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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ggtaaggtcttgtagtatgtaaagcagacatgcaagtttttttatgaaaataatgacatttaatttattctagtggtttataaggttttatctctatttgtaGCTCTGGCTGGTGCTTGGTGTTTTCTTGATGGCAACAATGTTGAGGATGTATGCAACATGTCAACAGCTTCAAGCACAGGCCCAAGCTCATGCAGCTGCA

Basic information

species Glycine max
transcript GLYMA18G04160.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G04160.1 (Glycine max), 3'ss of exon 5
lower sequence: AT3G55530.1 (Arabidopsis thaliana), 3'ss of exon 4
ggtaaggtcttgtagtatgtaaagcagacatgcaagtttttttatgaaaataatgacatttaatttattctagtggtttataaggttttatctctatttgtaGCTCTGGCTGGTGCTTGGTGTTTTCTTGATGGCAACAATGTTGAGGATGTATGCAACATGTCAACAGCTTCAAGCACAGGCCCAAGCTCATGCAGCTGCA-
||| || || | | ||||||||| | | | | | || ||| || | | ||| | ||||||||| ||||| |||||||| || || ||||||||||| | | | ||||||||||| || || ||||| |||||||| || || || ||||| || || |||
-----------gtatgattaaatacgtgagttaaagttttttccttttga----gttagtcgtctttcgggtgtgagtt-tgacatttccattaattttgtagCTGTGGCTTGTGCTTGGGGTGTTTTTGATGGCAACGACGCTTAGGATGTATGCTACTTGCCAACAACTTCAAGCTCATGCTCAGGCTCAGGCTGCAGCAG

upper sequence: GLYMA18G04160.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv06s0004g05080.t01 (Vitis vinifera), 3'ss of exon 3
ggtaaggtcttg-tagtatgtaaagcagacatgcaagtttttttatgaaaataatgacatttaatttattc--tagtggtttataaggtttt-------atctctatttgtaGCTCTGGCTGGTGCTTGGTGTTTTCTTGATGGCAACAATGTTGAGGATGTATGCAACATGTCAACAGCTTCAAGCACAGGCCCAAGCTCATGCAGCTGCA-
||| ||| | | || ||| | | |||| ||| ||| | |||||| ||| |||||| || ||| || | |||| || |||| ||| ||||||||||||| || | || | || || ||||| || | ||||||||||||||||| |||||||| || ||||| || |||||||||||||| || ||
-gtattttctcactggcatctaatgtgggcatgttagtctttct--gaaaattctgaagcataatttgttaaatagcaattgaagaggtattcatgtaaatctatatgtgtagCTCTGGCTAGTTGTGGGGTTCTTTTTTATGGCCACGAGCTTGAGGATGTATGCAACTTGTCAACAACTACAAGCTCATGCCCAAGCTCATGCTGCAGCTG

upper sequence: GLYMA18G04160.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv13s0019g01960.t01 (Vitis vinifera), 3'ss of exon 3
ggtaaggtcttgtagta------tgtaaagcagacatgcaagtttttttatgaaaataatgacatttaatttattcta---gtggtttataaggtttt----atctctatttgtaGCTCTGGCTGGTGCTTGGTGTTTTCTTGATGGCAACAATGTTGAGGATGTATGCAACATGTCAACAGCTTCAAGCACAGGCCCAAGCTCATGCAGCTGCA-
||| |||| | | || | || | || | | ||| | |||| || || | | |||| | || || | | | ||||||| |||||||||| ||||| | || ||||||| |||| | |||||||||||||| ||||| || |||||||| ||||| ||||||||||| || |||
-gtattttctttcattgagtttgtgcttggggagtatctacccttgtgcttagcaatgcttcagcttaaattgttgcacatgccatttaaagggccttcttaaccaatgtttgtagATCTGGCTGGTTCTTGGCATCTTTCTGATGGCCACAACCCTCAGGATGTATGCAACTTGTCAGCAACTTCAAGCTCAGGCACAAGCTCATGCTGCAGCAG

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|10845619|gb|BF068698.1|BF068698
EST:     CCAAACTTTCT                         GCTCTGGCTGGTGCTTGGTGTTTTCTTGATGGCAACAATGTTGAGGATGTA
genomic: CCAAACTTTCTggtaaggtct ... tctatttgtaGCTCTGGCTGGTGCTTGGTGTTTTCTTGATGGCAACAATGTTGAGGATGTA
EST: gi|208108153|gb|GD906613.1|GD906613
EST:     CTTCTGTTATTCATGATACTGAACTCTCACCAGATGTCCCCAAACTTTCT                         GCTCTGGCTGGTGCTTGGTGTTTTCTTGATGGCAACAATGTTGAGGATGTA
genomic: CTTCTGTTATTCATGATACTGAACTCTCACCAGATGTCCCCAAACTTTCTggtaaggtct ... tctatttgtaGCTCTGGCTGGTGCTTGGTGTTTTCTTGATGGCAACAATGTTGAGGATGTA
EST: gi|6481566|gb|AW200837.1|AW200837
EST:     CTTCTGTTATTCATGATACTGAACTCTCACCAGATGTCCCCAAACTTTCT                         GCTCTGGCTGGTGCTTGGTGTTTTCTTGATGGCAACAATGTTGAGGATGTA
genomic: CTTCTGTTATTCATGATACTGAACTCTCACCAGATGTCCCCAAACTTTCTggtaaggtct ... tctatttgtaGCTCTGGCTGGTGCTTGGTGTTTTCTTGATGGCAACAATGTTGAGGATGTA
EST: gi|21255789|gb|BQ452677.1|BQ452677
EST:     CTTCTGTTATTCATGATACTGAACTCTCACCAGATGTCCCCAAACTTTCT                         GCTCTGGCTGGTGCTTGGTGTTTTCTTGATGGCAACAATGTTGAGGATGTA
genomic: CTTCTGTTATTCATGATACTGAACTCTCACCAGATGTCCCCAAACTTTCTggtaaggtct ... tctatttgtaGCTCTGGCTGGTGCTTGGTGTTTTCTTGATGGCAACAATGTTGAGGATGTA
EST: gi|58016501|gb|CX703243.1|CX703243
EST:     TTCTGTTATTCATGATACTG-ACTTCTCACCAGATGTCCCCAAACTTTCT                         GCTCTGGCTGGTGCTTGGTGTTTTCTTGATGGCAACAATGTTGAGGATGTA
genomic: TTCTGTTATTCATGATACTGAAC-TCTCACCAGATGTCCCCAAACTTTCTggtaaggtct ... tctatttgtaGCTCTGGCTGGTGCTTGGTGTTTTCTTGATGGCAACAATGTTGAGGATGTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaataatgacatttaatttattctagtggtttataaggttttatctctatttgtaGCTCTGGCTGGTGCTTGGTGTTTTCTTGATGGCAACAATGTTGAGGATGTATGCAACATGTCAACAGCTTCAAGCACAGGCCCAAGCTCATGCAGCTGCA
          atttaat  putative branch site (score: 4)
 ttttatctctattt  putative PPT
 atgacatttaatttat  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
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggtaaggtcttgtagtatgtaaagcagacatgcaagtttttttatgaaaataatgacatttaatttattctagtggtttataaggttttatctctatttgtaGCTCTGGCTGGTGCTTGGTGTTTTCTTGATGGCAACAATGTTGAGGATGTATGCAACATGTCAACAGCTTCAAGCACAGGCCCAAGCTCATGCAGCTGCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC