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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCAGAACAGTTGTTTATTCCCAATTTTTGGAATCTTACAAGAGTGTGACAATTGAAGCCATGGCAAAAGCCTTTGGAGTGACAGTAGATTTCATTGATGTgtaagtaaatgcatatcacaaacccaattttggcttagtatttgtttagtttttagatgtcatagaaggcaactcattacatttttttgcttccag

Basic information

species Glycine max
transcript GLYMA17G13640.1
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G13640.1 (Glycine max), 5'ss of exon 7
lower sequence: LOC_Os02g38810.1 (Oryza sativa), 5'ss of exon 6
TCAGAACAGTTGTTTATTCCCAATTTTTGGAATCTTACAAGAGTGTGACAATTGAAGCCATGGCAAAAGCCTTTGGAGTGACAGTAGATTTCATTGATGTgtaagtaaatgcatatcacaaacccaattttggcttagtatttgtttagtttttagatgtcatagaaggcaactcattacatttttttgcttccag----------------------------
|  | || ||||| ||||| || |||||||| || ||||||||||||||||| ||||| |||||   ||| ||||| ||||| || |||||||| ||      ||||| ||| | ||||  | ||    || | ||  | |||||    ||  |   |||   | ||  ||     ||   ||  | ||||                                 
TGCGGACCGTTGTCTATTCACAGTTTTTGGAGTCATACAAGAGTGTGACAATGGAAGCGATGGCCGCAGCATTTGGTGTGACTGTTGATTTCATAGACC----Agtaagtgc-tgtcacccatccg-cattagttttatgtttgt--gattcctg--tgtaggacaaaacattcttttctgttcctgtgctgtggagataatatctccctttcatttgttccag

upper sequence: GLYMA17G13640.1 (Glycine max), 5'ss of exon 7
lower sequence: GRMZM2G093557_T01 (Zea mays), 5'ss of exon 7
TCAGAACAGTTGTTTATTCCCAATTTTTGGAATCTTACAAGAGTGTGACAATTGAAGCCATGGCAAAAGCCTTTGGAGTGACAGTAGATTTCATTGATGTgtaagtaaatgcatatcacaaacccaattttggctt---agtatttgtttagtttttagatgtcatagaaggcaactc-attacatttttttgcttccag
|  | || ||||| || || || ||| ||||||| ||||||||||||||||| |||||||||||    || ||||| || ||||| || || || ||   ||||||  | |  |    ||  ||||  |     ||   | | || ||  |   || |  | |  ||  | |  |||| | ||||               
TGCGCACTGTTGTCTACTCACAGTTTCTGGAATCGTACAAGAGTGTGACAATGGAAGCCATGGCTGCTGCATTTGGCGTCACAGTCGACTTTATAGACCAgtaagtgca-gtgtcagccatgcccatgtcaaagttctaaatgttagtacaagcttaacttttattatcatgtcactccaatacag--------------

upper sequence: GLYMA17G13640.1 (Glycine max), 5'ss of exon 7
lower sequence: Vv17s0000g10250.t01 (Vitis vinifera), 5'ss of exon 7
TCAGAACAGTTGTTTATTCCCAATTTTTGGAATCTTACAAGAGTGTGACAATTGAAGCCATGGCAAAAGCCTTTGGAGTGACAGTAGATTTCATTGATGTgtaagtaaatgcatatcacaaacccaattttggcttagtatttgtttagtttttagatgtcatagaaggcaactcattacatttttttgcttccag
|||| || || |||||||| ||||||||||||||||| |||||||| || ||||||||||||||||| |||||||| |||||||| || ||||||||| |||||||   |  ||||  ||     |  | ||  ||   | | ||| ||  |||     |   |||  | || | |  |     || || ||||||
TCAGGACTGTAGTTTATTCTCAATTTTTGGAATCTTATAAGAGTGTTACCATTGAAGCCATGGCAAAGGCCTTTGGGGTGACAGTGGAGTTCATTGATTTgtaagtggttttatatttcatggata-ctctgatttgcaagtggttaagcattt---catggcaga--gtaattta--aatccgttgtgtttccag

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|207825206|gb|GD795531.1|GD795531
EST:     ATTGAAGCCATGGCAAAAGCCTTTGGAGTGACAGTAGATTTCATTGATGT                         GGAGCTATCACGTTTTATTGCAGCAGGGAAGCTTCATTGTAAGATTGATAA
genomic: ATTGAAGCCATGGCAAAAGCCTTTGGAGTGACAGTAGATTTCATTGATGTgtaagtaaat ... ttgcttccagGGAGCTATCACGTTTTATTGCAGCAGGGAAGCTTCATTGTAAGATTGATAA
EST: gi|120494254|gb|EH222421.1|EH222421
EST:     ATTGAAGCCATGGCAAAAGCCTTTGGAGTGACAGTAGATTTCATTGATGT                         GGAGCTATCACGTTTTATTGCAGCAGGGAAGCTTCATTGTAAGATTGATAA
genomic: ATTGAAGCCATGGCAAAAGCCTTTGGAGTGACAGTAGATTTCATTGATGTgtaagtaaat ... ttgcttccagGGAGCTATCACGTTTTATTGCAGCAGGGAAGCTTCATTGTAAGATTGATAA
EST: gi|213610212|gb|DB974485.1|DB974485
EST:     ATTGAAGCCATGGCAAAAGCCTTTGGAGTGACAGTAGATTTCATTGATGT                         GGAGCTATCACGTTTTATTGCAGCAGGGAAGCTTCATTGTAAGATTGATAA
genomic: ATTGAAGCCATGGCAAAAGCCTTTGGAGTGACAGTAGATTTCATTGATGTgtaagtaaat ... ttgcttccagGGAGCTATCACGTTTTATTGCAGCAGGGAAGCTTCATTGTAAGATTGATAA
EST: gi|207716195|gb|GD697529.1|GD697529
EST:     TAGATTTCATTGATGT                         GGAGCTATCACGTTTTATTGCAGCAGGGAAGCTTCATTGTAAGATTGATAA
genomic: TAGATTTCATTGATGTgtaagtaaat ... ttgcttccagGGAGCTATCACGTTTTATTGCAGCAGGGAAGCTTCATTGTAAGATTGATAA
EST: gi|26268481|gb|CA819544.1|CA819544
EST:     ATTGAAGCCATGGCAAAAGCCTTTGGAGTGACAGTAGATTTCATTGATGT                         GGAGCTATCACGTTTTATTGCAGCAGGGAAGCTTCATTGTAAGATTGATAA
genomic: ATTGAAGCCATGGCAAAAGCCTTTGGAGTGACAGTAGATTTCATTGATGTgtaagtaaat ... ttgcttccagGGAGCTATCACGTTTTATTGCAGCAGGGAAGCTTCATTGTAAGATTGATAA
EST: gi|57574692|gb|CX547667.1|CX547667
EST:     ATTGAAGCCATGGCAAAAGCCTTTGGAGTGACAGTAGATTTCATTGATGT                         GGAGCTATCACGTTTTATTGCAGCAGGGAAGCTTCATTGTAAGATTGATAA
genomic: ATTGAAGCCATGGCAAAAGCCTTTGGAGTGACAGTAGATTTCATTGATGTgtaagtaaat ... ttgcttccagGGAGCTATCACGTTTTATTGCAGCAGGGAAGCTTCATTGTAAGATTGATAA
EST: gi|6951941|gb|AW424009.1|AW424009
EST:     ATTGAAGCCATGGCAAAAGCCTTTGGAGTGACAGTAGATTTCATTGATGT                         GGAGCTATCACGTTTTATTGCAGCAGGGAAGCTTCATTGTAAGATT
genomic: ATTGAAGCCATGGCAAAAGCCTTTGGAGTGACAGTAGATTTCATTGATGTgtaagtaaat ... ttgcttccagGGAGCTATCACGTTTTATTGCAGCAGGGAAGCTTCATTGTAAGATT
EST: gi|151400807|gb|EV270621.1|EV270621
EST:     ATTGAAGCCATGGCAAAAGCCTTTGGAGTGACAGTAGATTTCATTGATGT                         GGAGCTATCACGTTTTATTGCAGCAGGGAAGCTTCATTGTAAGATTGATAA
genomic: ATTGAAGCCATGGCAAAAGCCTTTGGAGTGACAGTAGATTTCATTGATGTgtaagtaaat ... ttgcttccagGGAGCTATCACGTTTTATTGCAGCAGGGAAGCTTCATTGTAAGATTGATAA
EST: gi|207775633|gb|GD747344.1|GD747344
EST:     AGTGACAGTAGATTTCATTGATGT                         GGAGCTATCACGTTTTATTGCAGCAGGGAAGCTTCATTGTAAGATTGATAA
genomic: AGTGACAGTAGATTTCATTGATGTgtaagtaaat ... ttgcttccagGGAGCTATCACGTTTTATTGCAGCAGGGAAGCTTCATTGTAAGATTGATAA
EST: gi|20497706|gb|BQ272636.1|BQ272636
EST:     ATTGAAGCCATGGCAAAAGCCTTTGGAGTGACAGTAGATTTCATTGATGT                         GGAGCTATCACGTTTTATTGCAGCAGGGAAGCTTCATTGTAAGATTGATAA
genomic: ATTGAAGCCATGGCAAAAGCCTTTGGAGTGACAGTAGATTTCATTGATGTgtaagtaaat ... ttgcttccagGGAGCTATCACGTTTTATTGCAGCAGGGAAGCTTCATTGTAAGATTGATAA
EST: gi|58019523|gb|CX706265.1|CX706265
EST:     ATTGAAGCCATGGCAAAAGCCTTTGGAGTGACAGTAGATTTCATTGATGT                         GGAGCTATCACGTTTTATTGCAGCAGGGAAGCTTCATTGTAAGATTGATAA
genomic: ATTGAAGCCATGGCAAAAGCCTTTGGAGTGACAGTAGATTTCATTGATGTgtaagtaaat ... ttgcttccagGGAGCTATCACGTTTTATTGCAGCAGGGAAGCTTCATTGTAAGATTGATAA
EST: gi|13788095|gb|BG650687.1|BG650687
EST:     ATTGAAGCCATGGCAAAAGCCTTTGGAGTGACAGTAGATTTCATTGATGT                         GGAGCTATCACGTTTTATTGCAGCAGGGAAGCTTCATTGTAAGATT
genomic: ATTGAAGCCATGGCAAAAGCCTTTGGAGTGACAGTAGATTTCATTGATGTgtaagtaaat ... ttgcttccagGGAGCTATCACGTTTTATTGCAGCAGGGAAGCTTCATTGTAAGATT
EST: gi|120494886|gb|EH223053.1|EH223053
EST:     ATTGAAGCCATGGCAAAAGCCTTTGGAGTGACAGTAGATTTCATTGATGT                         GGAGCTATCACGTTTTATTGCAGCAGGGAAGCTTCATTGTAAGATTGATAA
genomic: ATTGAAGCCATGGCAAAAGCCTTTGGAGTGACAGTAGATTTCATTGATGTgtaagtaaat ... ttgcttccagGGAGCTATCACGTTTTATTGCAGCAGGGAAGCTTCATTGTAAGATTGATAA
EST: gi|209706937|gb|BW683226.1|BW683226
EST:     ATTGAAGCCATGGCAAAAGCCTTTGGAGTGACAGTAGATTTCATTGATGT                         GGAGCTATCACGTTTTATTGCAGCAGGGAAGCTTCATTGTAAGATTGATAA
genomic: ATTGAAGCCATGGCAAAAGCCTTTGGAGTGACAGTAGATTTCATTGATGTgtaagtaaat ... ttgcttccagGGAGCTATCACGTTTTATTGCAGCAGGGAAGCTTCATTGTAAGATTGATAA
EST: gi|120494786|gb|EH222953.1|EH222953
EST:     ATTGAAGCCATGGCAAAAGCCTTTGGAGTGACAGTAGATTTCATTGATGT                         GGAGCTATCACGTTTTATTGCAGCAGGGAAGCTTCATTGTAAGATTGATAA
genomic: ATTGAAGCCATGGCAAAAGCCTTTGGAGTGACAGTAGATTTCATTGATGTgtaagtaaat ... ttgcttccagGGAGCTATCACGTTTTATTGCAGCAGGGAAGCTTCATTGTAAGATTGATAA
EST: gi|208070470|gb|GD872575.1|GD872575
EST:     AGTAGATTTCATTGATGT                         GGAGCTTATTCTACGTTTTATTGCAGCAGGGAAGCTTCATTGTAAGATTGA
genomic: AGTAGATTTCATTGATGTgtaagtaaat ... ttgcttccagGGAGC-TA-TC-ACGTTTTATTGCAGCAGGGAAGCTTCATTGTAAGATTGA
EST: gi|13791745|gb|BG654336.1|BG654336
EST:     ATTGAAGCCATGGCAAAAGCCTTTGGAGTGACAGTAGATTTCATTGATGT                         GGAGCTATCACGTTTTATTGCAGCAGGGAAGCTTCATTGTAAGATT
genomic: ATTGAAGCCATGGCAAAAGCCTTTGGAGTGACAGTAGATTTCATTGATGTgtaagtaaat ... ttgcttccagGGAGCTATCACGTTTTATTGCAGCAGGGAAGCTTCATTGTAAGATT
EST: gi|31561907|gb|CD487745.1|CD487745
EST:     ATTGAAGCCATGGCAAAAGCCTTTGGAGTGACAGTAGATTTCATTGATGT                         GGAGCTATCACGTTTTATTGCAGCAGGGAAGCTTCATTGTAAGATTGATAA
genomic: ATTGAAGCCATGGCAAAAGCCTTTGGAGTGACAGTAGATTTCATTGATGTgtaagtaaat ... ttgcttccagGGAGCTATCACGTTTTATTGCAGCAGGGAAGCTTCATTGTAAGATTGATAA
EST: gi|22930094|gb|BU547233.1|BU547233
EST:     ATTGAAGCCATGGCAAAAGCCTTTGGAGTGACAGTAGATTTCATTGATGT                         GGAGCTATCACGTTTTATTGCAGCAGGGAAGCTTCATTGTAAGATTGATAA
genomic: ATTGAAGCCATGGCAAAAGCCTTTGGAGTGACAGTAGATTTCATTGATGTgtaagtaaat ... ttgcttccagGGAGCTATCACGTTTTATTGCAGCAGGGAAGCTTCATTGTAAGATTGATAA
EST: gi|254314142|gb|GR831771.1|GR831771
EST:     ATTGAAGCCATGGCAAAAGCCTTTGGAGTGACAGTAGATTTCATTGATGT                         GGAGCTATCACGTTTTATTGCAGCAGGGAAGCTTCATTGTAAGATTGATAA
genomic: ATTGAAGCCATGGCAAAAGCCTTTGGAGTGACAGTAGATTTCATTGATGTgtaagtaaat ... ttgcttccagGGAGCTATCACGTTTTATTGCAGCAGGGAAGCTTCATTGTAAGATTGATAA
EST: gi|193529389|gb|FK487814.1|FK487814
EST:     AGTAGATTTCATTGATGT                         GGAGCTATCACGTTTTATTGCAGCAGGGAAGCTTCATTGTAAGATTGATAA
genomic: AGTAGATTTCATTGATGTgtaagtaaat ... ttgcttccagGGAGCTATCACGTTTTATTGCAGCAGGGAAGCTTCATTGTAAGATTGATAA
EST: gi|6227625|gb|AW156224.1|AW156224
EST:     ATTGAAGCCATGGCAAAAGCCTTTGGAGTGACAGTAGATTTCATTGATGT                         GGAGCTATCACGTTTTATTGCAGCANGGAAGCTTCATTGTAAGATT
genomic: ATTGAAGCCATGGCAAAAGCCTTTGGAGTGACAGTAGATTTCATTGATGTgtaagtaaat ... ttgcttccagGGAGCTATCACGTTTTATTGCAGCAGGGAAGCTTCATTGTAAGATT
EST: gi|193365972|gb|FK329441.1|FK329441
EST:     CCATGGCAAAAAGTCCTTTGGAGTGACAGTAGATTTCATTGATGT                         GGAGCTATCACGTTTTATTGCAGCAGGGAAGCTTCATTGTAAGATTGATAA
genomic: CCATGGC-AAAAG-CCTTTGGAGTGACAGTAGATTTCATTGATGTgtaagtaaat ... ttgcttccagGGAGCTATCACGTTTTATTGCAGCAGGGAAGCTTCATTGTAAGATTGATAA
EST: gi|58016465|gb|CX703207.1|CX703207
EST:     ATTGAAGCCATGGCAAAAGCCTTTGGAGTGACAGTAGATTTCATTGATGT                         GGAGCTATCACGTTTTATTGCAGCAGGGAAGCTTCATTGTAAGATTGATAA
genomic: ATTGAAGCCATGGCAAAAGCCTTTGGAGTGACAGTAGATTTCATTGATGTgtaagtaaat ... ttgcttccagGGAGCTATCACGTTTTATTGCAGCAGGGAAGCTTCATTGTAAGATTGATAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCAGAACAGTTGTTTATTCCCAATTTTTGGAATCTTACAAGAGTGTGACAATTGAAGCCATGGCAAAAGCCTTTGGAGTGACAGTAGATTTCATTGATGTgtaagtaaatgcatatcacaaacccaattttggcttagtatttgtttagtttttagatgtcatagaaggcaactcattacatttttttgcttccag

- - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG