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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tagtagtatctctatcatctgctttatccaatagcctttagctttccatttaattggcttccagatgttctgtaacaatatacattacttccaaatgcagGTGATTATTTGTGCAGTAGAGAGGTCCAACAAGCAATTCCCATTTTACAGAAAGCATATGGAGATAGCATGCATAAAGTTTTGCATGTTGGTCCTGATAC

Basic information

species Glycine max
transcript GLYMA0041S00280.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA0041S00280.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv18s0001g08530.t01 (Vitis vinifera), 3'ss of exon 3
--tagtagtatctctatcatctgcttt-atccaatagcctttagctttccatttaattggcttccagatgttctgtaacaatatacattacttccaaatgcagGTGATTATTTGTGCAGTAGAGAGGTCCAACAAGCAATTCCCATTTTACAGAAAGCATATGGAGATAGCATGCATAAAGTTTTGCATGTTGGTCCTGATAC
  | || || | |  |  || || ||| ||  |     || |   | |  || | | |  || |||| |  ||  ||  | |  |  |  | |  | |||||||||| | ||  ||||    ||| || ||    ||||||||  || |  ||||||| ||||| || |||||||||||||||||||||||||| || ||  |
cgtggttgtttttagaatatttgttttgatatatcgttctcttattatggatgttaat--ctaccagtttctcattagaagtg-agttatcctatatatgcagGTGACTTTTCATGCACAGCAGAAGTTCACTGGGCAATTCCATTTCTGAAGAAAGCTTATGGTGACAGCATGCATAAAGTTTTGCATGTTGGCCCAGACTC
















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|5606518|gb|AI900616.1|AI900616
EST:     GGAAACCGTATAGAATCTGTTAGCAGGGTTGAAG                         GTGATTATTTGTGCAGTAGAGAGGTCCAACAAGCAATTCCCATTTTACAGA
genomic: GGAAACCGTATAGAATCTGTTAGCAGGGTTGAAGgtagttttaa ... ccaaatgcagGTGATTATTTGTGCAGTAGAGAGGTCCAACAAGCAATTCCCATTTTACAGA
EST: gi|14125816|gb|BG790254.1|BG790254
EST:     GTGGAATTGGAAACCGTATAGAATCTGTTAGCAGGGTTGAAG                         GTGATTATTTGTGCAGTAGAGAGGTCCAACAAGCAATTCCCATTTTACAGA
genomic: GTGGAATTGGAAACCGTATAGAATCTGTTAGCAGGGTTGAAGgtagttttaa ... ccaaatgcagGTGATTATTTGTGCAGTAGAGAGGTCCAACAAGCAATTCCCATTTTACAGA
EST: gi|4397134|gb|AI496131.1|AI496131
EST:     GTGGAATTGGAAACCGTATAGAATCTGTTAGCAGGGTTGAAG                         GTGATTATTTGTGCAGTAGAGAGGTCCAACAAGCAATTCCCATTTTACAGA
genomic: GTGGAATTGGAAACCGTATAGAATCTGTTAGCAGGGTTGAAGgtagttttaa ... ccaaatgcagGTGATTATTTGTGCAGTAGAGAGGTCCAACAAGCAATTCCCATTTTACAGA
EST: gi|7684885|gb|AW755533.1|AW755533
EST:     GTGGAATTGGAAACCGTATAGAATCTGTTAGCAGGGTTGAAG                         GTGATTATTTGTGCAGTAGAGAGGTCCAACAAGCAATTCCCATTTTACAGA
genomic: GTGGAATTGGAAACCGTATAGAATCTGTTAGCAGGGTTGAAGgtagttttaa ... ccaaatgcagGTGATTATTTGTGCAGTAGAGAGGTCCAACAAGCAATTCCCATTTTACAGA
EST: gi|10237051|gb|BE805939.1|BE805939
EST:     GTGGAATTGGAAACCGTATAGAATCTGTTAGCAGGGTTGAAG                         GTGATTATTTGTGCAGTA
genomic: GTGGAATTGGAAACCGTATAGAATCTGTTAGCAGGGTTGAAGgtagttttaa ... ccaaatgcagGTGATTATTTGTGCAGTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccatttaattggcttccagatgttctgtaacaatatacattacttccaaatgcagGTGATTATTTGTGCAGTAGAGAGGTCCAACAAGCAATTCCCATTTTACAGAAAGCATATGGAGATAGCATGCATAAAGTTTTGCATGTTGGTCCTGATAC
                        ctgtaac  putative branch site (score: 3)
                                       ttacttcc  putative PPT
                           taacaatatacatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tagtagtatctctatcatctgctttatccaatagcctttagctttccatttaattggcttccagatgttctgtaacaatatacattacttccaaatgcagGTGATTATTTGTGCAGTAGAGAGGTCCAACAAGCAATTCCCATTTTACAGAAAGCATATGGAGATAGCATGCATAAAGTTTTGCATGTTGGTCCTGATAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - -catctgc
- - - - - - - - - - - - - - - - -gccttta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - gcttcca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttctgta