCAAACGGACAGCCCAAGTGGCTTCTTTCTCTTATCCCGGA
EST: gi|208326566|gb|GE124910.1|GE124910
EST:     GGCAAGATTACTTTGGAGACATACATTTCCCAGTTTCATA-TTGGTTAAG                         GTCTAACATGCCAAACGGACAGCCCAAGTGGCTTCTTTCTCTTATCCCGGA
genomic: GGCAAGATTACTTTGGAGACATACATTTCCCAGTTTCATATTTGGTTAAGgtgtgtatgc ... ttgcatacagGTCTAACATGCCAAACGGACAGCCCAAGTGGCTTCTTTCTCTTATCCCGGA
EST: gi|207688258|gb|GD672597.1|GD672597
EST:     ATTACTTTGGAGACATACATTTCCCAGTTTCATATTTGGTTAAG                         GTCTAACATGCCAAACGGACAGCCCAAGTGGCTTCTTTCTCTTATCCCGGA
genomic: ATTACTTTGGAGACATACATTTCCCAGTTTCATATTTGGTTAAGgtgtgtatgc ... ttgcatacagGTCTAACATGCCAAACGGACAGCCCAAGTGGCTTCTTTCTCTTATCCCGGA
EST: gi|208336761|gb|GE135151.1|GE135151
EST:     GGCAAGATTACTTTGGAGACATACATTTCCCAGTTTCATATTTGGTTAAG                         GTCTAACATGCCAAACGG-CAGCCCAAGTG
genomic: GGCAAGATTACTTTGGAGACATACATTTCCCAGTTTCATATTTGGTTAAGgtgtgtatgc ... ttgcatacagGTCTAACATGCCAAACGGACAGCCCAAGTG
EST: gi|192332805|gb|FK026806.1|FK026806
EST:     GACAAGATTACTTTGGAGACATACATTTCCCAGTTTCATATTTGGTTAAG                         GTCTAACATGCCAAACGGACAGCCCAAGTGGCTTCTTTCTCTTATCCCGGA
genomic: GGCAAGATTACTTTGGAGACATACATTTCCCAGTTTCATATTTGGTTAAGgtgtgtatgc ... ttgcatacagGTCTAACATGCCAAACGGACAGCCCAAGTGGCTTCTTTCTCTTATCCCGGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGGCTTGGCAAGATTACTTTGGAGACATACATTTCCCAGTTTCATATTTGGTTAAGgtgtgtatgcgtcgtgagccctccccgtgttatatgtctgaaatacattaagaggactccatgatgcatttgtacagtagtggctgtagtcagttattgt

- - - - GCAAGA
- - - - - - - - -  TTGGAG
- - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccctccc