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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATATGATAGTATTACTTCAAAAGACAAAAGTGGAAAGGATTGGTCATTCATACTTAAGCAGATAGGCATGTTCTCATTCACTGGCTTGAACAAGAACCAGgtaattgattcatgttattatgacttcttgcatgttatcaacttgtggcttttatacactatgttgagtcctatttcattgactatatcaacatattgactatgttgttcttaaatgatatctcatcag

Basic information

species Glycine max
transcript GLYMA17G33050.4
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G33050.4 (Glycine max), 5'ss of exon 10
lower sequence: LOC_Os02g55420.1 (Oryza sativa), 5'ss of exon 10
ATATGATAGTATTACTTCAAAAGACAAAAGTGGAAAGGATTGGTCATTCATACTTAAGCAGATAGGCATGTTCTCATTCACTGGCTTGAACAAGAACCAGgtaat---tgattcatgttattatg------acttcttgcatgttatcaacttgtggctttt--atacactatgttgagtcctatttcattgactatatcaacatattgactatgttgttcttaaatgatatctcatcag--
||||||||| | || |||| ||| | ||||| ||||| ||||| ||||| || | |||||||||||||||||| | ||| ||||||||||| | ||||| | || || | || | | ||||| | |||| ||| ||| || | ||| | |||| || | | | | | | ||| | | | | ||| | || | | | | | |
TTATGATAGTTTGTCTGCAAAGGACGACAGTGGCAAGGACTGGTCTTTCATTCTGAGGCAGATAGGCATGTTCTCCTACACGGGCTTGAACAAAACTCAGgtgacatatgctttaaattttcacagataacacttccattcttctatcgactggtgatttctccatatataatgt-gactgcaaacactgcaattcacacaatacactaagtattcttaatttgattcgtttgtatttgcag

upper sequence: GLYMA17G33050.4 (Glycine max), 5'ss of exon 10
lower sequence: AT4G31990.4 (Arabidopsis thaliana), 5'ss of exon 11
ATATGATAGTATTACTTCAAAAGACAAAAGTGGAAAGGATTGGTCATTCATACTTAAGCAGATAGGCATGTTCTCATTCACTGGCTTGAACAAGAACCAGgtaattgattcatgttattatgacttc--ttgcatgttatcaacttgtggcttttatacactatgttgagtcctatttcattgactatatcaacatattgactatgttgttcttaaatgatatctcatcag
|||||||| | |||||||||||| || || ||||| ||||| ||||| || ||||| || ||||||||||| ||||| ||| | ||||| |||||| | || ||| || || || | | | | || | ||| | | ||| | | || ||| | | ||
GTATGATAGCCTCGTTTCAAAAGACAAGAGCGGGAAGGACTGGTCCTTCATTCTGAAGCAAATTGGCATGTTCTCTTTCACCGGCCTAAACAAAGCTCAGgtatgccaacaattttaatactacacagattccctttggccttgtttagacttgtggtttgaagtttgtgctgttttcttttggtaacg--agcag-----------------------------------

upper sequence: GLYMA17G33050.4 (Glycine max), 5'ss of exon 10
lower sequence: Vv04s0008g06040.t01 (Vitis vinifera), 5'ss of exon 12
ATATGATAGTATTACTTCAAAAGACAAAAGTGGAAAGGATTGGTCATTCATACTTAAGCAGATAGGCATGTTCTCATTCACTGGCTTGAACAAGAACCAGgtaattgattcatgttattatgacttcttgcatgttatcaacttgtggcttttatacactatgttgagtcctatttcattgactatatcaacatattgactatgttgttcttaaatgatatctcatcag
|| ||| || | || ||||||| || ||||||||||||||||||| ||||| |||||||| ||||||||||||||||| || ||| ||| |||||||| | | | |||| | |||||| | | || ||||| | ||| || | ||||| || |||| || | | | | || || | | ||
ATTTGACAGCCTCTCTGCAAAAGATAAGTGTGGAAAGGATTGGTCATTTATACTAAAGCAGATTGGCATGTTCTCATTCACAGGGCTGAGCAAAGTTCAGgtaat--------gctctctcaacttttc-----ttatcagcat-tgaactttatgc-ttatatt---ttttattttttt--ttataggaaacgacaaaggaaaatattgataga-aaaat--------

upper sequence: GLYMA17G33050.4 (Glycine max), 5'ss of exon 10
lower sequence: PP1S245_98V6.2 (Physcomitrella patens), 5'ss of exon 10
ATATGATAGTATTACTTCAAAAGACAAAAGTGGAAAGGATTGGTCATTCATACTTAAGCAGATAGGCATGTTCTCATTCACTGGCTTGAACAAGAACCAGgtaattgattcatgttattatgacttcttgcatgttatcaacttgtggcttttatacactatgttgagtcctatttcattgactatatcaacatattgactatgttgttcttaaatgatatctcatcag
|||||| | |||| || ||||| ||||| ||||| |||||||| | || ||||| || || ||||| |||||||||||||||||||| |||||| | |||| || || | | || ||| | | || || || | | | | || | || | | ||| | | ||
GTATGATGAACTCTCTTCGAAGGACAAGAGTGGCAAGGACTGGTCATTTGTTCTCAAGCAAATCGGAATGTTTTCATTCACTGGCTTGAACAAAGCACAGgtatatt-ttcaatttctttaatttccatgagtgtgggtatcacgttactagcatgtcccaagctag--cccacgtcctagggcataactttgtgcactcttc--------------------------

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|192332684|gb|FK025341.1|FK025341
EST:     TTCACTAGCTTGAACAAGAACCAG                         AGTGACAACATGACAAACAAGTGGCACGTATACATGACAAAGGATGGAAGG
genomic: TTCACTGGCTTGAACAAGAACCAGgtaattgatt ... atctcatcagAGTGACAACATGACAAACAAGTGGCACGTATACATGACAAAGGATGGAAGG
EST: gi|58022546|gb|CX709287.1|CX709287
EST:     TACTTAAGCAGATAGGCATGTTCTCATTCACTGGCTTGAACAAGAACCAG                         AGTGACAACATGACAAACAAGTGGCACGTATACATGACAAAGGATGGAAGG
genomic: TACTTAAGCAGATAGGCATGTTCTCATTCACTGGCTTGAACAAGAACCAGgtaattgatt ... atctcatcagAGTGACAACATGACAAACAAGTGGCACGTATACATGACAAAGGATGGAAGG
EST: gi|51336363|gb|CO980229.1|CO980229
EST:     TACTTAAGCAGATAGGCATGTTCTCATTCACTGGCTTGAACAAGAACCAG                         AGTGACAACATGACAAACAAGTGGCACGTATACATGACAAAGGATGGAAGG
genomic: TACTTAAGCAGATAGGCATGTTCTCATTCACTGGCTTGAACAAGAACCAGgtaattgatt ... atctcatcagAGTGACAACATGACAAACAAGTGGCACGTATACATGACAAAGGATGGAAGG
EST: gi|193693875|gb|FK628193.1|FK628193
EST:     AACAAGAACCAG                         AGTGACAACATGACAAACAAGTGGCACGTATACATGACAAAGGATGGAAGG
genomic: AACAAGAACCAGgtaattgatt ... atctcatcagAGTGACAACATGACAAACAAGTGGCACGTATACATGACAAAGGATGGAAGG
EST: gi|120492269|gb|EH220436.1|EH220436
EST:     TACTTAAGCAGATAGGCATGTTCTCATTCACTGGCTTGAACAAGAACCAG                         AGTGACAACATGACANACAAGTGGCACGTATACATGACAAAGGATGGAAGG
genomic: TACTTAAGCAGATAGGCATGTTCTCATTCACTGGCTTGAACAAGAACCAGgtaattgatt ... atctcatcagAGTGACAACATGACAAACAAGTGGCACGTATACATGACAAAGGATGGAAGG
EST: gi|151403656|gb|EV273466.1|EV273466
EST:     TACTTAAGCAGATAGGCATGTTCTCATTCACTGGCTTGAACAAGAACCAG                         AGTGACAACATGACAAACAGGTGGCACGTATACATGACAAAGGATGGAAGG
genomic: TACTTAAGCAGATAGGCATGTTCTCATTCACTGGCTTGAACAAGAACCAGgtaattgatt ... atctcatcagAGTGACAACATGACAAACAAGTGGCACGTATACATGACAAAGGATGGAAGG
EST: gi|58022284|gb|CX709025.1|CX709025
EST:     TACTTAAGCAGATAGGCATGTTCTCATTCACTGGCTTGAACAAGAACCAG                         AGTGACAACATGACAAACAAGTGGCACGTATACATGACAAAGGATGGAAGG
genomic: TACTTAAGCAGATAGGCATGTTCTCATTCACTGGCTTGAACAAGAACCAGgtaattgatt ... atctcatcagAGTGACAACATGACAAACAAGTGGCACGTATACATGACAAAGGATGGAAGG
EST: gi|209711313|gb|BW683850.1|BW683850
EST:     TACTTAAGCAGATAGGCATGTTCTCATTCACTGGCTTGAACAAGAACCAG                         AGTGACAACATGACAAACAAGTGGCACGTATACATGACAAAGGATGGAAGG
genomic: TACTTAAGCAGATAGGCATGTTCTCATTCACTGGCTTGAACAAGAACCAGgtaattgatt ... atctcatcagAGTGACAACATGACAAACAAGTGGCACGTATACATGACAAAGGATGGAAGG
EST: gi|302141298|gb|HO212174.1|HO212174
EST:     TACTTAAGCAGATAGGCATGTTCTCATTCACTGGCTTGAACAAGAACCAG                         AGTGACAACATGACAAACAAGTGGCACGTATACATGACAAAGGATGGAAGG
genomic: TACTTAAGCAGATAGGCATGTTCTCATTCACTGGCTTGAACAAGAACCAGgtaattgatt ... atctcatcagAGTGACAACATGACAAACAAGTGGCACGTATACATGACAAAGGATGGAAGG
EST: gi|208329212|gb|GE126758.1|GE126758
EST:     TACTTAAGCAGATAGGCATGTTCTCATTCACTGGCTTGAACAAGAACCAG                         AGTGACAACATGACAAACAAGTGGCACGTATACATGACAAAGGATGGAAGG
genomic: TACTTAAGCAGATAGGCATGTTCTCATTCACTGGCTTGAACAAGAACCAGgtaattgatt ... atctcatcagAGTGACAACATGACAAACAAGTGGCACGTATACATGACAAAGGATGGAAGG
EST: gi|151395412|gb|EV265289.1|EV265289
EST:     TACTTAAGCAGATAGGCATGTTCTCATTCACTGGCTTGAACAAGAACCAG                         AGTGACAACATGACAAACAAGTGGCACGTATACATGACAAAGGATGGAAGG
genomic: TACTTAAGCAGATAGGCATGTTCTCATTCACTGGCTTGAACAAGAACCAGgtaattgatt ... atctcatcagAGTGACAACATGACAAACAAGTGGCACGTATACATGACAAAGGATGGAAGG
EST: gi|120491497|gb|EH219664.1|EH219664
EST:     TACTTAAGCAGATAGGCATGTTCTCATTCACTGGCTTGAACAAGAACCAG                         AGTGACAACATGACAAACAAGTGGCACGTATACATGACAAAGGATGGAAGG
genomic: TACTTAAGCAGATAGGCATGTTCTCATTCACTGGCTTGAACAAGAACCAGgtaattgatt ... atctcatcagAGTGACAACATGACAAACAAGTGGCACGTATACATGACAAAGGATGGAAGG
EST: gi|120530683|gb|EH258816.1|EH258816
EST:     TACTTAAGCAGATAGGCATGTTCTCATTCACTGGCTTGAACAAGAACCAG                         AGTGACAACATGACAAACAAGTGGCACGTATACATGACAAAGGATGGAAGG
genomic: TACTTAAGCAGATAGGCATGTTCTCATTCACTGGCTTGAACAAGAACCAGgtaattgatt ... atctcatcagAGTGACAACATGACAAACAAGTGGCACGTATACATGACAAAGGATGGAAGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATATGATAGTATTACTTCAAAAGACAAAAGTGGAAAGGATTGGTCATTCATACTTAAGCAGATAGGCATGTTCTCATTCACTGGCTTGAACAAGAACCAGgtaattgattcatgttattatgacttcttgcatgttatcaacttgtggcttttatacactatgttgagtcctatttcattgactatatcaacatattgactatgttgttcttaaatgatatctcatcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC