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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtacctttattcaactgtgcttcaattccccttccaatattttgtaaaagggggagggaccagcataagttaaccttttgtaatatttgttttttgcagATTGATGGTAAATTTGCCAGATGCCCCTAATCGAGCAAAAATATTGAAAGTTATACTGGCAAAAGAGGAATTGTCTCCTGATGTTGATTTAGATGCAGTT

Basic information

species Glycine max
transcript GLYMA17G13850.1
intron # 22
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G13850.1 (Glycine max), 3'ss of exon 22
lower sequence: Vv17s0000g01550.t01 (Vitis vinifera), 3'ss of exon 24
gtgag-tacctttattcaactgtgcttcaattccccttccaatattttgtaaaagggggagggaccagcataagttaaccttttgtaata-tttgttttttgcagATTGATGGTAAATTTGCCAGATGCCCCTAATCGAGCAAAAATATTGAAAGTTATACTGGCAAAAGAGGAATTGTCTCCTGATGTTGATTTAGATGCAGTT
|| ||  | |  |   | | | || ||  | |  ||| |   |||||    |||  ||||          | ||||   ||| ||||||  ||  | |||| ||| |||||||| |||||||||||||| || ||| ||||||| ||  | ||||| ||||||||||||||||| |||||||||||||||||||| |||||||||
gtaaggcatcactgagccattttg-ttggactatcctactt-tatttccacaaactgggac---------ttagtt---cttctgtaatggttcatcttttacagGTTGATGGTGAATTTGCCAGATGCTCCAAATAGAGCAAAGATTCTAAAAGTGATACTGGCAAAAGAGGACTTGTCTCCTGATGTTGATTTGGATGCAGTT
















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|16282350|gb|BI944969.1|BI944969
EST:     AACAGGCCTTTTGACCTTGACGAGGCTGTCATAAGGAGGATGCCAAGAAG                         ATTGATGGTAAATTTGCCAGATGCCCCTAATCGAGCAAAAATATTGAAAGT
genomic: AACAGGCCTTTTGACCTTGACGAGGCTGTCATAAGGAGGATGCCAAGAAGgtgagtacct ... ttttttgcagATTGATGGTAAATTTGCCAGATGCCCCTAATCGAGCAAAAATATTGAAAGT
EST: gi|254327049|gb|GR836658.1|GR836658
EST:     AACAGGCCTTTTGACCTTGACGAGGCTGTCATAAGGAGGATGCCAAGAAG                         ATTGATGGTAAATTTGCCAGATGCCCCTAATCGAGCAAAAATATTGAAAGT
genomic: AACAGGCCTTTTGACCTTGACGAGGCTGTCATAAGGAGGATGCCAAGAAGgtgagtacct ... ttttttgcagATTGATGGTAAATTTGCCAGATGCCCCTAATCGAGCAAAAATATTGAAAGT
EST: gi|7588236|gb|AW704036.1|AW704036
EST:     AACAGGCCTTTTGACCTTGACGAGGCTGTCATAAGGAGGATGCCAAGAAG                         ATTGATGGTAAATTTGCCAGATGCCCCTAATCGAGCAAAAATATTGAAAGT
genomic: AACAGGCCTTTTGACCTTGACGAGGCTGTCATAAGGAGGATGCCAAGAAGgtgagtacct ... ttttttgcagATTGATGGTAAATTTGCCAGATGCCCCTAATCGAGCAAAAATATTGAAAGT
EST: gi|15203099|gb|BI425867.1|BI425867
EST:     AACAGGCCTTTTGACCTTGACGAGGCTGTCATAAGGAGGATGCCAAGAAG                         ATTGATGGTAAATTTGCCAGATGCCCCTAATCGAGCAAAAATATTGAAAGT
genomic: AACAGGCCTTTTGACCTTGACGAGGCTGTCATAAGGAGGATGCCAAGAAGgtgagtacct ... ttttttgcagATTGATGGTAAATTTGCCAGATGCCCCTAATCGAGCAAAAATATTGAAAGT
EST: gi|193626107|gb|FK577003.1|FK577003
EST:     AACAGGCCTTTTGACCTTGACGAGGCTGTCATAAGGAGGATGCCAAGAAG                         ATTGATGGTAAATTTGCCAGATGCCCCTAATCGAGCAAAAATATTGAAAGT
genomic: AACAGGCCTTTTGACCTTGACGAGGCTGTCATAAGGAGGATGCCAAGAAGgtgagtacct ... ttttttgcagATTGATGGTAAATTTGCCAGATGCCCCTAATCGAGCAAAAATATTGAAAGT
EST: gi|13252456|gb|BG363367.1|BG363367
EST:     AACAGGCCTTTTGACCTTGACGAGGCTGTCATAAGGAGGATGCCAAGAAG                         ATTGATGGTAAATTTGCCAGATGCCCCTAATCGAGCAAAAATATTGAAAGT
genomic: AACAGGCCTTTTGACCTTGACGAGGCTGTCATAAGGAGGATGCCAAGAAGgtgagtacct ... ttttttgcagATTGATGGTAAATTTGCCAGATGCCCCTAATCGAGCAAAAATATTGAAAGT
EST: gi|22522568|gb|BU081379.1|BU081379
EST:     AACAGGCCTTTTGACCTTGACGAGGCTGTCATAAGGAGGATGCCAAGAAG                         ATTGATGGTAAATTTGCCAGATGCCCCTAATCGAGCAAAAATATTGAAAGT
genomic: AACAGGCCTTTTGACCTTGACGAGGCTGTCATAAGGAGGATGCCAAGAAGgtgagtacct ... ttttttgcagATTGATGGTAAATTTGCCAGATGCCCCTAATCGAGCAAAAATATTGAAAGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taaaagggggagggaccagcataagttaaccttttgtaatatttgttttttgcagATTGATGGTAAATTTGCCAGATGCCCCTAATCGAGCAAAAATATTGAAAGTTATACTGGCAAAAGAGGAATTGTCTCCTGATGTTGATTTAGATGCAGTT
                       agttaac  putative branch site (score: 3)
                                         tttgtttttt  putative PPT
                               ttttgtaatatttgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtacctttattcaactgtgcttcaattccccttccaatattttgtaaaagggggagggaccagcataagttaaccttttgtaatatttgttttttgcagATTGATGGTAAATTTGCCAGATGCCCCTAATCGAGCAAAAATATTGAAAGTTATACTGGCAAAAGAGGAATTGTCTCCTGATGTTGATTTAGATGCAGTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA