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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattttggtttttatgaattgggtgtgtgtgtgggggtgtgggggaggttctgctaagatgcagaatagttctaattgaatctaggattctcctatcatttttaacctggtcctttcaaggagtcttgtttttttaacaaaagcatttgacagATTCTAGAGGATATTTGGTTGATGAGGATGGATTTGACTACATGAAAATATCATTTTTGCGAGACATCAAAGCTCAACAAAGAAGTTTACG

Basic information

species Glycine max
transcript GLYMA08G20930.2
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G20930.2 (Glycine max), 3'ss of exon 10
lower sequence: AT1G51720.1 (Arabidopsis thaliana), 3'ss of exon 10
gtaattttggtttttatgaattgggtgtgtgtgtgggggtgtgggggaggttctgctaagatgcagaatagttctaattgaatctaggattctcctatcatttttaacctggtcctttc-aaggagtcttgtttttttaacaaaagcatttgacagATTCTAGAGGATATTTGGTTGATGAGGATGGATTTGACTACATGAAAATATCATTTTTGCGAGACATCAAAGCTCAACAAAGAAGTTTACG
                                                    ||||| |      || ||| | |   ||||  | |  ||    |    |||  ||  || | |  |  || |     | ||||  | |   || | |    ||||||| | |||||||||||| || || ||||||||||| || |||||| |  |||| ||| |||| || ||| ||||||| |||||| |  |
---------------------------------------------------gctgctcaag----gattagctttctgtgaaaat-gatttggttttcggtttgcaatttgattccatagaaagcaaacttttttgctgatgcaaacttcctgcagATTCAAAAGGATATTTGGTGGACGATGATGGATTTGATTATATGAAACTTGCATTCTTGAGAGATATAAAATCTCAACAGAGAAGTCTGAG

upper sequence: GLYMA08G20930.2 (Glycine max), 3'ss of exon 10
lower sequence: Vv09s0002g02530.t01 (Vitis vinifera), 3'ss of exon 9
gtaattttggtttttatgaattgggtgtgtgtgtgggggtgtgggggaggttctgctaagatgcagaatagttctaattgaatctaggattctcctatcatttttaacctggtcctttcaaggagtcttgtttttttaacaaaagcatttgacagATTCTAGAGGATATTTGGTTGATGAGGATGGATTTGACTACATGAAAATATCATTTTTGCGAGACATCAAAGCTCAACAAAGAAGTTTACG
                                                     |    |  | || |||     ||||     ||| || |    || |||| |  |    || | |  ||      |   |||   ||||||   |||  |||||||| |  || |||||||| ||||||||||||||||| ||||||||||||||||||||| |||| ||||||  |||||||||||||||  |
----------------------------------------------------tttaggatttacacaatgtggttaatcactactatgactagg-taccattgtatatgcagttcgtataaatcacatgcctttgccaacaaa--tattgtacagATTCAAAGGGTTATTTGGTGGATGAGGATGGATTTGATTACATGAAAATATCATTTTTGAGAGAGATCAAAAGTCAACAAAGAAGTTTGAG
















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|7924271|gb|AW830297.1|AW830297
EST:     TGTCTTGGAGAAGCTAATTGCTTATGGTGCTCTTCCCATGTCAGTATCAG                         ATTCTAGAGGATTATTTG-TTGATGAGGATGGATTTGAC
genomic: TGTCTTGGAGAAGCTAATTGCTTATGGTGCTCTTCCCATTTCAGTATCAGgtaattttgg ... catttgacagATTCTAGAGGAT-ATTTGGTTGATGAGGATGGATTTGAC
EST: gi|18735417|gb|BM528753.1|BM528753
EST:     TGTCTTGGAGAAGCTAATTGCTTATGGTGCTCTTCCCATTTCAGTATCAG                         ATTCTAGAGGATATTTGGTTGATGAGGATGGATTTGACTACATGAAAATAT
genomic: TGTCTTGGAGAAGCTAATTGCTTATGGTGCTCTTCCCATTTCAGTATCAGgtaattttgg ... catttgacagATTCTAGAGGATATTTGGTTGATGAGGATGGATTTGACTACATGAAAATAT
EST: gi|207749540|gb|GD720958.1|GD720958
EST:     TGTCTTGGAGAAGCTAATTGCTTATGGTGCTCTTCCCATTTCAGTATCAG                         ATTCTAGAGGATATTTGGTTGA
genomic: TGTCTTGGAGAAGCTAATTGCTTATGGTGCTCTTCCCATTTCAGTATCAGgtaattttgg ... catttgacagATTCTAGAGGATATTTGGTTGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttttaacctggtcctttcaaggagtcttgtttttttaacaaaagcatttgacagATTCTAGAGGATATTTGGTTGATGAGGATGGATTTGACTACATGAAAATATCATTTTTGCGAGACATCAAAGCTCAACAAAGAAGTTTACG
                                 ttttaac  putative branch site (score: 2)
                           ttgtttttttaacaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaattttggtttttatgaattgggtgtgtgtgtgggggtgtgggggaggttctgctaagatgcagaatagttctaattgaatctaggattctcctatcatttttaacctggtcctttcaaggagtcttgtttttttaacaaaagcatttgacagATTCTAGAGGATATTTGGTTGATGAGGATGGATTTGACTACATGAAAATATCATTTTTGCGAGACATCAAAGCTCAACAAAGAAGTTTACG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT