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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGCTGCGACATTTCTTGCATTTCATCCTCAAGACAATAATATTATTGCTATTGGCATGGAGGACTCTTCCATACAAATCTATAATGTTAGAGTGGACGAGgtattactctatgcacaatctagactagagctgttggttaagtttcataaaataatgattttttaaaattcgtacaagtctctccctctcctccttccacacaatgccttaagacattagtttagtttcatacgtcattggtgttttaaaaattttgacattgaccttttttgtttaatttgttttcatctag

Basic information

species Glycine max
transcript GLYMA17G12110.1
intron # 22
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G12110.2 (Glycine max), 5'ss of exon 22
lower sequence: Vv11s0016g05620.t01 (Vitis vinifera), 5'ss of exon 22
AGCTGCGACATTTCTTGCATTTCATCCTCAAGACAATAATATTATTGCTATTGGCATGGAGGACTCTTCCATACAAATCTATAATGTTAGAGTGGACGAGgtattactctatgcacaatctagactagagctgttggttaagtttcataaaataatgattttttaaaattcgtacaagtctctccctctcctccttccacacaatgccttaagacattagtttagtttcatacgtcattggtgttttaaaaattttgacattgaccttttttgtttaatttgttttcatctag
||| || |||||| | ||||| |||||||||||||||||||| ||||| || ||||||||||||||||| || ||||| ||||||||| | || ||||||||||| || ||| |  || ||    |   |   ||   |  |||  ||||           || | |  |||| ||| | |     |  |    ||  |||                                                                                            
AGCAGCAACATTTTTGGCATTCCATCCTCAAGACAATAATATCATTGCCATAGGCATGGAGGACTCTTCTATCCAAATATATAATGTTCGGGTTGACGAGgtatt-ctttattctgaagcttatattttgtgattctctttgttg-ataagcaggcagaagttgata--tcgttcaaat-tgggtatgccacattttgacag-------------------------------------------------------------------------------------------

upper sequence: GLYMA17G12110.2 (Glycine max), 5'ss of exon 22
lower sequence: PP1S99_260V6.1 (Physcomitrella patens), 5'ss of exon 21
AGCTGCGACATTTCTTGCATTTCATCCTCAAGACAATAATATTATTGCTATTGGCATGGAGGACTCTTCCATACAAATCTATAATGTTAGAGTGGACGAGgtattactctatgcacaatctagactagagctgttggttaagtttcataaaataatgattttttaaaattcgtacaagtctctccctctcctccttccacacaatgccttaagacattagtttagtttcatacgtcattggtgttttaaaaattttgacattgaccttttttgtttaatttgttttcatctag
||| || || ||||||||||||||||| |||||||| ||||| |||||||| || ||||| || ||  | || || || ||||||||| | ||||| |||||||             ||| || |      ||   | |||||| |      |  |||||| | | |  | ||     |   |   ||||    ||  | | ||  |  |     ||  | ||| |   | |  ||  || ||||   |                                            
AGCAGCTACTTTTCTTGCATTTCATCCACAAGACAACAATATCATTGCTATCGGAATGGAAGATTCGACAATTCAGATTTATAATGTTCGTGTGGATGAGgtat----------gttatcaagtcc----ttgccagataagttgcgctt--ttgtgatttgtcaca-cttgtgttgatgcatatgtctcggt-tttaatataagactgtcgttgatacgcttaat--aagatttctctgctgttcacag-------------------------------------------
















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|208162409|gb|GD963140.1|GD963140
EST:     TTGGCATGGAGGACTCTTCCATACAAATCTATAATGTTAGAGTGGACGAG                         GTCAAAACTAAGCTAAAGGGTCATCAGAAGAGAATTACTGGTCTTGCCTTT
genomic: TTGGCATGGAGGACTCTTCCATACAAATCTATAATGTTAGAGTGGACGAGgtattactct ... tttcatctagGTCAAAACCAAGCTAAAAGGTCATCAGAAGAGAATTACTGGTCTTGCCTTT
EST: gi|208122623|gb|GD925401.1|GD925401
EST:     TTGGCATGGAGGACTCTTCCATACAAATCTATAATGTTAGAGTGGACGAG                         GTCAAAACCAAGCTAAAAGGTCATCAGAAGAGAATTACTGGTCTTGCCTTT
genomic: TTGGCATGGAGGACTCTTCCATACAAATCTATAATGTTAGAGTGGACGAGgtattactct ... tttcatctagGTCAAAACCAAGCTAAAAGGTCATCAGAAGAGAATTACTGGTCTTGCCTTT
EST: gi|302141350|gb|HO212226.1|HO212226
EST:     TTGGCATGGAGGACTCTTCCATACAAATCTATAATGTTAGAGTGGACGAG                         GTCAAAACCAAGCTAAAAGGTCGTCAGAAGAGAATTACTGGTCTTGCCTTT
genomic: TTGGCATGGAGGACTCTTCCATACAAATCTATAATGTTAGAGTGGACGAGgtattactct ... tttcatctagGTCAAAACCAAGCTAAAAGGTCATCAGAAGAGAATTACTGGTCTTGCCTTT
EST: gi|254332906|gb|GR850156.1|GR850156
EST:     TTGGCATGGAGGACTCTTCCATACAAATCTATAATGTTAGAGTGGACGAG                         GTCAAAACCAAGCTAAAAGGTCATCAGAAGAGAATTACTGGTCTTGCCTTT
genomic: TTGGCATGGAGGACTCTTCCATACAAATCTATAATGTTAGAGTGGACGAGgtattactct ... tttcatctagGTCAAAACCAAGCTAAAAGGTCATCAGAAGAGAATTACTGGTCTTGCCTTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGCTGCGACATTTCTTGCATTTCATCCTCAAGACAATAATATTATTGCTATTGGCATGGAGGACTCTTCCATACAAATCTATAATGTTAGAGTGGACGAGgtattactctatgcacaatctagactagagctgttggttaagtttcataaaataatgattttttaaaattcgtacaagtctctccctctcctccttccacacaatgccttaagacattagtttagtttcatacgtcattggtgttttaaaaattttgacattgaccttttttgtttaatttgttttcatctag

- - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA