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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatgctgcgtgattattgtctctgtgatgttggagcttggaagttttctctggatttattgtgttatttgtggaacagGACAAGAGGATTACAACAGATTAAGACCTTTGAGTTACCGTGGTGCCGATGTTTTCATATTGGCTTTCTCTCTCATAAGCAAGGCCAGTTATGAAAATGT

Basic information

species Glycine max
transcript GLYMA11G08380.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G08380.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os02g02840.1 (Oryza sativa), 3'ss of exon 2
gtaatgctgcgtgattattgtctctgtgatgttggagcttggaagttttctctggatttattgtgttatt--tgtgga-----acagGACAAGAGGATTACAACAGATTAAGACCTTTGAGTTACCGTGGTGCCGATGTTTTCATATTGGCTTTCTCTCTCATAAGCAAGGCCAGTTATGAAAATGT
|||||   |      |  | |||     ||  || |   | |   | ||||    | |||||  ||| ||  |  |||     ||||| || ||||||||||||||| | |||||  ||||||| ||||| || ||||||||| |  |||| ||||| || || ||||||||||| ||||| |||||
gtaatctggttgcgctgctatct----aattctgcatgcttgttttcttctaccaagttattaagtttttccttcggaataccacagGTCAGGAGGATTACAACAGACTGAGACCACTGAGTTATCGTGGAGCTGATGTTTTCCTTCTGGCCTTCTCGCTAATCAGCAAGGCCAGCTATGAGAATGT

upper sequence: GLYMA11G08380.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM5G846811_T01 (Zea mays), 3'ss of exon 2
------------------gtaatgctgcgtgattattgtctctgtgatgttggagcttggaagttttct-ctggatttattg--tgttatttgtggaac------agGACAAGAGGATTACAACAGATTAAGACCTTTGAGTTACCGTGGTGCCGATGTTTTCATATTGGCTTTCTCTCTCATAAGCAAGGCCAGTTATGAAAATGT
                   |  | ||  |    | ||  | |  |  ||      |||     || | |     | |  |||    | || | || |||      ||| |||||||||||||||||| | |||||  |||| || ||||| || ||||||||  |  |||||||||| || || || |||||||| ||||| |||||
gtgaccagctatcctattttgttactttgatgcttttcccccctttgtgcatatcctttttccttgtttatcaaaatggttgaacttcatctttgcaactgccgcagGTCAAGAGGATTACAACAGACTGAGACCACTGAGCTATCGTGGAGCTGATGTTTTTCTTCTGGCTTTCTCACTGATCAGTAAGGCCAGCTATGAGAATGT

upper sequence: GLYMA11G08380.1 (Glycine max), 3'ss of exon 3
lower sequence: AT4G35950.1 (Arabidopsis thaliana), 3'ss of exon 2
gtaatgctgcgtgattattgtctctgtgatgttggagcttggaagttttctc--tggattt------attgtgttatttgtgga-acagGACAAGAGGATTACAACAGATTAAGACCTTTGAGTTACCGTGGTGCCGATGTTTTCATATTGGCTTTCTCTCTCATAAGCAAGGCCAGTTATGAAAATGT
    |  ||  |||| ||    |   | ||  | |      ||  ||| ||   || ||        ||| |||| || ||  |  |||| |||||||| || |||||||||||||||||||||||||||||||| |||||||||||  | || ||||||||||| || ||||| |||||||| |||||
---gtaatgaatgatgatccaattcataatccttggtgagagagctttccttgatgaatcggtcgaaattatgtttttggtttatgcagGGCAAGAGGACTATAACAGATTAAGACCTTTGAGTTACCGTGGTGCTGATGTTTTCATTCTTGCCTTCTCTCTCATTAGTAAGGCTAGTTATGAGAATGT

upper sequence: GLYMA11G08380.1 (Glycine max), 3'ss of exon 3
lower sequence: AT2G17800.2 (Arabidopsis thaliana), 3'ss of exon 3
gtaatg-ctgcgtgattattgtctct----gtgatgttgg-agcttggaagttttc--tctggatttattgtgttatttgtg-gaacagGACAAGAGGATTACAACAGATTAAGACCTTTGAGTTACCGTGGTGCCGATGTTTTCATATTGGCTTTCTCTCTCATAAGCAAGGCCAGTTATGAAAATGT
||| || ||   | ||     |||      ||  |   || ||||  |   |||    |||| |  | |||| || ||  ||  |||||| || |||||||| |||||||||||||||||||||||||| ||||| ||||||||||| || || |||||||| || || ||||| |||||||| |||||
gtactgactaaataatagggatcttacttagtagtagcggcagctatgggatttggggtctgaaacttttgttttgttgttgtaaacagGGCAGGAGGATTATAACAGATTAAGACCTTTGAGTTACCGCGGTGCTGATGTTTTCATCTTAGCATTCTCTCTTATCAGTAAGGCTAGTTATGAGAATGT

upper sequence: GLYMA11G08380.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv04s0023g03860.t01 (Vitis vinifera), 3'ss of exon 3
-----------gtaatgctgcgtgattattgtctctg--tgatgttggagcttggaagttttctctggattt-attgtgttatttgtggaacagGACAAGAGGATTACAACAGATTAAGACCTTTGAGTTACCGTGGTGCCGATGTTTTCATATTGGCTTTCTCTCTCATAAGCAAGGCCAGTTATGAAAATGT
           || |          || |||| |     |  |     |  ||   | | || | ||| | | | | |||| | | ||||||||| || ||||||||||||||||| |||||||||||||| || || || ||||||||||||||||| ||||||||||| ||||||||||| |||||||||||
gtagcttcacagtcacttgtttccttttttgttttcaattactaacaaacattttgattattttatggctctgaatttgttctctttggaacagGGCAGGAGGATTACAACAGATTGAGACCTTTGAGTTATCGCGGGGCAGATGTTTTCATATTGGCATTCTCTCTCATCAGCAAGGCCAGCTATGAAAATGT

upper sequence: GLYMA11G08380.1 (Glycine max), 3'ss of exon 3
lower sequence: PP1S257_74V6.1 (Physcomitrella patens), 3'ss of exon 2
----------gtaatgctgcgtgattattgtctctgtgatgttggagcttggaa-gttttctctggatttattgtgtta---------tttgtggaac--agGACAAGAGGATTACAACAGATTAAGACCTTTGAGTTACCGTGGTGCCGATGTTTTCATATTGGCTTTCTCTCTCATAAGCAAGGCCAGTTATGAAAATGT
          | | |    | | |  |   | ||  | | |    ||| ||||| | | |   |  |||| |   | |          || || ||||  ||| ||||| |||||||||||| |  ||||| | |||||| | ||||||||||| ||  || |||| ||||||||||| |||||||| |||||||||||  |
tttcgcatcagaagtctcaccttac-accat-tcactcaaggaacagcctggaacgatcttattacatttgtgacgatggagatagttttcgttgaacgcagGTCAAGAAGATTACAACAGACTCCGACCTCTTAGTTACAGGGGTGCCGATGTGTTTTTACTGGCATTCTCTCTCATCAGCAAGGCTAGTTATGAAAACAT

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|5606072|gb|AI900170.1|AI900170
EST:     TGTGGTTGTCAATGGGAGCATTGTGAATCTGGGTTTGTGGGATACTGCTG                         GACAAGAGGATTACAACAGATTAAGACCTTTGAGTTACCGTGGTGCCGATG
genomic: TGTGGTTGTCAATGGGAGCATTGTGAATCTGGGTTTGTGGGATACTGCTGgtaatgctgc ... tgtggaacagGACAAGAGGATTACAACAGATTAAGACCTTTGAGTTACCGTGGTGCCGATG
EST: gi|58017044|gb|CX703786.1|CX703786
EST:     TGTGGTTGTCAATGGGAGCATTGTGATTCTGGGTTTGTGGGATACTGCTG                         GACAAGAGGATTACAACAGATTAAGACCTTTGAGTTACCGTGGTGCCGATG
genomic: TGTGGTTGTCAATGGGAGCATTGTGAATCTGGGTTTGTGGGATACTGCTGgtaatgctgc ... tgtggaacagGACAAGAGGATTACAACAGATTAAGACCTTTGAGTTACCGTGGTGCCGATG
EST: gi|19054119|gb|BM732786.1|BM732786
EST:     TGTGGTTGTCAATGGGAGCATTGTGAATCTGGGTTTGTGGGATACTGCTG                         GACAAGAGGATTATAACAGATTAAGACCTTTGAGTTACCGTGGTGCCGATG
genomic: TGTGGTTGTCAATGGGAGCATTGTGAATCTGGGTTTGTGGGATACTGCTGgtaatgctgc ... tgtggaacagGACAAGAGGATTACAACAGATTAAGACCTTTGAGTTACCGTGGTGCCGATG
EST: gi|58016803|gb|CX703545.1|CX703545
EST:     TGTGGTTGTCAATGGGAGCATTGTGAATCTGGGTTTGTGGGATACTGCTG                         GACAAGAGGATTACAACAGATTAAGACCTTTGAGTTACCGTGGTGCCGATG
genomic: TGTGGTTGTCAATGGGAGCATTGTGAATCTGGGTTTGTGGGATACTGCTGgtaatgctgc ... tgtggaacagGACAAGAGGATTACAACAGATTAAGACCTTTGAGTTACCGTGGTGCCGATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgatgttggagcttggaagttttctctggatttattgtgttatttgtggaacagGACAAGAGGATTACAACAGATTAAGACCTTTGAGTTACCGTGGTGCCGATGTTTTCATATTGGCTTTCTCTCTCATAAGCAAGGCCAGTTATGAAAATGT
                              atttattgtgttattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatgctgcgtgattattgtctctgtgatgttggagcttggaagttttctctggatttattgtgttatttgtggaacagGACAAGAGGATTACAACAGATTAAGACCTTTGAGTTACCGTGGTGCCGATGTTTTCATATTGGCTTTCTCTCTCATAAGCAAGGCCAGTTATGAAAATGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG