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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attcatgttactgctgtttcttaatgtatactttcatgactttgcgtcaacttgaaatgtaactttattttttgttgttgtttttttcctttcactgtagCTTACTGAAGAATTGTCAAGGGTTGAGGGGAAGCTGAAGTTAACAGAATCTCTTCTAGAAAGCAAA

Basic information

species Glycine max
transcript GLYMA08G05100.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G05100.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os12g44340.1 (Oryza sativa), 3'ss of exon 2
attcat-gttactgctgtttcttaatgtatactttcatgactttgcgtcaacttgaaatgtaactttattttttgttgttgtttttttcctttcactgta-gCTTACTGAAGAATTGTCAAGGGTTGAGGGGAAGCTGAAGTTAACAGAATCTCTTCTAGAAAGCAAA
 | ||| || |  ||| ||   | ||   |    |||    ||    |    ||    ||        | |  ||   |||  || | | |  |  |||| |||||| ||||||||| ||| ||| || |||||||||||| | ||||| ||||| || |||||||| 
ctgcattgtcaaagcttttgacttatacttgtagtcaaactttaagattttttttttttgagggagactatcctgactttgccttctgcat--cgatgtaagCTTACGGAAGAATTGACAAAGGTGGATGGGAAGCTGAAGCTTACAGAGTCTCTCCTCGAAAGCAAG

upper sequence: GLYMA08G05100.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv01s0011g05790.t01 (Vitis vinifera), 3'ss of exon 2
attcatgttactgctgtttcttaatgtatactttcatgactttgcgtcaacttgaaatgtaactttattttttgttgttgtttttttccttt-cactgtagCTTACTGAAGAATTGTCAAGGGTTGAGGGGAAGCTGAAGTTAACAGAATCTCTTCTAGAAAGCAAA
 |  |  ||| | || ||| ||  | || |  || |  |  ||  ||         ||| |    |  | |||    ||||||| |||   |  ||  ||| ||||||||||| |||||| ||| |||| |||||| ||||||||||||||||||||||||||||| 
-tggaaattatttctttttatttgtctaaatctttagaatgttatgtgtttagagcatgcactgattctgttttcccttgttttcttctactgtaccttagATTACTGAAGAACTGTCAAAGGTGGAGGAGAAGCTTAAGTTAACAGAATCTCTTCTAGAAAGCAAG
















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|193479800|gb|FK445481.1|FK445481
EST:     TCAAAGCCTTGAGGCTCTCCGAACGACTCAGAGAAA-GGCCGTTGAAGAG                         CTTACTGAAGAATTGTCAAGGGTTGAGGGGAAGCTGAAGTTAACAGAATC
genomic: TCAAAGCCTTGAGGCTCTCCGAACGACTCAGAGAAAAGGCCGTTGAAGAGgtcactttct ... ttcactgtagCTTACTGAAGAATTGTCAAGGGTTGAGGGGAAGCTGAAGTTAACAGAATC
EST: gi|193351595|gb|FK317129.1|FK317129
EST:     TCAAAGCCTTGAGGCTCTCCGAACGACTCAGAGAAAAGGCCGTTGAAGAG                         CTTACTGAAGAATTGTCAAGGGTTGAGGGGAAGCTGAAGTTAACAGAATCT
genomic: TCAAAGCCTTGAGGCTCTCCGAACGACTCAGAGAAAAGGCCGTTGAAGAGgtcactttct ... ttcactgtagCTTACTGAAGAATTGTCAAGGGTTGAGGGGAAGCTGAAGTTAACAGAATCT
EST: gi|193555690|gb|FK513237.1|FK513237
EST:     TCAAAGCCTTGAGGCTCTCCGAACGACTCAGAGAAAAGGCCGTTGAAGAG                         CTTACTGAAGAATTGTCAAGGGTTGAGGGGAAGCTGAAGTTAACAGAATCT
genomic: TCAAAGCCTTGAGGCTCTCCGAACGACTCAGAGAAAAGGCCGTTGAAGAGgtcactttct ... ttcactgtagCTTACTGAAGAATTGTCAAGGGTTGAGGGGAAGCTGAAGTTAACAGAATCT
EST: gi|24205768|gb|BU965021.1|BU965021
EST:     TCAAAGCCTTGAGGCTCTCCGAACGACTCAGAGAAAAGGCCGTTGAAGAG                         CTTACTGAAGAATTGTCAAGGGTTGAGGGGAAGCTGAAGTTAACAGAATCT
genomic: TCAAAGCCTTGAGGCTCTCCGAACGACTCAGAGAAAAGGCCGTTGAAGAGgtcactttct ... ttcactgtagCTTACTGAAGAATTGTCAAGGGTTGAGGGGAAGCTGAAGTTAACAGAATCT
EST: gi|207737366|gb|GD716950.1|GD716950
EST:     TCAAAGCCTTGAGGCTCTCCGAACGACTCAGAGAAAAGGCCGTTGAAGAG                         CTTACTGAAGAATTGTCAAGGGTTGAGGGGGAAGCTGAAGTTAACAGAATC
genomic: TCAAAGCCTTGAGGCTCTCCGAACGACTCAGAGAAAAGGCCGTTGAAGAGgtcactttct ... ttcactgtagCTTACTGAAGAATTGTCAAGGGTTGAGGGG-AAGCTGAAGTTAACAGAATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtcaacttgaaatgtaactttattttttgttgttgtttttttcctttcactgtagCTTACTGAAGAATTGTCAAGGGTTGAGGGGAAGCTGAAGTTAACAGAATCTCTTCTAGAAAGCAAA
           atgtaac  putative branch site (score: 3)
                 ctttattttttgttgt  CT-rich tract
              taactttattttttgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attcatgttactgctgtttcttaatgtatactttcatgactttgcgtcaacttgaaatgtaactttattttttgttgttgtttttttcctttcactgtagCTTACTGAAGAATTGTCAAGGGTTGAGGGGAAGCTGAAGTTAACAGAATCTCTTCTAGAAAGCAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- tcatgtt
- - - - - ctgctgt
- - - - - - - - - - - - - - - - -tcatgac