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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtcgtagtttattattttaatattttcattttatgaacatgttcttttcctgttgtgctaagatctgatttattggatccctggtggtcactattgtctctaattctttgtcgttggagttgccagGTTGATCCAGTAGTTTACAATATGTTGCATGAAGATCCTGGTAATATCAGCTACTCAGCTGTTGGTGGCTTATCTGATCAGATCAGGGAATTGAGGGAGT

Basic information

species Glycine max
transcript GLYMA04G03180.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G03180.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv18s0001g13090.t01 (Vitis vinifera), 3'ss of exon 3
--------------------------------------------------gtaagtcgtagtttattattttaatattttcattttatgaacatgttcttttcc--tgttgtgctaagatctgatt-tattggatccctggtggtcactattgtct--ctaattctttgt----cgttggagtt-gccagGTTGATCCAGTAGTTTACAATATGTTGCATGAAGATCCTGGTAATATCAGCTACTCAGCTGTTGGTGGCTTATCTGATCAGATCAGGGAATTGAGGGAGT
                                                   ||| |    |    |    || ||  || |    | ||  |||| |  ||| |    || |  | ||     ||  ||   ||     |   ||   | | ||    || ||    |||     | ||  |||    ||||||||||||| ||||| || |||||||| ||||||||||||||| |||||||||||||||| ||||| ||||| ||||| ||| | ||| | ||||| |
gtaagttaccatggttctctatgtggactttgctgtgtaataccaactggataacttagtggcattagaattgatgattactccatttggtcatgattattttcaacattttagttagtgacaatcataaaagaaaaaagagagtttgtgtggttctcctgatagactgtgctatgatgatgtttaatagGTTGATCCAGTTGTTTATAACATGTTGCACGAAGATCCTGGTAATGTCAGCTACTCAGCTGTGGGTGGGTTATCAGATCAAATCCGAGAACTCAGGGAAT

upper sequence: GLYMA04G03180.1 (Glycine max), 3'ss of exon 3
lower sequence: PP1S13_419V6.1 (Physcomitrella patens), 3'ss of exon 3
gtaagtcgtagtttattattttaatattttcattttatgaacatgttcttttcctgttgtgctaagatctgatttattggatccctggtggtcactattgtctctaattctttgtcgttggagttgccagGTTGATCCAGTAGTTTACAATATGTTGCATGAAGATCCTGGTAATATCAGCTACTCAGCTGTTGGTGGCTTATCTGATCAGATCAGGGAATTGAGGGAGT
                          ||   || ||||    |||||  |     ||||    ||  ||  | |   |    | ||| |  |   | ||||   |   |     |  || | |  |  |||||||||| ||||| ||||| ||| | || || || ||||||||||| ||||||||||||||||| ||  ||  ||| || ||  | ||| |  | ||||
--------------------------ttaggatcttat----atgtttgtgagtcgttggtaaaatttccaaatatcttctccgctgatttttcgttttgtgcatttgtgcgcttgattcgtgcggttagGTTGATCCCGTAGTGTACAACATGCTTCACGAGGACCCTGGTAATATTAGCTACTCAGCTGTTGGAGGACTAAGTGACCAAATTCGAGAACTTCGTGAGT

upper sequence: GLYMA04G03180.1 (Glycine max), 3'ss of exon 3
lower sequence: PP1S91_182V6.1 (Physcomitrella patens), 3'ss of exon 3
gtaagtcgtagtttattattttaatattttcattttatgaacatgttcttttcctgttgtgctaagatctgatttattggatccctggtggtcactattgtctctaattctttgtcgttggagttgccagGTTGATCCAGTAGTTTACAATATGTTGCATGAAGATCCTGGTAATATCAGCTACTCAGCTGTTGGTGGCTTATCTGATCAGATCAGGGAATTGAGGGAGT
            || ||   |  |||  |    | | | ||||   ||| | | |  | |||  |           ||| || |||     | |  | |||   |   ||| ||   |||    ||  |||||||||| || || ||||||||| |||| || || ||||| ||||| ||||||||||| ||||| ||  |   |||||| ||| | ||  |  | ||||
------------ttgtt-catagatacctgggctgtctaaacagtgtctgtgcttactttgccga-----------ttgtatgcctttatataaaaaatgtgcatg--tctgtgcgattg----tgttagGTTGATCCCGTTGTGTACAATATGCTGCACGAGGACCCTGGAAATATTAGCTACTCAGCCGTTGGAGGACTCAGTGATCAAATCCGAGAGCTCCGTGAGT

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|151405441|gb|EV275255.1|EV275255
EST:     TGGTTCTTGATATGACAACACTCACCATAATGCGAGCTCTTCCTCGAGAA                         GCTGATCCAGTAGTTTACAATATGTTGCATGAAGATCCTGGTAATATCAGC
genomic: TGGTTCTTGATATGACAACACTCACCATAATGCGAGCTCTTCCTCGAGAAgtaagtcgta ... gagttgccagGTTGATCCAGTAGTTTACAATATGTTGCATGAAGATCCTGGTAATATCAGC
EST: gi|7285516|gb|AW598003.1|AW598003
EST:     TGGTTCTTGATATGACAACACTCACCATAATGCGAGCTCTTGCTCGAGAA                         GTTGATCCAGTAGTTTACAATATGTTGCATGAAGATCCTGATAATATCAGC
genomic: TGGTTCTTGATATGACAACACTCACCATAATGCGAGCTCTTCCTCGAGAAgtaagtcgta ... gagttgccagGTTGATCCAGTAGTTTACAATATGTTGCATGAAGATCCTGGTAATATCAGC
EST: gi|254341452|gb|GR850665.1|GR850665
EST:     TGGTTCTTGATATGACAACACTCACCATAATGCGAGCTCTTCCTCGAGAA                         GTTGATCCAGTAGTTTACAATATGTTGCATGAAGATCCTGGTAATATCAGC
genomic: TGGTTCTTGATATGACAACACTCACCATAATGCGAGCTCTTCCTCGAGAAgtaagtcgta ... gagttgccagGTTGATCCAGTAGTTTACAATATGTTGCATGAAGATCCTGGTAATATCAGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attggatccctggtggtcactattgtctctaattctttgtcgttggagttgccagGTTGATCCAGTAGTTTACAATATGTTGCATGAAGATCCTGGTAATATCAGCTACTCAGCTGTTGGTGGCTTATCTGATCAGATCAGGGAATTGAGGGAGT
                          ctctaat  putative branch site (score: 3)
                             taattcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtcgtagtttattattttaatattttcattttatgaacatgttcttttcctgttgtgctaagatctgatttattggatccctggtggtcactattgtctctaattctttgtcgttggagttgccagGTTGATCCAGTAGTTTACAATATGTTGCATGAAGATCCTGGTAATATCAGCTACTCAGCTGTTGGTGGCTTATCTGATCAGATCAGGGAATTGAGGGAGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA