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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctactagttatatatagggctgggatcttctatgcatgcatacttttttgttgcttctggtgtctttgattatcttatgcgttcattctcaaatttgcagCCACGGGTGGAAGCTGCCATGGTTAATGCCAGAATACGCAAAACTGTCAGAGCAAACCAAGCCAAAGTTGGGTACATTGGGCCTGCCACTGATTTCAACT

Basic information

species Glycine max
transcript GLYMA11G33480.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G33480.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G145854_T01 (Zea mays), 3'ss of exon 4
---ctactagttatatatagggctgggatcttctatgcatgc--atacttttttgttgcttctggtgtctttgattatcttatgcgttcattctcaaatttgcagCCACGGGTGGAAGCTGCCATGGTTAATGCCAGAATACGCAAAACTGTCAGAGCAAACCAAGCCAAAGTTGGGTACATTGGGCCTGCCACTGATTTCAACT
    |      | |||||   ||||   | | |    |||||  ||| |   || |||    |    | ||  |||  |  ||   ||  | |         |||||| ||||||||||||| |||||||| ||||| || || || ||||| | |||||  ||||| || |||||||||||||| ||| |  |||| || ||||
attttgtctcctctatat---gctgccttttacacgtcatgctgatattaagttattgtgaatataatattgtattggcacattgttttgtgccatgga--acagCCAAGGGTGGAAGCTGCTATGGTTAACGCCAGGATTCGGAAGACTGTTAAAGCAACACAAGCAAAGGTTGGGTACATTGGTCCTCCAGCTGACTTTAACT

upper sequence: GLYMA11G33480.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G126038_T01 (Zea mays), 3'ss of exon 4
ctactagttatatatagggctgggatcttctatgcatgc-atacttttttgttgcttc-tggtgtctttgattatcttatg---cgttcattctcaaatttg---cagCCACGGGTGGAAGCTGCCATGGTTAATGCCAGAATACGCAAAACTGTCAGAGCAAACCAAGCCAAAGTTGGGTACATTGGGCCTGCCACTGATTTCAACT
    |   |  |||||  ||      ||| ||  || |  || || || ||  | ||  | |||  | | ||  | | |||   ||||| || |    | ||   |||||| ||||||||||||| |||||||||||||| || || || ||||| | |||||  ||||| || || || |||||||| ||| |  |||| |||||||
--gtttcctccatatactgc------cttttagtcacgtgatgctgttatgaagttttattgtgaatataatattataatggcacgttctttttgtgctgtggaacagCCAAGGGTGGAAGCTGCTATGGTTAATGCCAGGATTCGGAAGACTGTTAAAGCAACACAAGCAAAGGTGGGCTACATTGGTCCTCCAGCTGACTTCAACT

upper sequence: GLYMA11G33480.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv14s0006g02020.t01 (Vitis vinifera), 3'ss of exon 4
--ctactagttatatatagggctgg-gatcttctatg-catgcatacttttttgttgcttctggtgtctttgattatcttatgcgttcattctcaaatttgcagCCACGGGTGGAAGCTGCCATGGTTAATGCCAGAATACGCAAAACTGTCAGAGCAAACCAAGCCAAAGTTGGGTACATTGGGCCTGCCACTGATTTCAACT
  ||     |   ||   ||| ||  |   |||| ||   ||  ||  || |   |     |  ||   ||  || |  ||     ||||  |||| || ||||||| ||||||||||| ||||||| |||||| |||| || ||||| ||   |||||  || ||||| || || |||||||||||||| |||||||||||||
ttctgtggatgggatgatgggatgatgggtttctgtggtttgagtaacttataagtatgatttatg---ttacttgttctaatttgtcataatcaa-ttggcagCCAAGGGTGGAAGCTCCCATGGTAAATGCCCGAATCCGGAAAACAGTACAAGCAACTCATGCCAAGGTGGGTTACATTGGGCCTGCAACTGATTTCAACT

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|308098271|gb|HO760012.1|HO760012
EST:     CATTGCTGGTCTTGAAAAAAGCGGATGCGTTCCTGTTGGTTGGCACCCAT                         CCCCGGGTGGAAGCTGCCTTGGTTAATGACAGAATACGCAAATCTGTCTGA
genomic: CATTGCTGGTCTTGAAAAA-GCGGATGCGTTCCTGTTGGTTGGCACCCAGgtatatctct ... aaatttgcagCCACGGGTGGAAGCTGCCATGGTTAATGCCAGAATACGCAAAACTGTCAGA
EST: gi|308098030|gb|HO761201.1|HO761201
EST:     CCATTGCTGGTCTTGAAAAAGCGGATGCGTTCCTGTTGGTTGGCACCCAG                         CCACGGGTGGAAGCTGCCATGGTTAATGCCAGAATACGCAAAACTGTCAGA
genomic: C-ATTGCTGGTCTTGAAAAAGCGGATGCGTTCCTGTTGGTTGGCACCCAGgtatatctct ... aaatttgcagCCACGGGTGGAAGCTGCCATGGTTAATGCCAGAATACGCAAAACTGTCAGA
EST: gi|308098031|gb|HO761202.1|HO761202
EST:     CATTGCTGGTCTTGAAAAAGCGGATGCGTTCCTGTTGGTTGGCCACCCAG                         CCACGGGTGGAAGCTGCCATGGTTAATGCCAGAATACGCAAAACTGTCAG
genomic: -ATTGCTGGTCTTGAAAAAGCGGATGCGTTCCTGTTGGTTGGC-ACCCAGgtatatctct ... aaatttgcagCCACGGGTGGAAGCTGCCATGGTTAATGCCAGAATACGCAAAACTGTCAG
EST: gi|26058530|gb|CA801444.1|CA801444
EST:     GCATTGCTGGTCTTGAAAAAGCGGATGCGTTCCTGTTGGTTGGCACCCAG                         CCACGGGTGGAAGCTGCCATGGTTAATGCCAGAATACGCAAAACTGTCAGA
genomic: GCATTGCTGGTCTTGAAAAAGCGGATGCGTTCCTGTTGGTTGGCACCCAGgtatatctct ... aaatttgcagCCACGGGTGGAAGCTGCCATGGTTAATGCCAGAATACGCAAAACTGTCAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttgttgcttctggtgtctttgattatcttatgcgttcattctcaaatttgcagCCACGGGTGGAAGCTGCCATGGTTAATGCCAGAATACGCAAAACTGTCAGAGCAAACCAAGCCAAAGTTGGGTACATTGGGCCTGCCACTGATTTCAACT
                  ctttgat  putative branch site (score: 5)
                   tttgattatcttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctactagttatatatagggctgggatcttctatgcatgcatacttttttgttgcttctggtgtctttgattatcttatgcgttcattctcaaatttgcagCCACGGGTGGAAGCTGCCATGGTTAATGCCAGAATACGCAAAACTGTCAGAGCAAACCAAGCCAAAGTTGGGTACATTGGGCCTGCCACTGATTTCAACT

- - - - - - - - -ggctggg
- - - - - - - - - - - - - - - - -gcatgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtctttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cttatgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cattctc