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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCTGCCCATGAGAAGATTGGAGTTGTTGATTCTCAGTGGATTGTTCACCAAGGTCTTCCCTCACTAGGGAATCAGgtactttgtttgtcatgatttctctagacttgacatttttactcaaaaatctggctgtaatttatgcttattaatattccttttctttgcag

Basic information

species Glycine max
transcript GLYMA18G01710.1
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G01710.1 (Glycine max), 5'ss of exon 13
lower sequence: AT3G26440.4 (Arabidopsis thaliana), 5'ss of exon 12
CCTGCCCATGAGAAGATTGGAGTTGTTGATTCTCAGTGGATTGTTCACCAAGGTCTTCCCTCACTAGGGAATCAGgtactttgtttgtca----tgatttctctagacttgacatttttactcaaaaatctggctgtaatttatgcttattaatattccttttctttgcag----------
||||| |||||||||||||| ||||| |||||||| |||||  |||| |||    |||| ||  |||| |  |||||  ||   |  |||    | || |  ||| |||  ||    ||| | |  |   |   |||   |  |  | | ||  |     | |||                
CCTGCACATGAGAAGATTGGTGTTGTGGATTCTCAATGGATCATTCATCAAAAGATTCCTTCTTTAGGCAGCCAGgttattaaatgatcaaactttatcttcctatactcaactacattatttactagcttctttgttcatagttttaactatgagatgatctctcaaatacattgatcag

upper sequence: GLYMA18G01710.1 (Glycine max), 5'ss of exon 13
lower sequence: AT1G13000.2 (Arabidopsis thaliana), 5'ss of exon 12
CCTGCCCATGAGAAGATTGGAGTTGTTGATTCTCAGTGGATTGTTCACCAAGGTCTTCCCTCACTAGGGAATCAGgtactttgt----ttgtcatgatttctctagacttgacat-ttttactcaaaaatctggctgtaatttatgcttattaatattccttttctttgcag
||||| ||||||||||| |||||||| |||||||| |||||  | || |||  |||||| ||  |||| |  ||||| |||          ||   |||||  || |  |    | ||||  ||| | ||       | ||| |   || ||  | ||| ||||    |   
CCTGCACATGAGAAGATAGGAGTTGTGGATTCTCAATGGATCATACATCAATCTCTTCCTTCTTTAGGCAGCCAGgttcttgacaataccttctcaatttcagtacaagtattctgttttgttcatatat-------tgattcagattttttggttttctttttaccag---

upper sequence: GLYMA18G01710.1 (Glycine max), 5'ss of exon 13
lower sequence: Vv14s0036g00790.t01 (Vitis vinifera), 5'ss of exon 1
-------------------------CCTGCCCATGAGAAGATTGGAGTTGTTGATTCTCAGTGGATTGTTCACCAAGGTCTTCCCTCACTAGGGAATCAGgtactttgtttgtcatgatttctctagacttgacatttttactcaaa-aatctggctgtaatttatgcttat-taatattccttttctttgcag-----------------
                         |||||||||||||| ||||||||||| |||||||| ||||| ||||| |||  | ||||||  || ||||| ||||||  |  | | |||  |    | |  |||  ||||||||| | | | || |    ||||||  |    | | | | ||    |      | |                  
TGGAACTTCCTCGTCTTTGAAACAACCTGCCCATGAGAAAATTGGAGTTGTAGATTCTCAATGGATCGTTCATCAAACTGTTCCCTTGCTCGGGAACCAGgtaaatcatct-tcagaaaaattttctact--acatttttatttatataaacgttttgtaatgaaaagatctatgaaatagaatactggagtaaccattatgtttttatag

upper sequence: GLYMA18G01710.1 (Glycine max), 5'ss of exon 13
lower sequence: Vv00s0187g00030.t01 (Vitis vinifera), 5'ss of exon 8
CCTGCCCATGAGAAGATTGGAGTTGTTGATTCTCAGTGGATTGTTCACCAAGGTCTTCCCTCACTAGGGAATCAGgtactttgtttgtcatgatttctctagacttgacatttttactcaaa-aatctggctgtaatttatgcttat-taatattccttttctttgcag-----------------
|||||||||||||| ||||||||||| |||||||| |||||  |||| |||  | ||||||| || ||||| ||||||  |  | | |||  |    | |  |||  ||||||||| | | | || |    ||||||  |    | | | | ||    |      | |                  
CCTGCCCATGAGAAAATTGGAGTTGTAGATTCTCAATGGATCATTCATCAAACTTTTCCCTCGCTTGGGAACCAGgtaaatcatct-tcagaaaaattttctact--acatttttatttatataaacgttttgtaatgaaaagatctatgaaatagaatactggagtaaccgttatgtttttatag

upper sequence: GLYMA18G01710.1 (Glycine max), 5'ss of exon 13
lower sequence: Vv01s0137g00770.t01 (Vitis vinifera), 5'ss of exon 13
CCTGCCCATGAGAAGATTGGAGTTGTTGATTCTCAGTGGATTGTTCACCAAGGTCTTCCCTCACTAGGGAATCAGgtactttgtttgtcatgatttctctagacttgacattt--ttactcaaaaatctggctgtaa-----tttatgcttattaatatt----------ccttttctttgcag
|||||||||||||| |||||||| || |||||||| ||||| ||||| |||  | ||||||| || ||||| ||||||  |  | | |||  |    | |  |||  |  |||  |||   |||  | | |   | |     | ||||      |||| |          |  | | |||  ||
CCTGCCCATGAGAAAATTGGAGTCGTAGATTCTCAATGGATCGTTCATCAAACTGTTCCCTCGCTTGGGAACCAGgtaaatcatct-tcagaaaacttttctactacatttttatttatataaatgttttgtaatgaaaagatctatgaaatagaatactggattaaccgctatgtttttatag

upper sequence: GLYMA18G01710.1 (Glycine max), 5'ss of exon 13
lower sequence: Vv17s0000g02780.t01 (Vitis vinifera), 5'ss of exon 1
-------------------------CCTGCCCATGAGAAGATTGGAGTTGTTGATTCTCAGTGGATTGTTCACCAAGGTCTTCCCTCACTAGGGAATCAGgtactttgtttgtcatgatttctctagacttgacatt-tttactcaaaaatctggctgtaa-----tttatgcttattaatatt-------ccttt---tctttgcag
                         |||||||||||||| ||||||||||| |||||||| ||||| ||||| |||  | ||||||| || ||||| ||||||  |  | |      |  | |            || ||||   |||  | | |   | |     | ||||      |||| |       || ||   | |||  ||
TGGAACTTCCTCGTCTTTGAAACAACCTGCCCATGAGAAAATTGGAGTTGTAGATTCTCAATGGATCGTTCATCAAACTGTTCCCTCGCTTGGGAACCAGgtaaataatcttcagaaaaattttctactacattgttatttatataaacgttttgtaatgaaaagatctatgaaatagaatactggagtaaccgttatgtttttatag

upper sequence: GLYMA18G01710.1 (Glycine max), 5'ss of exon 13
lower sequence: Vv13s0106g00570.t01 (Vitis vinifera), 5'ss of exon 4
CCTGCCCATGAGAAGATTGGAGTTGTTGATTCTCAGTGGATTGTTCACCAAGGTCTTCCCTCACTAGGGAATCAGgtactttgtttgtcatgatttctctagacttgacatttttactcaaa-aatctggctgtaatttatgcttat-taatattccttttctttgcag-----------------
|||||||||||||| ||||||||||| ||||||||  |||| ||||| |||  | ||||||| || ||||| ||||||  |  | | |||  |    | |  |||  ||||||||| | | | || |    ||||||  |    | | | | ||    |      | |                  
CCTGCCCATGAGAAAATTGGAGTTGTAGATTCTCAAGGGATCGTTCATCAAACTGTTCCCTCGCTTGGGAACCAGgtaaatcatct-tcagaaaaattttctact--acatttttatttatataaacgttttgtaatgaaaagatctatgaaatagaatactggagtaaccgttatgtttttatag

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|208113070|gb|GD912445.1|GD912445
EST:     TTGATTCTCAGTGGATTGTTCACCAAGGTCTTCCCTCACTAGGGAATCAG                         GGTGAATCTCAAACAGGGAAATCACGGTGGCAGG
genomic: TTGATTCTCAGTGGATTGTTCACCAAGGTCTTCCCTCACTAGGGAATCAGgtactttgtt ... ttctttgcagGGTGAATCTCAAACAGGGAAATCACGGTGGCAGG
EST: gi|6726342|gb|AW310696.1|AW310696
EST:     TTGATTCTCAGTGGATTGTTCACCAAGGTCTTCCCTCACTAGGGAATCAG                         GGTGAATCTCAAACAGGGAAATCACGGTGGCAGGGG
genomic: TTGATTCTCAGTGGATTGTTCACCAAGGTCTTCCCTCACTAGGGAATCAGgtactttgtt ... ttctttgcagGGTGAATCTCAAACAGGGAAATCACGGTGGCAGGGG
EST: gi|19348792|gb|BM893324.1|BM893324
EST:     TTGATTCTCAGTGGATTGTTCACCAAGGTCTTCCCTCACTAGGGAATCAG                         GGTGAATCTCAAACAGGGAAATCACGGTGGCAGGGG
genomic: TTGATTCTCAGTGGATTGTTCACCAAGGTCTTCCCTCACTAGGGAATCAGgtactttgtt ... ttctttgcagGGTGAATCTCAAACAGGGAAATCACGGTGGCAGGGG
EST: gi|192319062|gb|FK010626.1|FK010626
EST:     TTGATTCTCAGTGGATTGTTCACTAAGGTCTTCCCTCACTAGGGAATCAG                         GGTGAATCTCAAACAGGGAAATCACGGTGGCAGGGG
genomic: TTGATTCTCAGTGGATTGTTCACCAAGGTCTTCCCTCACTAGGGAATCAGgtactttgtt ... ttctttgcagGGTGAATCTCAAACAGGGAAATCACGGTGGCAGGGG
EST: gi|208125922|gb|GD925978.1|GD925978
EST:     TGATTCTCAGTGGATTGTTCACCAAGGTCTTCCCTCACTAGGGAATCAG                         GGTGAATCTCAAACAGGGAAATCACGGTGGCAGGGG
genomic: TGATTCTCAGTGGATTGTTCACCAAGGTCTTCCCTCACTAGGGAATCAGgtactttgtt ... ttctttgcagGGTGAATCTCAAACAGGGAAATCACGGTGGCAGGGG
EST: gi|254315636|gb|GR825445.1|GR825445
EST:     TTGATTCTCAGTGGATTGTTCACCAAGGTCTTCCCTCACTAGGGAATCAG                         GGTGAATCTCAAACAGGGAAATCACGGTGGCAGGGG
genomic: TTGATTCTCAGTGGATTGTTCACCAAGGTCTTCCCTCACTAGGGAATCAGgtactttgtt ... ttctttgcagGGTGAATCTCAAACAGGGAAATCACGGTGGCAGGGG
EST: gi|254347136|gb|GR856806.1|GR856806
EST:     TTGATTCTCAGTGGATTGTTCACCAAGGTCTTCCCTCACTAGGGAATCAG                         GGTGAATCTCAAACAGGGAAATCACGGTGGCAGGGG
genomic: TTGATTCTCAGTGGATTGTTCACCAAGGTCTTCCCTCACTAGGGAATCAGgtactttgtt ... ttctttgcagGGTGAATCTCAAACAGGGAAATCACGGTGGCAGGGG
EST: gi|193385504|gb|FK349858.1|FK349858
EST:     TTGATTCTCAGTGGATTGTTCACCAAGGTCTTCCCTCACTAGGGAATCAG                         GGTGAATCTCAAACAGGGAAATCACGGTGGCAGGGG
genomic: TTGATTCTCAGTGGATTGTTCACCAAGGTCTTCCCTCACTAGGGAATCAGgtactttgtt ... ttctttgcagGGTGAATCTCAAACAGGGAAATCACGGTGGCAGGGG
EST: gi|192302164|gb|FG995816.1|FG995816
EST:     TTGATTTTCAGTGGATTGTTCACCAAGGTTTTCCCTCACTAGGGAATCAG                         GGTGAATTTCAAACAGGGAAATCACGGTGGCAGGGG
genomic: TTGATTCTCAGTGGATTGTTCACCAAGGTCTTCCCTCACTAGGGAATCAGgtactttgtt ... ttctttgcagGGTGAATCTCAAACAGGGAAATCACGGTGGCAGGGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCTGCCCATGAGAAGATTGGAGTTGTTGATTCTCAGTGGATTGTTCACCAAGGTCTTCCCTCACTAGGGAATCAGgtactttgtttgtcatgatttctctagacttgacatttttactcaaaaatctggctgtaatttatgcttattaatattccttttctttgcag

- - - - - - - - - - - - - - - - - AGTGGA