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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attaattctcttatgtggttgtaccttcaattcaatttttggtgtaaatacatttgttgtgttgttaatgatatatacttatttactatcttccttgcagGGAGCATTTACTGAACAGCATTTTGATCAGGATCTGAATTTTCTTGCTACTGAGGAGGATCCTGTAACAAAAAGG

Basic information

species Glycine max
transcript GLYMA20G24820.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G24820.2 (Glycine max), 3'ss of exon 12
lower sequence: GRMZM2G151236_T03 (Zea mays), 3'ss of exon 9
---attaattc---tcttatgtggttgtaccttcaattcaatttttggtgtaaatacatttgttgtgttgttaatgatatatacttatttactatcttccttgcagGGAGCATTTACTGAACAGCATTTTGATCAGGATCTGAATTTTCTTGCTACTGAGGAGGATCCTGTAACAAAAAGG
   ||   |||   ||||| |||    | |    | |||  |  ||| | | || | ||      || | | ||||| |  |   ||   ||| ||    |   |||| || ||||||   || || |||||||| ||||| ||||||| |||||| |||||||||||||| ||||||| |
catatctgttcaactcttaagtgaacttgcaaatacttctctaattgat-tgaacaaataaaa-atgctctaaatga-acgtgtcta---actttccatttcatagGGTGCCTTTACTATGCAACACTTTGATCAAGATCTCAATTTTCATGCTACCGAGGAGGATCCTGTGACAAAAACG

upper sequence: GLYMA20G24820.2 (Glycine max), 3'ss of exon 12
lower sequence: GRMZM2G147811_T02 (Zea mays), 3'ss of exon 10
attaattctcttatgtggt---tgtaccttcaattcaatttttggtgtaaatacatttgttg-tgttgttaatgatatatacttatttactatcttccttgcagGGAGCATTTACTGAACAGCATTTTGATCAGGATCTGAATTTTCTTGCTACTGAGGAGGATCCTGTAACAAAAAGG
  ||  | |||  ||   |   || |  | ||| |   | | |  | | | |  |    |    | || |    ||  ||   | | ||   | |   ||| |||| || ||||||   || || || ||||| ||||| ||||||| |||||| |||||||||||||| ||||||| |
-ctatatatctggtgcactctttgaatttgcaaatacttctctaat-tgattgaaccgataaacgctgctctaaatgaatg--tgtctaacttttgttttgtagGGTGCCTTTACTATGCAACACTTCGATCAAGATCTCAATTTTCATGCTACCGAGGAGGATCCTGTGACAAAAACG

upper sequence: GLYMA20G24820.2 (Glycine max), 3'ss of exon 12
lower sequence: Vv01s0011g03350.t01 (Vitis vinifera), 3'ss of exon 10
atta-attctcttatgtggt-tgtaccttca-attcaatttttggtgtaaatacatttgttgtgttgttaatgatatatacttatttactatcttccttgcagGGAGCATTTACTGAACAGCATTTTGATCAGGATCTGAATTTTCTTGCTACTGAGGAGGATCCTGTAACAAAAAGG
 ||| |||    ||| || | ||||       |||  ||| | | | ||| |    |     || | | |||  | | | ||  ||| || ||||| || ||||||||||||||||| ||||| ||||||||||| || ||||| | ||| ||||||||||||||||| ||||| | |
-ttacatttgtatatatgttctgtatggctgcattacattgtggatataattcttctctaattgctttgaatattttttgctc-ttttctttcttc-ttacagGGAGCATTTACTGATCAGCACTTTGATCAGGACCTTAATTTCCATGCCACTGAGGAGGATCCTGTCACAAAGAAG

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|254316086|gb|GR825895.1|GR825895
EST:     GGCTTCACATGGAACTGAAGGGCCCTTTTCCAAAGAAGATGCTGCGTAAG                         GGAGCATTTACTGAACAGCATTTTGATCAGGATCTGAATTTTCTTGCTACT
genomic: GGCTTCACATGGAACTGAAGGGCCCTTTTCCAAAGAAGATGCTGCGTAAGgtaaacatat ... ttccttgcagGGAGCATTTACTGAACAGCATTTTGATCAGGATCTGAATTTTCTTGCTACT
EST: gi|5761013|gb|AI966376.1|AI966376
EST:     CCAAAGAAGATGCTGCGTAAG                         GGAGCATTTACTGAACAGCATTTTGATCAGGATCTGAATTTTCTTGCTACT
genomic: CCAAAGAAGATGCTGCGTAAGgtaaacatat ... ttccttgcagGGAGCATTTACTGAACAGCATTTTGATCAGGATCTGAATTTTCTTGCTACT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaatacatttgttgtgttgttaatgatatatacttatttactatcttccttgcagGGAGCATTTACTGAACAGCATTTTGATCAGGATCTGAATTTTCTTGCTACTGAGGAGGATCCTGTAACAAAAAGG
                 tgttaat  putative branch site (score: 3)
                                    tttactatcttcctt  putative PPT
                ttgttaatgatatata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attaattctcttatgtggttgtaccttcaattcaatttttggtgtaaatacatttgttgtgttgttaatgatatatacttatttactatcttccttgcagGGAGCATTTACTGAACAGCATTTTGATCAGGATCTGAATTTTCTTGCTACTGAGGAGGATCCTGTAACAAAAAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - gtggttg
- - - - - - - - - - - accttca
- - - - - - - - - - - - - - - - - - -tttggtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - tgttgtg